- compbio-allhands@cgl.ucsf.edu - RBVI Mailing Lists

[Compbio-allhands] Fwd: Postdoc position in the SIBYLS group
by Andrej Sali 14 Mar '17

14 Mar '17

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Michal Hammel <mhammel(a)lbl.gov> > Subject: Postdoc position in the SIBYLS group > Date: March 14, 2017 at 5:04:26 PM MDT > To: Michal Hammel <mhammel(a)lbl.gov> > Cc: Jane Tanamachi <JTanamachi(a)lbl.gov> > > Dear Colleagues, > > I would like to draw your attention to a postdoc position in the SIBYLS group i at the Lawrence Berkeley National Laboratory in Berkeley. Please, spread this advertisement to students that could be interested in this position. > Thanks and best regards > > Michal Hammel > > > > __________________ > Michal Hammel PhD > Scientist at Advanced Light Source > Lawrence Berkeley National Laboratory > > 1 Cyclotron Road MS 6R2100 > Berkeley, CA 94720 > (phone) 510-495-8179 > (cell) 510-457-6317 > > mhammel(a)lbl.gov > ____________________ > >

1 0

[Compbio-allhands] ICHS Seminar Series: Udi Manber, 4/19 @ 4pm
by Rizk-Jackson, Angela 13 Mar '17

13 Mar '17

We hope you will join us for the following talk in our ICHS Seminar Series (flyer attached): "Healthcare as an information business” Udi Manber, PhD Professor and Director of Digital Transformation, Department of Medicine, UCSF Technical Advisor, Institute for Computational Health Sciences, UCSF Former head of Google Search (2009-2014) Wednesday, April 19, 2017 @ 4pm Lecture: 4-5pm Reception: 5-6pm (refreshments will be served) Mission Bay Campus: 1550 4th St, Genentech Hall, Byers Auditorium (Simulcast in Toland Hall at Parnassus Campus) RSVPs Appreciated: click here<https://ucsf.co1.qualtrics.com/SE/?SID=SV_eVB5Fapad8DCcZf> Hosted by Robert Wachter, MD, Chair of the Department of Medicine Contact: Angela.Rizk-jackson(a)ucsf.edu<mailto:Angela.Rizk-jackson@ucsf.edu>

1 0

[Compbio-allhands] Fwd: Atomwise Job Openings
by Brian Shoichet 09 Mar '17

09 Mar '17

---------- Forwarded message ---------- From: Michael Mysinger <michael(a)atomwise.com> Date: Thu, Mar 9, 2017 at 5:26 PM Subject: Atomwise Job Openings To: Brian Shoichet <shoichet(a)cgl.ucsf.edu>, John Irwin <jji(a)cgl.ucsf.edu>, Michael Keiser <keiser(a)keiserlab.org> Hello Brian, John, and Mike, Atomwise is hiring for 3 different positions, including a computational chemist, a data engineer, and an infrastructure engineer. The relevant link is: http://www.atomwise.com/careers/ It would be great if you can get the word out for those that may be interested. Cheers, Michael -- Michael Mysinger Principal Scientist Atomwise San Francisco, CA -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

1 0

[Compbio-allhands] Postdoctoral Position in Computer Aided Drug Design at the University of Notre Dame
by Matthew O'Meara 08 Mar '17

08 Mar '17

Dear all I talked with several of you during the study section last month about a position in the CAMD core I direct here at Notre Dame. I finally got around to putting up the position ad on the CCL (also copied below). If you have strong candidates, (either from your own group or someone else you know) please encourage them to apply. Thanks for your help Olaf =========== Postdoctoral Position in Computer Aided Drug Design at the University of Notre Dame The Warren Family Center for Drug Discovery and Development ( http://drugdiscovery.nd.edu) invites applications for a postdoctoral position in its Computer Aided Molecular Design (CAMD) core facility. Together with the director of the CAMD core, Prof. Olaf Wiest, the successful candidate will work closely with organic, medicinal, and biochemists as well as biologists from Notre Dame and other research institutions to develop models used in the design and development of bioactive compounds. Currently, a number of projects in the areas of cancer, infectious and neurodegenerative diseases as well as rare and neglected diseases are studied in close collaboration with experimentalists from different backgrounds , which allows the rapid testing of the models. After an initial period, this postdoctoral position could be converted into a staff-level position at the University of Notre Dame. Required qualifications - PhD in chemistry or a related field with relevant research experience - Documented experience with two or more of the tools of computer aided drug design such as protein modelling and structure prediction, docking/virtual screening, molecular dynamics simulations, free energy calculations, cheminformatics and databases, ADME/Tox and PD/PK predictions - Demonstrated problem solving abilities - Ability to effectively collaborate with researchers from a variety of backgrounds (organic and medicinal chemistry, chemical, molecular and cell biology, biochemistry), working on multiple projects simultaneously. - Excellent verbal and written communication and presentation skills Responsibilities - Independently conduct research with guidance from the director of the CAMD - Manage interactions with the customers of the CAMD core facility - Plan work load and provide cost estimates and timelines to CAMD customers - Publications in peer review journals, conference talks and posters - Participate in writing of proposals, patents, and publications of CAMD customers - Training and supervision of junior researchers - Acquisition of new projects To apply, please email curriculum vitae, publication list, reference letters (or names and contact information) of at least three individuals familiar with your work, and a statement of research experience to camd(a)nd.edu. Review of application will begin 3/20/2017 and will continue until the position is filled.

1 0

[Compbio-allhands] Fwd: Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL
by Grabe, Michael 06 Mar '17

06 Mar '17

Dear biophysics/comp community. Please see the workshop details on MD simulations below. Best Michael ---------------------------------------------------------- Michael Grabe Associate Professor University of California, San Francisco Cardiovascular Research Institute Department of Pharmaceutical Chemistry 555 Mission Bay Blvd South, Room 452T, MC 3122 San Francisco, California 94143 415-502-2874 (office) 415-476-8173 (fax) Begin forwarded message: From: João Ribeiro KS <jribeiro(a)ks.uiuc.edu<mailto:jribeiro@ks.uiuc.edu>> Subject: Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL Date: March 6, 2017 at 2:49:16 PM PST To: <michael.grabe(a)ucsf.edu<mailto:michael.grabe@ucsf.edu>> Cc: Emad Tajkhorshid <emad(a)life.illinois.edu<mailto:emad@life.illinois.edu>> Dear Michael Grabe, I hope this email finds you well. Please forgive the late notice, but I would like to let you know that the NIH Center for Macromolecular Modeling & Bioinformatics is once again hosting the "Hands-on" Workshop on Computational Biophysics, this time in Urbana, Illinois. Announcement: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/ Program: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/program.html Instructors: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/instructors.html Application Deadline: March 10th, 2017 Enrollment limited to 25 participants. Would you be kind and forward this email to your students and individuals you think that might be interested? Thank you Best wishes Joao Ribeiro Brief description: This workshop will be presented by members of the NIH Center for Macromolecular Modeling & Bioinformatics at Urbana-Champaign. Topics will cover instruction in state-of-the-art molecular dynamics simulation and free energy techniques using NAMD<https://www-s.ks.uiuc.edu/Research/namd/>, bacterial cells simulation with Lattice Microbes<http://www.scs.illinois.edu/schulten/lm/> (LM) and biomolecular visualization and analysis with VMD<https://www-s.ks.uiuc.edu/Research/vmd/>. Morning lecture presentations will introduce fundamental theory and concepts, while afternoon hands-on computer laboratory sessions will allow participants to apply NAMD, LM and VMD directly in a series of guided tutorials. The workshop is designed for all students and researchers in computational and/or biophysical fields who seek to extend their expertise to include biomolecular simulations. Experimentalists and non-specialists are encouraged to attend and will benefit particularly from instruction in the use of QwikMD<https://www-s.ks.uiuc.edu/Research/qwikmd/>, a new teaching software incorporating NAMD and VMD that significantly lowers the learning curve for novice users. -- ……………………………………………………... João Vieira Ribeiro Theoretical and Computational Biophysics Group Beckman Institute, University of Illinois jribeiro(a)ks.uiuc.edu<mailto:jribeiro@ks.uiuc.edu> +1 (217) 3000380

1 0

[Compbio-allhands] 3/9/17 Seminar with Steve Elledge
by Flowers, Nicole 03 Mar '17

03 Mar '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Steve Elledge Harvard Breaking Bad: How Aneuploidy Drives Cancer March 9, 2017 S. Bandyopadhyay, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: An exciting opportunity for highly talented graduate students and post-docs in your research group
by Brian Shoichet 01 Mar '17

01 Mar '17

FYI. ---------- Forwarded message ---------- From: Timothy A Grese <grese_timothy_a(a)lilly.com> Date: Fri, Feb 24, 2017 at 7:19 AM Subject: An exciting opportunity for highly talented graduate students and post-docs in your research group To: "bshoichet(a)gmail.com" <bshoichet(a)gmail.com> Dear Professor Shoichet, Greetings! I am writing to inform you about an exciting opportunity for highly talented graduate students and post-docs in your research group. You may be aware that Eli Lilly is expanding its research presence on the West Coast at the San Diego Biotechnology facility. As part of this expansion, we are establishing a Medicinal and Synthetic Chemistry group there. We are looking for select individuals to join this group and participate in our mission to provide innovative health care solutions to patients. We are reaching out to select chemistry faculty to help us identify exceptional candidates that meet this need. In addition to classical synthetic and medicinal chemistry approaches, our expanded research center in San Diego will (i) emphasize the application of automation to chemical design, synthesis and testing; (ii) take advantage of the proximity to our world-class structural biology capabilities; (iii) work at the interface of small and large molecule approaches; and (iv) explore unique and innovative methods to collaborate with West Coast research institutions. A job description for the position is included with this letter. We are currently targeting Ph.D. and Post-Doctoral students that will be ready to begin their independent career in 2018. As this is a new research group and the facilities are still being completed, some existing Lilly chemistry leadership and scientists that will work within this group have not yet relocated to San Diego. To facilitate the interview process and ensure that the right individuals are available to meet with candidates, we plan to conduct on-site interviews during a 1-2 week period in June/July of 2017. Therefore we are requesting your assistance to help identify qualified and interested candidates in advance of the normal 2017 recruiting season. Kevin Oberg and Jacqueline Wurst will be accepting CV’s and research summaries until April 17 at the email addresses below. Kevin Oberg, PhD koberg(a)lilly.com Jacqueline Wurst, PhD jwurst(a)lilly.com Where there are sufficient numbers of candidates at a single university or institution, we would like to conduct on-campus interviews in April/May. Alternatively, discussions with potential candidates can be done over the phone before any invitations are made to visit the Lilly San Diego site for in-person interviews. Thank you for your assistance in helping us to identify talented candidates for this exciting opportunity. If you have any questions regarding our new research group or the recruiting process, please feel free to contact me. _____________________________________________________________ *Timothy A. Grese, Ph.D.* Chief Scientific Officer, Discovery Chemistry Research and Technologies Eli Lilly and Company Lilly Corporate Center, Indianapolis IN 46285 U.S.A. 317.276.1356 <(317)%20276-1356> (office) | 317.985-6825 <(317)%20985-6825> (mobile) grese_timothy_a(a)lilly.com | www.lilly.com [image: LillyLogo_EmailSig2.jpg] CONFIDENTIALITY NOTICE: This email message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. -- Brian Shoichet, Professor, UCSF *http://www.bkslab.org/contact.php <http://www.bkslab.org/contact.php>* By Courtesy: UofT Fac. of Pharmacy

1 0

[Compbio-allhands] RESCHEDULED: 3/8 ICHS Seminar Series with Jure Leskovec
by Rizk-Jackson, Angela 01 Mar '17

01 Mar '17

Hello All, Due to a conflict with the recently scheduled Biohub Investigator orientation meeting, Jure Leskovec will not be available to give his talk as part of the ICHS Seminar Series set for March 8 at 2pm. We are working with Jure to reschedule the seminar for sometime in mid-late May. Please remove this event from your calendar and look for a notification of the revised date/time in the coming days. Apologies for any inconvenience. Best, Angela Angela Rizk-Jackson, Ph.D. Director of Operations Institute for Computational Health Sciences University of California, San Francisco (415) 514-0537 Angela.Rizk-Jackson(a)ucsf.edu<mailto:Angela.Rizk-Jackson@ucsf.edu> <http://ichs.ucsf.edu/> <https://mail.ucsf.edu/owa/Angela.Rizk-jackson@ucsf.edu/ICHS.ucsf.edu> <applewebdata://B868DB3E-8FDA-4C59-B156-AEA5C76C0163/UrlBlockedError.aspx> ICHS.ucsf.edu<http://ichs.ucsf.edu/> <http://ichs.ucsf.edu/>

1 0

[Compbio-allhands] 3/2/17 Seminar with Alexander Mankin
by Flowers, Nicole 24 Feb '17

24 Feb '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Alexander Mankin University of Illinois at Chicago Stopping the stopping: how one inhibitor can interfere with termination of translation in two different ways March 2, 2017 D. Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 2/23/17 Seminar with James Noonan
by Flowers, Nicole 17 Feb '17

17 Feb '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) James Noonan Yale Genetic models of human evolution February 23, 2017 N. Ahituv, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] ICHS Seminar Series: Jure Leskovec, 3/8 @ 2pm
by Rizk-Jackson, Angela 16 Feb '17

16 Feb '17

We hope you will join us for the following talk in our ICHS Seminar Series (flyer attached): "Scaled computation & inferential methods in biomedicine: Machine learning for biomedical applications” Jure Leskovec, PhD Associate Professor of Computer Science, Stanford University Chief Scientist, Pinterest Wednesday, March 8, 2017 @ 2pm Lecture: 2-3pm Reception: 3-3:30pm (light refreshments will be served) Mission Bay Campus: 1550 4th St, Rock Hall Auditorium About the Speaker: Jure’s research focuses on mining and modeling large social and information networks, their evolution, and diffusion of information and influence over them; and at Pinterest he works on machine learning problems. Contact: Angela.Rizk-jackson(a)ucsf.edu<mailto:Angela.Rizk-jackson@ucsf.edu>

1 0

[Compbio-allhands] Fwd: Recruitment of associate professor in chemoinformatics / bioinformactics
by Brian Shoichet 16 Feb '17

16 Feb '17

FYI ---------- Forwarded message ---------- From: Ruth Brenk <Ruth.Brenk(a)uib.no> Date: Thu, Feb 16, 2017 at 4:18 AM Subject: Recruitment of associate professor in chemoinformatics / bioinformactics To: Brian Shoichet <bshoichet(a)gmail.com> Hi Brian, the University of Bergen (Norway) is currently recruiting 5 associate professors in the are of chemoinformatics / bioinformatics ( https://www.jobbnorge.no/en/available-jobs/job/134177/assoc iate-professors-in-bioinformatics-up-to-five-positions). It would be great if you could spread to the news to suitable candidates. Regards Ruth -- Prof. Dr. Ruth Brenk University of Bergen Department of Biomedicine Ruth.Brenk(a)uib.no +47 55586070 Visitor adress: Mail address: Jonas Lies vei 91 Postboks 7804 5020 Bergen 5020 Bergen Norway Norway -- Brian Shoichet, Professor, UCSF *http://www.bkslab.org/contact.php <http://www.bkslab.org/contact.php>* By Courtesy: UofT Fac. of Pharmacy

1 0

[Compbio-allhands] Fwd: An announcement from COMP Together
by magdalena K 14 Feb '17

14 Feb '17

COMP Together event will be held on Thursday, please see announcement > Begin forwarded message: > > From: comp_together(a)acscomp.org > Subject: An announcement from COMP Together > Date: January 18, 2017 at 11:24:34 PM PST > To: Magdalena Korczynska <xtal.ca(a)gmail.com> > Reply-To: BinQing Wei <wei.binqing(a)gmail.com> > > The COMP Together champions in your area would like to announce the following event: > > Speaker: JW Feng (Denali), Alberto Gobbi & Ben Sellers (Genentech), Mario Cardozo (Nurix) > Title: SF Bay Area COMP Together Mini-Talk Series > Date: 2017-02-16 > Time: 6:00 PM > Event ID: 36 > Sponsor: NIBR > > Location > UCSF Mission Bay > 1700 4th St. BH212 > > San Francisco CA 94158 > > Description and Notes > Description: > Software expenditure and headcount for computational chemistry are often closely scrutinized at pharma and biotech companies. Some of us are working at smaller biotech or startups where the limitations tend to be even more severe. This meeting aims to promote sharing of strategies & tools to help address those challenges, including leveraging open-source software and cloud computing. > > Schedule: > > 6-7pm, check-in & networking (pizza and drinks provided) > > 7-7:20pm, talk #1, JW Feng (Denali) > Title: Computational chemistry challenges and opportunities at a biotech startup > > 7:20-8pm, talk #2, Ben Sellers & Alberto Gobbi (Genentech) > Title: Chemalot and chemalot_knime versatile open source tools for many of your cheminformatics and computational chemistry tasks. > > 8-8:20pm, discussion moderated by Mario Cardozo (Nurix) > > Notes: > Non-UCSF affiliated participants please enter through the main entrance of Genentech Hall (600 16th St., San Francisco, CA 94158) and sign in at the security desk. > > Public parking is available at the UCSF Mission Bay surface lots. For more information, please visit: http://campuslifeservices.ucsf.edu/transportation/services/parking/public_p… > > On-street parking is also available on 4th street and 16th street. > > > > > If you would like to attend this COMP Together event, please visit the COMP website and register using the > http://app.acscomp.org/COMP_Together/meeting_signup.php?event_id=36. > > If you have any questions about this event, please contact BinQing Wei atwei.binqing(a)gmail.com. > > If you would like to update your COMP Together registration or unsubscribe, please visit http://app.acscomp.org/COMP_Together/reg_update/update_login.php

1 0

[Compbio-allhands] Fwd: Mobley lab hiring postdoc
by Andrej Sali 14 Feb '17

14 Feb '17

> Begin forwarded message: > > From: David Mobley <dmobley(a)uci.edu> > Subject: Mobley lab hiring postdoc > Date: February 14, 2017 at 6:32:18 AM PST > To: David Mobley <dmobley(a)mobleylab.org> > > Dear Colleagues, > > I'm currently hiring a postdoc working on free energy calculations and applications to problems relating to pharmaceutical drug discovery. I'm ideally looking for someone with significant software development experience and expertise in MD and/or MC. > > Please pass along this brief advertisement to anyone suitable you might be aware of: http://mobleylab.org/2017/02/14/postdoc-position-currently-available/ <http://mobleylab.org/2017/02/14/postdoc-position-currently-available/> > > The position is available as early as March 1, and applications should be received by Feb. 21. > > Thanks so much, > David Mobley > > -- > David Mobley > Associate Professor > Department of Pharmaceutical Sciences > Department of Chemistry > 3134B Natural Sciences I > University of California, Irvine > Irvine, CA 92697 > dmobley(a)uci.edu <mailto:dmobley@uci.edu> > work (949) 824-6383 > cell (949) 385-2436 >

1 0

[Compbio-allhands] SAVE THE DATE- PETER KOLLMAN LECTURESHIP- APRIL 13, 2017
by Flowers, Nicole 13 Feb '17

13 Feb '17

SAVE THE DATE- THURSDAY, April 13, 2017 AT 3:00 PM Ron Dror Stanford PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS LIVE WEBCAST— URL TBA Reception in Byers Hall 2rd Floor Lounge at 4:30 pm. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 2/16/17 Seminar with Jeff Kelly
by Flowers, Nicole 10 Feb '17

10 Feb '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Jeff Kelly Scripps Adapting Proteostasis to Ameliorate Degenerative Diseases Linked to Protein Aggregation February 16, 2017 M. Kampmann, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Claus Seidel seminar, Feb 8
by Andrej Sali 08 Feb '17

08 Feb '17

“Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems in vitro and in live cells” 11am, Feb 8, BH 212 -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

1 1

[Compbio-allhands] Fwd: Vacancy Bioinformatics professor Radboudumc Nijmegen
by Andrej Sali 06 Feb '17

06 Feb '17

> Begin forwarded message: > > From: <Han.Brunner(a)radboudumc.nl> > Subject: Vacancy Bioinformatics professor Radboudumc Nijmegen > Date: February 6, 2017 at 2:32:52 AM PST > To: Undisclosed recipients:; > > Dear colleague, > > This is to ask whether you might have ideas about a position that we would like to fill here at Radboudumc Nijmegen. > > We are looking for a professor and head of bioinformatics. We have some very good bioinformaticians already, focusing on specific areas such as human genetics, molecular biology, and immunology. We are now looking for a full professor to lead the central bioinformatics core. Ideally, we would hope to find someone who has active research going and who would also be interested in the broader development of information science and method development to make biomedical sciences more informative! > > Let me know if you have any ideas for a candidate who might be interested in moving to the Netherlands. > > Best wishes > > Han Brunner > > > > Monday-Wednesday, and alternating Fridays > Radboud UMC > Department of Human Genetics 855 > Donders Institute for Brain, Cognition and Behaviour > PO Box 9101 > 6500HB Nijmegen > The Netherlands > Tel: +31-243614017 > Han.Brunner(a)RadboudUMC.nl <mailto:Han.Brunner@RadboudUMC.nl> > > Thursdays and alternating Fridays > Maastricht University Medical Center > Department of Clinical Genetics > PO Box 5800 > 6202AZ Maastricht > The Netherlands > Tel: +31-433871349 > Han.Brunner(a)MUMC.NL <mailto:Han.Brunner@MUMC.NL> > > > > > Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. > The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629. >

1 0

[Compbio-allhands] Fwd: Claus Seidel Seminar
by Andrej Sali 03 Feb '17

03 Feb '17

> Begin forwarded message: > > From: "Ha, Steve" <Steve.ha(a)ucsf.edu> > Subject: Claus Seidel Seminar > Date: February 2, 2017 at 2:21:51 PM PST > To: "SaliLab Mail (salilab(a)salilab.org)" <salilab(a)salilab.org> > > Hi everyone, > > Dr. Seidel is having a seminar next Wednesday Feb 8th. 11am - Byers Hall 212. > > Steve

1 0

[Compbio-allhands] 2/9/17 Seminar with Dorothea Fiedler
by Flowers, Nicole 03 Feb '17

03 Feb '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Dorothea Fiedler University of Berlin Elucidating the role of inositol pyrophosphates in cellular signaling February 9, 2017 D. Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Summer Internship openings at Genentech in the computational chemistry group
by Brian Shoichet 31 Jan '17

31 Jan '17

FYI. ---------- Forwarded message ---------- From: Daniel Ortwine <ortwine.daniel(a)gene.com> Date: Tue, Jan 31, 2017 at 12:05 PM Subject: Summer Internship openings at Genentech in the computational chemistry group To: Brian Shoichet <shoichet(a)cgl.ucsf.edu> Hello Brian! I am contacting you to ask if you know of any candidate that might be suitable for internship positions that we have open for this coming summer in the computational chemistry group at Genentech. Short descriptions of each position and the position requirements can be found below. These internships can start at different times during the summer. We are recruiting for these positions now! It would be great if you could suggest candidates that fit the profiles and/or circulate the job descriptions among your students. Any student that would like to apply for a position should send a cover letter and their CV to Genentech via the the link provided below: https://www.gene.com/careers/detail/00450980/Intern-Discovery-Chemistry- Computational-Chemistry Here is some information on the logistics of the internship: - Internships are scheduled for the duration of 12 weeks - There will be 3-4 intern start dates in June 2017. - Interns are paid an hourly rate based on their degree level. - Recent (within 2 years) graduates of BS/BA or MS/MA programs are eligible. They are paid based on their most recent degree completed. - Travel assistance is given to all intern candidates - Interns are eligible to use the Genentech bus system at no cost, which connects the Genentech campus to several locations in the San Francisco bay area for morning and evening commutes. - All interns must clear a background check. - Interns do not receive medical/dental benefits and do not accrue vacation - We do not currently offer formal housing assistance for interns. However, we do provide networking assistance so interns can contact each other to make living arrangements. I am also happy to answer any questions you or any candidates might have. With best regards, Dan Project 1: The intern will work with Alberto Gobbi to implement and evaluate a method for computing strain energies of drug molecules in their bound conformation. The strain energy is a component of the binding energy and significantly contributes to the strength of a small molecule protein interaction. A drug that binds its protein target without increasing its strain energy may be given at a lower dose, thereby reducing the risk of toxicity. Part of the work includes evaluating open source and commercial software for computing molecular energies at a quantum mechanical level. The other part will be the development of an automated workflow to perform the calculation on an in-house computer cluster at Genentech. The candidate will learn about small molecule energetics, binding conformations, and ligand protein interactions. This work may also lead to a publication of a manuscript and or open source software. Candidates must be full-time undergraduate or graduate students, with a working knowledge of chemistry, familiarity with the Unix operating system and programming experience (preferably in Java or Python). A familiarity with computational chemistry software is a plus. Project 2: The intern will work with Paul Gibbons to improve our ability to use existing software to aid the design of small organic molecules. The work will include evaluating virtual libraries, improving them, evaluating current workflows for virtual molecule modification and proposing/ implementing improved workflows. The intern should have knowledge of basic UNIX commands and some scripting. In addition, the candidate must be a full-time undergraduate or graduate student who has completed a full year of undergraduate organic chemistry. Formal coursework in computer science would be advantageous but is not essential. -- Daniel Ortwine Computational Drug Discovery Genentech, Inc. 1 DNA Way, ms 18b South San Francisco, CA 94080 Office 650-225-2749 <(650)%20225-2749> Cell 925-323-0504 <(925)%20323-0504> email ortwine.daniel(a)gene.com -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

1 0

[Compbio-allhands] 2/2/17 Seminar with Eric Alm
by Flowers, Nicole 27 Jan '17

27 Jan '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Eric Alm MIT The ecology of the human microbiome in health and disease February 2, 2017 L. Morinishi, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Open position for a Postdoc in 3DGenomics in Barcelona (CNAG-CRG)
by Andrej Sali 25 Jan '17

25 Jan '17

Sent from my iPhone Begin forwarded message: > From: Marc Marti Renom <martirenom(a)cnag.crg.eu> > Date: January 25, 2017 at 9:33:59 AM GMT > To: Marc Marti Renom <martirenom(a)cnag.crg.eu> > Subject: Open position for a Postdoc in 3DGenomics in Barcelona (CNAG-CRG) > > Dear colleagues and friends, > > Could you please forward this email to anybody in your research institutions who could be interested in a computational biology postdoc in 3DGenomics? > > Detailed information can be found in the attached PDF or in this link: https://recruitment.crg.eu/content/jobs/position/postdoctoral-position-stru… > > Many thanks in advance! > Marc > ... > OPEN PostDoc POSITION IN THE LAB! https://recruitment.crg.eu/content/jobs/position/postdoctoral-position-stru… > > Marc A. Marti-Renom, ICREA Research Professor > Structural Genomics Group Leader > Centre Nacional d’Anàlisi Genòmica - Centre de Regulació Genòmica (CNAG-CRG) > Parc Científic de Barcelona – Torre I (10th floor) > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email: martirenom(a)cnag.crg.eu > Web: http://marciuslab.org · http://cnag.crg.eu · http://crg.cat > > CRG PhD positions available at “la Caixa” INPhINIT Doctoral fellowships programme http://www.inphinitlacaixa.org > Application deadline: February 2, 2017 > “This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklowdowska- Curie grant agreement No. 713673” > > *** Consider the environment. Print responsibly. *** > > > > > > >

1 0

[Compbio-allhands] 1/26/17 Seminar with Gerhard Wagner
by Flowers, Nicole 20 Jan '17

20 Jan '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Gerhard Wagner Harvard Engineering nanodiscs for membrane protein studies January 26, 2017 D. Asarnow, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 1/19/17 Seminar with Joachim Frank
by Flowers, Nicole 13 Jan '17

13 Jan '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Joachim Frank Columbia Time-resolved cryo-EM: first biological results with the mixing/spraying microfluidic chip January 19, 2017 R. Woldeyes, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: job opening at Novartis Emeryville
by Andrej Sali 09 Jan '17

09 Jan '17

> Begin forwarded message: > > From: Dave Barkan <davebarkan(a)gmail.com> > Subject: job opening at Novartis Emeryville > Date: January 9, 2017 at 3:49:18 PM PST > To: Andrej Sali <sali(a)salilab.org> > > Hey Andrej! > > Hope things are going well in Mission Bay! > > We have another job opening here in Emeryville for an entry-level Investigator position in our Infectious Diseases Bioinformatics group. Talented post-docs and recent PhD graduates from bioinformatics-focused labs at UCSF would be good candidates. Could you please circulate the following link? > > https://sjobs.brassring.com/tgwebhost/jobdetails.aspx?jobId=2444628&Partner… <https://sjobs.brassring.com/tgwebhost/jobdetails.aspx?jobId=2444628&Partner…> > > Thanks! > Dave

1 0

[Compbio-allhands] 1/12/17 Seminar with Kimberly Reynolds
by Flowers, Nicole 06 Jan '17

06 Jan '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Kimberly Reynolds University of Texas, Southwestern A conserved evolutionary unit in central metabolism January 12, 2017 Y. Birman, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Job for a Masters or PhD Bioinformatician - Scientific Software Developer
by Andrej Sali 06 Jan '17

06 Jan '17

> Begin forwarded message: > > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: FW: Job for a Masters or PhD Bioinformatician - Scientific Software Developer > Date: January 6, 2017 at 8:18:25 AM PST > > > Dear colleague – I’d be grateful if you would advertise. We are looking for strong web development skills and a Masters or PhD is the ideal qualification. > Thanks > > Mike > ******************************************** > m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > > > From: Sternberg, Michael J E > Sent: 06 January 2017 16:15 > To: Sternberg, Michael J E > Subject: Job for a Masters or PhD Bioinformatician - Scientific Software Developer > > Scientific Software Developer > Imperial College London – Structural Bioinformatics Group - Department of Life Sciences > Location: > London > Salary: > £35,140 to £43,350 per annum > Hours: > Full Time > Contract Type: > Contract / Temporary > Closes: > 5th February 2017 > Job Ref: > NS 2017 001 PB > Applications are invited for a Scientific Software Developer to join the Structural Bioinformatics Group of Prof Mike Sternberg, within the Department of Life Sciences based at the South Kensington Campus. The post holder will work as a member of a small team developing the PhyreRisk dynamic web portal which will provide the bioscience and biomedical communities with a resource relating human genetic variation, disease, protein structure and biological pathways. > > The post will focus on the development of a dynamic web site to map genetic variants onto experimental and predicted structures of proteins. You must have at least a Master’s postgraduate degree (or equivalent), and ideally a PhD (or equivalent) from a course that involved substantial computational work such as computer science, physics, chemistry, mathematics or computational-biology/bioinformatics or a comparable vocational qualification together with comparable experience in a relevant role. You must have demonstrable strong programming experience required to develop a substantive dynamic web site to a professional standard using HTML/JavaScript/Django and server side languages (Java, Perl-CGI), ideally applied to a scientific problem. You must also have demonstrable strong programming experience for data processing and/or algorithm development in a high level language such as C, C++ or Python (or a close equivalent), ideally applied to a scientific problem. > > This is a full time position, funded by the Wellcome Trust until 30 November 2019. > > For initial enquiries please contact Professor Michael Sternberg by email: m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > The preferred method of application is online via our websitehttp://www3.imperial.ac.uk/employment <http://www3.imperial.ac.uk/employment> (please select “Job Search” then enter the job title or vacancy reference number including spaces – NS 2017 001 PB. Please complete and upload an application form as directed and attach a full CV. > > ******************************************** > Professor Michael J E Sternberg > Director Centre for Integrative Systems Biology and Bioinfomatics (CISBIO) > Room 306 - Sir Ernst Chain Building > Department of Life Sciences > Imperial College London, London SW7 2AZ,UK > m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > http://www3.imperial.ac.uk/cisbio <http://www3.imperial.ac.uk/cisbio> (CISBIO) > www.sbg.bio.imperial.ac.uk <http://www.sbg.bio.imperial.ac.uk/> (Group's research) > > Tel +44 (0)20 7594 5212 > ****************************************************************************

1 0

[Compbio-allhands] Fwd: Postdoc position in computational biology
by Andrej Sali 05 Jan '17

05 Jan '17

> Begin forwarded message: > > From: pau bernado <pau.bernado(a)cbs.cnrs.fr> > Subject: Postdoc position in computational biology > Date: January 5, 2017 at 1:03:02 AM PST > To: Alessandro Barducci <barducci(a)cbs.cnrs.fr> > > Dear Colleagues, > > I would like to draw your attention to a postdoc position in computational biology in the group of Alessandro Barducci at the Centre de Biochimie Structurale in Montpellier. Please, spread this advertisement to students that could be interested in this position. > Thanks and best regards > > Pau Bernado

1 0

[Compbio-allhands] Fwd: Junior GL positions at CRG (Barcelona)
by Andrej Sali 22 Dec '16

22 Dec '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Marc Marti Renom <martirenom(a)cnag.crg.eu> > Subject: Junior GL positions at CRG (Barcelona) > Date: December 22, 2016 at 12:27:38 AM PST > To: Joe DeRisi <joe(a)derisilab.ucsf.edu>, Tomas Marques Bonet <tomas.marques(a)upf.edu>, Victor Corces <vgcorces(a)gmail.com>, Patsy Babbitt <babbitt(a)cgl.ucsf.edu>, José Luís Gómez-Skarmeta <jlgomska(a)upo.es>, Francesc Aviles <FrancescXavier.Aviles(a)uab.es>, "Tobias A. Knoch" <t.a.knoch(a)erasmusmc.nl>, Giacomo Cavalli <giacomo.cavalli(a)igh.cnrs.fr>, Andrej Sali <sali(a)salilab.org>, Maya Topf <mayatopf(a)gmail.com>, Luis Serrano Pubul <luis.serrano(a)crg.eu>, Phil Bourne <bourne(a)sdsc.edu>, Gerd Blobel <blobel(a)email.chop.edu>, Modesto Orozco <modesto(a)mmb.pcb.ub.es>, Ismael Mingarro <mingarro(a)uv.es>, "Cristina Marino-Buslje" <cmb(a)leloir.org.ar>, Bosco Ho <bosco(a)maxwell.ucsf.edu>, Alfonso Valencia <avalencia(a)cnio.es>, F. Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es>, Jordi Quintana <jquintana(a)pcb.ub.es>, Olivier Neyrolles <olivier.neyrolles(a)gmail.com>, Kerstin Bystricky <kerstin(a)biotoul.fr>, "F. Xavier de la Cruz" <xdmcri(a)ibmb.csic.es>, Matt Jacobson <matt(a)cgl.ucsf.edu>, Ana Pombo <Ana.Pombo(a)mdc-berlin.de>, Santiago Elena Fito <sfelena(a)ibmcp.upv.es>, "Fyodor Kondrashov" <Fyodor.Kondrashov(a)crg.eu>, Andras Fiser <andras(a)fiserlab.org>, Peter Fraser <peter.fraser(a)babraham.ac.uk>, Lluís Ribas de Pouplana <lluis.ribas(a)irbbarcelona.org>, Javier Santoyo <jsantoyo(a)cipf.es>, Rob Russell <russell(a)embl.de>, "George Church" <gc(a)harvard.edu>, Cedric Notredame <Cedric.Notredame(a)crg.eu>, "David Jones" <dtj(a)cs.ucl.ac.uk>, Salvador Aznar-Benitah <salvador.aznar-benitah(a)irbbarcelona.org>, Emidio Capriotti <emidio.capriotti(a)gmail.com>, Roderic Guigo Serra <roderic.guigo(a)crg.eu>, Genevieve Almouzni <Genevieve.almouzni(a)curie.fr>, Ferran Azorin <fambmc(a)ibmb.csic.es>, Wouter de Laat <w.delaat(a)hubrecht.eu>, "William Stafford Noble" <william-noble(a)u.washington.edu>, Boris Turk <boris.turk(a)ijs.si>, Chris Burge <chris(a)CCR-081.mit.edu>, Ugo Bastolla <ubastolla(a)cbm.uam.es>, Isidre Gibert <Isidre.Gibert(a)uab.es>, Amadeo Caflisch <caflisch(a)bioc.unizh.ch>, Cedric Govaerts <cedric(a)cmpharm.ucsf.edu>, "Howard Chang" <howchang(a)stanford.edu>, Franca Fraternali <ffranca(a)nimr.mrc.ac.uk>, Rosa Angelo <anrosa76(a)gmail.com>, Torsten Schwede <Torsten.Schwede(a)unibas.ch>, Ben Lehner Gmail <lehner.ben(a)gmail.com>, "Tom Misteli" <mistelit(a)mail.nih.gov>, John Overington <joverington(a)mac.com>, Xavier Deupi <xdeupi(a)gmail.com>, Karsten Rippe <Karsten.Rippe(a)bioquant.uni-heidelberg.de>, Jordi Mestres <jmestres(a)imim.es>, Christos Ouzounis <ouzounis(a)certh.gr>, "M. S. Madhusudhan" <madhusudhan(a)iiserpune.ac.in>, Thomas Blundell <tom(a)cryst.bioc.cam.ac.uk>, Tyler Scott Alioto <talioto(a)pcb.ub.cat>, Adam Godzik <adam(a)ljcrf.edu>, "David Baker" <dabaker(a)u.washington.edu>, Toni Gabaldon Estevan <toni.gabaldon(a)crg.eu>, Damien Devos <damien.devos(a)gmail.com>, Job Dekker <jobdekker1(a)gmail.com>, Anna Tramontano <anna.tramontano(a)uniroma1.it>, "Fred Davis" <fred(a)salilab.org>, Gicquel Brigitte <bgicquel(a)pasteur.fr>, "Fatima Al-Shahrour" <falshahrour(a)cnio.es>, Attila Nemeth <attila.nemeth(a)vkl.uni-regensburg.de>, Leonardo Pardo <leonardo.pardo(a)uab.es>, Silvio Tosatto <silvio(a)cribi.unipd.it>, "Francisco Pancho Melo-Ledermann" <pancho.melo(a)gmail.com>, Ana Conesa <aconesa(a)cipf.es>, David Reverter <dreverter(a)yahoo.es>, Francesc Canals <fcanals(a)vhebron.net>, Joan Seoane <jseoane(a)vhio.net>, Jerónimo Bravo <jbravo(a)ibv.csic.es>, Casadio Rita <casadio(a)biocomp.unibo.it>, "Jaume Bertranpetit" <jaume.bertranpetit(a)upf.edu>, Frank Grosveld <f.grosveld(a)erasmusmc.nl>, Mark Gerstein <Mark.Gerstein(a)yale.edu>, "Steven Brenner" <brenner(a)compbio.berkeley.edu>, Joaquin Dopazo <joaquin.dopazo(a)gmail.com>, Tom Ferrin <tef(a)cgl.ucsf.edu>, Baldomero Oliva <baldo.oliva(a)gmail.com>, Eswar Narayanan <eswar.n(a)gmail.com>, Leonid Mirny <leonid(a)mit.edu>, Emanuele Paci <e.paci(a)leeds.ac.uk>, "Antonio Barbadilla Prados" <Antonio.Barbadilla(a)uab.es>, Dmitry Korkin <korkin(a)salilab.org>, Bosi Stefania <stefania.bosi(a)gmail.com>, Agusti Lledos <agusti(a)klingon.uab.es>, "imartins(a)clinic.ub.es" <imartins(a)clinic.ub.es>, Frank Alber <alber(a)usc.edu>, Henk Stunnenberg <H.Stunnenberg(a)ncmls.ru.nl>, Francisco Paco Enguita <fenguita(a)medicina.ulisboa.pt>, Xavier Daura <xavier.daura(a)uab.cat>, Mario Nicodemi <nicodem(a)na.infn.it>, "Marcelo Nollmann" <marcnol(a)gmail.com>, Daniel Jost <daniel.jost(a)imag.fr>, "Edith Heard" <edith.heard(a)curie.fr>, Jim Hughes <jim.hughes(a)imm.ox.ac.uk>, "Stephen Taylor" <stephen.taylor(a)imm.ox.ac.uk>, Wendy Bickmore <Wendy.Bickmore(a)igmm.ed.ac.uk>, Arcadi Navarro <arcadi.navarro(a)upf.edu> > > Dear friends, > > We have two openings for junior group leader positions at the CRG in Barcelona. These are non-tenured, up to 9 year positions for outstanding young scientists to build their research groups. Successful candidates are offered 45 square meters of equipped lab space (that can host up to 7-9 lab members), salaries for the group leader, one postdoc, one PhD student and a technician during the 9 years (plus possibly additional positions through internal open calls), and a consumables annual budget of about 80K EUR. The Institute has strong core facilities and a collegial and collaborative atmosphere that favors strong interactions between the groups. In its 14 years of existence, junior group leaders of the CRG have gone on to senior positions at excellent Institutes, including HemlholtzZentrum Munich, IGBMC Strasbourg, Imperial College London, IRB Barcelona, Oxford University, University of California or University of Vienna. > > More information can be found in this link: > > https://recruitment.crg.eu/content/jobs/position/two-junior-group-leader-po… <https://recruitment.crg.eu/content/jobs/position/two-junior-group-leader-po…> > > The positions are thematically open, with an emphasis on integrative biology, i.e. multidisciplinary efforts that provide integrated views of biological processes. > > I would greatly appreciate if you could bring these positions to the attention of suitable candidates and if you could publicize them widely at your Institutions. > > Many thanks in advance and all the best for the holidays and new year, > > Marc > > ... > OPEN PhD POSITION IN THE LAB! https://recruitment.crg.eu/content/jobs/position/phd-fellowship-structural-… <https://recruitment.crg.eu/content/jobs/position/phd-fellowship-structural-…> > Marc A. Marti-Renom, ICREA Research Professor > Structural Genomics Group Leader > Centre Nacional d’Anàlisi Genòmica - Centre de Regulació Genòmica (CNAG-CRG) > Parc Científic de Barcelona – Torre I (10th floor) > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email: martirenom(a)cnag.crg.eu <mailto:martirenom@cnag.crg.eu> > Web: http://marciuslab.org <http://marciuslab.org/> · http://cnag.crg.eu <http://cnag.crg.eu/> · http://crg.cat <http://crg.cat/> > > CRG PhD positions available at “la Caixa” INPhINIT Doctoral fellowships programme http://www.inphinitlacaixa.org <http://www.inphinitlacaixa.org/> > Application deadline: February 2, 2017 > “This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklowdowska- Curie grant agreement No. 713673” > > *** Consider the environment. Print responsibly. *** > > > > > > > >

1 0

[Compbio-allhands] Fwd: computational chemistry opening at Lilly San Diego
by Andrej Sali 19 Dec '16

19 Dec '16

> Begin forwarded message: > > From: Michal Vieth <vieth_michal(a)lilly.com> > Subject: computational chemistry opening at Lilly San Diego > Date: December 19, 2016 at 7:14:52 AM PST > To: "Andrej Sali (sali(a)salilab.org) (sali(a)salilab.org)" <sali(a)salilab.org> > > https://careers.lilly.com/job/san-diego/research-scientist-computational-ch… <https://careers.lilly.com/job/san-diego/research-scientist-computational-ch…> > > I’m moving there in mid March > > Happy Holidays, > Best, > michal > > > *************************************************************** > Dr hab. Michal Vieth, PhD > Discovery Chemistry Research > Lilly Research Laboratories, Indianapolis, IN 46285 > (317)277-3959, m.vieth(a)lilly.com <mailto:m.vieth@lilly.com> > *************************************************************** > This e-mail message (including any attachments) contains information that may be confidential and/or privileged. If you are not the intended recipient, please do not read, use, copy or disclose to anyone the e-mail message (or attachments) or any information contained in the e-mail message (or attachments). If you have received or obtained this e-mail message (or attachments) in error, please notify the sender by return e-mail (m.vieth(a)lilly.com <mailto:m.vieth@lilly.com>)

1 0

[Compbio-allhands] systems biology talk today
by Grabe, Michael 12 Dec '16

12 Dec '16

Dear Comp Bio folks, Oleg Igoshin will speak today in CVRI about his theory and experiments on the following topic: "Making cell-fate-decisions: lessons from sporulating bacteria” Oleg Igoshin, Ph.D. Associate Professor Dept. of Bioengineering & Center for Theoretical and Biological Physics Rice University Date: Today - Monday December 12, 2016 Time: 2-3 pm Place: CVRI First floor (SC-159) Host: Michael Grabe Please share with anyone that may be interested. Best Michael ---------------------------------------------------------- Michael Grabe Associate Professor University of California, San Francisco Cardiovascular Research Institute Department of Pharmaceutical Chemistry 555 Mission Bay Blvd South, Room 452T, MC 3122 San Francisco, California 94143 415-502-2874 (office) 415-476-8173 (fax)

1 0

[Compbio-allhands] Fwd: NIST/NRC Postdoctoral Research--hydrogen/deuterium exchange MS
by Andrej Sali 12 Dec '16

12 Dec '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Hudgens, Jeffrey W (Fed)" <jeffrey.hudgens(a)nist.gov> > Subject: NIST/NRC Postdoctoral Research--hydrogen/deuterium exchange MS > Date: December 12, 2016 at 7:36:13 AM PST > To: "Hudgens, Jeffrey W (Fed)" <jeffrey.hudgens(a)nist.gov> > > Dear Colleague, > > INVITATION: I wish to invite applications for postdoctoral research at NIST. My laboratory program focuses on topics involving hydrogen/deuterium exchange mass spectrometry (HDX-MS) of proteins and biological drugs; however, theapplicant needs no prior experience in this area. Please forward this e-mail to any candidates who can benefit from this opportunity. > > BACKGROUND: Through a head-to-head competition administered by the National Research Council of the National Academy of Sciences, NIST awards approximately 60 new fellowships to recent PhD recipients in science, mathematics, and engineering. The competition is judged from each applicant’s research proposal, letters of reference, transcripts, and publications. Appointments are for two years at an annual stipend of $67,588 per year, plus moving expenses, an allowance for professional expenses and travel, and cost-shared health insurance. Applicants must be U.S. citizens. > > Associateships are awarded to persons who have held the doctorate for less than five years at the time of application. (Candidates may apply before their PhD degree is conferred.) Electronic applications for the next competition are due on 1 FEB (5:00 PM EST), and supporting documents (e.g., letters, transcripts) must be received by 15 FEB (5:00 PM EST). Postdoctoral appointments are usually announced in late SEP for start dates beginning in JAN-JUN 2016 (sometimes earlier). > > THE PROPOSAL: The application includes a proposal describing research that the candidate will conduct during his/her tenure. My interests are quite broad and afford much creativity to the candidate: > · H/D exchange mass spectrometry (HDX-MS) for biopharmaceutical analysis <http://www.nist.gov/mml/bmd/hdx-ms.cfm> > · Expanding the application of HDX-MS to new protein types, > · Studies of protein-protein and protein-ligand interactions, and > · Enhancing HDX-MS resolution and dynamic range. > > Candidates should contact me to discuss their project and proposal preparation. The formal description of the HDX-MS research opportunity is available at the NRC website. > > Helpful NIST and NRC web-links are: > My Website: https://www.nist.gov/people/jeffrey-w-hudgens <https://www.nist.gov/people/jeffrey-w-hudgens> > My HDX-MS Opportunity: http://nrc58.nas.edu/RAPLab10/Opportunity/Opportunity.aspx?LabCode=50&ROPCD… <http://nrc58.nas.edu/RAPLab10/Opportunity/Opportunity.aspx?LabCode=50&ROPCD…> > NIST Announcement: http://www.nist.gov/iaao/postdoc.cfm <http://www.nist.gov/iaao/postdoc.cfm> > NRC E-Application: http://sites.nationalacademies.org/PGA/RAP/PGA_046398 <http://sites.nationalacademies.org/PGA/RAP/PGA_046398> > > From personal experience I can testify that the NIST/NRC program is a terrific opportunity that enables emergent scientists to jumpstart their careers. I encourage potential candidates to contact me today. > > Best wishes, > > Dr. Jeffrey W. Hudgens (hudgens(a)NIST.gov <mailto:hudgens@NIST.gov>) > Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD 20850 > Tel. 240-314-6485 Fax. 240-314-6255 >

1 0

[Compbio-allhands] Fwd: Junior group leader in bioinformatics, in Krakow, Poland (Jagiellonian University – Malopolska Centre of Biotechnology)
by Andrej Sali 09 Dec '16

09 Dec '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Janusz Bujnicki <iamb(a)genesilico.pl> > Subject: Junior group leader in bioinformatics, in Krakow, Poland (Jagiellonian University – Malopolska Centre of Biotechnology) > Date: December 9, 2016 at 1:28:17 PM PST > To: "Janusz M. Bujnicki" <iamb(a)genesilico.pl> > > Dear All, > > Please spread the word and share this advertisement with anyone who may be interested. > > Thanks, > Janusz > > ----------------------- > > Malopolska Centre of Biotechnology is seeking a talented and dynamic scientist early in his/her career to establish a research group in the field of computational biology/bioinformatics. > > Title > Computational biology Group Leader > > Requirements > Ph.D in computational biology or bioinformatics > An excellent track record of scientific publications > Excellent written and oral communication in English, presentation skills > > Desirable: diverse experience in international, interdisciplinary, and collaborative environment, experience with grant/fellowship applications, project management and supervision of junior researchers > > Responsibilities > Implementing excellent research, leading MCB’s bioinformatics facility staff and managing its computational infrastructure. > > Opportunities > The Team Leader will have the opportunity to develop an innovative research program in their own scientific area of interest and additionally will be expected to collaborate closely with other research teams at the MCB, in the fields of genomics, biochemistry, biotechnology and structural biology, in a highly collaborative and interdisciplinary environment. We offer salary commensurate with experience. In addition, two PhD scholarships and ½ position for technician financed from the MCB budget will be at the disposal of the team leader. > > Applications > Deadline for application is 10th January 2017 > Applications should be submitted in the pdf format (max size: 50 MB) by email to beata.binieda(a)uj.edu.pl Include “Computational Biology Group Leader” and your first and last names in the email subject. > > Applications should include: a curriculum vitae, copies of three most important papers, a short description of one key achievement (up to 1 page), a statement of research interests and a research proposal that takes into account potential collaborations at the MCB (up to 2 pages), and contact details of at least two potential referees. > > The application must contain the following statement: „In accordance with the personal data protection act from 29th August 1997, I hereby agree to process and to store my personal data by the Institution for recruitment purposes”. > > Contact info > e-mail: mcb(a)uj.edu.pl > > Links to Naturejobs.com: > http://www.nature.com/naturejobs/science/jobs/600183-computational-biology-… > and job.sciencecareers.com: > http://jobs.sciencecareers.org/job/434664/computational-biology-group-leade…

1 0

[Compbio-allhands] 12/1/16 Seminar with Ivan Dikic
by Flowers, Nicole 23 Nov '16

23 Nov '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Ivan Dikic University of Frankfurt Ubiquitin and Autophagy Networks in Health and Disease December 1, 2016 N. Jura, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Vertex Fellowship: Seeking Candidates
by Brian Shoichet 17 Nov '16

17 Nov '16

FYI...seems interesting. They are very strong scientifically at Vertex. Brian ---------- Forwarded message ---------- From: Georgia McGaughey <georgia_mcgaughey(a)vrtx.com> Date: Thu, Nov 17, 2016 at 12:05 PM Subject: Vertex Fellowship: Seeking Candidates To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu> Cc: Kelly Lewis <kelly_lewis(a)vrtx.com> Hi Brian, I hope this email finds you well. I’m writing to ask for your help as we seek candidates for the second class of the Vertex Fellows program. Vertex Fellows get to work as part of a team to create transformative medicines for patients with serious diseases, learn about the variety of functions that contribute to getting these medicines to patients, and receive mentorship from senior leaders. Our goal with the Vertex Fellowship is to attract some of the most talented scientists and physicians to join Vertex for one year of immersive learning about the science of discovering and developing medicines, and, in the process, expose us to innovative ways of thinking. The response in our first year was fantastic. We received 134 high quality applications for a handful of positions. The 4 Fellows that joined us in September are enthusiastic about how much they are learning and they are already adding value to our teams. The 2016 Fellows are as follows: · *Bart Borek*, PhD, from the Hasty lab at the BioCircuits Institute at UCSD · *Alexandra Cantley*, PhD, from the Clardy lab at Harvard · *Kevin Daniel*, PhD, from the Langer and Anderson labs at the Koch Institute at MIT · *Rob Komorowski*, PhD, from the Bear lab at the Picower Institute at MIT Each Fellow gets embedded within an existing project team based on his or her interests and experience and our needs. In addition, we provide Fellows with a week of intensive training on the science of drug discovery and the business of creating medicines as well as other group training opportunities throughout the year. The program is intentionally short(one year) so it augments rather than replaces a traditional postdoc, residency or business school experience. We expect to hire 5 - 7 Fellows across our global sites to start in September 2017. We will provide career advice and mentorship to help the fellows as they consider options, including open positions at Vertex, toward the end of the program. I am asking for your help with identifying potential Fellows who would be excited about such an opportunity. *Do you know anyone who might be a good fit? Applications are due by Jan 31.* I'm attaching a 1-page flyer with more information. I’d be particularly grateful if you would pass this along to any potential Fellows whom you think might be interested. Please do let me know what questions or feedback you have about the program. Thanks for your help, -Georgia Georgia McGaughey, Ph.D. *Vertex Pharmaceuticals* 50 Northern Ave, Building A, 3027, Boston, MA 02210 Office: 617.961.1652, Cell: 215.565.6125 g <Anne-Laure_Grillot(a)vrtx.com>eorgia_mcgaughey(a)vrtx.com This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you. -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

1 0

[Compbio-allhands] Hands-On Workshop on Integrative Modeling and Simulations
by Andrej Sali 17 Nov '16

17 Nov '16

Hands-On Workshop on Integrative Modeling and Simulations There's still time to apply for the Hands-On Workshop on Integrative Modeling and Simulations, to be held at UCSF on December 12-16. The workshop is presented jointly by members of the Theoretical and Computational Biophysics Group at UIUC and the group of Andrej Sali at UCSF. Topics will cover biomolecular simulations, visualization, and analysis with NAMD, QwikMD, and VMD, cryo-EM modeling with MDFF and Rosetta-MDFF, and integrative modeling techniques with the IMP software. The full program can be found here: http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco2016/program.html <http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco2016/program.html> Registration is free, however attendance is limited to 25 participants, selected based on application. For more information, and to apply, visit: http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco2016/index.html <http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco2016/index.html> Questions can be addressed to: workshop+sanfran2016(a)ks.uiuc.edu <mailto:workshop+sanfran2016@ks.uiuc.edu><mailto:workshop%2Bsanfran2016@ks.uiuc.edu <mailto:2Bsanfran2016@ks.uiuc.edu>>. -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

1 0

[Compbio-allhands] FW: Stevan Hubbard's seminar on Friday
by Flowers, Nicole 17 Nov '16

17 Nov '16

UCSF Helen Diller Family Comprehensive Cancer Center Friday Seminar Series presents Stevan Hubbard, PhD Professor Skirball Institute of Biomolecular Medicine NYU School of Medicine Structural insights into hyperactivation of JAK2 tyrosine kinase in myeloproliferative neoplams November 18, 2016, 4:00-5:00 PM HD 160 Bakar Auditorium 1450 3rd Street, Helen Diller Family Cancer Research Building Mission Bay Campus Host: Natalia Jura, PhD more info: Geraldine Pacheco email: gpacheco(a)cc.ucsf.edu phone: 476-5448 Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546 From: "Jura, Natalia" <Natalia.Jura(a)ucsf.edu<mailto:Natalia.Jura@ucsf.edu>> Date: Wednesday, November 16, 2016 at 10:49 PM To: Nicole Flowers <nicole.flowers(a)ucsf.edu<mailto:nicole.flowers@ucsf.edu>> Subject: Stevan Hubbard's seminar on Friday Hi Nicole, Could you please forward this announcement to the BBC seminar mailing list? Stevan Hubbard’s seminar is at 4PM this Friday at the Cancer Center. Thank you!, Natalia _ -- Natalia Jura, Ph.D. Assistant Professor Cardiovascular Research Institute MC:3122 Department of Cellular and Molecular Pharmacology University of California San Francisco 555 Mission Bay Blvd South, Rm 452W San Francisco, CA 94158-9001 Phone: 415 514 1133 Fax: 415 476 8173 Lab Website: http://www.cvri.ucsf.edu/~jura

1 0

[Compbio-allhands] 11/17/16 Braisted Lecture with David Eisenberg
by Flowers, Nicole 14 Nov '16

14 Nov '16

UCSF-UCB Andrew Braisted Award Lectureship David Eisenberg, Ph.D. University of California, Los Angeles Pathogenic vs. Reversible Amyloid Thursday, November 17, 2014 4 pm Genentech Hall Byers Auditorium UCSF Mission Bay Campus Simulcast to Parnassus, Room 161 Contact: Jim Wells, Charles Craik Sponsor: The Andrew Braisted Lecture Fund Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 11/10/16 Seminar with Ken Prehoda
by Flowers, Nicole 03 Nov '16

03 Nov '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Ken Prehoda University of Oregon The ties that bind— evolution of a protein interaction domain family November 10, 2016 W. Lim, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Seminar, Dr. Martin Flavius et al, Amgen, “Translating Insights From Human Genetics to Drug Development”
by Andrej Sali 31 Oct '16

31 Oct '16

a broad research presentation by Amgen, aimed at our students, postdocs, and faculty. by their heads of Cardio Metabolic Resdearch (Aarif Khakoo) and Oncology and Inflammation Research (Martin Flavius). RH-102, 12pm, Mon Oct 31 -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

1 1

[Compbio-allhands] 11/3/16 Seminar with Jason Moore
by Flowers, Nicole 28 Oct '16

28 Oct '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Jason Moore University of Pennsylvania An Automated Data Science Assistant November 3, 2016 R. Hernandez, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] FoldIt development job posting
by Matthew O'Meara 26 Oct '16

26 Oct '16

---------- Forwarded message ---------- From: Steven Combs <steven.combs1(a)gmail.com> Date: Wed, Oct 26, 2016 at 10:00 AM Subject: job posting To: Matthew O'Meara <mattjomeara(a)gmail.com>, Scott Horowitz < horowsah(a)umich.edu> Hi Matt, Could you post htis to the compbio-allhands mailing list board? We are looking for a developer for Foldit. They would be HHMI employee. Foldit Developer Position: The Bardwell laboratory and the Foldit development team are looking to hire a computer programmer to develop the Foldit game. Foldit is a computer game that challenges players to solve real biochemistry problems. The candidate would interface with current Foldit developers and experimental collaborators to improve the ability of Foldit to interface with biochemical data. The ideal candidate would have considerable programming experience in C++ and experience with large-scale code-bases. Past experience or knowledge of biochemistry, molecular biology, or X-ray crystallography is recommended. Work location could be at the primary Foldit development site in Seattle, or tertiary sites in Boston or Ann Arbor. Salary will be determined based on education level and experience. If interested, please contact Molly Wysong at mewysong(a)umich.edu.

1 0

[Compbio-allhands] 10/27/16 Seminar with Roberto Chica- GH N114
by Flowers, Nicole 21 Oct '16

21 Oct '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall N114 Livestream: https://lecture.ucsf.edu/ets/Catalog/Full/f94c469bb908465691ec810f578ecbb221 Roberto Chica University of Ottawa Engineering protein conformational landscapes using multistage computational protein design October 27, 2016 J. Fraser, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: 12 postdoc positions in Montpellier. One in NMR of disordered proteins
by Andrej Sali 21 Oct '16

21 Oct '16

> Begin forwarded message: > > From: pau bernado <pau.bernado(a)cbs.cnrs.fr> > Subject: 12 postdoc positions in Montpellier. One in NMR of disordered proteins > Date: October 21, 2016 at 4:16:56 AM PDT > To: pau bernado <pau.bernado(a)cbs.cnrs.fr> > > Dear Colleague, > > I would like to draw your attention to the opening of 12 postdoctoral positions in Montpellier funded by the EpiGenMed Labex program (https://www.epigenmed.fr <https://www.epigenmed.fr/>). One of these position is for a two-year postdoc in NMR to work in our group at the Centre de Biochimie Structurale (CBS) in Montpellier. > > The project focuses in the study of a family of Intrinsically Disordered Proteins that modulate Nuclear Receptor gene transcription. Successful candidates should have a strong background in solution NMR. Expertise in protein expression and purification is highly recommended. Previous experience in Small-Angle X-ray Scattering (SAXS) and computational methods will be positively evaluated. Find attached a more detailed description of the position. Please, spread this information to students or postdocs that could be interested. > > Thanks a lot for your collaboration and best regards > > Pau Bernadó

1 0

[Compbio-allhands] seminar TODAY, Jan Ellenberg, "Imaging the assembly of protein complexes and the dynamics of protein networks in dividing human cells"
by Andrej Sali 19 Oct '16

19 Oct '16

TODAY, 12pm, Oct 19, MH-1406 eg, https://elifesciences.org/content/5/e19071 -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

1 1

[Compbio-allhands] Fwd: An announcement from COMP Together at UCSF 2016-10-26
by Magdalena Korczynska 18 Oct '16

18 Oct '16

> Begin forwarded message: > > From: comp_together(a)acscomp.org > Subject: An announcement from COMP Together > Date: October 14, 2016 at 1:28:40 PM PDT > To: Magdalena Korczynska <mkucsf(a)gmail.com> > Reply-To: Siegfried Leung <siegfried.leung(a)circlepharma.com> > > The COMP Together champions in your area would like to announce the following event: > > Speaker: Eric Martin (Novartis), BinQing Wei (Genentech) > Title: SF Bay Area COMP Together Mini-Talk Series > Date: 2016-10-26 > Time: 6:30 PM > Event ID: 35 > Sponsor: NIBR > > Location > UCSF Mission Bay > 1700 4th St. BH212 > > San Francisco CA 94158 > > Description and Notes > Schedule: > > 6:30 – 7 pm: check-in & networking (pizza and drinks provided) > > 7 – 7:30 pm: Talk #1 > Title: Rational Bioavailability Design: Global Sensitivity Analysis of Physiologically-Based Pharmacokinetics (GSA of PBPK) > Speaker: Eric Martin (Novartis) > > 7:30 – 8.00 pm: Talk #2 > Title: Computational Design of Non-peptide Linkers with Restricted Protease Cleavability for Antibody-Drug Conjugates > Speaker: BinQing Wei (Genentech) > > Notes: > Non-UCSF affiliated participants please enter through the main entrance of Genentech Hall (600 16th St., San Francisco, CA 94158) and sign in at the security desk. > > Public parking is available at the UCSF Mission Bay surface lots. For more information, please visit: > http://campuslifeservices.ucsf.edu/transportation/services/parking/public_p… > > On-street parking is also available on 4th street and 16th street. > > > If you would like to attend this COMP Together event, please visit the COMP website and register using the > http://app.acscomp.org/COMP_Together/meeting_signup.php?event_id=35. > > If you have any questions about this event, please contact Siegfried Leung at 6503181743 or siegfried.leung(a)circlepharma.com. > > If you would like to update your COMP Together registration or unsubscribe, please visit http://app.acscomp.org/COMP_Together/reg_update/update_login.php

1 0

[Compbio-allhands] Fwd: AMMA: PhD position (Auckland, New Zealand & A*STAR, Singapore)
by Andrej Sali 18 Oct '16

18 Oct '16

> Begin forwarded message: > > From: Elizabeth Yuriev <elizabeth.yuriev(a)monash.edu> > Subject: AMMA: PhD position (Auckland, New Zealand & A*STAR, Singapore) > Date: October 18, 2016 at 4:02:56 PM PDT > To: undisclosed-recipients:; > > sent on behalf of Jane Allison > > > > A PhD position is available on computational studies of antimicrobial peptides and cell membranes, to be hosted between my research group at Massey University (Auckland, New Zealand) and that of Peter Bond (A*STAR, Singapore) - see attached for more information. I would greatly appreciate it if you could circulate this to any students whom you think might be interested, and/or advertise it further in your Institute or department. > > Many thanks, > > Jane > > > -- > > Jane R Allison > Senior Lecturer > Rutherford Discovery Fellow > Institute of Natural and Mathematical Sciences Massey University Auckland New Zealand > > > > > > > > Cheers, > Elizabeth > > ********************************************** > Dr Elizabeth Yuriev > Secretary, Association of Molecular Modellers of Australasia (AMMA) > Senior Lecturer, Faculty of Pharmacy and Pharmaceutical Sciences > Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences > Monash University (Parkville Campus), 381 Royal Parade, Parkville VIC 3052, Australia > Tel: Int +61 3 9903 9611, E-mail: elizabeth.yuriev(a)monash.edu <mailto:elizabeth.yuriev@monash.edu>, www.pharm.monash.edu.au <http://www.pharm.monash.edu.au/> >

1 0

[Compbio-allhands] Fwd: Bioinformatics Software Developer - Mike Sternberg's Group Imperial - Protein Structure and Disease Variants
by Andrej Sali 17 Oct '16

17 Oct '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: FW: Bioinformatics Software Developer - Mike Sternberg's Group Imperial - Protein Structure and Disease Variants > Date: October 17, 2016 at 1:31:30 PM PDT > To: Undisclosed recipients:; > > > Dear Colleague/ I’d be grateful if you would let suitable applicants know of this opportunity. > > ------------------------------------------------------------------------------------------------------------------------------- > > Bioinformatics Software Developer : Mapping genetic variants to protein structures > Group of Prof Mike Sternberg > Department of Life Sciences > South Kensington Campus > Imperial College London > > Salary £35,140-£43,350 per annum > > Applications are invited for a Bioinformatics Software Developer to join the Structural Bioinformatics Group. The post holder will work as a member of a small team developing the software for the PhyreRisk portal which will provide a dynamic web portal to deliver to the community a resource relating human genetic variation, disease, protein structure and biological pathways. > > You must have a Masters in bioinformatics or a closely related discipline in computational biology or vocational qualification and experience in a relevant role. A PhD Degree (or equivalent) in bioinformatics or a closely related discipline in computational biology is desirable. You must have demonstrable strong programming experience developing a substantive dynamic web site to a professional standard using HTML/JavaScript/Django and server side languages (Java, Perl-CGI) applied to a biological problem is essential. You must also have a proven programming experience that results in the development of at least two of the following within a biological context: (i) a substantive and robust algorithm, (ii) a substantial dynamic web-site or (iii) a substantial relational database. > > This is a full time position, funded by the Wellcome Trust for up to 36 months. > Closing date is > 6 November 2016 (midnight GMT) > > For informal enquiries contact Prof Mike Sternberg > m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > > For application procedure and further details see: > https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf… <https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf…> > > > > > ******************************************** > Professor Michael J E Sternberg > Director Centre for Integrative Systems Biology and Bioinfomatics (CISBIO) > Room 306 - Sir Ernst Chain Building > Department of Life Sciences > Imperial College London, London SW7 2AZ,UK > m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > http://www3.imperial.ac.uk/cisbio <http://www3.imperial.ac.uk/cisbio> (CISBIO) > www.sbg.bio.imperial.ac.uk <http://www.sbg.bio.imperial.ac.uk/> (Group's research) > > Tel +44 (0)20 7594 5212 > ****************************************************************************

1 0

[Compbio-allhands] seminar, Jan Ellenberg, "Imaging the assembly of protein complexes and the dynamics of protein networks in dividing human cells"
by Andrej Sali 17 Oct '16

17 Oct '16

12pm, Oct 19, MH-1406 -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

1 0

[Compbio-allhands] Seminar, Jan Ellenberg, “Imaging the assembly of protein complexes and the dynamics of protein networks in dividing human cells”
by Andrej Sali 14 Oct '16

14 Oct '16

Wed, Oct 19, 12-1pm, MH-1406 -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

1 0

[Compbio-allhands] 10/20/16 Seminar with Yong Xiong
by Flowers, Nicole 14 Oct '16

14 Oct '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Yong Xiong Yale HIV Capsid Pattern Sensing by the Host October 20, 2016 J. Gross, Host This seminar is sponsored by the HARC Center BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Following up: recruiting postdoc for GROMACS improvements and development
by Jacobson, Matt 12 Oct '16

12 Oct '16

- Matt Begin forwarded message: From: Michael R Shirts <Michael.Shirts(a)Colorado.EDU<mailto:Michael.Shirts@Colorado.EDU>> Subject: Following up: recruiting postdoc for GROMACS improvements and development Date: October 12, 2016 at 4:18:09 PM PDT To: Michael R Shirts <Michael.Shirts(a)Colorado.EDU<mailto:Michael.Shirts@Colorado.EDU>> Cc: Peter Kasson <kasson(a)virginia.edu<mailto:kasson@virginia.edu>> Hi, all- Thanks very much for the responses to my previous email. We have hired one postdoc (located at the U. of Virginia) on the NIH-sponsored collaborative project to improve GROMACS robustness and functionality I emailed you about before. However, I am still recruiting one postdoctoral researcher to join my group here at CU Boulder. Perhaps you knew someone for whom this fall was not a good starting time, but January might be; we’d love to hear from them. As discussed before, the work on the Colorado side involves statistical physics to test and diagnose simulation validity, improving the testing framework, and new Monte Carlo methods. Strong software engineering skills are a must, and we would particularly appreciate active members of the molecular simulation development community. As always, members of groups under-represented in the molecular simulation field are especially encouraged to apply. Please refer anyone you think appropriate or have them apply at the link below. The Shirts research group in the Department of Chemical and Biological Engineering is hiring a highly capable research associate to help develop the GROMACS molecular simulation package. GROMACS is an open-source project with a strong international development community as well as a 10,000+ user base. This position is part of a new NIH funded collaborative effort between the Shirts group and the Kasson group (at the University of Virginia) to improve the robustness, functionality, and usability of GROMACS, offering the candidate the opportunity to positively affect the work of thousands of researchers across the globe. Candidates will have the opportunity to learn state-of-the-art simulation methodology and work collaboratively with a global team of developers. This position requires a Ph.D. in Chemistry, Chemical Engineering, Physics, Computer Science or a related field. It requires very strong statistical mechanical, molecular simulation and theoretical skills, as well as significant software engineering experience and ability. Experience in C++ and Python is preferred, as well as experience with version control, code review systems, and team-oriented software development. Competitive candidates will have a track record of scientific success in graduate study with a strong publication record. Apply at https://cu.taleo.net/careersection/2/jobdetail.ftl?job=05979&lang=en&sns_id… ~~~~~~~~~~~~~~~~ Michael Shirts Associate Professor michael.shirts(a)colorado.edu<mailto:michael.shirts@colorado.edu> http://www.colorado.edu/lab/shirtsgroup/ Phone: (303) 735-7860 Office: JSCBB C123 Department of Chemical and Biological Engineering University of Colorado Boulder

1 0

[Compbio-allhands] 10/13/16 Seminar with Eckhard Jankowsky
by Flowers, Nicole 07 Oct '16

07 Oct '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Eckhard Jankowsky Case Western RNA helicases in translation initiation and granule formation. October 13, 2016 J. Gross & D. Weinberg, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 10/6/16 Seminar with Jonathan Gable
by Flowers, Nicole 06 Oct '16

06 Oct '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Jonathan Gable Clements Lecture Targeting a Dynamic Protein-Protein Interface to Inhibit a Critical Herpesvirus Enzyme October 6, 2016 D. Agard, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 1

[Compbio-allhands] 10/4/16 Seminar with Ruth Ley
by Flowers, Nicole 04 Oct '16

04 Oct '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Tuesday, 12 Noon Genentech Hall Auditorium NO SIMULCAST Ruth Ley Max Planck Institute Tübingen Genetic determinants of the gut micro biome and links to phenotype October 4, 2016 S. Lyalina, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 1

[Compbio-allhands] Knapp Seminar (Monday October 3rd 2:30 pm, CVRI 441)
by Grabe, Michael 02 Oct '16

02 Oct '16

Hi everyone, I wanted to remind you of the following lecture tomorrow: Walter Knapp Free University of Berlin Computing pKa values in proteins Smith CVRI Building 4th floor Room 441 Monday October 3rd 2:30 pm Walter’s website can be found here: http://agknapp.chemie.fu-berlin.de/agknapp/ Please share this posting with interested members of your lab. Best Michael PS - I apologize if you get this email twice. ---------------------------------------------------------- Michael Grabe Associate Professor University of California, San Francisco Cardiovascular Research Institute Department of Pharmaceutical Chemistry 555 Mission Bay Blvd South, Room 452T, MC 3122 San Francisco, California 94143 415-502-2874 (office) 415-476-8173 (fax)

1 0

[Compbio-allhands] Seminar in CVRI (Walter Knapp)
by Grabe, Michael 27 Sep '16

27 Sep '16

Hi everyone, Walter Knapp from the Free University of Berlin will be visiting my lab next Monday October 3rd and giving a seminar in CVRI titled: Computing pKa values in proteins Smith CVRI Building 4th floor Room 441 Monday October 3rd 2:30 pm Walter’s website can be found here: http://agknapp.chemie.fu-berlin.de/agknapp/ Please share this posting with anyone that may be interested, and let me know if you want to meet with him during the day. Best Michael l---------------------------------------------------------- Michael Grabe Associate Professor University of California, San Francisco Cardiovascular Research Institute Department of Pharmaceutical Chemistry 555 Mission Bay Blvd South, Room 452T, MC 3122 San Francisco, California 94143 415-502-2874 (office) 415-476-8173 (fax)

1 0

[Compbio-allhands] Fwd: Faculty position openings
by Jacobson, Matt 25 Sep '16

25 Sep '16

Not sure which lists this has gone out to so apologies if it’s a duplicate - Matt Begin forwarded message: From: Talent Project <talents(a)cuhk.edu.cn<mailto:talents@cuhk.edu.cn>> Subject: Faculty position openings Date: September 25, 2016 at 5:25:03 PM PDT To: Talent Project <talents(a)cuhk.edu.cn<mailto:talents@cuhk.edu.cn>> Dear Colleague, We have the pleasure to announce an ambitious hiring plan for faculty members at all ranks in areas of Science and Engineering at The Chinese University of Hong Kong, Shenzhen [CUHK(SZ)]. CUHK(SZ) is a research intensive University executed with the highest international standards and traditions. English is the official language. The University extends the core values and educational philosophy of The Chinese University of Hong Kong, Hong Kong. Operated under a modern and transparent management system that values academic freedom, CUHK(SZ) contributes to higher education by nurturing graduates at all levels with broad international outlook, sound scholarship and commitment to society. Besides education, the University also contributes to the long-term prosperity of Shenzhen and China by its leading work in research and entrepreneurship. The campus (http://www.cuhk.edu.cn/en/index.html) is located in a picturesque area of Shenzhen (http://www.eyeshenzhen.com/, http://v.qq.com/x/page/m0308sptsyb.html) one of the fastest growing communities in the World. The University offers the right candidate an excellent salary package, competitive startup funds and space. The City and Longang Municipal District also offer generous signing bonuses and financial incentives (http://www.cuhk.edu.cn/UploadFiles/TalentsProgramOutline.pdf) While the University welcomes applicants from all areas of expertise, current strengths include Computer Science and Engineering, Electronic Information Engineering, Robotics and Control, New Energy Science and Engineering, Statistics and Data Science, Mathematics and Applied Mathematics, Bioinformatics, Biological Sciences and Biomedical Engineering, Design and Manufacturing Systems, Physics, Chemistry, and Materials Science. A number of multi-million dollar research centers have already been set up. Cluster hiring for the right groups are also considered. The University expects to hire 150 to 200 new faculty in the next five years. By joining us, the person will become a member of one of the best run educational and research institutions in the world. We should be much obliged if you would kindly broadcast this information to those who might be interested in this announcement. For interested individuals, please send CV and/or inquiries to talents4sse(a)cuhk.edu.cn<mailto:talents4sse@cuhk.edu.cn>. Sincerely, S Y Tong (David) Director, President’s Special Unit in Faculty Recruitment The Chinese University of Hong Kong, Shenzhen

1 0

[Compbio-allhands] 9/29/16 Seminar with Jennifer Cochran
by Flowers, Nicole 22 Sep '16

22 Sep '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Jennifer Cochran Stanford Engineered Proteins for Visualizing and Treating Cancer September 29, 2016 B. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 9/22/16 Seminar with Grant Jensen- NOTE ROOM
by Flowers, Nicole 22 Sep '16

22 Sep '16

Just a reminder that today’s BBC Seminar will be in Mission Hall 1400. Thank you, Nicole Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546 From: Nicole Flowers <nicole.flowers(a)ucsf.edu<mailto:nicole.flowers@ucsf.edu>> Date: Friday, September 16, 2016 at 9:44 AM To: CCB Student List <CCB_STUDENTS(a)LISTSRV.UCSF.EDU<mailto:CCB_STUDENTS@LISTSRV.UCSF.EDU>>, BMI Students List <BMI_STUDENTS(a)LISTSRV.UCSF.EDU<mailto:BMI_STUDENTS@LISTSRV.UCSF.EDU>>, "bpstudents(a)listserv.ucsf.edu<mailto:bpstudents@listserv.ucsf.edu>" <bpstudents(a)listserv.ucsf.edu<mailto:bpstudents@listserv.ucsf.edu>>, "BBCFACULTY(a)LISTSRV.UCSF.EDU<mailto:BBCFACULTY@LISTSRV.UCSF.EDU>" <BBCFACULTY(a)LISTSRV.UCSF.EDU<mailto:BBCFACULTY@LISTSRV.UCSF.EDU>> Cc: "Alvarez-Buylla, Arturo" <AlvarezBuyllaA(a)ucsf.edu<mailto:AlvarezBuyllaA@ucsf.edu>>, "abul.abbas(a)ucsf.edu<mailto:abul.abbas@ucsf.edu>" <abul.abbas(a)ucsf.edu<mailto:abul.abbas@ucsf.edu>>, "adam.gazzaley(a)ucsf.edu<mailto:adam.gazzaley@ucsf.edu>" <adam.gazzaley(a)ucsf.edu<mailto:adam.gazzaley@ucsf.edu>>, "allan.basbaum(a)ucsf.edu<mailto:allan.basbaum@ucsf.edu>" <allan.basbaum(a)ucsf.edu<mailto:allan.basbaum@ucsf.edu>>, "Butte, Atul" <Atul.Butte(a)ucsf.edu<mailto:Atul.Butte@ucsf.edu>>, "brian.black(a)ucsf.edu<mailto:brian.black@ucsf.edu>" <brian.black(a)ucsf.edu<mailto:brian.black@ucsf.edu>>, "Hueschen, Christina" <Christina.Hueschen(a)ucsf.edu<mailto:Christina.Hueschen@ucsf.edu>>, "Cunha, Gerald" <gerald.cunha(a)ucsf.edu<mailto:gerald.cunha@ucsf.edu>>, "david.erle(a)ucsf.edu<mailto:david.erle@ucsf.edu>" <david.erle(a)ucsf.edu<mailto:david.erle@ucsf.edu>>, David Morgan <david.morgan(a)ucsf.edu<mailto:david.morgan@ucsf.edu>>, Deanna Kroetz <deanna.kroetz(a)ucsf.edu<mailto:deanna.kroetz@ucsf.edu>>, "edward.goetzl(a)ucsf.edu<mailto:edward.goetzl@ucsf.edu>" <edward.goetzl(a)ucsf.edu<mailto:edward.goetzl@ucsf.edu>>, "Gupta, Nalin" <Nalin.Gupta(a)ucsf.edu<mailto:Nalin.Gupta@ucsf.edu>>, "hal.chapman(a)ucsf.edu<mailto:hal.chapman@ucsf.edu>" <hal.chapman(a)ucsf.edu<mailto:hal.chapman@ucsf.edu>>, "Bourne, Henry" <Henry.Bourne(a)ucsf.edu<mailto:Henry.Bourne@ucsf.edu>>, "jason.cyster(a)ucsf.edu<mailto:jason.cyster@ucsf.edu>" <jason.cyster(a)ucsf.edu<mailto:jason.cyster@ucsf.edu>>, "Chang, Jeremy" <Jeremy.Chang(a)ucsf.edu<mailto:Jeremy.Chang@ucsf.edu>>, "Ye, Chun" <Jimmie.Ye(a)ucsf.edu<mailto:Jimmie.Ye@ucsf.edu>>, Joachim Li <joachim.li(a)ucsf.edu<mailto:joachim.li@ucsf.edu>>, "john.rubenstein(a)ucsf.edu<mailto:john.rubenstein@ucsf.edu>" <john.rubenstein(a)ucsf.edu<mailto:john.rubenstein@ucsf.edu>>, "jon.levine(a)ucsf.edu<mailto:jon.levine@ucsf.edu>" <jon.levine(a)ucsf.edu<mailto:jon.levine@ucsf.edu>>, "Thompson-Peer, Katherine" <Katherine.Thompson-Peer(a)ucsf.edu<mailto:Katherine.Thompson-Peer@ucsf.edu>>, Keith Mostov <keith.mostov(a)ucsf.edu<mailto:keith.mostov@ucsf.edu>>, "Kriegstein, Arnold" <Arnold.Kriegstein(a)ucsf.edu<mailto:Arnold.Kriegstein@ucsf.edu>>, "larry.tecott(a)ucsf.edu<mailto:larry.tecott@ucsf.edu>" <larry.tecott(a)ucsf.edu<mailto:larry.tecott@ucsf.edu>>, "Lowenstein, Daniel" <Lowenstein(a)ucsf.edu<mailto:Lowenstein@ucsf.edu>>, "Lee-Baird, Marissa" <Marissa.Lee-Baird(a)ucsf.edu<mailto:Marissa.Lee-Baird@ucsf.edu>>, "mary.dallman(a)ucsf.edu<mailto:mary.dallman@ucsf.edu>" <mary.dallman(a)ucsf.edu<mailto:mary.dallman@ucsf.edu>>, "mary.elting(a)ucsf.edu<mailto:mary.elting@ucsf.edu>" <mary.elting(a)ucsf.edu<mailto:mary.elting@ucsf.edu>>, "Matija.Peterlin(a)ucsf.edu<mailto:Matija.Peterlin@ucsf.edu>" <Matija.Peterlin(a)ucsf.edu<mailto:Matija.Peterlin@ucsf.edu>>, Melissa Paraiso <Melissa.Paraiso(a)ucsf.edu<mailto:Melissa.Paraiso@ucsf.edu>>, Mike Wilson <Michael.A.Wilson(a)nasa.gov<mailto:Michael.A.Wilson@nasa.gov>>, "michael.lazarus(a)ucsf.edu<mailto:michael.lazarus@ucsf.edu>" <michael.lazarus(a)ucsf.edu<mailto:michael.lazarus@ucsf.edu>>, "millo.pasquini(a)ucsf.edu<mailto:millo.pasquini@ucsf.edu>" <millo.pasquini(a)ucsf.edu<mailto:millo.pasquini@ucsf.edu>>, Noleine Blizzard <Noleine.Blizzard(a)ucsf.edu<mailto:Noleine.Blizzard@ucsf.edu>>, "pao-tien.chuang(a)ucsf.edu<mailto:pao-tien.chuang@ucsf.edu>" <pao-tien.chuang(a)ucsf.edu<mailto:pao-tien.chuang@ucsf.edu>>, Peter Sargent <peter.sargent(a)ucsf.edu<mailto:peter.sargent@ucsf.edu>>, "Philip.Coffino(a)ucsf.edu<mailto:Philip.Coffino@ucsf.edu>" <Philip.Coffino(a)ucsf.edu<mailto:Philip.Coffino@ucsf.edu>>, "Philippe.Gascard(a)ucsf.edu<mailto:Philippe.Gascard@ucsf.edu>" <Philippe.Gascard(a)ucsf.edu<mailto:Philippe.Gascard@ucsf.edu>>, "pui.kwok(a)ucsf.edu<mailto:pui.kwok@ucsf.edu>" <pui.kwok(a)ucsf.edu<mailto:pui.kwok@ucsf.edu>>, Raul Andino <Raul.Andino(a)ucsf.edu<mailto:Raul.Andino@ucsf.edu>>, "rik.derynck(a)ucsf.edu<mailto:rik.derynck@ucsf.edu>" <rik.derynck(a)ucsf.edu<mailto:rik.derynck@ucsf.edu>>, "Nicoll, Roger" <Roger.Nicoll(a)ucsf.edu<mailto:Roger.Nicoll@ucsf.edu>>, "Packman, Seymour" <Seymour.Packman(a)ucsf.edu<mailto:Seymour.Packman@ucsf.edu>>, "Sam.Pleasure(a)ucsf.edu<mailto:Sam.Pleasure@ucsf.edu>" <Sam.Pleasure(a)ucsf.edu<mailto:Sam.Pleasure@ucsf.edu>>, "Scott.Baraban(a)ucsf.edu<mailto:Scott.Baraban@ucsf.edu>" <Scott.Baraban(a)ucsf.edu<mailto:Scott.Baraban@ucsf.edu>>, "Hickey, Scott" <Scott.Hickey(a)ucsf.edu<mailto:Scott.Hickey@ucsf.edu>>, "shaun.coughlin(a)ucsf.edu<mailto:shaun.coughlin@ucsf.edu>" <shaun.coughlin(a)ucsf.edu<mailto:shaun.coughlin@ucsf.edu>>, "Sretavan, David" <David.Sretavan(a)ucsf.edu<mailto:David.Sretavan@ucsf.edu>>, "takashi.mikawa(a)ucsf.edu<mailto:takashi.mikawa@ucsf.edu>" <takashi.mikawa(a)ucsf.edu<mailto:takashi.mikawa@ucsf.edu>>, Thanh Lam <thanh.lam(a)ucsf.edu<mailto:thanh.lam@ucsf.edu>>, "thea.tlsty(a)ucsf.edu<mailto:thea.tlsty@ucsf.edu>" <thea.tlsty(a)ucsf.edu<mailto:thea.tlsty@ucsf.edu>>, "Ullian, Erik" <Erik.Ullian(a)ucsf.edu<mailto:Erik.Ullian@ucsf.edu>>, "Yee, Laura" <Laura.Yee2(a)ucsf.edu<mailto:Laura.Yee2@ucsf.edu>>, "Shen, Yin" <Yin.Shen(a)ucsf.edu<mailto:Yin.Shen@ucsf.edu>>, "ying-hui.fu(a)ucsf.edu<mailto:ying-hui.fu@ucsf.edu>" <ying-hui.fu(a)ucsf.edu<mailto:ying-hui.fu@ucsf.edu>>, "YuhNung.Jan(a)ucsf.edu<mailto:YuhNung.Jan@ucsf.edu>" <YuhNung.Jan(a)ucsf.edu<mailto:YuhNung.Jan@ucsf.edu>>, "Balmain, Allan" <Allan.Balmain(a)ucsf.edu<mailto:Allan.Balmain@ucsf.edu>>, "akreitzer(a)gladstone.ucsf.edu<mailto:akreitzer@gladstone.ucsf.edu>" <akreitzer(a)gladstone.ucsf.edu<mailto:akreitzer@gladstone.ucsf.edu>>, "Albertson, Donna" <Donna.albertson(a)ucsf.edu<mailto:Donna.albertson@ucsf.edu>>, "allhands(a)compbio.ucsf.edu<mailto:allhands@compbio.ucsf.edu>" <allhands(a)compbio.ucsf.edu<mailto:allhands@compbio.ucsf.edu>>, "Weiss, Art" <Art.Weiss(a)ucsf.edu<mailto:Art.Weiss@ucsf.edu>>, "barondes(a)cgl.ucsf.edu<mailto:barondes@cgl.ucsf.edu>" <barondes(a)cgl.ucsf.edu<mailto:barondes@cgl.ucsf.edu>>, "Cheyette, Ben" <bc(a)ucsf.edu<mailto:bc@ucsf.edu>>, "Bhatnagar, Rajendr" <Rajendr.Bhatnagar(a)ucsf.edu<mailto:Rajendr.Bhatnagar@ucsf.edu>>, "bishop(a)cgl.ucsf.edu<mailto:bishop@cgl.ucsf.edu>" <bishop(a)cgl.ucsf.edu<mailto:bishop@cgl.ucsf.edu>>, Jeff Blaney <blaney.jeff(a)gene.com<mailto:blaney.jeff@gene.com>>, "Seaman, William" <William.Seaman(a)ucsf.edu<mailto:William.Seaman@ucsf.edu>>, Robert Chalkley <chalkley(a)cgl.ucsf.edu<mailto:chalkley@cgl.ucsf.edu>>, "charles.ordahl(a)ucsf.edu<mailto:charles.ordahl@ucsf.edu>" <charles.ordahl(a)ucsf.edu<mailto:charles.ordahl@ucsf.edu>>, "chris(a)phy.ucsf.edu<mailto:chris@phy.ucsf.edu>" <chris(a)phy.ucsf.edu<mailto:chris@phy.ucsf.edu>>, "Cleaver, James" <James.Cleaver(a)ucsf.edu<mailto:James.Cleaver@ucsf.edu>>, "clifford.lowell(a)ucsf.edu<mailto:clifford.lowell@ucsf.edu>" <clifford.lowell(a)ucsf.edu<mailto:clifford.lowell@ucsf.edu>>, "cope(a)phy.ucsf.edu<mailto:cope@phy.ucsf.edu>" <cope(a)phy.ucsf.edu<mailto:cope@phy.ucsf.edu>>, "damsky(a)cgl.ucsf.edu<mailto:damsky@cgl.ucsf.edu>" <damsky(a)cgl.ucsf.edu<mailto:damsky@cgl.ucsf.edu>>, "david.wofsy(a)ucsf.edu<mailto:david.wofsy@ucsf.edu>" <david.wofsy(a)ucsf.edu<mailto:david.wofsy@ucsf.edu>>, "Sheppard, Dean" <Dean.Sheppard(a)ucsf.edu<mailto:Dean.Sheppard@ucsf.edu>>, "defranco(a)cgl.ucsf.edu<mailto:defranco@cgl.ucsf.edu>" <defranco(a)cgl.ucsf.edu<mailto:defranco@cgl.ucsf.edu>>, "Hanahan, Doug" <Doug.Hanahan(a)ucsf.edu<mailto:Doug.Hanahan@ucsf.edu>>, "dieter.gruenert(a)ucsf.edu<mailto:dieter.gruenert@ucsf.edu>" <dieter.gruenert(a)ucsf.edu<mailto:dieter.gruenert@ucsf.edu>>, Dirk Bussiere <dirksen.bussiere(a)novartis.com<mailto:dirksen.bussiere@novartis.com>>, "Ron, Dorit" <Dorit.Ron(a)ucsf.edu<mailto:Dorit.Ron@ucsf.edu>>, "dsrivastava(a)gladstone.ucsf.edu<mailto:dsrivastava@gladstone.ucsf.edu>" <dsrivastava(a)gladstone.ucsf.edu<mailto:dsrivastava@gladstone.ucsf.edu>>, Erin Simonds <erin.simonds(a)gmail.com<mailto:erin.simonds@gmail.com>>, "fathi.karouia(a)nasa.gov<mailto:fathi.karouia@nasa.gov>" <fathi.karouia(a)nasa.gov<mailto:fathi.karouia@nasa.gov>>, "Brodsky, Frances" <Frances.Brodsky(a)ucsf.edu<mailto:Frances.Brodsky@ucsf.edu>>, Kati Medzihradszky <folkl(a)cgl.ucsf.edu<mailto:folkl@cgl.ucsf.edu>>, "gail.r.martin(a)ucsf.edu<mailto:gail.r.martin@ucsf.edu>" <gail.r.martin(a)ucsf.edu<mailto:gail.r.martin@ucsf.edu>>, "Davis, Graeme" <Graeme.Davis(a)ucsf.edu<mailto:Graeme.Davis@ucsf.edu>>, "gevan(a)cc.ucsf.edu<mailto:gevan@cc.ucsf.edu>" <gevan(a)cc.ucsf.edu<mailto:gevan@cc.ucsf.edu>>, "Jan , Lily" <Lily.Jan(a)ucsf.edu<mailto:Lily.Jan@ucsf.edu>>, "Guo, Su" <Su.Guo(a)ucsf.edu<mailto:Su.Guo@ucsf.edu>>, Christine Guthrie <guthrie(a)cgl.ucsf.edu<mailto:guthrie@cgl.ucsf.edu>>, "heberleinu(a)janelia.hhmi.org<mailto:heberleinu@janelia.hhmi.org>" <heberleinu(a)janelia.hhmi.org<mailto:heberleinu@janelia.hhmi.org>>, "hjr(a)phy.ucsf.edu<mailto:hjr@phy.ucsf.edu>" <hjr(a)phy.ucsf.edu<mailto:hjr@phy.ucsf.edu>>, "Horton, Jonathan" <Jonathan.Horton(a)ucsf.edu<mailto:Jonathan.Horton@ucsf.edu>>, "hypusine(a)gmail.com<mailto:hypusine@gmail.com>" <hypusine(a)gmail.com<mailto:hypusine@gmail.com>>, "Bluestone, Jeffrey (Private)" <Jeff.Bluestone(a)ucsf.edu<mailto:Jeff.Bluestone@ucsf.edu>>, "Lansman, Jeffry" <jeff.lansman(a)ucsf.edu<mailto:jeff.lansman@ucsf.edu>>, "Engel, Joanne" <Joanne.Engel(a)ucsf.edu<mailto:Joanne.Engel@ucsf.edu>>, "Fike, John" <John.Fike(a)ucsf.edu<mailto:John.Fike@ucsf.edu>>, "Imboden, John" <john.imboden(a)ucsf.edu<mailto:john.imboden@ucsf.edu>>, "jlee111(a)mac.com<mailto:jlee111@mac.com>" <jlee111(a)mac.com<mailto:jlee111@mac.com>>, "johanna.jansen(a)novartis.com<mailto:johanna.jansen@novartis.com>" <johanna.jansen(a)novartis.com<mailto:johanna.jansen@novartis.com>>, J Gray <jwgray(a)lbl.gov<mailto:jwgray@lbl.gov>>, Kim Osborn <kim.osborn(a)gladstone.ucsf.edu<mailto:kim.osborn@gladstone.ucsf.edu>>, "knudsen(a)cgl.ucsf.edu<mailto:knudsen@cgl.ucsf.edu>" <knudsen(a)cgl.ucsf.edu<mailto:knudsen@cgl.ucsf.edu>>, Irwin Kuntz <kuntz(a)cgl.ucsf.edu<mailto:kuntz@cgl.ucsf.edu>>, "LaVail, Jennifer" <Jennifer.LaVail(a)ucsf.edu<mailto:Jennifer.LaVail@ucsf.edu>>, "Li, Lili" <Lili.Li(a)ucsf.edu<mailto:Lili.Li@ucsf.edu>>, "ljp(a)ucsf.edu<mailto:ljp@ucsf.edu>" <ljp(a)ucsf.edu<mailto:ljp@ucsf.edu>>, "lmucke(a)gladstone.ucsf.edu<mailto:lmucke@gladstone.ucsf.edu>" <lmucke(a)gladstone.ucsf.edu<mailto:lmucke@gladstone.ucsf.edu>>, "Locksley, Richard" <Richard.Locksley(a)ucsf.edu<mailto:Richard.Locksley@ucsf.edu>>, "loren(a)phy.ucsf.edu<mailto:loren@phy.ucsf.edu>" <loren(a)phy.ucsf.edu<mailto:loren@phy.ucsf.edu>>, "Correia, Maria" <almira.correia(a)ucsf.edu<mailto:almira.correia@ucsf.edu>>, Mark Von Zastrow <mark.vonzastrow(a)ucsf.edu<mailto:mark.vonzastrow@ucsf.edu>>, "McCormick, Frank" <Frank.mccormick(a)ucsf.edu<mailto:Frank.mccormick@ucsf.edu>>, "merz(a)phy.ucsf.edu<mailto:merz@phy.ucsf.edu>" <merz(a)phy.ucsf.edu<mailto:merz@phy.ucsf.edu>>, "Hebrok, Matthias" <Matthias.Hebrok(a)ucsf.edu<mailto:Matthias.Hebrok@ucsf.edu>>, "mike.mccune(a)ucsf.edu<mailto:mike.mccune@ucsf.edu>" <mike.mccune(a)ucsf.edu<mailto:mike.mccune@ucsf.edu>>, "msb(a)phy.ucsf.edu<mailto:msb@phy.ucsf.edu>" <msb(a)phy.ucsf.edu<mailto:msb@phy.ucsf.edu>>, "Wabl, Matthias" <Matthias.Wabl(a)ucsf.edu<mailto:Matthias.Wabl@ucsf.edu>>, "nms(a)ucsf.edu<mailto:nms@ucsf.edu>" <nms(a)ucsf.edu<mailto:nms@ucsf.edu>>, Patrick O'farrell <ofarrell(a)cgl.ucsf.edu<mailto:ofarrell@cgl.ucsf.edu>>, "olivijuly(a)gmail.com<mailto:olivijuly@gmail.com>" <olivijuly(a)gmail.com<mailto:olivijuly@gmail.com>>, "Oppenheimer, Norman" <Norman.Oppenheimer(a)ucsf.edu<mailto:Norman.Oppenheimer@ucsf.edu>>, "peter.ohara(a)ucsf.edu<mailto:peter.ohara@ucsf.edu>" <peter.ohara(a)ucsf.edu<mailto:peter.ohara@ucsf.edu>>, Peter Sargent <peter.sargent(a)ucsf.edu<mailto:peter.sargent@ucsf.edu>>, "Pinkel, Dan" <Dan.pinkel(a)ucsf.edu<mailto:Dan.pinkel@ucsf.edu>>, "R.A. Bradshaw" <rablab(a)uci.edu<mailto:rablab@uci.edu>>, "richard.m.lawn(a)gmail.com<mailto:richard.m.lawn@gmail.com>" <richard.m.lawn(a)gmail.com<mailto:richard.m.lawn@gmail.com>>, "Kelly, Regis" <Regis.Kelly(a)qb3.org<mailto:Regis.Kelly@qb3.org>>, "sbaekkeskov(a)ucsf.edu<mailto:sbaekkeskov@ucsf.edu>" <sbaekkeskov(a)ucsf.edu<mailto:sbaekkeskov@ucsf.edu>>, "scoyle79(a)gmail.com<mailto:scoyle79@gmail.com>" <scoyle79(a)gmail.com<mailto:scoyle79@gmail.com>>, "sfinkbeiner(a)gladstone.ucsf.edu<mailto:sfinkbeiner@gladstone.ucsf.edu>" <sfinkbeiner(a)gladstone.ucsf.edu<mailto:sfinkbeiner@gladstone.ucsf.edu>>, "sgl(a)phy.ucsf.edu<mailto:sgl@phy.ucsf.edu>" <sgl(a)phy.ucsf.edu<mailto:sgl@phy.ucsf.edu>>, Martin Shetlar <shetlar(a)cgl.ucsf.edu<mailto:shetlar@cgl.ucsf.edu>>, Anita Sil <sil(a)cgl.ucsf.edu<mailto:sil@cgl.ucsf.edu>>, "Prusiner, Stanley" <Stanley.Prusiner(a)ucsf.edu<mailto:Stanley.Prusiner@ucsf.edu>>, "steven.rosen(a)ucsf.edu<mailto:steven.rosen@ucsf.edu>" <steven.rosen(a)ucsf.edu<mailto:steven.rosen@ucsf.edu>>, "stimulusartifact(a)gmail.com<mailto:stimulusartifact@gmail.com>" <stimulusartifact(a)gmail.com<mailto:stimulusartifact@gmail.com>>, "stryker(a)phy.ucsf.edu<mailto:stryker@phy.ucsf.edu>" <stryker(a)phy.ucsf.edu<mailto:stryker@phy.ucsf.edu>>, "Kornberg, Tom" <Tom.Kornberg(a)ucsf.edu<mailto:Tom.Kornberg@ucsf.edu>>, Jon Trinidad <trinidad(a)cgl.ucsf.edu<mailto:trinidad@cgl.ucsf.edu>>, "vincent514(a)gmail.com<mailto:vincent514@gmail.com>" <vincent514(a)gmail.com<mailto:vincent514@gmail.com>>, "vlingappa(a)prosetta.com<mailto:vlingappa@prosetta.com>" <vlingappa(a)prosetta.com<mailto:vlingappa@prosetta.com>>, William Weiss <waweiss(a)gmail.com<mailto:waweiss@gmail.com>>, "wgreene(a)gladstone.ucsf.edu<mailto:wgreene@gladstone.ucsf.edu>" <wgreene(a)gladstone.ucsf.edu<mailto:wgreene@gladstone.ucsf.edu>>, "yinshen2000(a)gmail.com<mailto:yinshen2000@gmail.com>" <yinshen2000(a)gmail.com<mailto:yinshen2000@gmail.com>>, "yw.kan(a)ucsf.edu<mailto:yw.kan@ucsf.edu>" <yw.kan(a)ucsf.edu<mailto:yw.kan@ucsf.edu>>, "zena.werb(a)ucsf.edu<mailto:zena.werb@ucsf.edu>" <zena.werb(a)ucsf.edu<mailto:zena.werb@ucsf.edu>>, "Kanter, Joan" <Joan.Kanter(a)ucsf.edu<mailto:Joan.Kanter@ucsf.edu>>, "Donnella, Hayley" <Hayley.Donnella(a)ucsf.edu<mailto:Hayley.Donnella@ucsf.edu>>, "Titus, Erron" <Erron.Titus(a)ucsf.edu<mailto:Erron.Titus@ucsf.edu>> Subject: 9/22/16 Seminar with Grant Jensen BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Mission Hall 1400 Livestream: https://lecture.ucsf.edu/ets/Catalog/Full/f94c469bb908465691ec810f578ecbb221 Grant Jensen CalTech Structural biology in vivo through electron cryotomography September 22, 2016 B. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Two open positions on molecule visualization and virtual reality in Paris
by Tom Ferrin 21 Sep '16

21 Sep '16

FYI... -------- Forwarded Message -------- Subject: Two open positions on molecule visualization and virtual reality in Paris Date: Thu, 22 Sep 2016 01:03:38 +0200 From: baaden(a)smplinux.de To: tef(a)cgl.ucsf.edu Dear Colleague, It's already 2,5 years since Faraday discussion #169. I hope this message finds you well. Because of your interest for molecular visualization, I thought I share the following in the hope you can circulate it, or even direct candidates towards me :) Thanks in advance! We have two open positions in Paris, France, both relating to molecule and network visualization developments in Unity3D, and one specifically to VR. We are looking to hire ASAP and funds are available. The first position is for a postdoc on Development and Application of a Virtual Reality Immersive Modelling Platform for Enabling Drug Discovery. You can find an html version at [1] and PDF at [2]. The second position is for an engineer (or postdoc) on Computational Analysis, Visualization and Modeling of Redox Signaling Networks. You can find an html version at [3] and PDF at [4]. Thank you, Marc [1] http://www.baaden.ibpc.fr/ns16/pdoc1.html [2] http://www.baaden.ibpc.fr/ns16/pdoc1.pdf [3] http://www.baaden.ibpc.fr/ns16/inge1.html [4] http://www.baaden.ibpc.fr/ns16/inge1.pdf -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217

1 0

[Compbio-allhands] Fwd: Computational Biology faculty search at USC
by Andrej Sali 20 Sep '16

20 Sep '16

Sent from my iPhone Begin forwarded message: > From: Frank Uwe Alber <alber(a)usc.edu> > Date: September 20, 2016 at 7:42:19 AM PDT > To: Andrej Sali <sali(a)salilab.org> > Subject: Computational Biology faculty search at USC > > Hi Andrej, > > I just wanted to let you know that we are having a faculty search for one (or two) open rank positions, in case you know people who would like to apply. > > Here is the link: https://jobs.usc.edu/postings/74647 > > Best wishes, > Frank > > > ----------- > https://jobs.usc.edu/postings/74647 > > Requisition ID > 2002954 > Position ID > P01473861 > Academic Title > Assistant, Associate or Full Professor in Computational Biology > Department > Biological Sciences > Location > University Park Campus > Employment Type > Full-Time > > > The Department of Biological Sciences in the Dana and David Dornsife College of Letters, Arts and Sciences at the University of Southern California invites applications for Open Rank tenured Associate or Full Professor or tenure-track Assistant Professor positions in the broad area of Computational Biology. Applicants will be evaluated based on the overall originality of their work and promise for establishing a strong independent research program. > > Successful candidates will join the Molecular and Computational Biology section within Biological Sciences at USC, located in Los Angeles, California. We have a robust Ph.D. program in Computational Biology and Bioinformatics, which emphasizes both rigorous mathematical training and immersive co-localization with experimental biologists. The anticipated start date is August 16, 2017, and applicants must have received a Ph.D. (or equivalent) degree by time of appointment. > > Review of applications will begin November 1st, 2016 and continue until the position is filled. In order to be considered for this position, all candidates must apply via the “CLICK HERE” link at the top or bottom of this page. Please submit, in a single PDF file, a curriculum vita, a cover letter, a statement of research accomplishments and future research plans, and the contact information of at least three references. Please direct inquiries to: oginskis(a)usc.edu . > > USC is an equal-opportunity educator and employer, proudly pluralistic and firmly committed to providing equal opportunity for outstanding persons of every race, gender, creed and background. The University particularly encourages women, members of underrepresented groups, veterans and individuals with disabilities to apply. USC will make reasonable accommodations for qualified individuals with known disabilities unless doing so would result in an undue hardship. Further information is available by contacting uschr(a)usc.edu. > >

1 0

[Compbio-allhands] Fwd: Group Leader Position at EMBL
by Andrej Sali 19 Sep '16

19 Sep '16

> Begin forwarded message: > > From: "Jan Ellenberg" <jan.ellenberg(a)embl.de> > Subject: Group Leader Position at EMBL > Date: September 19, 2016 at 12:39:55 AM PDT > To: sali(a)salilab.org > > Dear Andrej, > > I would like to draw your attention to two openings for a group leader position in the Cell Biology and Biophysics Unit at EMBL Heidelberg, as recently advertised in Nature and Science. > > We are looking for outstanding junior scientists with a background in biology, physics, chemistry or mathematics that want to pursue original and interdisciplinary research in cutting edge molecular cell biology, especially also in the areas of chemical biology and fluorescent probe development, image analysis and/bioimage informatics and computational modelling of complex dynamic biological processes. > > We generally hire group leaders early in their careers, often after their first postdoc and sometimes immediately after their PhD, and provide them with very generous internal support and a highly collaborative environment for their first independent position. We therefore strongly encourage highly promising young male and especially also female candidates to apply. > > I would very much appreciate if you could bring the attached advertisement to the attention of suitable candidates or let me know if I should contact them personally. > > Thanks so much for help with this recruitment, > All the best, > Jan > > Jan Ellenberg > Cell Biology and Biophysics Unit > European Molecular Biology Laboratory (EMBL) > Meyerhofstr. 1 > D-69117 Heidelberg > Germany > > T +49-6221-3878328 > F +49-6221-3878512 > jan.ellenberg(a)embl.de <mailto:jan.ellenberg@embl.de> > www.embl.de/research/units/cbb/ellenberg/index.html <http://www.embl.de/research/units/cbb/ellenberg/index.html> > > > >

1 0

[Compbio-allhands] 9/22/16 Seminar with Grant Jensen
by Flowers, Nicole 16 Sep '16

16 Sep '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Mission Hall 1400 Livestream: https://lecture.ucsf.edu/ets/Catalog/Full/f94c469bb908465691ec810f578ecbb221 Grant Jensen CalTech Structural biology in vivo through electron cryotomography September 22, 2016 B. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Greg Landrum will talk about RDKit Tomorrow Tues Sept 13 10am in BH313
by John Irwin 12 Sep '16

12 Sep '16

Greg Landrum will be talking about his toolkit RDKit tomorrow. Tues Sept 13 10am in BH313 Over the past 5 years or so, RDKit had changed the landscape of chemoinformatics and has had a huge impact on our research. John

1 0

[Compbio-allhands] Fwd: Faculty opening in Computational Biology
by Andrej Sali 12 Sep '16

12 Sep '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Ilya Vakser <vakser(a)ku.edu> > Subject: Faculty opening in Computational Biology > Date: September 12, 2016 at 10:14:21 AM PDT > To: Ilya Vakser <vakser(a)ku.edu> > > Dear Colleagues, > We would highly appreciate if you attract attention of qualified individuals to a tenure-track faculty opening in Computational Biology at The University of Kansas - see the ad attached. > Thank you very much! > Ilya > > ------ > Ilya Vakser > Professor and Director > Computational Biology Program and Center for Computational Biology > Professor > Department of Molecular Biosciences > The University of Kansas > 2030 Becker Dr. > Lawrence, KS 66045 > vakser(a)ku.edu <mailto:vakser@ku.edu>, +1-785-864-1057 > www.compbio.ku.edu <http://www.compbio.ku.edu/> > >

1 0

[Compbio-allhands] Fwd: PhD and postdoc positions avaiable
by Andrej Sali 06 Sep '16

06 Sep '16

> Begin forwarded message: > > From: Kresten Lindorff-Larsen <lindorff(a)bio.ku.dk> > Subject: PhD and postdoc positions avaiable > Date: September 6, 2016 at 11:15:31 AM PDT > To: Kresten Lindorff-Larsen <lindorff(a)bio.ku.dk> > > Dear colleagues > > We're looking to hire several postdocs and a ph.d. student working on various aspects of computational biology and integrative structural biology. If you know of any strong candidates that are looking for positions, I would appreciate it if you would pass on the adverts on to them, or have them contact me directly. > > For the postdoc positions, we are looking for people with a strong background in molecular dynamics simulations as well as people with hands on experience interpreting experimental data using computational simulation methods. > > Postdoc positions (deadline for applications Sept 15th): > http://employment.ku.dk/faculty/?show=850415 <http://employment.ku.dk/faculty/?show=850415> > Ph.d. position (deadline for applications Sept 16th): > http://employment.ku.dk/phd/?show=851613 <http://employment.ku.dk/phd/?show=851613> > > The positions advertised above have starting dates between now and february, but we will also be hiring 1-2 additional people over the next year, so if you know of candidates who have a longer timeframe, that is also of interest. > > > Regards > Kresten > > > > > -- > Prof. Kresten Lindorff-Larsen > Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science > Department of Biology, University of Copenhagen > Rm. 3.2.11, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark > Mobile: +45 4267 0074 ; Office: +45 3532 2027 > > >

1 0

[Compbio-allhands] Fwd: Comp Chem open position at Biogen
by Jacobson, Matt 26 Aug '16

26 Aug '16

- Matt Begin forwarded message: From: Govinda Bhisetti <govinda.bhisetti(a)biogen.com<mailto:govinda.bhisetti@biogen.com>> Subject: Comp Chem open position at Biogen Date: August 26, 2016 at 9:05:02 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Prof. Jacobson I have an open position in my group. Likely to have one more next year. Please see the attachment for the job description. Mark Murcko suggested that I contact you to find post-docs in your group with suitable training/experience who might be interested to work at Biogen. Please ask interested candidates to contact me. Thanks and regards. -Govinda Govinda Rao Bhisetti, PhD Principal Investigator and Head of Computational Chemistry Chem & Mol Therapeutics Biogen | 225 Binney Street | Cambridge, MA | 02142 Email: govinda.bhisetti(a)biogen.com<mailto:john.smith@biogen.com>| Direct: 617 914 7273 | Mobile: 781 325 6029 [cid:d748c923-d57c-4042-af36-219dd386c41c@ucsf.edu]

1 0

[Compbio-allhands] Fwd: Comp Chem open position at Biogen
by Brian Shoichet 26 Aug '16

26 Aug '16

---------- Forwarded message ---------- From: Govinda Bhisetti <govinda.bhisetti(a)biogen.com> Date: Fri, Aug 26, 2016 at 8:40 AM Subject: Comp Chem open position at Biogen To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu> Hi Brian, I have an open position in my group. Likely to have one more next year. Please see the attachment for the job description. Please let me know if you have anyone suitable for this position in your group who would be interested to work at Biogen. Regards. -Govinda *Govinda Rao Bhisetti, PhD* Principal Investigator and Head of Computational Chemistry Chem & Mol Therapeutics Biogen | 225 Binney Street | Cambridge, MA | 02142 Email: govinda.bhisetti(a)biogen.com <john.smith(a)biogen.com>| Direct: 617 914 7273 | Mobile: 781 325 6029 [image: unknown.png] -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

1 0

[Compbio-allhands] Fwd: WANTED: Talented computational chemists
by Jacobson, Matt 26 Aug '16

26 Aug '16

- Matt Begin forwarded message: Subject: WANTED: Talented computational chemists Date: August 26, 2016 at 7:54:50 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Matt, The Modeling and Informatics group at Merck is seeking creative, self-motivated entry level PhD computational chemists with exceptional interpersonal and problem solving skills to join our scientific teams in Boston, MA or West Point, PA. If you have (or know of) any talented students who might be interested, could you please ask them to apply online here<https://merck.taleo.net/careersection/int_merckunitedstates_10880_en/jobdet…>? The job code is CHE004912. And thanks for already sending along Katrina. She’s great! - Kate M. Katharine Holloway, Ph.D. | Senior Principal Scientist | Structural Chemistry | Merck & Co WP14-1101 | 215-652-7425 (Office) |

1 0

[Compbio-allhands] Fwd: job opportunity: computational epidemiology
by Jacobson, Matt 09 Aug '16

09 Aug '16

- Matt Begin forwarded message: From: Jaline Gerardin <jgerardin(a)idmod.org<mailto:jgerardin@idmod.org>> Subject: job opportunity: computational epidemiology Date: August 9, 2016 at 2:26:39 PM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, "rebecca.brown3(a)ucsf.edu<mailto:rebecca.brown3@ucsf.edu>" <rebecca.brown3(a)ucsf.edu<mailto:rebecca.brown3@ucsf.edu>> Hi Matt and Rebecca, Would you mind recirculating our job posting to the compbio/iPQB listservs? We’re looking for someone with a strong quantitative background and a couple years of experience with coding/scripting. Previous knowledge of malaria and disease modeling are absolutely not required. The pay is competitive for Research Scientist positions, and Seattle is a great place to live! Thanks, and hope this finds you well. Jaline jgerardin(a)idmod.org<mailto:jgerardin@idmod.org> ________________________________ TITLE: Research Scientist – Malaria LOCATION: Bellevue, WA, USA The Institute for Disease Modeling (IDM) team is composed of research scientists and software professionals who focus on creating powerful and innovative disease modeling and data analysis tools to help researchers and policy makers understand diseases, their causes, the way they spread, and the best types of interventions to use for the particular situation faced. IDM partners with selected universities, NGOs, government ministries, and other research and public health institutions focused on researching new ways to understand and combat diseases both locally and globally. We seek a full-time Research Scientist to work as part of the IDM malaria team and collaborate on the development, refinement, and utilization of sophisticated infectious disease models for epidemiological research and eradication-campaign planning. The IDM team architects advanced models of disease transmission, develops computational tools to inform global disease eradication policy, conducts innovative analysis of epidemiologically- and policy-relevant data (programmatic data, financial data, clinical trials data, and cluster surveys data), and identifies epidemiologically critical knowledge gaps. As part of our work, we routinely collaborate with groups at the World Health Organization, the Center for Disease Control, PATH, the Bill and Melinda Gates Foundation, ministries of health in the developing world, as well as universities and research institutes. As part of this group, the researcher will design and build new modules for the existing malaria disease model. The researcher will configure, calibrate, and exercise disease models to answer questions aimed at refining the malaria research agenda, improving understanding of disease dynamics, informing effective public health campaigns, and guiding rational development of new public-health interventions. The research, models, and results will be presented to key stakeholders, displayed at conferences, and published in academic journals. Joining our group provides unique opportunities to interact with global-health policymakers, to collaborate with world-class research laboratories and non-profit organizations, and to contribute to global and national disease-eradication strategies. Responsibilities: · Reviews scientific literature and determines which aspects of biology, demography, geography, and climate are relevant to the model. · Builds new modules for existing disease models; builds and develops new disease models. · Works closely with the modelers, programmers, and statisticians on the team to refine the models and use them to conduct sensitivity analyses, explore tradeoffs among possible interventions, and optimize eradication plans for time, cost, or other factors. · Finds sources for the necessary input data to the models and helps to organize the necessary data for input to the models. · Writes software code (in C/C++) to implement model features. · Collects, analyzes, and presents data on model results and performance. · Assists in the preparation of research articles and conference presentations communicating the project and its results to the scientific community. Key Qualifications and Required Skills: · Ph.D. in a quantitative field (e.g. Applied Mathematics, Statistics, Epidemiology, Quantitative Biology) · Numerical analysis, dynamical systems, stochastic processes, and biostatistics. · Read and write research articles in biology and applied mathematics. · Principles, techniques, and tools of computational epidemiology. · Work extended hours to meet a deadline; demonstrated ability to work productively as part of a small team. · At least 2 years’ experience in C/C++ software development. · Proficiency in at least one data-analysis or scripting language (e.g. MATLAB, python, R) · Multiple published articles in peer-reviewed scientific journals (to be submitted with application). · Knowledge of developing-world public health issues and the malaria disease system preferred.

1 0

[Compbio-allhands] Fwd: Recruiting two postdocs for GROMACS improvements and development
by Jacobson, Matt 02 Aug '16

02 Aug '16

- Matt Begin forwarded message: From: Michael R Shirts <Michael.Shirts(a)Colorado.EDU<mailto:Michael.Shirts@Colorado.EDU>> Subject: Recruiting two postdocs for GROMACS improvements and development Date: August 2, 2016 at 1:22:52 AM PDT To: Michael R Shirts <Michael.Shirts(a)Colorado.EDU<mailto:Michael.Shirts@Colorado.EDU>> Cc: Peter Kasson <kasson(a)virginia.edu<mailto:kasson@virginia.edu>> Hello, all- Myself and Peter Kasson, in close cooperation with Erik Lindahl and Mark Abraham at KTH, have recently obtained funding for GROMACS development work on the US side. We now have two postdoc positions open, as detailed below, one based in Virginia and one in Colorado. We’d love it if you could pass on this email to current or former students of yours, or others you may know who may be interested. The mandate on the Virginia side involves API design and implementation and cloud- and dataflow-based parallelization, while on the Colorado side it involves statistical physics to test and diagnose simulation validity, improving the testing framework, and new Monte Carlo methods. Strong software engineering skills are a must, and we would particularly appreciate active members of the molecular simulation development community. As always, members of groups under-represented in the molecular simulation field are especially encouraged to apply. Please refer anyone you think appropriate or apply at the links below. Thanks! Michael Shirts ------------------------ The Shirts research group in the Department of Chemical and Biological Engineering is hiring a highly capable research associate to help develop the GROMACS molecular simulation package. GROMACS is an open-source project with a strong international development community as well as a 10,000+ user base. This position is part of a new NIH funded collaborative effort between the Shirts group and the Kasson group (at the University of Virginia) to improve the robustness, functionality, and usability of GROMACS, offering the candidate the opportunity to positively affect the work of thousands of researchers across the globe. Candidates will have the opportunity to learn state-of-the-art simulation methodology and work collaboratively with a global team of developers. This position requires a Ph.D. in Chemistry, Chemical Engineering, Physics, Computer Science or a related field. It requires very strong statistical mechanical, molecular simulation and theoretical skills, as well as significant software engineering experience and ability. Experience in C++ and Python is preferred, as well as experience with version control, code review systems, and team-oriented software development. Competitive candidates will have a track record of scientific success in graduate study with a strong publication record. Apply at https://cu.taleo.net/careersection/2/jobdetail.ftl?job=05979&lang=en&sns_id… ----------- The Kasson laboratory located within the Department of Molecular Physiology & Biological Physics at the University of Virginia seeks a talented postdoctoral scholar to help further the development of the GROMACS molecular simulation package. GROMACS is an open-source project with a strong international development community as well as a 10,000+ user base. The Kasson and Shirts laboratories have recently secured funding to contribute new development to GROMACS. We are seeking a postdoctoral scholar with strong software engineering skills to help build this widely-used scientific software package. This scholar will gain experience in and exposure to the broad base of GROMACS users and developers as well as skills in API design and parallel cloud-computing analytics. Skills not only in C++ and Python programming but also version control and code review systems are essential. A track record of contributions to open-source software is desired as well. Scientific background related to simulation science is desired; competitive candidates will have a track record of scientific success in graduate study with a strong publication record. For inquiry into the position, please refer to the posting number 0619061. Apply at https://jobs.virginia.edu/applicants/Central?quickFind=79490 ~~~~~~~~~~~~~~~~ Michael Shirts Associate Professor michael.shirts(a)colorado.edu<mailto:michael.shirts@colorado.edu> http://www.colorado.edu/lab/shirtsgroup/ Phone: (303) 735-7860 Office: JSCBB D317 Department of Chemical and Biological Engineering University of Colorado Boulder

1 0

[Compbio-allhands] Fwd: Tenure-Track Assistant Professor in Biochemistry position
by Brian Shoichet 19 Jul '16

19 Jul '16

FYI. ---------- Forwarded message ---------- From: Spencer Anthony-Cahill <Spencer.Anthony-Cahill(a)wwu.edu> Date: Mon, Jul 18, 2016 at 6:15 PM Subject: Tenure-Track Assistant Professor in Biochemistry position To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu> Dear Professor Shoichet: I am reaching out to prominent structural biologists and biophysicists to bring to your attention a job posting we have for a tenure track assistant professorship in biochemistry. Western Washington University is a predominantly undergraduate institution. Our mission is to primarily serve our undergraduate population and engage them in meaningful research projects, which are commonly funded through federal grants and often result in quality peer-reviewed publications. Additionally, our Masters graduate program has grown over the past few years, which also bolsters our research infrastructure. We are keenly interested in attracting outstanding new faculty members who are motivated to work in this environment and excel in both teaching and research. We are particularly interested in candidates with interests in biochemistry and/or biophysics. If you know of any quality candidates that would be a good fit for our department, please encourage them to apply. Here is the link to our job posting: https://jobs.wwu.edu/JobPosting.aspx?JPID=7056 With best regards, Spencer. Spencer Anthony-Cahill, Ph.D. Professor of Chemistry, and Department Chair Email: Spencer.Anthony-Cahill(a)wwu.edu Tel: 360 650 3071 Morse Hall (CB) 270 516 High Street Bellingham, WA 98225-9150 -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

1 0

[Compbio-allhands] Fwd: Job ads
by Jacobson, Matt 07 Jul '16

07 Jul '16

- Matt Begin forwarded message: From: "Lexa, Katrina W" <katrina.lexa(a)merck.com<mailto:katrina.lexa@merck.com>> Subject: Job ads Date: July 7, 2016 at 7:22:44 AM PDT To: Matt Jacobson <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt! A good friend of mine from Michigan works in the Chemistry department at Rollins College, just outside of Orlando. They’re hiring for a tenure-track assistant level professor position to start in August 2017, and they’re hoping for someone with a computational background: http://jobs.rollins.edu/cw/en-us/job/492307/assistant-professor-chemistry Also, Merck is hiring for two computational positions, one in Boston https://taleo.msd.com/careersection/merck_external_career_section/jobdetail… And one in West Point PA https://taleo.msd.com/careersection/merck_external_career_section/jobdetail… If you know anyone who might be interested, please pass the word along. Thanks! Hope everything in SF is going well, ------------------------------- Katrina Lexa Merck & Co., Inc. 126 East Lincoln Ave RY800-C364 Rahway, NJ 07065 phone: (732) 594-7058 office: RY800-D365 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

1 0

[Compbio-allhands] Fwd: Research Associate (postdoc) in Structural Bioinformatics of Genetic Variants @ Imperial London
by Andrej Sali 01 Jul '16

01 Jul '16

> Begin forwarded message: > > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: FW: Research Associate (postdoc) in Structural Bioinformatics of Genetic Variants @ Imperial London > Date: July 1, 2016 at 11:29:38 AM GMT+2 > To: Undisclosed recipients:; > > Please forward to suitable applicants > Thanks > > Mike > > > > Imperial College London – Structural Bioinformatics of Genetic Variants > > > Salary £33,860-£42,830 per annum > > South Kensington Campus > > Applications are invited for a Research Associate position to join Prof Mike Sternberg’s Structural Bioinformatics Group at the South Kensington Campus, Imperial College London. The post holder will work as a member of a small team developing the software for the PhyreRisk portal which will provide a web portal to deliver to the community a resource relating human genetic variation, disease, protein structure and biological pathways. > > The post holder will be responsible for developing the PhyreRisk database and provide support to users of Phyre Risk. You will collaborate closely with other members of the team modelling protein structure and you will be involved in disseminating PhyreRisk to the community. You will also be expected to apply the portal to specific problems including those at the Institute of Cancer Research in London. In addition you will also assist with the teaching and the administration of research groups. > > You must have a PhD (or equivalent) involving substantial development of software to study biological systems at the genetic or molecular level. You will have proven programming experience that results in the development of a substantive and robust algorithm, web-site or database tackling a problem in protein modelling or the analysis of genetic variants. Extensive knowledge of either modelling protein structure or the analysis of genetic variants together with extensive experience of developing either web site using JavaScript/HTML (or equivalent) or an SQL (or equivalent) database for use by the bioscience and biomedical communities are essential. You must also be able to demonstrate an understanding of the application of statistics in bioinformatics. > > You must be able to express scientific concepts (especially those in bioinformatics) precisely and clearly, both verbally and in writing, and have experience of developing high-level code to a professional standard of robustness and clarity. Ability to identify the technical and scientific steps that need to be accomplished to develop novel and complex bioinformatics software with minimal supervision is highly desirable. > > You must have excellent verbal and written communication skills, and be able to write clearly and succinctly for publication. You must be able to relate well with others, form positive relationships with a wide range of people and to work as part of a team, as well as independently and be able to prioritise in respond to deadlines. You must have a pro-active attitude in the planning of research work, and have a creative approach to problem-solving. > > This is a full time position, funded by the Wellcome Trust for up to three years. > > > Deadline: 30 July 2016 (midnight BST) > > > > For initial enquiries please contact Professor Michael Sternberg by <>email: m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > > > Full details on how to apply see: > > https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf… <https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf…>..

1 0

[Compbio-allhands] Fwd: Hiring computational chemist at Denali Therapeutics
by Brian Shoichet 20 Jun '16

20 Jun '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "JW Feng" <feng(a)dnli.com> Date: Jun 20, 2016 7:46 PM Subject: Hiring computational chemist at Denali Therapeutics To: <shoichet(a)cgl.ucsf.edu> Cc: Hi Brian, This is JW Feng at Denali Therapeutics, a neuroscience startup in South San Francisco. We met while I was a computational chemist at Genentech. I joined Denali a year ago to lead the data science group and we are looking for an outstanding computational chemist to join our growing team. As you may know, Denali raised a historic biotech series A funding at $217 million. We have a world class team of scientists to discover drugs to treat neurodegenerative diseases. It would be great if you can recommend students or postdocs that would be interested in the job. Online job description: http://www.denalitherapeutics.com/careers?gh_jid=235936 Best, JW ___________________ JW Feng, Ph.D. Denali Therapeutics Inc. 201 Gateway Blvd. South San Francisco, CA 94080 | (650) 270-0628

1 0

[Compbio-allhands] Fwd: Postdoc opening at Stanford
by Jacobson, Matt 10 Jun '16

10 Jun '16

- Matt Begin forwarded message: From: Ron Dror <rondror(a)stanford.edu<mailto:rondror@stanford.edu>> Subject: Postdoc opening at Stanford Date: June 10, 2016 at 1:15:01 AM PDT Dear colleagues, I have an opening for a postdoc to lead one or more projects in my group at Stanford. If you can recommend a promising candidate, please let me know. I’d welcome applications from outstanding researchers with backgrounds in molecular simulation (either methods development or biological applications), molecular modeling, protein design, or related areas. A description of the position is below. Best, Ron Applications are invited for postdoctoral research positions in Prof. Ron Dror’s lab at Stanford University. Successful applicants will use a variety of computational techniques to address key scientific questions in biochemistry and to enable advances in drug discovery, particularly for G-protein-coupled receptors (GPCRs), which represent the largest class of drug targets. This work will be carried out in close collaboration with world-class experimentalists. Candidates must have an outstanding record of research and academic performance, strong communication skills, and an ability to work independently and collaborate effectively. Experience with molecular dynamics simulation, enhanced sampling methods, programming, protein design, or molecular modeling of membrane proteins is desirable, but candidates are not expected to have experience in all of these areas. Dr. Dror’s lab focuses on computational approaches to studying the spatial organization and dynamics of biomolecules and cells. Our work spans fields ranging from biophysics and computational chemistry to high-performance computing, image processing, and machine learning. We have access to substantial computational and experimental facilities and are based in an interdisciplinary biosciences building immediately adjacent to Stanford’s medical, science, and engineering schools. Stanford, one of the world’s top universities, is located on a beautiful campus in the San Francisco Bay Area. Stanford has long been a magnet for talent in computing and the biosciences, and is considered the birthplace and spiritual center of Silicon Valley, an unparalleled center of technological and scientific innovation. Stanford University is an equal opportunity employer. To apply, please send the following to drorlabopenings(a)gmail.com<mailto:drorlabopenings@gmail.com>: a CV, a cover letter explaining your interest in the position, contact information for three referees, and a document you wrote that has not been edited by anyone else (for example, a report, an early draft of a manuscript, or an email to a colleague about a scientific topic). -- Ron Dror Associate Professor of Computer Science and, by courtesy, Molecular and Cellular Physiology and Structural Biology Stanford University http://drorlab.stanford.edu/

1 0

[Compbio-allhands] Fwd: Postdoc opening at Stanford
by Andrej Sali 10 Jun '16

10 Jun '16

> Begin forwarded message: > > From: Ron Dror <rondror(a)stanford.edu> > Subject: Postdoc opening at Stanford > Date: June 10, 2016 at 1:17:03 AM PDT > To: "Lennart.Nilsson(a)ki.se" <Lennart.Nilsson(a)ki.se>, "bojan.zagrovic(a)univie.ac.at" <bojan.zagrovic(a)univie.ac.at>, "hgrubmu(a)gwdg.de" <hgrubmu(a)gwdg.de>, "c.de.graaf(a)vu.nl" <c.de.graaf(a)vu.nl>, "gerhard.hummer(a)biophys.mpg.de" <gerhard.hummer(a)biophys.mpg.de>, "schlick(a)nyu.edu" <schlick(a)nyu.edu>, "p.carloni(a)grs-sim.de" <p.carloni(a)grs-sim.de>, "ursula.roethlisberger(a)epfl.ch" <ursula.roethlisberger(a)epfl.ch>, "Michael.Grabe(a)ucsf.edu" <Michael.Grabe(a)ucsf.edu>, "sali(a)salilab.org" <sali(a)salilab.org>, "peter(a)kolblab.org" <peter(a)kolblab.org>, Koby Levy <Koby.Levy(a)weizmann.ac.il> > Cc: Ron Dror <ron.dror(a)stanford.edu> > > Dear colleagues, > > I have an opening for a postdoc to lead one or more projects in my group at Stanford. If you can recommend a promising candidate, please let me know. I’d welcome applications from outstanding researchers with backgrounds in molecular simulation (either methods development or biological applications), molecular modeling, protein design, or related areas. A description of the position is below. > > Best, > Ron > > > Applications are invited for postdoctoral research positions in Prof. Ron Dror’s lab at Stanford University. Successful applicants will use a variety of computational techniques to address key scientific questions in biochemistry and to enable advances in drug discovery, particularly for G-protein-coupled receptors (GPCRs), which represent the largest class of drug targets. This work will be carried out in close collaboration with world-class experimentalists. > > Candidates must have an outstanding record of research and academic performance, strong communication skills, and an ability to work independently and collaborate effectively. Experience with molecular dynamics simulation, enhanced sampling methods, programming, protein design, or molecular modeling of membrane proteins is desirable, but candidates are not expected to have experience in all of these areas. > > Dr. Dror’s lab focuses on computational approaches to studying the spatial organization and dynamics of biomolecules and cells. Our work spans fields ranging from biophysics and computational chemistry to high-performance computing, image processing, and machine learning. We have access to substantial computational and experimental facilities and are based in an interdisciplinary biosciences building immediately adjacent to Stanford’s medical, science, and engineering schools. > > Stanford, one of the world’s top universities, is located on a beautiful campus in the San Francisco Bay Area. Stanford has long been a magnet for talent in computing and the biosciences, and is considered the birthplace and spiritual center of Silicon Valley, an unparalleled center of technological and scientific innovation. > > Stanford University is an equal opportunity employer. > > To apply, please send the following to drorlabopenings(a)gmail.com <mailto:drorlabopenings@gmail.com>: a CV, a cover letter explaining your interest in the position, contact information for three referees, and a document you wrote that has not been edited by anyone else (for example, a report, an early draft of a manuscript, or an email to a colleague about a scientific topic). > > -- > > Ron Dror > Associate Professor of Computer Science and, by courtesy, Molecular and Cellular Physiology and Structural Biology > Stanford University > http://drorlab.stanford.edu/ <http://drorlab.stanford.edu/>

1 0

[Compbio-allhands] Fwd: An announcement from COMP Together
by Magdalena Korczynska 02 Jun '16

02 Jun '16

June COMP Together. > Begin forwarded message: > > From: comp_together(a)acscomp.org > Subject: An announcement from COMP Together > Date: June 2, 2016 at 8:43:50 AM PDT > To: Magdalena Korczynska <mkucsf(a)gmail.com> > Reply-To: BinQing Wei <wei.binqing(a)gmail.com> > > The COMP Together champions in your area would like to announce the following event: > > Speaker: Max Kuhn, Pfizer > Ignacio Aliagas, Genentech > Title: Two talks on machine learning and applications in drug discovery > Date: 2016-06-28 > Time: 6:00 PM > Event ID: 34 > Sponsor: Gilead > > Location > Gilead > 333 Lakeside Drive > > Foster City CA 94404 > > Description and Notes > 6-7 pm networking over pizza & drinks > > 7-7:45pm 1st talk, Max Kuhn, Pfizer > > Title: Under the Hood of Cubist > Abstract: Cubist model rules are a relatively unknown machine learning model that has been extensively utilized in QSAR. The model is related to work published by Ross Quinlan in the early 90’s but had remained closed source until 2010. This talk will describe the model and its mechanics and an illustrative example will be shown to demonstrate the result. > > 7:45-8:15pm 2nd talk, Ignacio Aliagas, Genentech > > Title: The Importance of Being Earnest: Assessing Risk in Model Predictions > Abstract: QSAR models for the prediction of properties and DMPK end points can play a very important role to guide synthesis and advance compounds in the drug discovery paradigm. For prediction models to be used efficiently and with ease, integration with other modeling tools and software can facilitate their use. At the same time, it is critical to provide validation tools to quickly inform on the models’ domain of applicability within a given therapeutic project or chemical series. We describe a probabilistic approach to model prediction and how various QSAR models and validation tools are being delivered to drug discovery scientists at Genentech. > > 8:30pm End > > > If you would like to attend this COMP Together event, please visit the COMP website and register using the > http://app.acscomp.org/COMP_Together/meeting_signup.php?event_id=34. > > If you have any questions about this event, please contact BinQing Wei atwei.binqing(a)gmail.com. > > If you would like to update your COMP Together registration or unsubscribe, please visit http://app.acscomp.org/COMP_Together/reg_update/update_login.php

1 0

[Compbio-allhands] Fwd: Job openings at Schrodinger
by Brian Shoichet 02 Jun '16

02 Jun '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF ---------- Forwarded message ---------- From: "Devleena Shivakumar" <devleena.shivakumar(a)schrodinger.com> Date: Jun 2, 2016 1:03 AM Subject: Job openings at Schrodinger To: "Brian Shoichet" <bshoichet(a)gmail.com> Cc: Hi Brian, We are looking to hire Applications Scientists in San Diego, Boston and Europe Job Description: Schrödinger, a technology leader specializing in software solutions for life science research and development, is searching for an Applications Scientist to be based in Boston. Applications Scientists work on applying Schrodinger's computational chemistry software to address challenging problems in drug discovery. The position also involves the development of new computational methods for drug discovery, scientific publications, and helping customers with using Schrodinger software. Responsibilities include drug discovery project support, engaging in scientific discussions with customers, giving presentations at conferences, demonstrating optimal use of the software, and providing customer training. Applications Scientists gain familiarity with our entire suite of structure-based and ligand-based software, including packages for docking, molecular simulations, homology modeling, pharmacophore modeling, cheminformatics, and quantum mechanics. A strong background in molecular modeling and computational chemistry with application to biological problems is highly desired. Exceptional communication skills, an outgoing personality, and a willingness to travel are required. Experience working on drug discovery projects is highly desirable. *Requirements:* - Ph.D. in computational chemistry or biophysics plus experience with pharmaceutical applications of molecular modeling software tools - Excellent interpersonal, communication, and organizational skills - Strong problem-solving ability - A broad knowledge of molecular modeling theory and applications - Ability to conduct independent research *Preferred:* - Post-doctoral research and/or relevant experience in the commercial sector - Biologics modeling and *in silico *protein engineering - Python programming experience If you know anyone looking to join my super amazing team, please have them contact me directly. Anyone from your group would be great! Best, Devleena -- Devleena Shivakumar, Ph.D. Senior Applications Scientist Schrödinger, Inc. http://www.schrodinger.com (201) 455-4980 (Phone) (212) 295-5801 (FAX) http://www.linkedin.com/in/devleena

1 0

[Compbio-allhands] Christos Ouzounis seminar Friday, June 3, 2 pm, BH212
by Patricia Babbitt 31 May '16

31 May '16

Hi all, Christos Ouzounis is giving an informal seminar this Friday, detailed in the subject line of this email. He has been a major contributor to many aspects of the field and was a founding officer of the International Society for Computational Biology. One of his early efforts was the development of clustering algorithms for biological networks, including creation of TRIBE-MCL, an approach used for rapid and accurate clustering of protein sequences into families. The method relies on the Markov cluster (MCL) algorithm for the assignment of proteins into families based on precomputed sequence similarity information (PMID: 11917018). The title of Friday's talk is "Comparative Genomics 2.0: From reading to writing" -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Sydney Russell Leed, +1 415-514-1214, 415-514-9816 Sydney.RussellLeed(a)ucsf.edu <mailto:Sydney.RussellLeed@ucsf.edu>

1 0

[Compbio-allhands] Christos Ouzounis seminar Friday, June 3, 2 pm, BH212
by Patricia Babbitt 31 May '16

31 May '16

Hi all, Christos Ouzounis is giving an informal seminar this Friday, detailed in the attached flyer. He has been a major contributor to many aspects of the field and was a founding officer of the International Society for Computational Biology. One of his early efforts was the development of clustering algorithms for biological networks, including creation of TRIBE-MCL, an approach used for rapid and accurate clustering of protein sequences into families. The method relies on the Markov cluster (MCL) algorithm for the assignment of proteins into families based on precomputed sequence similarity information (PMID: 11917018). The title of Friday's talk is "Comparative Genomics 2.0: From reading to writing" -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Sydney Russell Leed, +1 415-514-1214, 415-514-9816 Sydney.RussellLeed(a)ucsf.edu <mailto:Sydney.RussellLeed@ucsf.edu>

1 0

[Compbio-allhands] a computational / structural biology job at Biodesy, South San Francisco
by Andrej Sali 24 May '16

24 May '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

1 0

[Compbio-allhands] Fwd: A New Job Posting for 'Computational Protein Engineering' at Amgen Thousand Oaks
by Jacobson, Matt 19 May '16

19 May '16

- Matt From: <Alba>, Ben <balbaphd(a)amgen.com<mailto:balbaphd@amgen.com>> Date: Thursday, May 19, 2016 at 10:01 AM To: Charles Craik <charles.craik(a)ucsf.edu<mailto:charles.craik@ucsf.edu>> Subject: A New Job Posting for 'Computational Protein Engineering' at Amgen Thousand Oaks Hi Charly, I hope you are well!! Thousand Oaks is looking for a talented ‘Computational Protein Engineer’ (e.g. PhD. in computational biophysics or related fields). Do you have any candidates who might fit this bill? Best, Ben http://careers.amgen.com/job-en/6072153/scientist-computational-protein-eng… Scientist – Computational Protein Engineering and Design Category: Scientific Job ID: R-14827 Location: Thousand Oaks, CA Posted Date:May 13, 2016 Amgen is seeking a scientist with expertise in computational protein engineering and design to join the Therapeutic Discovery Department at our campus in Thousand Oaks, CA. The candidate will be part of multidisciplinary teams that seek to advance our biologics drug discovery programs, spanning multiple modalities including therapeutic proteins, antibodies, and bispecific molecules. The work involves protein structure analysis and modeling, biophysical property prediction, protein-protein interaction analysis, as well as novel molecular design. Basic Qualifications: Doctorate degree OR Master’s degree & 4 years of scientific experience OR Bachelor’s degree & 6 years of scientific experience Preferred Qualifications: PhD. in computational biophysics or related fields Strong track record of research accomplishment with three or more scientific publications or conference presentations in the area of computational protein modeling and design Strong communication and interpersonal skills and the ability to work flexibly in a cross-functional team environment Experience in antibody modeling and engineering Experience with one or more protein modeling software packages (MOE, Discovery Studio, Schrodinger, etc.). Experience working on a biologics project in a biopharmaceutical setting. Amgen is an Equal Opportunity employer and will consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability status. Benjamin Alba, Ph.D. Senior Scientist Biologics Amgen, Inc. 1120 Veterans Blvd Drop Zone ASF5/234 South San Francisco, CA 94080 650-228-4943 (cell); 650-244-3119 (desk) "This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message."

1 0

[Compbio-allhands] Fwd: Recommendations for job positions @ GSK
by Brian Shoichet 19 May '16

19 May '16

FYI. ---------- Forwarded message ---------- From: Brian Shoichet <shoichet(a)cgl.ucsf.edu> Date: Thu, May 19, 2016 at 9:38 AM Subject: Re: Recommendations for job positions @ GSK To: Eric Manas <eric.s.manas(a)gsk.com> Cc: Constantine Kreatsoulas <constantine.x.kreatsoulas(a)gsk.com>, Kris Brown <Kristin.K.Brown(a)gsk.com> Hi Guys, I'll keep my eyes open, and pass this around. No one in my lab is quite ready yet, but there are certainly other talented folks in the comp. chem. groups here at UCSF. brian On Thu, May 19, 2016 at 9:14 AM, Eric Manas <eric.s.manas(a)gsk.com> wrote: > Hi Brian, > > Just to chime in...some of the skill sets we are looking for are around > protein modeling, physics of equilibrium binding and kinetics, structure > based design...etc. As Kris suggested we'd be happy to chat more at any > time. > > Eric > > Sent from my iPhone > > On May 19, 2016, at 5:02 PM, Kris Brown <Kristin.K.Brown(a)gsk.com> wrote: > > Dear Brian: > > > > I wanted to reach out to let you know that we are currently recruiting for > several open positions in the computational molecular design group at GSK. > The job descriptions are given as links below. If you know of anyone who > might be interested please feel free to pass along the job descriptions and > my contact information. I’d be happy to schedule a phone call if you’d like > to hear more detail about what these positions entail. > > > > Best Regards, > > Kris Brown > > > > > > Grade 7 Cheminformatics: WD64811 - http://tinyURL.gsk.com/91fd3f > <http://tinyurl.gsk.com/91fd3f> > > Grade 6/7 Data Science: WD59234 - http://tinyURL.gsk.com/2e27fa > <http://tinyurl.gsk.com/2e27fa> > > Grade 7 Investigator: WD58496 - http://tinyURL.gsk.com/55ac18 > <http://tinyurl.gsk.com/55ac18> > > > > > > *Kristin Brown* > > *Director**, Molecular Design US* > > Computational & Modeling Sciences > > RD Platform Technology & Science > > > > *GlaxoSmithKline* > > 709 Swedeland Road UW2412, King of Prussia, PA 19406 > > *Email *Kristin.K.Brown(a)gsk.com > > *Tel *610-270-4638 > > > > -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

1 0

[Compbio-allhands] 5/19/16 Seminar with Xiaowei Zhuang
by Flowers, Nicole 13 May '16

13 May '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Xiaowei Zhuang Harvard Illuminating Biology at the Nanoscale with Single-molecule and Super-resolution Imaging May 19, 2016 B. Huang, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] computational postdoc @ ucsf
by Michael Keiser 10 May '16

10 May '16

FYI. Recommendations & help getting the word out much appreciated! -- We're looking for highly motivated postdoctoral candidates with a background in machine learning, systems pharmacology, computational chemistry, bioinformatics, or a related field. The candidate would work to integrate deep learning with pharmacology. The project involves the design of deep neural networks for the prediction of small molecule binding activities and their role in phenotypic screens. Desired, albeit not strictly required, skills include experience with theano, lasagne/keras, TensorFlow, pandas, and sklearn. Expertise with CUDA and/or massive dataset analysis (e.g., NoSQL, AWS, Google Cloud) is a plus. A productive track record with at least one first-author publication is required. We seek a driven individual who will lead his/her research independently and communicate frequently and clearly to the field. Just north of Silicon Valley, the Keiser lab’s location at UCSF Mission Bay directly adjoins SoMa district and the heart of SF’s tech and artificial intelligence startup scene. Interested candidates should submit a CV and arrange that three letters of reference be sent directly to apply(a)keiserlab.org. Please reference “postdoc-dnn”. -- Michael J Keiser, PhD Assistant Professor, UCSF Dept Pharmaceutical Chemistry Dept Bioengineering & Therapeutic Sciences Institute for Neurodegenerative Diseases p/1-415-886-7651 keiserlab.org <http://www.keiserlab.org> calendly.com/mjke

1 0

[Compbio-allhands] Fwd: Comp Chem position at MD Anderson Cancer Center
by Jacobson, Matt 10 May '16

10 May '16

-- Matt Sent from my iPhone Begin forwarded message: From: "Cross,Jason B" <JBCross(a)mdanderson.org<mailto:JBCross@mdanderson.org>> Date: May 10, 2016 at 9:32:58 AM PDT To: "'matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>'" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Comp Chem position at MD Anderson Cancer Center Dear Dr. Jacobson, I’m contacting you to let you know that I currently have a junior position available, appropriate for a newly minted PhD or someone completing their post-doctoral training. The position is in the Institute for Applied Cancer Science (IACS) at the University of Texas MD Anderson Cancer Center in Houston, providing computational chemistry support for ongoing drug discovery projects. IACS is part of the cancer moonshots program and has essentially been built as a “biotech” within the cancer center, populated mostly by ex-pharma drug discovery scientists, and is a great environment for junior scientists to learn and contribute to exciting projects. If you have current or former students, or know of others within your network, that would be interested, I would appreciate if you could forward this information. Links to the position description and the MD Anderson IACS website are listed below. Interested applicants will need to apply through the career website, but can also forward their CVs directly to me. Job posting<https://mdanderson.referrals.selectminds.com/jobs/institute-rsch-investigat…> Institute for Applied Cancer Science<http://www.cancermoonshots.org/platforms/institute-for-applied-cancer-scien…> Thank you for your time and consideration. Best regards, Jason Jason Cross, Ph.D. Institute Senior Research Scientist Institute for Applied Cancer Science University of Texas – MD Anderson Cancer Center South Campus Research Bldg 3 (3SCR3.3438) Houston, TX 77054 Office: 713-745-7499 Email: jbcross(a)mdanderson.org<mailto:jbcross@mdanderson.org> The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

1 0

[Compbio-allhands] Fwd: job opportunity in disease modeling
by Jacobson, Matt 09 May '16

09 May '16

- Matt Begin forwarded message: From: Jaline Gerardin <jgerardin(a)idmod.org<mailto:jgerardin@idmod.org>> Subject: job opportunity in disease modeling Date: May 9, 2016 at 11:37:29 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, My team at the Institute for Disease Modeling<http://www.idmod.org/> is looking to hire a few research scientists. Could you circulate our job posting below to the compbio listserv? This is a great opportunity for anyone with a quantitative background who wants to continue doing research but not necessarily in an academic environment. Previous knowledge of malaria or epidemiology is not required. Thanks, Jaline TITLE: Research Scientist – Malaria LOCATION: Bellevue, WA, USA The Institute for Disease Modeling (IDM) team is composed of research scientists and software professionals who focus on creating powerful and innovative disease modeling and data analysis tools to help researchers and policy makers understand diseases, their causes, the way they spread, and the best types of interventions to use for the particular situation faced. IDM partners with selected universities, NGOs, government ministries, and other research and public health institutions focused on researching new ways to understand and combat diseases both locally and globally. We seek a full-time Research Scientist to work as part of the IDM malaria team and collaborate on the development, refinement, and utilization of sophisticated infectious disease models for epidemiological research and eradication-campaign planning. The IDM team architects advanced models of disease transmission, develops computational tools to inform global disease eradication policy, conducts innovative analysis of epidemiologically- and policy-relevant data (programmatic data, financial data, clinical trials data, and cluster surveys data), and identifies epidemiologically critical knowledge gaps. As part of our work, we routinely collaborate with groups at the World Health Organization, the Center for Disease Control, PATH, the Bill and Melinda Gates Foundation, ministries of health in the developing world, as well as universities and research institutes. As part of this group, the researcher will design and build new modules for the existing malaria disease model. The researcher will configure, calibrate, and exercise disease models to answer questions aimed at refining the malaria research agenda, improving understanding of disease dynamics, informing effective public health campaigns, and guiding rational development of new public-health interventions. The research, models, and results will be presented to key stakeholders, displayed at conferences, and published in academic journals. Joining our group provides unique opportunities to interact with global-health policymakers, to collaborate with world-class research laboratories and non-profit organizations, and to contribute to global and national disease-eradication strategies. Responsibilities: · Reviews scientific literature and determines which aspects of biology, demography, geography, and climate are relevant to the model. · Builds new modules for existing disease models; builds and develops new disease models. · Works closely with the modelers, programmers, and statisticians on the team to refine the models and use them to conduct sensitivity analyses, explore tradeoffs among possible interventions, and optimize eradication plans for time, cost, or other factors. · Finds sources for the necessary input data to the models and helps to organize the necessary data for input to the models. · Writes software code (in C/C++) to implement model features. · Collects, analyzes, and presents data on model results and performance. · Assists in the preparation of research articles and conference presentations communicating the project and its results to the scientific community. Key Qualifications and Required Skills: · Ph.D. in a quantitative field (e.g. Applied Mathematics, Statistics, Epidemiology, Quantitative Biology) · Numerical analysis, dynamical systems, stochastic processes, and biostatistics. · Read and write research articles in biology and applied mathematics. · Principles, techniques, and tools of computational epidemiology. · Work extended hours to meet a deadline; demonstrated ability to work productively as part of a small team. · At least 2 years’ experience in C/C++ software development. · Proficiency in at least one data-analysis or scripting language (e.g. MATLAB, python, R) · Multiple published articles in peer-reviewed scientific journals (to be submitted with application). · Knowledge of developing-world public health issues and the malaria disease system preferred. Jaline Gerardin Senior Research Scientist jgerardin(a)idmod.org<mailto:jgerardin@idmod.org> T - 425.691.3343 [cid:image001.png@01D1A9E7.29107920] This message may contain confidential information which may also be legally privileged information. If you are not an intended recipient of the message, please delete it and notify the sender via reply email. Any unauthorized dissemination, distribution or copying of the material in this message, and any attachments to the message, is strictly forbidden.

1 0

[Compbio-allhands] 5/12/16 Seminar with Chris Voigt
by Flowers, Nicole 06 May '16

06 May '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Chris Voigt MIT Cello: A programming language for living cells May 12, 2016 W. Lim, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 5/5/16 Seminar with David Savage
by Flowers, Nicole 29 Apr '16

29 Apr '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) David Savage UC Berkeley Fixed: Synthetic biological approaches for probing cellular physiology May 5, 2016 J. Fraser, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] helpers needed for Software Carpentry Workshops April 29 and 30 at Mission Bay
by Patricia C. Babbitt 26 Apr '16

26 Apr '16

The UCSF Library is hosting a Software Carpentry Python workshop this Friday and Saturday, April 29th and 30th at Mission Bay and we need your help to make it successful! We will have 80 UCSF researchers at this event – 46 beginners and 34 advanced beginners. Here is what we need: 1 person with technical competence in Python who is willing to be helpers to the Software Carpentry Instructors during both days of the bootcamp. Workshops will run from 9 - 5 on Friday and Saturday (workshop info can be found here:http://bsmith89.github.io/2016-04-29-ucsf/). As a helper you will have the interpersonal skills to spot people who are confused and help them get unstuck during the practical sessions. Helpers are vital to keeping workshops flowing smoothly. More details on the role of the helper is here:https://software-carpentry.org/workshops/checklists/helpers.html Here is what you will get if you are the right person for this role: * $100 Visa Gift Card * Breakfast and coffee/snacks each day * An opportunity to learn the material well enough to teach it yourself in the future * Credit on the workshop materials and you can put this effort on your CV as service to the UCSF community, showing you have teaching experience in these areas If you are interested in this opportunity please emailariel.deardorff(a)ucsf.edu<mailto:ariel.deardorff@ucsf.edu> to get more details and see if you are a good fit for this role. -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Sydney Russell Leed, +1 415-514-1214, 415-514-9816 Sydney.RussellLeed(a)ucsf.edu <mailto:Sydney.RussellLeed@ucsf.edu>

1 0

[Compbio-allhands] Fwd: IGBMC call for Group Leader positions
by Andrej Sali 26 Apr '16

26 Apr '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org <mailto:assistant@salilab.org>, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org <mailto:sali@salilab.org>; Web http://salilab.org <http://salilab.org/> > Begin forwarded message: > > From: Directeur IGBMC <directeur.igbmc(a)igbmc.fr> > Subject: IGBMC call for Group Leader positions > Date: April 26, 2016 at 7:53:10 AM PDT > To: Undisclosed recipients:; > > > Dear Colleagues, > > The IGBMC is currently seeking outstanding scientists to take-up group leader positions within its Departements of Functional Genomics, Development and Stem Cells, and Integrated Structural Biology. Our attractive new call has just been launched and will be opened until July 30th 2016 (see attached advertisement). > > We would be grateful if you could post the attached poster to your notice board and disseminate the information to your organization/network and to people who might be interested. > > Many thanks in advance. > > With best regards, > > > Dr. Bertrand SERAPHIN > IGBMC Director > > > //\//\//\//\//\//\//\//\//\//\//\//\/ > > Bertrand Séraphin > > IGBMC > CNRS UMR 7104/INSERM U964/UDS > 1 Rue Laurent Fries > BP 10142 > 67404 Illkirch CEDEX > France > > Tel +33 (0)3 88 65 32 16 > Fax +33 (0)3 88 65 32 03 > > //\//\//\//\//\//\//\//\//\//\//\//\/ >

1 0

[Compbio-allhands] Fwd: Antibody & Protein Engineering positions at Bayer - San Francisco
by Andrej Sali 25 Apr '16

25 Apr '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org <mailto:assistant@salilab.org>, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org <mailto:sali@salilab.org>; Web http://salilab.org <http://salilab.org/> > Begin forwarded message: > > From: Shaun Lippow <slippow(a)gmail.com> > Subject: Antibody & Protein Engineering positions at Bayer - San Francisco > Date: April 25, 2016 at 1:09:10 PM PDT > To: Shaun Lippow <shaun.lippow(a)bayer.com> > > Hi all, > > Apologies for the mass email, but I'd like to get your help to distribute two great positions now open in my group. Please forward (or apply!). Applications should go through Bayer's website but recommendations direct to me are welcome and I'll try to expedite. Thanks! > > Position #1: Technical Staff Research Scientist - Antibody and Protein Engineering > Group/Department: Protein Platform Technologies group, in the Lead Discovery department > Company/Location: Bayer, US Innovation Center, Mission Bay, San Francisco > Primary Responsibilities: (1) Support antibody lead discovery, set strategies, manage projects; (2) Develop novel antibody technologies. See attached Job Description for more info > Minimum Experience: PhD with 4+ years relevant experience or equivalent -- but stellar new PhDs welcome to apply and position level will be adjusted accordingly > Start Date: ASAP > To Apply: www.career.bayer.us <http://www.career.bayer.us/> reference code 0000162405 (link here <https://career.bayer.us/job/Technical-Staff-Research-Scientist-Antibody-and…>) > > Position #2: Industrial Post Doc - Antibody and Protein Engineering > Group/Department: Protein Platform Technologies group, in the Lead Discovery department > Company/Location: Bayer, US Innovation Center, Mission Bay, San Francisco > Primary Responsibility: Develop novel protein and antibody technologies. See attached Job Description for more info > Minimum Experience: PhD or equivalent > Start Date: ASAP > To Apply: www.career.bayer.us <http://www.career.bayer.us/> reference code 0000162426 (link here <https://career.bayer.us/job/Industrial-Post-Doc-Ab-Protein-Engineer--000016…>) > > Best regards, > Shaun >

1 0

[Compbio-allhands] 4/28/16 Seminar with Debbie Nickerson
by Flowers, Nicole 22 Apr '16

22 Apr '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Debbie Nickerson University of Washington Lessons learned from scaling the analysis of Mendelian conditions April 28, 2016 T. Friedrich, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: opening in Computational Proteing Engineering at Illumina
by Jacobson, Matthew 21 Apr '16

21 Apr '16

-- Matt Sent from my iPhone Begin forwarded message: From: "Peisajovich, Sergio" <speisajovich(a)illumina.com<mailto:speisajovich@illumina.com>> Date: April 21, 2016 at 11:26:08 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: opening in Computational Proteing Engineering at Illumina Dear Matt, I am a former postdoc from Wendell’s lab who is now working in Protein Engineering at Illumina. I am contacting you regarding an opening for a computational protein scientist in our Protein Engineering group, based in San Diego. I am attaching the job description here, I was hoping you could circulate this among postdocs or grad students in your lab that you believe are close to move on with their careers. If anyone is interested, please forward them my contact info, they can reach out to me directly. Please let me know if you have any questions or need more information. Thanks so much for your help on this. Cheers sergio Sergio Peisajovich, Ph.D. Associate Director, Scientific Research Illumina, Inc Tel:(858) 255-5451 speisajovich(a)illumina.com<mailto:speisajovich@illumina.com> www.illumina.com<http://www.illumina.com/>

1 0

[Compbio-allhands] Fwd: opening in Computational Proten Engineering at Illumina
by Andrej Sali 21 Apr '16

21 Apr '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Peisajovich, Sergio" <speisajovich(a)illumina.com> > Subject: opening in Computational Proten Engineering at Illumina > Date: April 21, 2016 at 11:16:42 AM PDT > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Andrej, > > I am a former postdoc from Wendell’s lab who is now working in protein engineering at Illumina. > > I am contacting you regarding an opening for a computational protein scientist in our Protein Engineering group at Illumina, based in San Diego. > > I am attaching the job description here, I was hoping you could circulate this among postdocs or grad students in your lab that you believe are close to move on with their careers. If anyone is interested, please forward them my contact info, they can reach out to me directly. > > Please let me know if you have any questions or need more information. > > Thanks so much for your help on this, > > Best > > sergio > Sergio Peisajovich, Ph.D. > Associate Director, Scientific Research > Illumina, Inc > Tel:(858) 255-5451 > speisajovich(a)illumina.com <mailto:speisajovich@illumina.com> > www.illumina.com <http://www.illumina.com/> >

1 0

[Compbio-allhands] Fwd: Employment opportunities in computational protein modeling for students and postdocs
by Andrej Sali 14 Apr '16

14 Apr '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org <mailto:assistant@salilab.org>, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org <mailto:sali@salilab.org>; Web http://salilab.org <http://salilab.org/> > Begin forwarded message: > > From: Greg Lakatos <glakatos(a)zymeworks.com> > Subject: Fwd: Employment opportunities in computational protein modeling for students and postdocs > Date: April 14, 2016 at 11:00:48 AM PDT > To: sali(a)salilab.org > > Dear Professor Sali, > > I apologize for contacting you again, however the job postings didn't make it through with my previous email. > > Thank you again, > > Greg > > > From: Greg Lakatos <glakatos(a)zymeworks.com> > To: <sali(a)salilab.org> > Sent: 4/14/2016 10:54 AM > Subject: Employment opportunities in computational protein modeling for students and postdocs > > Dear Professor Sali, > > I am writing on behalf of Zymeworks Inc., a computational biotechnology company located in Vancouver, Canada. Zymeworks has developed a set of computational protein modeling tools that have been successfully used to design a novel antibody-based drug platform. As part of our on-going efforts to improve our protein modeling capabilities, we are currently recruiting scientists to join our simulation and modeling team. I have attached copies of our current job postings, and I would be grateful if you could forward these postings to members of your group, or any other students or postdocs who may be interested. More information about Zymeworks is available at our website (www.zymeworks.com <http://www.zymeworks.com/>). I am also happy to answer questions about our openings, and I can be reached at glakatos(a)zymeworks.com <mailto:glakatos@zymeworks.com> > > Thank you for your time and assistance. > > Sincerely, > > Greg Lakatos > Principal Scientist and Simulations Team Lead > Zymeworks Inc. > > > > Notice of Confidentiality: The information transmitted is intended only for the > person or entity to which it is addressed and may contain confidential and/or > privileged material. Any review, re-transmission, dissemination or other use of > or taking of any action in reliance upon this information by persons or entities > other than the intended recipient is prohibited. If you received this in error > please contact the sender immediately by return electronic transmission and then > immediately delete this transmission including all attachments without copying, > distributing or disclosing the same.

1 0

[Compbio-allhands] Fwd: Employment opportunities in computational protein modeling for students and postdocs
by Jacobson, Matthew 14 Apr '16

14 Apr '16

- Matt Begin forwarded message: From: Greg Lakatos <glakatos(a)zymeworks.com<mailto:glakatos@zymeworks.com>> Subject: Employment opportunities in computational protein modeling for students and postdocs Date: April 14, 2016 at 10:49:03 AM PDT To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Professor Jacobson, I am writing on behalf of Zymeworks Inc., a computational biotechnology company located in Vancouver, Canada. Zymeworks has developed a set of computational protein modeling tools that have been successfully used to design a novel antibody-based drug platform. As part of our on-going efforts to improve our modeling tools, we are currently recruiting scientists to join our simulation and modeling team. I have attached copies of our current job postings and I would be grateful if you could forward these postings to members of your group, or any other students or postdocs who may be interested. More information about Zymeworks is available at our website (www.zymeworks.com<http://www.zymeworks.com>). I am also happy to answer questions about our openings, and I can be reached at glakatos(a)zymeworks.com<mailto:glakatos@zymeworks.com> Thank you for your time and assistance. Sincerely, Greg Lakatos Principal Scientist and Simulations Team Lead Zymeworks Inc. Notice of Confidentiality: The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, re-transmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error please contact the sender immediately by return electronic transmission and then immediately delete this transmission including all attachments without copying, distributing or disclosing the same.

1 0

[Compbio-allhands] Fwd: Computational Biology Position
by Brian Shoichet 08 Apr '16

08 Apr '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "Susie Stephens" <susie.stephens(a)gmail.com> Date: Apr 9, 2016 1:33 AM Subject: Computational Biology Position To: <bshoichet(a)gmail.com> Cc: Hi Brian, How are you doing? Are you aware of any computational biologists with 2-5 years of experience who would be interested in working at Pfizer with a focus on target discovery and validation in oncology and immuno-oncology? If you know of someone it would be great if you could point them in my direction, or have them apply for the job at https://globaljobs.pfizer.com/pages/jobs.aspx using Job Id 1010987. Thanks for you rhelp. Best, Susie

1 0

[Compbio-allhands] 4/14/16 Seminar with Ian Wilson- NOTE LOCATION
by Flowers, Nicole 08 Apr '16

08 Apr '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall N114 NO SIMULCAST. URL for live capture will be sent out on 4/13/16. HARC Center Speaker: Ian Wilson Scripps Broad neutralization of viral pathogens April 14, 2016 B. Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: job opportunity in Seattle area
by Jacobson, Matthew 05 Apr '16

05 Apr '16

- Matt Begin forwarded message: From: Jaline Gerardin <gerardin(a)gmail.com<mailto:gerardin@gmail.com>> Subject: job opportunity in Seattle area Date: April 5, 2016 at 9:17:13 PM PDT To: Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, We have an interesting position open at the interface of software and research. Could you forward to compbio-allhands? thanks, Jaline -------------------------------------------------------------------------------------------------- Open position at Institute for Disease Modeling, Bellevue WA: The IDM Research Software Engineer will work on an elite team of software developers along with testers and researchers at IDM tasked with developing software tools for all stages of the disease modeling pipeline. This pipeline includes designing and querying large data for climate, demographic, and transportation data for input to the disease modeling software; specifying and commissioning simulation jobs on a high performance computing cluster; detailed simulation of disease transmission dynamics; data reduction and analysis of simulation output; and workstation and web based data visualization tools. This position focuses on building tools and applications to support the different disease teams. Full job posting: http://iv.avature.net/careers/JobDetail/Bellevue-Wa-Washington-United-State… Institute for Disease Modeling: www.idmod.org<http://www.idmod.org/>

1 0

[Compbio-allhands] Fwd: Hands-On Computer Aided Drug Design Workshop @ UCSF, San Francisco - Friday Apr. 15
by Jacobson, Matthew 05 Apr '16

05 Apr '16

I don’t recall whether this has been distributed on this list previously If you want to learn MOE ... - Matt Begin forwarded message: From: Audrey Bonin <abonin(a)chemcomp.com<mailto:abonin@chemcomp.com>> Subject: Hands-On Computer Aided Drug Design Workshop @ UCSF, San Francisco - Friday Apr. 15 Date: April 5, 2016 at 11:33:07 AM PDT To: Audrey Bonin <abonin(a)chemcomp.com<mailto:abonin@chemcomp.com>> Dear Friends and Colleagues , I would like to invite you to our hands-on computer-aided drug design workshops which will take place at UCSF - April 15th, 2016. The workshops are open to the public and all interested parties are welcome to attend - no prior software experience is required to participate. Please find course information and related details below. The workshop is free but pre-registration is required since places are limited, to register please visit : http://www.chemcomp.com/Workshops-North_America.htm Lunch, and refreshments will be provided during the workshops, please bring your own laptop to the workshop*. Date: CCG Workshops - Friday April 15, 2016 Location: UCSF - Smith Cardiovascular Research Bldg (CVRI), 555 Mission Bay Blvd S., first floor seminar room. ================================================================ 08:30-09:00 Morning break* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - 09:00-12:00 Structure-Based Drug Design and Ligand Modification Molecular Surfaces and Maps / Ligand Interactions / Conformational Searching / Ligand Optimization / Ligand Selectivity / Protein Alignments and Superposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - 12:00-13:00 Lunch* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - 13:00-17:00 Antibody Modeling and Protein Engineering in MOE Protein-Protein Interactions / Protein Properties / Developability / Hot Spot Analysis / Antibody Modeling / Molecular Surfaces / Protein-protein docking ================================================================ *Continental breakfast and lunch will be provided. ================================================================ -- Course title: Structure-Based Drug Design and Ligand Modification Course description: The course covers MOE applications for interactive structure based design. Examples include active site visualization, protein-ligand contact analysis and ligand modification/optimization in the receptor pocket. Conformational searching and analysis of the ligand to assess ligand flexibility will be discussed. A protocol for aligning and superposing protein complexes in the context of protein selectivity will be studied. Course title: Antibody Modeling and Protein Engineering in MOE Course description: The course covers approaches for structure-based biologics design and includes protein-protein interactions analysis, in silico protein engineering, affinity modeling and antibody homology modeling. The interaction of a co-crystallized antibody-antigen complex will be evaluated by generating and examining the molecular surface topology and visualizing protein-protein interactions in 3D and 2D. The application of protein engineering tools for homology modeling and conducting property optimization of an antibody-antigen complex in the context developability will be studied.All the steps necessary for producing and assessing antibody homology models will be described. Methods for evaluating the structure of protein and antibody models will be discussed. *If you don't have access to MOE, please communicate with me prior to the workshop, I will set up a demo key for you so you can follow along on your personal laptop. Regards, Audrey Bonin, M. Sc. Chemistry Academic Services Manager Chemical Computing Group T. +1 514 393-1055<tel:%2B1%20514%20393-1055> abonin(a)chemcomp.com<mailto:abonin@chemcomp.com> | www.chemcomp.com<http://www.chemcomp.com/> Follow us on Twitter! @CCG_MOE

1 0

[Compbio-allhands] Fwd: Editorial
by Brian Shoichet 03 Apr '16

03 Apr '16

---------- Forwarded message ---------- From: Patrick Walters <wpwalters(a)gmail.com> Date: Sun, Apr 3, 2016 at 8:29 AM Subject: Re: Editorial To: Brian Shoichet <shoichet(a)cgl.ucsf.edu> W e're looking for someone with MD expertise (see below). I think this could be a huge opportunity for someone of that phenotype. Please let me know if you know of anyone who would be interested in joining our band. Best, Pat ------- Relay Therapeutics is seeking a highly motivated computational chemist to join our rapidly growing team. This individual will utilize cutting edge computational methods, in conjunction with information generated by a variety of biophysical techniques, to design novel therapeutics targeted to allosteric sites. In this role, the ideal candidate will work as part of a multidisciplinary team to integrate computational and experimental insights and drive drug discovery. *Responsibilities* - Carry out analyses that combine computational and experimental data to develop testable hypotheses that drive drug discovery programs - Collaborate with scientists throughout the company to maximize the impact of computational efforts on projects - Work collaboratively with external computational groups to develop and refine new computational methods - Ensure effective communication of computational results across departments and teams - Develop new approaches to streamline and enhance computational workflows *Preferred Qualifications* - Ph.D. in Computational Chemistry, Computational Biology, Biophysics, or a related discipline - 1 to 5 years of industrial or postdoctoral experience - Demonstrated expertise applying wide variety of modern computational chemistry methods - Demonstrated expertise in structure-based drug design - In depth knowledge of molecular dynamics and its application to drug discovery - Facility working in a Unix/Linux environment - Ability to program in at least 1 modern scripting language (e.g. Python) - Strong interpersonal and communications skills - Ability to conduct independent research >>>> >>>> -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

1 0

[Compbio-allhands] 4/7/16 Seminar with Ronen Marmorstein
by Flowers, Nicole 01 Apr '16

01 Apr '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Ronen Marmorstein University of Pennsylvania Molecular mechanisms of post-translational and co-translational protein acetylation April 7, 2016 D. Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Postdoc openings
by Matt Jacobson 29 Mar '16

29 Mar '16

Positions at Livermore national lab -- Matt Sent from my iPhone Begin forwarded message: From: "Wong, Sergio E." <wong105(a)llnl.gov<mailto:wong105@llnl.gov>> Date: March 29, 2016 at 4:33:31 PM EDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Postdoc openings Hi; Here are the links to two postdoc positions in our group: http://careers-ext.llnl.gov/jobs/5183154-postdoctoral-research-staff-member… http://careers-ext.llnl.gov/jobs/5183258 Thanks; -Sergio

1 0

[Compbio-allhands] Fwd: Summer internship opportunity in CompBio at Bayer for distribution
by Andrej Sali 24 Mar '16

24 Mar '16

> Begin forwarded message: > > From: Shaun Lippow <shaun.lippow(a)bayer.com> > Subject: Summer internship opportunity in CompBio at Bayer for distribution > Date: March 24, 2016 at 10:32:37 AM PDT > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Andrej, > > I’m a senior scientist at Bayer in Mission Bay and am requesting help to distribute a summer internship opportunity in computational biology for an upper-level undergrad or a graduate student. The topic is our sequence-based immunogenicity prediction, which I know is of interest to your lab or at least complementary to the structure-based MHC/TCR approach. > > I’ve attached the internship description. Applicants should apply through our company website (not directly to me): > https://career.bayer.us/job/Computational-Biology-Summer-Intern--0000159445… <https://career.bayer.us/job/Computational-Biology-Summer-Intern--0000159445…> > > Best regards, > Shaun > > > > > The information contained in this e-mail is for the exclusive use of the intended recipient(s) and may be confidential, proprietary, and/or legally privileged. Inadvertent disclosure of this message does not constitute a waiver of any privilege. If you receive this message in error, please do not directly or indirectly use, print, copy, forward, or disclose any part of this message. Please also delete this e-mail and all copies and notify the sender. Thank you. > > For alternate languages please go to http://bayerdisclaimer.bayerweb.com <http://bayerdisclaimer.bayerweb.com/> > >

1 0

[Compbio-allhands] postdoc fellow position
by Hao Li 16 Mar '16

16 Mar '16

*FYI. * * * *Postdoctoral Fellow position in Computational Biology and Bioinformatics* We are seeking for a highly motivated postdoctoral fellow, who has good programming skills and extensive genomics/epigeneomics data analysis experience, to study transcriptional regulation networks in mammalian systems using ChIP-seq, RNA-seq and Hi-C data. Candidates should send CV and arrange to have 3 letters of recommendation letters sent directly to michael.zhang(a)utdallas.edu <mailto:michael.zhang@utdallas.edu>. Michael Zhang, Ph.D. Cecil H. and Ida Green Distinguished Chair Professor Director, Center for Systems Biology Department of Biological Sciences The University of Texas at Dallas -- ------------------------------------- Hao Li, Professor Dept. of Biochemistry and Biophysics Director, Larry L. Hillblom Center for the Biology of Aging University of California, San Francisco 1700 4th Street, Room 403A, Box 2542 San Francisco, CA 94143-2542 For direct delivery: Use Zip code 94158 office phone: (415)502-8187 Fax: (415)514-2617 email: haoli(a)genome.ucsf.edu http://mobydick.ucsf.edu/~haoli/ ------------------------------------

1 0

[Compbio-allhands] Vertex Fellow Program
by Andrej Sali 09 Mar '16

09 Mar '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

1 0

[Compbio-allhands] Fwd: Vertex Fellows Program
by Brian Shoichet 04 Mar '16

04 Mar '16

Might be an interesting opportunity, even for faculty. Brian Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "Jonathan Moore" <jonathan_moore(a)vrtx.com> Date: Mar 4, 2016 6:10 AM Subject: Vertex Fellows Program To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu> Cc: Dear Brian, I hope all is well. I'm writing to tell you about a new Fellowship program we're launching at Vertex, and to ask for your help with identifying great candidates. The new Vertex Fellowship is intended to attract some of the most talented scientists and physicians to join Vertex for one year of immersive learning about the science of drug discovery and, in the process, expose us to diverse and innovative ways of thinking. Each Vertex Fellow will be embedded with a drug discovery project team based on their interests and our needs. In addition, we will provide Fellows with didactic multi-disciplinary training on the science of drug discovery. The program is intentionally short (one year) so it augments rather than replaces traditional postdoctoral training. David Altshuler (CSO) will personally oversee the program together with our most senior scientists (Principal Research Fellows). We expect to take on 3 - 6 Vertex Fellows across our sites in the Fall of 2016. We will provide career advice and mentorship to help the fellows on their way to a successful career in biomedical science. I am asking for your help with identifying potential Fellows who would be excited about such an opportunity. Fellows could be finishing a PhD, MD or joint program, or completing clinical training. We will also consider faculty who have a sabbatical and would be interested in the experience. (Kit Parker, a faculty member at Harvard, is currently spending a sabbatical at Vertex.) In short, Vertex Fellows will: · Learn about drug discovery at an innovative biotechnology company · Help patients by contributing to transformative medicines · Advance a scientific idea rapidly and effectively in a team-based environment · Receive mentorship from scientific, medical and business leaders · Join a community of Fellows that will span Vertex and academia · Accelerate their careers by learning new skills in a different setting *Do you know anyone who might be a good fit?* I'm attaching a 1-page flyer with more information. Please let me know what questions or feedback you have about the program. I’d be particularly grateful if you would pass this along to any potential Fellows whom you think might be interested. Thanks for your help, Jon Jonathan M. Moore Principal Research Fellow and Vice President Exploratory Biochemistry Vertex Pharmaceuticals Incorporated 50 Northern Avenue Boston, MA 02210 Phone: 617-341-6444 This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

1 0

[Compbio-allhands] 3/10/16 Seminar with Tuuli Lappalainen
by Flowers, Nicole 04 Mar '16

04 Mar '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Tuuli Lappalainen New York Genome Center & Columbia University Functional variation in the human genome: lessons from the transcriptome March 10, 2016 T. Friedrich, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 3/3/16 Seminar with Carrie Partch
by Flowers, Nicole 26 Feb '16

26 Feb '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Carrie Partch UC Santa Cruz Dissecting the molecular basis for circadian timekeeping March 3, 2016 D. Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Recommendations for computational chemist position
by Jacobson, Matt 24 Feb '16

24 Feb '16

- Matt Begin forwarded message: From: David Weinberg <david.weinberg(a)ucsf.edu<mailto:david.weinberg@ucsf.edu>> Subject: Fwd: Recommendations for computational chemist position Date: February 24, 2016 at 2:12:57 PM PST To: Brian Shoichet <bshoichet(a)gmail.com<mailto:bshoichet@gmail.com>>, Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt and Brian, Jaime suggested that you guys might know someone that's a good fit for this position at Moderna Therapeutics (with whom I collaborate). See below for the details and let me know if you want me to pass on anyone's name. Best, David ------------------------------- David Weinberg, PhD UCSF Faculty Fellow University of California, San Francisco Department of Cellular and Molecular Pharmacology Office: Genentech Hall S572F // Lab: Genentech Hall S576 Phone: (415) 514-9723 // Fax: (415) 514-4112 david.weinberg(a)ucsf.edu<mailto:david.weinberg@ucsf.edu> // deweinberg(a)gmail.com<mailto:deweinberg@gmail.com> ---------- Forwarded message ---------- From: Iain McFadyen <Iain.McFadyen(a)modernatx.com<mailto:Iain.McFadyen@modernatx.com>> Date: Wed, Feb 24, 2016 at 12:10 PM Subject: Recommendations for computational chemist position To: Iain McFadyen <Iain.McFadyen(a)modernatx.com<mailto:Iain.McFadyen@modernatx.com>> I’m looking for a talented and creative computational chemist to work on structure-based design of modified nucleotides, cap analogs, tail modifications, and lipid components in collaboration with our chemistry group. If you know of someone that might fit that description, please let me know! Thanks, and hope you don’t mind this random question – I’m trying to cast as wide a net as possible. Iain P Please consider the environment before printing this email Confidentiality notice and disclaimer: The information in this message and any attachments is intended for the exclusive use of the addressee(s), is confidential and may be privileged or otherwise protected from disclosure. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, of any such information by persons or entities other than the intended addressee(s) is prohibited. If you have received this message in error and are not the intended addressee, please notify the sender immediately and delete this message and any attachments from your system without reading or disclosing them. If you are not the intended addressee, be advised that any use of the information in this message and any attachment is prohibited and may be unlawful, and you must not copy this message or attachment or disclose the contents to any other person.

1 0

[Compbio-allhands] Fwd: Postdoctoral position on integrating structural biology with big data to engineer next generation vaccines
by Andrej Sali 20 Feb '16

20 Feb '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Jens Meiler" <jens(a)meilerlab.org> > Subject: Postdoctoral position on integrating structural biology with big data to engineer next generation vaccines > Date: February 20, 2016 at 12:52:56 PM PST > To: "James Crowe" <james.crowe(a)vanderbilt.edu> > > Please distribute widely: > > The laboratories of James E. Crowe and Jens Meiler are looking immediately > for outstanding postdoctoral candidates that will join a team of graduate > and post-graduate researchers co-advised by both mentors. The candidates > would work to integrate structural biology with big data to engineer next > generation vaccines targeting influenza, HIV, Ebola, or Marburg viruses. The > project involves computational design of broadly neutralizing antibodies, > computational engineering of vaccine candidates, and experimental structural > and functional characterization of these. Skills that are a plus, but not > all would be required, include programming/scripting, experimental > structural biology (X-ray, NMR, EM, ...), Rosetta modeling, immunology. If > interested, please submit a CV and arrange three letters of reference sent > to jens(a)meilerlab.org and james.crowe(a)vanderbilt.edu. > > ==================================================================== > > Jens Meiler, Ph.D. > Chancellor Faculty Fellow > Associate Professor > Vanderbilt University > Departments of Chemistry, Pharmacology, and Biomedical Informatics Center > for Structural Biology, Institute for Chemical Biology > > ==================================================================== > > office: MRBIII, Room 5144 B, 465 21st Ave South, Nashville, TN 37240 > mail : 7330 Stevenson Center, Station B 351822, Nashville, TN 37235 > e-mail: jens(a)meilerlab.org > WWW: www.meilerlab.org > Twitter: https://twitter.com/MeilerLab > Phone: +1 (615) 936-5662 > Fax: +1 (615) 936-2211 > Assistant: h.darling(a)vanderbilt.edu > > ==================================================================== > > >

1 0

[Compbio-allhands] 2/25/16 Seminar with Michael Rosen
by Flowers, Nicole 19 Feb '16

19 Feb '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Michael Rosen UT Southwestern Physical Mechanisms of Cell Organization on Micron Length Scales February 25, 2016 J. Lobel, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Post Doc @ Imperial - Developing a structure-based database of genetic variants
by Andrej Sali 15 Feb '16

15 Feb '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: Post Doc @ Imperial - Developing a structure-based database of genetic variants > Date: February 15, 2016 at 1:58:05 AM PST > To: Undisclosed recipients:; > > I would be grateful if you would forward to suitable finishing PhD students and postdocs > Many thanks Mike > ------------------------------------- > > > Research Associate in Bioinformatics > Developing > > Imperial College, South Kensington Campus > Department of Life Sciences/Faculty of Natural Sciences > Salary £33,860-£42,830 per annum > > Applications are invited for a Research Associate position to join the Structural Bioinformatics Group, within the Department of Life Sciences based at the South Kensington Campus. The post holder will work as a member of a small team developing the software for the PhyreRisk portal which will provide a web portal to deliver to the community a resource relating human genetic variation, disease, protein structure and biological pathways. > The post holder will be responsible for developing the PhyreRisk database and provide support to users of Phyre Risk. You will collaborate closely with other members of the team modelling protein structure and you will be involved in disseminating PhyreRisk to the community. You will also be expected to apply the portal to specific problems including those at the Institute of Cancer Research in London. In addition you also assist with the teaching and the administration of research groups. > > You must have a PhD (or equivalent) involving substantial development of software to study biological systems at the genetic or molecular level. You will have proven programming experience that results in the development of a substantive and robust algorithm, web-site or database tackling a problem in protein modelling or the analysis of genetic variants. Extensive knowledge of either modelling protein structure or the analysis of genetic variants together with extensive experience of developing either web site using JavaScript/HTML (or equivalent) or an SQL (or equivalent) database for use by the bioscience and biomedical communities are essential. Understanding of the application of statistics in bioinformatics is also essential. You must have the ability to express scientific concepts verbally and in writing, especially those in bioinformatics, precisely and clearly. Ability to develop high-level code to a professional standard of robustness and clarity is also essential. Ability to identify the technical and scientific steps that need to be accomplished to develop novel and complex bioinformatics software with minimal supervision is highly desirable. > You must have excellent verbal and written communication skills, and be able to write clearly and succinctly for publication. You must be able to relate well with others, form positive relationships with a wide range of people and to work as part of a team, as well as independently and be able to prioritise in respond to deadlines. You must have a pro-active attitude in the planning of research work, and have a creative approach to problem-solving. > This is a full time position, funded by the Welcome Trust for up to three years. > Closing Date : 14 March 2016 (midnight GMT) > > How To Apply: Our preferred method of application is online via > https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf… <https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf…>. > Should you have any queries please contact: Professor Michael Sternberg by email:m.sternberg@imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> Alternatively, if you are unable to apply online, please contact dols.recruitment(a)imperial.ac.uk <mailto:dols.recruitment@imperial.ac.uk> by email to request an application form > > > > ******************************************** > Professor Michael J E Sternberg > Director Centre for Integrative Systems Biology and Bioinformatics (CISBIO) > Room 306 - Sir Ernst Chain Building > Department of Life Sciences > Imperial College London, London SW7 2AZ,UK > m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > http://www3.imperial.ac.uk/cisbio <http://www3.imperial.ac.uk/cisbio> (CISBIO) > www.sbg.bio.imperial.ac.uk <http://www.sbg.bio.imperial.ac.uk/> (Group's research) > > Tel +44 (0)20 7594 5212 > ****************************************************************************

1 0

[Compbio-allhands] 2/18/16 Seminar with Erin O'Shea
by Flowers, Nicole 12 Feb '16

12 Feb '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Erin O'Shea Harvard Timekeeping by a Three Protein Circadian Clock February 18, 2016 J. Weissman, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 2/11/16 Seminar with Alice Ting
by Flowers, Nicole 05 Feb '16

05 Feb '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Alice Ting MIT Spatially-Resolved Proteomic Mapping of Living Cells Reveals New Proteins and Functions in the Mitochondria and Neuronal Synapse February 11, 2016 J Perez Bermejo, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 2/4/16 Seminar with Taekjip Ha
by Flowers, Nicole 29 Jan '16

29 Jan '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Taekjip Ha University of Illinois at Urbana-Champaign Surprising Physics of DNA on the Genome Scale February 4, 2016 T. Lee, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 1/28/16 NO BBC SEMINAR
by Flowers, Nicole 28 Jan '16

28 Jan '16

There is no BBC Seminar today, January 28, 2016. Thank you, Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Job opening for Genetic Bioinformatics at NIDA
by Tom Ferrin 27 Jan '16

27 Jan '16

-------- Forwarded Message -------- Subject: Job opening for Genetic Bioinformatics at NIDA Date: Wed, 27 Jan 2016 17:45:58 +0000 From: Pollock, Jonathan (NIH/NIDA) [E] <jpollock(a)nida.nih.gov> To: tef(a)cgl.ucsf.edu <tef(a)cgl.ucsf.edu> Dear Colleague: Dear Dr. Ferrin, I wish to bring to your attention a job opening in my branch, The Genetics, Epigenetics, and Developmental Neuroscience Branch, in the Division of Neuroscience and Behavior at NIDA for the position of program director in Genetic Bioinformatics. The posting on USAjobs became active on 1/27/16 and will close 2/5/16. Here are links to the vacancy announcement: DE: https://www.usajobs.gov/GetJob/ViewDetails/427694600. The DE vacancy is open to all US Citizens so applicants who currently do not work for the Federal government should apply to this announcement. MP: _https://www.usajobs.gov/GetJob/ViewDetails/427699100. _The Merit Promotion vacancy is for those candidates who currently work or are former Federal employees. The announcement is open only to US Citizens. Underrepresented minorities are encouraged to apply. The position is at the GS-14 level ($108,887 to $141,555) and is located at NIDA headquarters in Rockville, MD. The ideal candidate will have a doctorate in neuroscience, molecular biology, or genetics/epigenetics with research experience in bioinformatics and genetics/epigenetics. The successful candidate can have a huge impact on public health, on the direction of science and will have the opportunity to write papers that analyze existing datasets. Much of the health burden stems from substance abuse and addiction. Specifically the duties of the job are to * provide technical leadership and guidance in bioinformatics of human genome and epigenomic data. * plan and direct research program activities in the area of associated data science * analyze trends and data to assess the adequacy of research being conducted and proposed epigenetics and genetics of addiction and drug abuse. * identify gaps in existing scientific research. * identify advances and developments in bioinformatics, research design and statistical genetics. * propose a comprehensive and cohesive research plan outlining the direction and long-term goals to be accomplished. * analyze the scientific merit of current and projected research programs. * identify and recommend the program direction of new research. * assess the scientific progress of research or clinical programs to ensure that objectives are being attained. * develop new analytical tools to analyze data from established data infrastructure. * lead program and researchers in managing and analyzing new and emerging data resources. * provide advice to grantees/contractors during preparation of applications/proposals. * advise and evaluate grants/awards, cooperative agreements of biomedical research in genetics/epigenetics. * recommend and distribute research funding for new research initiatives/efforts. * Initiate appropriate action relative to the grantee/contractor when research progress is inadequate. * administer unsolicited grant/contract proposals and provide support regarding funding options and areas of program emphasis. * establish or participate in panels to review research proposals or reports, including the criteria and standards for the panel to follow. * evaluate the technical and scientific merit of funding applications and proposals being submitted for approval. * examine the technical and scientific merit of research proposals. * manage research fund distribution amongst competing interests within an organization. I would appreciate your assistance in this search process and welcome your application or nomination of applicants whom you feel could provide the leadership and scientific excellence required of this position. I would appreciate your forwarding this announcement to scientists who may be well qualified for the position. I would be particularly interested in your calling this employment opportunity to the attention of well-qualified applicants from traditionally under-represented groups. The announcement is open only to US Citizens Feel free to contact me, Jonathan D. Pollock, Ph.D., Chief, Genetics, Epigenetics, and Developmental Neuroscience Branch with any questions regarding this announcement. Sincerely, Jonathan D. Pollock, Ph.D. Jonathan D. Pollock, Ph.D. Chief Genetics, Epigenetics, and Developmental Neuroscience Branch Division of Neuroscience and Behavior National Institute on Drug Abuse, NIH 6001 Executive Blvd, Rm. 4267 Bethesda, MD 20892 Tel. 301-435-1309 Email. jpollock(a)mail.nih.gov <mailto:jpollock@mail.nih.gov> Skype: Dogmacentral1

1 0

[Compbio-allhands] Fwd: Job opening for Genetic Bioinformatics at NIDA
by Andrej Sali 27 Jan '16

27 Jan '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Pollock, Jonathan (NIH/NIDA) [E]" <jpollock(a)nida.nih.gov> > Subject: Job opening for Genetic Bioinformatics at NIDA > Date: January 27, 2016 at 9:42:22 AM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > > > > Dear Dr. Sali, > > I wish to bring to your attention a job opening in my branch, The Genetics, Epigenetics, and Developmental Neuroscience Branch, in the Division of Neuroscience and Behavior at NIDA for the position of program director in Genetic Bioinformatics. The posting on USAjobs became active on 1/27/16 and will close 2/5/16. Here are links to the vacancy announcement: > > DE: https://www.usajobs.gov/GetJob/ViewDetails/427694600 <https://www.usajobs.gov/GetJob/ViewDetails/427694600>. The DE vacancy is open to all US Citizens so applicants who currently do not work for the Federal government should apply to this announcement. > > MP: https://www.usajobs.gov/GetJob/ViewDetails/427699100 <https://www.usajobs.gov/GetJob/ViewDetails/427699100>. The Merit Promotion vacancy is for those candidates who currently work or are former Federal employees. > > The announcement is open only to US Citizens. Underrepresented minorities are encouraged to apply. > > The position is at the GS-14 level ($108,887 to $141,555) and is located at NIDA headquarters in Rockville, MD. The ideal candidate will have a doctorate in neuroscience, molecular biology, or genetics/epigenetics with research experience in bioinformatics and genetics/epigenetics. The successful candidate can have a huge impact on public health, on the direction of science and will have the opportunity to write papers that analyze existing datasets. Much of the health burden stems from substance abuse and addiction. > > Specifically the duties of the job are to > > provide technical leadership and guidance in bioinformatics of human genome and epigenomic data. > plan and direct research program activities in the area of associated data science > analyze trends and data to assess the adequacy of research being conducted and proposed epigenetics and genetics of addiction and drug abuse. > identify gaps in existing scientific research. > identify advances and developments in bioinformatics, research design and statistical genetics. > propose a comprehensive and cohesive research plan outlining the direction and long-term goals to be accomplished. > analyze the scientific merit of current and projected research programs. > identify and recommend the program direction of new research. > assess the scientific progress of research or clinical programs to ensure that objectives are being attained. > develop new analytical tools to analyze data from established data infrastructure. > lead program and researchers in managing and analyzing new and emerging data resources. > provide advice to grantees/contractors during preparation of applications/proposals. > advise and evaluate grants/awards, cooperative agreements of biomedical research in genetics/epigenetics. > recommend and distribute research funding for new research initiatives/efforts. > Initiate appropriate action relative to the grantee/contractor when research progress is inadequate. > administer unsolicited grant/contract proposals and provide support regarding funding options and areas of program emphasis. > establish or participate in panels to review research proposals or reports, including the criteria and standards for the panel to follow. > evaluate the technical and scientific merit of funding applications and proposals being submitted for approval. > examine the technical and scientific merit of research proposals. > manage research fund distribution amongst competing interests within an organization. > > I would appreciate your assistance in this search process and welcome your application or nomination of applicants whom you feel could provide the leadership and scientific excellence required of this position. I would appreciate your forwarding this announcement to scientists who may be well qualified for the position. I would be particularly interested in your calling this employment opportunity to the attention of well-qualified applicants from traditionally under-represented groups. > > The announcement is open only to US Citizens > > > Feel free to contact me, Jonathan D. Pollock, Ph.D., Chief, Genetics, Epigenetics, and Developmental Neuroscience Branch with any questions regarding this announcement. > > > Sincerely, > > > > Jonathan D. Pollock, Ph.D. > > > Jonathan D. Pollock, Ph.D. > Chief > Genetics, Epigenetics, and Developmental Neuroscience Branch > Division of Neuroscience and Behavior > National Institute on Drug Abuse, NIH > 6001 Executive Blvd, Rm. 4267 > Bethesda, MD 20892 > Tel. 301-435-1309 > Email. jpollock(a)mail.nih.gov <mailto:jpollock@mail.nih.gov> > Skype: Dogmacentral1

1 0

[Compbio-allhands] computational jobs at Third Rock startup
by Jacobson, Matt 25 Jan '16

25 Jan '16

Job descriptions below. I have been working with Third Rock to start this company, which will focus exclusively on allosteric drug discovery. The company has not been officially announced and these job descriptions are preliminary, but they are looking to identify good candidates in anticipation of a rapid launch. Anyone interested can send CV/resume to the CSO, Mark Murcko (mark.murcko(a)gmail.com<mailto:mark.murcko@gmail.com>) or to me (matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>). Feel free to forward. Thanks, Matt ============================ POSITION #1 Relay Therapeutics is seeking a highly motivated computational chemist to join our rapidly growing team. This individual will utilize cutting edge computational methods, in conjunction with information generated by a variety of structural and biophysical techniques, to design novel therapeutics targeted to allosteric sites. In this role, the ideal candidate will work as part of a multidisciplinary team to integrate computational and experimental insights and drive drug discovery. Responsibilities * Carry out analyses that combine computational and experimental data to develop testable hypotheses that drive drug discovery programs * Collaborate with scientists throughout the company as well as academic founders and other external advisors to maximize the impact of computational efforts on projects * Work collaboratively with external computational groups to develop and refine new computational methods * Ensure effective communication of computational results across departments and teams * Develop new approaches to streamline and enhance computational workflows [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif] Preferred Qualifications * Ph.D. in Computational Chemistry, Computational Biology, Biophysics, or a related discipline * 1 to 5 years of industrial or postdoctoral experience * Demonstrated expertise applying wide variety of modern computational chemistry methods to drug discovery * Demonstrated expertise in structure-based drug design * In depth knowledge of molecular dynamics and its application to drug discovery * Facility working in a Unix/Linux environment * Ability to program in at least 1 modern scripting language (e.g. Python) * Strong interpersonal and communications skills * Ability to conduct independent research ========================================= POSITION #2 Relay Therapeutics seeks a skilled, creative scientific software developer to develop novel computational workflows to streamline our drug discovery efforts. The ideal candidate will combine scientific knowledge and full-stack web development skills to design and develop user interfaces as well as back-end infrastructure. Responsibilities * Work collaboratively with scientists to understand needs for data flow, access and analysis * Develop scripts and applications to streamline scientific workflows * Develop web-based user interfaces to support data input and analysis * Utilize commercial, as well as internally developed software to design and maintain an infrastructure to facilitate decision making in drug discovery Preferred Qualifications * BA or BS in Chemistry, Biology, Physics or a related discipline * 2 to 5 years experience developing software to support pharmaceutical research * Demonstrated knowledge of Cheminformatics * Demonstrated ability to program in Python and JavaScript * Experience with at least one modern JavaScript framework (e.g. Angular, React, ExtJS) * Expertise with databases and SQL * Experience programming with commercial or open source cheminformatics toolkits (e.g. OEChem, RDKit, Open Babel) * - Matt

1 1

[Compbio-allhands] Fwd: position for biophysicist at Biodesy
by Andrej Sali 22 Jan '16

22 Jan '16

fyi > Begin forwarded message: > > From: Joshua Salafsky <joshua.salafsky(a)biodesy.com> > Subject: position for biophysicist at Biodesy > Date: January 22, 2016 at 4:35:19 PM PST > To: Andrej Sali <sali(a)salilab.org>, "Shoichet, Brian" <bshoichet(a)gmail.com> > > Hi guys, > In case you happen to know of anyone suitable, we are looking for an experimental with some experience with computational structural biology (please see attached). > > Thanks, > Josh > > Joshua Salafsky, PhD > > Founder & Chief Scientific Officer > Biodesy, Inc. > 384 Oyster Point Boulevard, #8 > South San Francisco, CA 94080 > > (415) 640-6210 > joshua.salafsky(a)biodesy.com <mailto:joshua.salafsky@biodesy.com>

1 0

[Compbio-allhands] Fwd: 1/26/16 Seminar with Aled Edwards
by Jacobson, Matt 20 Jan '16

20 Jan '16

- Matt Begin forwarded message: From: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> Subject: 1/26/16 Seminar with Aled Edwards Date: January 20, 2016 at 4:07:52 PM PST To: <PSPGFACULTY(a)LISTSRV.UCSF.EDU<mailto:PSPGFACULTY@LISTSRV.UCSF.EDU>> Reply-To: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> PSPG Graduate Program/CERSI Seminar Series Pharmaceutical Sciences & Pharmacogenomics Center for Excellence in Regulatory Science & Innovation Tuesdays, 12 Noon Rock Hall Auditorium Simulcast to Parnassus Campus N225 Aled Edwards University of Toronto Open source discovery of new drug targets using chemical probes January 26, 2016 B. Shoichet, Host Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546 ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?TICKET=NzM2MDEzIG1hdHQuamFjb2Jzb25AVUNTR…> from this mailing list.

1 0

[Compbio-allhands] PETER KOLLMAN LECTURESHIP- JANUARY 21, 2016
by Flowers, Nicole 20 Jan '16

20 Jan '16

Michael Gilson UC San Diego The Physical Basis of Computer-Aided Drug Design Thursday, January 21, 2016 12:00 PM PETER A. KOLLMAN LECTURESHIP Genentech Hall Byers Auditorium UCSF Mission Bay Campus Simulcast to Parnassus Campus S-161 Webcast: http://lecture.ucsf.edu/ets/Play/a4adc34fa08b46fa9388e9e0aab8f5f41d Reception in Byers Hall 3rd Floor Lounge at 3:30 pm. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

2 1

[Compbio-allhands] Fwd: Postdoc Position in NMR
by Andrej Sali 13 Jan '16

13 Jan '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: pau bernado <pau.bernado(a)cbs.cnrs.fr> > Subject: Postdoc Position in NMR > Date: January 13, 2016 at 9:47:54 AM GMT+1 > To: pau bernado <pau.bernado(a)cbs.cnrs.fr>, Nathalie Sibille <nathalie.sibille(a)cbs.cnrs.fr> > > Dear Colleague, > > Our group is opening a two-year postdoc position in NMR to work at the Centre de Biochimie Structurale (CBS) in Montpellier. Please, spread this information to students or postdocs that could be interested. > Candidates should have a strong background in solution NMR. Expertise in protein expression and purification, or computational approaches is highly recommended. The project aims at studying Intrinsically Disordered Proteins related with cell signaling and neurodegenerative diseases. Find attached a more detailed description of the position. > > Thanks a lot for your collaboration and best regards > > Pau Bernadó > > > >

1 0

[Compbio-allhands] Fwd: Senior level faculty search in computational biology at UMass Amherst
by Andrej Sali 12 Jan '16

12 Jan '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Lila Gierasch <gierasch(a)biochem.umass.edu> > Subject: Senior level faculty search in computational biology at UMass Amherst > Date: January 12, 2016 at 11:39:21 PM GMT+1 > To: Ken Dill <dill(a)maxwell.compbio.ucsf.edu>, D Thirumalai <thirum(a)umd.edu>, Angel Garcia <angel(a)rpi.edu>, Vijay Pande <pande(a)stanford.edu>, Rohit Pappu <pappu(a)wustl.edu>, Jose Onuchic <jonuchic(a)rice.edu>, George Makhatadze <makhag(a)rpi.edu>, case <case(a)biomaps.rutgers.edu>, brookscl(a)umich.edu, pwolynes(a)ucsd.edu, brunger(a)stanford.edu, Andrej Sali <sali(a)salilab.org>, David Baker <dabaker(a)u.washington.edu>, Oliver Brock <oliver.brock(a)tu-berlin.de>, George Rose <grose(a)jhu.edu>, Dave Thirumalai <thirum(a)umd.edu>, Ruth Nussinov <ruthn(a)ncifcrf.gov>, "David A. Agard" <agard(a)msg.ucsf.edu>, Vince Hilser <hilser(a)jhu.edu>, Chris Sander C <sanderc(a)mskcc.org>, eugene(a)belok.harvard.edu, palsson(a)ucsd.edu, ronlevy(a)temple.edu, chan(a)arrhenius.med.utoronto.ca, sali(a)salilab.org, Arnie Hagler <athagler(a)gmail.com>, bh6(a)columbia.edu, Woody Sherman <woody.sherman(a)gmail.com> > > Hi friends- > > I wanted to let you know about a faculty search at UMass Amherst in computational biology and to ask your help in spreading the word about this exciting opportunity. Within the broad area of computational biology, we would be delighted to have applicants from any of a wide range of topics: including molecular-level modeling, such as protein-protein interactions, docking of small molecules, simulations of dynamics and conformational change; analysis of large data sets and –omic results; or modeling of systems and networks. This search has been launched under the aegis of our new Institute for Applied Life Sciences (IALS), and we seek a mid-career scientist whose star is rising and whose research is directed towards therapeutic goals, such as target discovery. In addition, we want to attract someone who enjoys collaboration and has synergistic research interests with IALS scientists in areas like protein homeostasis, cancer, immunology, drug delivery, and more. Interested candidates can take a look at the IALS faculty research themes at: https://www.umass.edu/ials/ <https://www.umass.edu/ials/> > It’s a very exciting time at UMass Amherst, and we are looking for a number of new hires in addition to the computational biologist (see the attached ad). The state has invested in the campus to the tune of $140M to start IALS, and many new core facilities have been created and others enhanced (see https://www.umass.edu/ials/core-facilities <https://www.umass.edu/ials/core-facilities>). For a computational biologist, it is also exciting that we are establishing a new College of Information and Computer Sciences (www.cics.umass.edu <http://www.cics.umass.edu/>), and the campus is a partner in the Green High Performance Computing Center located in nearby Holyoke, MA (www.mghpcc.org/) > > Please help spread the word. The Amherst area is a great place to live, the Five-Colleges Inc collaboration is a super aspect, and UMass Amherst is truly blossoming. The search is now open, and consideration of candidates will continue until we fill the position. > > Best, > > Lila > > > > > > Lila M. Gierasch > Distinguished Professor > Depts. of Biochemistry & Molecular Biology and Chemistry > Life Sciences Laboratories Room N331 > 240 Thatcher Way > University of Massachusetts, Amherst > Amherst, Massachusetts 01003-9364 > Tel 413-545-6094 > Fax 413-545-1289 > email: gierasch(a)biochem.umass.edu <mailto:gierasch@biochem.umass.edu> > http://www.biochem.umass.edu/biochem/gierasch/index.html <http://www.biochem.umass.edu/biochem/gierasch/index.html> > http://people.chem.umass.edu/gieraschlab > > >

1 0

[Compbio-allhands] Fwd: job opening at Novartis Emeryville
by Andrej Sali 11 Jan '16

11 Jan '16

Sent from my iPhone Begin forwarded message: > From: Dave Barkan <davebarkan(a)gmail.com> > Date: January 11, 2016 at 5:07:08 PM GMT+1 > To: Andrej Sali <sali(a)salilab.org> > Subject: job opening at Novartis Emeryville > > Hey Andrej! > > Hope things are going well. We have an opening for an entry-level Investigator position in our Infectious Diseases group in Emeryville. Talented post-docs from bioinformatics-focused labs at UCSF, or newly minted PhD graduate students, would be good candidates. Could you please circulate the following link? > > http://jobs.brassring.com/1033/ASP/TG/cim_jobdetail.asp?partnerid=13617&sit… > > Thanks! > Dave

1 0

[Compbio-allhands] Fwd: LabEx LERMIT - "New Group Leader" Call
by Brian Shoichet 11 Jan '16

11 Jan '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "Aurelie Lando" <aurelie.lando(a)u-psud.fr> Date: Jan 11, 2016 2:04 AM Subject: LabEx LERMIT - "New Group Leader" Call To: "atartar" <andre.tartar(a)univ-lille2.fr>, "Ralph Schermuly" < Ralph.Schermuly(a)innere.med.uni-giessen.de>, "Francois Ballet" < fballet(a)medicen.org>, "Lehr Claus-Michael" <lehr(a)mx.uni-saarland.de>, "Harding, Sian E" <sian.harding(a)imperial.ac.uk>, "Houslay, Miles" < miles.houslay(a)kcl.ac.uk>, "Kevin Harrington" <Kevin.Harrington(a)icr.ac.uk>, "Beat Ernst" <beat.ernst(a)unibas.ch>, "michel.bouvier(a)umontreal.ca" < michel.bouvier(a)umontreal.ca>, "jlederer(a)umaryland.edu" < jlederer(a)umaryland.edu>, "lederer(a)umbi.umd.edu" <lederer(a)umbi.umd.edu>, "Ulf Lindahl" <ulf.lindahl(a)imbim.uu.se>, "Storm, G." <G.Storm(a)uu.nl>, "Mark Sansom" <mark.sansom(a)bioch.ox.ac.uk>, "Gunda Georg" <georg(a)umn.edu>, " vera.regitz-zagrosek(a)charite.de" <vera.regitz-zagrosek(a)charite.de>, " carlo.croce(a)osumc.edu" <carlo.croce(a)osumc.edu>, "Meijer Manros" < meijer(a)manros-therapeutics.com>, "stephen.archer(a)queensu.ca" < stephen.archer(a)queensu.ca>, "Hossam Haick" <hhossam(a)tx.technion.ac.il>, "Sam Gellman" <gellman(a)chem.wisc.edu>, "Juliano, Rudolph L" < rudy_juliano(a)med.unc.edu>, "Kungl, Andreas (andreas.kungl(a)uni-graz.at)" < andreas.kungl(a)uni-graz.at>, "Tom Blundell" <tom(a)cryst.bioc.cam.ac.uk>, "Uchegbu, Ijeoma" <ijeoma.uchegbu(a)ucl.ac.uk>, "Brian Shoichet" < bshoichet(a)gmail.com>, "Maria Jose Alonso" <mariaj.alonso(a)usc.es>, " jsamitier(a)ub.edu" <jsamitier(a)ub.edu> Cc: "rodolphe.fischmeister(a)inserm.fr" <rodolphe.fischmeister(a)inserm.fr>, " david.bonnaffe(a)u-psud.fr" <david.bonnaffe(a)u-psud.fr> *New Group Leader Call 2016 - LabEx LERMIT * The Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LabEx LERMIT) is launching an international call for an outstanding new group leader willing to establish an independent research group within one of the LERMIT partner laboratories. The content of this call is attached. The dead-line for application is May 17th, 2016. Thank you to spread widely this offer among your contacts and especially junior scientists who may be interested in establishing their research activity in France. Rodolphe Fischmeister Coordinator David Bonnaffé Vice-Coordinator P/O Aurélie Lando -- Dr.Aurélie Lando Administrative Project Manager LabEx LERMITwww.labex-lermit.fr Faculté de Pharmacie Tour D1 1er étage Université Paris-Sud 5 Rue Jean-Baptiste Clément 92296 Châtenay-Malabry Cedexaurelie.lando(a)u-psud.fr tel : +33 (0)1 46 83 52 46

1 0

[Compbio-allhands] Fwd: Help with a post doc??
by Andrej Sali 23 Dec '15

23 Dec '15

Sent from my iPhone Begin forwarded message: > From: John Aitchison <John.Aitchison(a)systemsbiology.org> > Date: December 23, 2015 at 3:24:38 PM PST > To: John Aitchison <john.aitchison(a)cidresearch.org> > Subject: Help with a post doc?? > > Hi Friends, > I am looking for a post-doc to pick up on a great project involving systems biology and dengue virus. The ideal person would have experience, be interested in, systems cell biology in the context of infectious disease. I would greatly appreciate passing this on to any exceptional people you think might be interested. > Thank you, and happy holidays, > John > > John Aitchison, PhD > Professor > Institute for Systems Biology >

1 0

[Compbio-allhands] Fwd: Postdoc merging structure-based drug design with physiologically-based pharmacokinetic simulations
by Jacobson, Matt 11 Dec '15

11 Dec '15

- Matt Begin forwarded message: From: "Martin, Eric" <eric.martin(a)novartis.com<mailto:eric.martin@novartis.com>> Subject: Postdoc merging structure-based drug design with physiologically-based pharmacokinetic simulations Date: December 11, 2015 at 4:36:47 PM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, I recently obtained funding to extend the work we have been doing in adapting physiologically-based pharmacokinetic simulations to drug lead optimization. Given your groups work in both structure-based virtual screening and on PK parameters like membrane permeability, serum albumin binding, PgP efflux, and brain exposure, I think your students would be very well prepared to take on this challenging interdisciplinary postdoctoral project. I would appreciate your passing this opportunity along to any appropriate students. Best wishes, Eric Rational Bioavailability Design using Physiologically-Based Pharmacokinetics Simulations This computational postdoctoral project is at the interface of several scientific disciplines: chemistry, enzyme kinetics, pharmacokinetics, mathematical simulations, and statistics. Structure-based drug design (SBDD) is the main computational tool for improving binding affinity during lead optimization (LO), but does not address whole animal efficacy. We have recently developed methodology to perform reliable physiologically-based pharmacokinetic (PBPK) simulations of absorption, distribution, metabolism and elimination (ADME) not just for a few, well studied, late-stage compounds, but for entire medchem series, using only inputs computed from chemical structure. These whole-animal simulations only require about 15 rat PK studies for training, typically available early enough to impact LO. We analyze thousands of these simulations with partial least squares regression (PLS) based global sensitivity analysis to identify which few of perhaps a dozen compound properties dominate improved bioavailability across each entire series, as well as for each specific compound. Furthermore, the PLS function provides a very good approximation of the full PBPK simulation for that series. While this work has extended PBPK modeling to LO, it does not yet suggest specific compounds to synthesize, and does not account for how whole-animal ADME interacts with molecular binding kinetics to determine target occupancy over time, and therefore efficacy. We now aim to integrate interactive SBDD and in silico compound evolution with multi-objective scoring functions that include both affinity and the PLS approximation of exposure, and to incorporate binding kinetics into the full PBPK simulations. This multi-scale systems biology approach to drug design would complete a path from SBDD, through binding-kinetics enabled PBPK and pharmacodynamics, enabling SBDD not just of ligand binding, but of in vivo efficacy. The goal is ambitious, yet the risks are minimized because the components are established methods, and we can draw on internal Novartis experts in all the required disciplines. Eric Martin Director, Computational Chemistry Novartis Institutes for BioMedical Research, Inc. 5300 Chiron Way Emeryville, CA 94608-2916, USA eric.martin(a)novartis.com<mailto:eric.martin@novartis.com> (510)879-9657

1 0

[Compbio-allhands] 12/3/15 Seminar with Jay Shendure
by Flowers, Nicole 01 Dec '15

01 Dec '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Jay Shendure University of Washington New methods in human genetics December 3, 2015 N. Emami, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Michael Chimenti Referral
by Jacobson, Matt 25 Nov '15

25 Nov '15

- Matt Begin forwarded message: From: Kate Nelson <knelson(a)payettegroup.com<mailto:knelson@payettegroup.com>> Subject: Michael Chimenti Referral Date: November 25, 2015 at 2:26:22 PM PST To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, Michael Chimenti passed along your information. I’m hiring a Principal Bioinformatician in the Bay Area and Michael said that you often circulate job postings via a listserv. It’s a long shot, but I thought I’d pass along the JD in case you wanted to share with your network. JD --> https://goo.gl/o9g5r7 Job description Principal Bioinformatician It was only a matter of time before the big data explosion impacted the food we eat, buy, and sell. We’re the team that wants to make sure that what we think is in our food products, is actually in it. Our analytics platform transforms quality control, analytics, and safety in the global food industry. Built on the foundation of a robust big data engine, our proprietary platform translates quantifiable molecular tests into actionable food data insights. We’re using the same tools and technologies used by clinical genomicists to perform fast and accurate affordable genomic analysis at scale. As our Principal Bioinformatician, you will work directly with the VP of Engineering and be responsible for the development statistical algorithms, methods, and programs for analysis of genomics data. You'll have unparalleled food quality data and domain experts within the company to grow and develop both personally and professionally. With our recent funding, it’s a great time to join us! Food fraud is bigger than ever and this is your chance to solve a real world problem – there is nothing else like this in the world and you could have the opportunity to work on it. Responsibilities • Develop and maintain robust software tools to improve the speed, accuracy, and automation of our analysis pipeline in the cloud • Evaluate third-party tools and libraries we may wish to leverage in our pipeline • Develop novel data analysis and data-mining methods to optimize the performance and accuracy of our platform • Work closely with our science and product team to help define product requirements, spec technical requirements, develop project plans and generate test cases Key responsibilities Requirements • B.S. in Math, Computer Science, Physics, Engineering or equivalent • Minimum 2 years of experience in bioinformatics in industry setting, with strong experience in developing algorithms processing next-generation sequencing data • Familiar with cloud computing and working in cloud environment • Proficiency with SQL and UNIX shells • Proven development experience with an object-oriented language • Strong communication skills both written and verbal with engineers and product marketers • Ability to work independently in a fast paced and high performing environment Preferred Skills • Proven ability to develop algorithms dealing with large-scale data • Extensive experience in biostatistics, advanced mathematics and system modeling • Expertise in Python Thanks in advance and if you have any questions, feel free to reach out! Cheers- Kate Nelson Sr. Technical Recruiter Payette Group 650-326-0760 ext. 104 LinkedIn<https://goo.gl/avPNOa> Twitter<https://goo.gl/GO1Uuw>

1 0

[Compbio-allhands] faculty positions at Shanghaitech, Shanghai
by Andrej Sali 23 Nov '15

23 Nov '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

1 0

[Compbio-allhands] SAVE THE DATE- PETER KOLLMAN LECTURESHIP- JANUARY 21, 2016
by Flowers, Nicole 19 Nov '15

19 Nov '15

SAVE THE DATE- THURSDAY, January 21, 2016 AT 12:00 PM Michael Gilson UC San Diego PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS S-161 Reception in Byers Hall 3rd Floor Lounge at 3:30 pm. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Reminder: Janet Iwasa Seminar TODAY 2-3 PM
by Jacobson, Matt 16 Nov '15

16 Nov '15

Not sure if this got sent out to this list - Matt Begin forwarded message: From: "Brewer, Melanie" <Melanie.Brewer(a)ucsf.edu<mailto:Melanie.Brewer@ucsf.edu>> Subject: Reminder: Janet Iwasa Seminar TODAY 2-3 PM Date: November 16, 2015 at 9:15:28 AM PST To: Melanie Bennett Brewer <melaniebbrewer(a)gmail.com<mailto:melaniebbrewer@gmail.com>> Janet Iwasa of the University of Utah will give a HARC-sponsored seminar “Animating Molecules” TODAY Nov. 16, 2-3 PM in Genentech Hall Room N114. Janet is an award-winning animator and TED speaker who uses 3D animation to provide new insights into macromolecular and cellular systems. Come hear about Janet’s work and learn how we might collaborate with her to animate some of the pathways studied in HARC. ------------------------------------------------------- Melanie Bennett Brewer, Ph.D. Program Manager, The HARC Center University of California, San Francisco Genentech Hall S572, MC 2280 600 16th Street San Francisco, CA 94158-2517 HARC Website: harc.ucsf.edu<http://harc.ucsf.edu/> View my publications at Google Scholar<http://scholar.google.com/citations?hl=en&user=HhJKtigAAAAJ&view_op=list_wo…> Connect on: Linked In<https://www.linkedin.com/profile/view?id=35890499&trk=nav_responsive_tab_pr…>

1 0

[Compbio-allhands] faculty jobs at iHuman, ShaghaiTech
by Andrej Sali 11 Nov '15

11 Nov '15

Computational Biology Faculty Positions at the iHuman Institute, ShanghaiTech University The iHuman Institute at ShanghaiTech University was established to understand human cell signaling at a level beyond what is achievable today. The institute encourages interdisciplinary research combining chemistry, biology, imaging, and structural biology of the cellular components involved in signal transduction. Academic basic science and applied industry research is integrated, providing researchers with unique opportunities. The Institute is recruiting 2 regular tenured and/or tenure-track faculty in 2015 in the areas of computer-aided drug design (CADD) and whole cell modeling. Junior level position applicants should have a Ph.D. degree in computational biology/chemistry, as well as 3+ years postdoctoral or industrial experience. Senior position applicants are expected be leading scientists in their research area. The successful applicant will be expected to establish an independent, internationally recognized research program and to hire and supervise postgraduate, graduate and undergraduate students. Each group is encouraged to recruit up to 10 members and be highly collaborative with other laboratories in different disciplines. A strong core infrastructure has been established within the institute to serve the faculty needs. All financial support is provided by the institute. Importantly, grant writing is not required, particularly for junior faculty members so they can focus on creative research and mentoring of their first students. Initial Research Support Package: The Institute will provide internationally competitive start-up funds plus support of Research Associates and Post-Doctoral Fellows up to 10 full time lab members. Research laboratory and office space will be provided to match the research needs. Faculty have access to some of the world’s best research facilities and resources of the Chinese Academy of Science including the National Protein Center, Shanghai Synchrotron, and Chinese National Compound Library. Compensation and Benefits: Starting salary will be competitive at the international level and commensurate with qualifications and experience. We offer a comprehensive benefits package including health benefits as well as subsidized campus housing. The iHuman Institute will also sponsor applications of national and local Talent Programs based on individuals’ qualification and experience. The iHuman Institute is located in Shanghai, China, which is an exciting and rapidly growing global center of excellence for scientific research. Application Procedure: Submit a cover letter, a 2-3 page statement of research interests, a CV and the names and addresses of three individuals who can serve as references to the mail addresses given below: The iHuman Institute ShanghaiTech University, Building 8, 319 Yueyang Road, Shanghai 200031, China Email: iHuman(a)shanghaitech.edu.cn <mailto:iHuman@shanghaitech.edu.cn> Review of applications will start immediately and will continue until positions are filled. For more information, please visit our website: ihuman.shanghaitech.edu.cn -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

1 0

[Compbio-allhands] Job openings at Veracyte, South San Francisco
by Seung Joong Kim 10 Nov '15

10 Nov '15

Hi all, Veracyte (South San Francisco) has two job openings in a senior level. 1. DAT: Senior Scientist/Associate Director, Machine Learning 2. R&D Lab: Principal Scientist/Associate Director, Discovery R&D Please see the attached word files for job description. Thanks a lot! About Veracyte Veracyte is pioneering molecular cytology; we are dedicated to helping people avoid unnecessary invasive procedures just to get a diagnosis and to reducing healthcare costs at the same time. We use rigorous science to unlock genomic answers from tiny numbers of cells obtained through minimally invasive methods before surgery is needed. We launched our first product the Afirma® Thyroid FNA Analysis, with a genomic test at its core in record time and have already helped save thousands of patients from unnecessary surgery due to ambiguous thyroid nodule biopsy results. Our genomic test is offered by hundreds of physicians around the country, is covered by Medicare and private payers, and is clinically validated, including in a multicenter study published in the New England Journal of Medicine. Earlier this year, we entered the pulmonology space with the launch of Percepta. The Percepta test uses advanced genomic technology to help patients avoid unnecessary invasive, risky procedures on suspicious lung nodules or lesions that were initially found on computed tomography (CT) scans. Percepta is clinically validated, with its key studies recently published in the New England Journal of Medicine. Looking to our pulmonology pipeline, we are also developing a product to target idiopathic pulmonary fibrosis. The Wall Street Journal named us to its list of top-50 venture capital-funded companies in 2011, BayBio honored us with its Fast Start award in 2012, and In Vivo: The Business and Medicine Report featured us recently as a model for how to build a molecular cytology company. In 2014 and 2015 our employees voted us a Bay Area News Group Top Workplace. Veracyte affords equal employment opportunities to all qualified persons, regardless of race, color, religion, national origin, age, sex, disability, sexual orientation, gender expression, veteran or marital status. Veracyte participates in E-Verify in the United States. - Seung Joong Kim -- Seung Joong Kim, Ph.D. Postdoctoral Scholar, Andrej Sali group Department of Bioengineering and Therapeutic Sciences University of California at San Francisco (UCSF) 1-217-649-2147 http://salilab.org/~sjkim

1 0

[Compbio-allhands] Fwd: DBDS Faculty Search
by Patricia C. Babbitt 09 Nov '15

09 Nov '15

-------- Forwarded Message -------- Subject: DBDS Faculty Search Date: Mon, 9 Nov 2015 17:39:40 +0000 From: Laura Dunkin-Hubby <lhubby(a)stanford.edu> To: babbitt(a)cgl.ucsf.edu <babbitt(a)cgl.ucsf.edu> Dear Dr. Babbitt, I am writing on behalf of Dr. Carlos Bustamante to ask your help in identifying candidates for an Assistant, Associate or Full Professor position in the new Department of Biomedical Data Science (DBDS) at the Stanford University School of Medicine. This appointment will be in the University Tenure Line (UTL). The predominant criterion for appointment in the University Tenure Line is a major commitment to research and teaching. We define biomedical data science as the study of biomedical data and information, of how such data and information may be structured, and of how analysis and processing of biomedical data and information will lead to new discoveries and to advances in health and healthcare. We are particularly interested in candidates dedicated to the development of novel computational and statistical methods for acquiring, representing, storing, analyzing, and applying biological and clinical data at all scales, who can apply their expertise in biomedical informatics and/or biostatistics to meet departmental goals. Further information on the Department of Biomedical Data Science can be found at[dbds.stanford.edu]dbds.stanford.edu. Applicants should have demonstrated strong ability and interest in conducting both methodological and collaborative research, and in teaching. We expect the successful candidate to conduct a vigorous, independent research program, to advise students, and to assist in program administration. Formal teaching in the classroom will be encouraged. An MD, MD/PhD, or PhD in biostatistics, statistics, biomedical informatics, computer science, biomedical engineering or a related area is required. Faculty rank will be determined by the qualifications and experiences of the successful candidate. Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty. It welcomes nominations of and applications from women, members of minority groups, protected veterans and individuals with disabilities, as well as from others who would bring additional dimensions to the university's research, teaching and clinical missions. I would appreciate your forwarding this announcement to individuals whom you feel would be particularly suited for this position. Interested candidates should send a copy of their curriculum vitae, a brief letter outlining their research and teaching interests, and arrange for three letters of reference to be submitted to: Euan Ashley, MD, PhD and Daniel Rubin, MD, MS Search Committee Co-Chairs Department of Biomedical Data Science Stanford University School of Medicine DBDSjobs_SOM(a)stanford.edu<mailto:DBDSjobs_SOM@stanford.edu> Applications will continue to be accepted and considered until the opening is filled. Sincerely yours, Carlos D. Bustamante, PhD Chair, Department of Biomedical Data Science Stanford University School of Medicine - Laura Dunkin-Hubby Administrative Assistant to Dr. Carlos Bustamante Stanford Center for Computational, Evolutionary and Human Genomics T 650.725.5067<file://localhost/tel/+1-650-723-2643> * cehg.stanford.edu -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Josel Tongson, +1 415-514-1214, 415-514-4861 GraciaJoselina.Tongson(a)ucsf.edu

1 0

[Compbio-allhands] 11/12/15 Seminar with Xuewu Zhang
by Flowers, Nicole 06 Nov '15

06 Nov '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Xuewu Zhang UT Southwestern Regulation mechanisms of the neuronal axon guidance receptor plexin November 12, 2015 N. Jura, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: potential comp chem position at Merck
by Jacobson, Matt 30 Oct '15

30 Oct '15

- Matt Begin forwarded message: From: "McMasters, Daniel R" <daniel_mcmasters(a)merck.com<mailto:daniel_mcmasters@merck.com>> Subject: RE: potential comp chem position at Merck Date: October 30, 2015 at 5:59:45 AM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, Thanks! Any help getting the word out to potential candidates is appreciated. We actually have two openings for computational chemists, one each in Boston and West Point, PA (Philadelphia area). There is also an opening for a cheminformatician/comp tox as well as one for a crystallographer. Here are the links for applicants to apply, and of course anyone can feel free to email me at any time. -Daniel Computational chemistry: https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft… Cheminformatics & computational toxicology: https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft… Crystallography: https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft…

1 0

[Compbio-allhands] Fwd: Still open places for our course on modeling 3D genomes and genomic domains
by Andrej Sali 30 Oct '15

30 Oct '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > Date: October 30, 2015 at 11:27:49 AM PDT > To: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > Subject: Still open places for our course on modeling 3D genomes and genomic domains > > Dear Friends and Colleagues, > > Apologies for the mass posting. > > We still have open positions for people who may be interested in our TADbit Course at the Gulbenkian Institute in Oeiras (near Lisbon) in Portugal. > > See the details here http://gtpb.igc.gulbenkian.pt/bicourses/CSDM15/ <http://gtpb.igc.gulbenkian.pt/bicourses/CSDM15/> or in the attached poster. > > Pass it along to whom you may think could be interested. > > Thanks in advance! > Marc A. Marti-Renom > > > > > ... > Marc A. Marti-Renom, ICREA Research Professor > Structural Genomics Group Leader > Centre Nacional d’Anàlisi Genòmica - Centre de Regulació Genòmica (CNAG-CRG) > Parc Científic de Barcelona – Torre I (10th floor) > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email: martirenom(a)cnag.crg.eu <mailto:martirenom@cnag.crg.eu> > Web: http://marciuslab.org <http://marciuslab.org/> · http://cnag.crg.eu <http://cnag.crg.eu/> · http://crg.cat <http://crg.cat/> > > *** Consider the environment. Print responsibly. *** > > CRG/”la Caixa” – Severo Ochoa FELLOWSHIPS AVAILABLE TO CARRY OUT PhD > STUDIES AT THE CENTER FOR GENOMIC REGULATION (CRG), BARCELONA > MORE INFORMATION AND ONLINE APPLICATION AT: http:// <http://www.crg.eu/lacaixa_fellowships>www.crg.eu/lacaixa_fellowships <http://www.crg.eu/lacaixa_fellowships> > > > > > > > > > > > > > >

1 0

[Compbio-allhands] Fwd: The Rockefeller University - Fellow Position
by Jacobson, Matt 30 Oct '15

30 Oct '15

- Matt Begin forwarded message: From: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Subject: The Rockefeller University - Fellow Position Date: October 30, 2015 at 9:44:01 AM PDT To: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Dear Colleague: The Center for Studies in Physics and Biology, at The Rockefeller University, expects to have a small number of postdoctoral fellowships available for appointments in September 2016. We are seeking theoretical physicists, mathematicians and computer scientists with a demonstrable interest in the interface between their discipline and biology. The Fellows are to be at that stage of career as to function as independent members of the Center, free to work alone or in collaboration with any members of The Rockefeller University faculty. Would you be so kind as to post the attached notice, and share this within your department and with your peers and colleagues. Many thanks! Melanie J. Lee Administrative Assistant Center for Studies in Physics and Biology Rockefeller University 1230 York Avenue New York, NY 10065-6399 Tel: 212-327-8636 Fax: 212-327-8544

1 0

[Compbio-allhands] Fwd: open CC position
by Jacobson, Matt 29 Oct '15

29 Oct '15

- Matt Begin forwarded message: From: "Lexa, Katrina W" <katrina.lexa(a)merck.com<mailto:katrina.lexa@merck.com>> Subject: open CC position Date: October 29, 2015 at 1:45:42 PM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, Another comp chemist job ad went up for the Structural Chemistry dept – they are looking primarily for people coming out of a postdoc. https://taleo.msd.com/careersection/merck_external_career_section/jobdetail… They are hoping to fill several slots, so please pass along. Thanks! ------------------------------- Katrina Lexa Merck & Co., Inc. 126 East Lincoln Ave RY800-C364 Rahway, NJ 07065 phone: (732) 594-7058 office: RY800-D365 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

1 0

[Compbio-allhands] Volunteers needed to help with upcoming Software Carpentry workshops at UCSF on R and Python
by Patricia C. Babbitt 28 Oct '15

28 Oct '15

Hi all, The UCSF Institute for Computational Health Sciences and the UCSF Library have set up a collaboration to bring in Software Carpentry to teach two bootcamp workshops, one an R and the other on Python on Nov. 20 and 21. The content is geared to grad students and postdocs who want to develop basic skills with these tools. Both will run for two days, 9 am to 5 pm. Volunteers are needed to help the Software Carpentry Instructors in providing assistance to workshop learners during practical sessions. While not a paid gig, breakfast and coffee/snacks will be offered in the afternoon of each day. You will be listed on the workshop materials and website as helpers and you can put this effort on your CV as service to the UCSF community and to show you have teaching experience in these areas. You can check out a similar recent boot camp to get a feel for the content and whether your expertise is a good fit: https://richford.github.io/2015-10-22-uw/ The roles for the helpers are described at https://software-carpentry.org/workshops/checklists/helpers.html If you're interested in doing this, please send an email to babbitt(a)cgl.ucsf.edu. I'm happy to answer questions you may have before deciding if you want to sign up for this. We'll take folks who are a fit on a first come, first served basis. If you decide to participate, we will also ask for your feedback on the experience, as having some expert eyes on the content and format of the boot camps and syllabi will be helpful for future workshops we want to mount on biostats and bioinformatics for the broad UCSF community. Getting your opinions about how best to do that would be helpful to us. If you're interested in participating as instructors in some of these later workshops, please let me know that as well. Thanks. Patsy Babbitt -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Josel Tongson, +1 415-514-1214, 415-514-4861 GraciaJoselina.Tongson(a)ucsf.edu

1 0

[Compbio-allhands] Fwd: Tenure-Track Openings in Computational Biology at Carnegie Mellon University
by Jacobson, Matt 25 Oct '15

25 Oct '15

-- Matt Sent from my iPhone Begin forwarded message: From: "Robert F. Murphy" <murphy(a)cmu.edu<mailto:murphy@cmu.edu>> Date: October 25, 2015 at 5:15:54 PM PDT Subject: Re: Tenure-Track Openings in Computational Biology at Carnegie Mellon University ======================================== Tenure-track Faculty Positions Available We seek outstanding researchers who are developing and applying rigorous computational methods in all areas of biology for tenure-track positions in the Computational Biology Department within the School of Computer Science. We especially seek candidates working on automated analysis and modeling of biological and medical images, and those addressing problems in neurobiology using computational methods, although outstanding candidates from all areas will be enthusiastically considered. The department has extensive strengths in methods underlying genome-based personalized medicine (genome association for complex phenotypes, dynamic network models, efficient sequence analysis), bioimage informatics (analysis and modeling of cell and tissue organization, perturbation and differentiation), modeling and simulation of biological systems at various levels, and application of active machine learning to biological problems. A critical focus is that we do not simply build systems to reproduce or automate tasks that humans can do, but build machine learning and vision systems that answer questions and build models in ways well beyond human capabilities and that can be the driver behind choice of further experiments. Additional information on the department may be found at http://www.cbd.cmu.edu. We particularly encourage applications from candidates who have a demonstrated track record in mentoring and nurturing female and under-represented minority students. Appointments will be made either entirely in the Computational Biology Department or jointly with other departments in the University (as appropriate to the background and interests of the candidate and at a level commensurate with experience). New faculty members will be expected to both contribute to and benefit from the collaborative spirit that is a hallmark of Carnegie Mellon University and from opportunities to collaborate with other institutions in the Pittsburgh region. Applications should be submitted through the faculty application system at https://webapps.cs.cmu.edu/FacultyApplication/SCS/Welcome. Completed applications must be received by January 4, 2016. Carnegie Mellon is an EEO/Affirmative Action Employer - M/F/Disability/Veteran ======================= Robert F. Murphy, Ph.D. Ray and Stephanie Lane Professor of Computational Biology and Professor of Biological Sciences, Biomedical Engineering, and Machine Learning Head, Computational Biology Department, School of Computer Science, Carnegie Mellon University 7723 Gates and Hillman Centers, 5000 Forbes Ave., Pittsburgh, PA 15213 Phone: 412-268-3480, FAX: 412-268-2977, email: murphy(a)cmu.edu<mailto:murphy@cmu.edu>, Skype: rfmurphy1953 Personal Home Page: http://www.andrew.cmu.edu/user/murphy Honorary Professor, University of Freiburg and External Senior Fellow, Freiburg Institute for Advanced Studies

1 0

[Compbio-allhands] 10/29/15 Seminar with Chris Garcia
by Flowers, Nicole 23 Oct '15

23 Oct '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Chris Garcia Stanford Turning cell surface receptor signaling through ligand engineering: Type I receptors versus GPCR October 29, 2015 J. Kung, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 10/22/15 Seminar with Andrew Ward
by Flowers, Nicole 16 Oct '15

16 Oct '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Andrew Ward Scripps High-resolution cryoEM structures of viral glycoproteins and neutralizing antibodies October 22, 2015 W. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Structural biology faculty positions at CUNY ASRC
by Andrej Sali 15 Oct '15

15 Oct '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Kevin Gardner <Kevin.Gardner(a)asrc.cuny.edu> > Date: October 15, 2015 at 2:38:07 PM PDT > To: "sali(a)salilab.org" <sali(a)salilab.org> > Subject: Structural biology faculty positions at CUNY ASRC > > Dear Andrej: > > I’m writing today <https://urldefense.proofpoint.com/v2/url?u=http-3A__airmail.calendar_2015-2…> to ask for your help in identifying outstanding applicants for two open tenure-track faculty positions at the CUNY Advanced Science Research Center, a new interdisciplinary research center located in New York City. I believe these might be very good fits for potential trainees of yours with expertise in integrative structural biology, as detailed below. > > As you might be aware, I moved to the CUNY ASRC in Fall 2014 as the facility opened, providing 200,000 ft2 of laboratory space that has turned into a highly interactive and collaborative environment which integrates structural biologists with colleagues in neuroscience, photonics, nanoscience and environmental sciences. Combining world-class experts in these areas with state-of-the-art NMR, EM, mass spec, crystallization and other instrumentation and colleagues both in the building and at the adjacent CCNY Center for Discovery and Innovation and New York Structural Biology Center, the ASRC offers a unique opportunity for research programs to flourish among normally-disparate fields. > > Continuing our growth this year, we are looking for two new tenure-track faculty to join the ASRC’s Structural Biology Initiative at the Assistant, Associate or Full Professor level. To do so, I ask for your help at bringing this opportunity to the attention of outstanding scientists with strong records of significant research accomplishments in structural biology, broadly defined as the use of a wide range of experimental and computational approaches to tackle fundamental questions of the molecular mechanisms inherent to biological processes. > > Candidates are expected to have advanced degrees (Ph.D., M.D. or equivalent) in biophysics, biochemistry, chemistry or related areas plus postdoctoral research experience. Final faculty ranks will be determined by the qualifications and experience of successful candidates, with our primary criteria being a demonstrated commitment to research and teaching. Individuals filling these positions are expected to serve major roles in the research and education programs of the ASRC, along with the teaching mission ns of one of the colleges within the CUNY system. > > Applicants should electronically submit 1). a curriculum vitae, 2). a 1-2 page cover letter summarizing research accomplishments, future directions and views on interdisciplinary research, and 3). a brief (3 page max) description of proposed research, and arrange to have at least three letters of recommendation submitted on their behalf to the Structural Biology Initiative Search Committee c/o Dr. Kevin Gardner, at Academic Jobs Online <https://urldefense.proofpoint.com/v2/url?u=https-3A__academicjobsonline.org…>https://academicjobsonline.org/ajo/jobs/6092 <https://urldefense.proofpoint.com/v2/url?u=https-3A__academicjobsonline.org…>, Job# 6092. All application materials must be received by October 31, 2015 <https://urldefense.proofpoint.com/v2/url?u=http-3A__airmail.calendar_2015-2…>. > > For more information, please see our websites at <http://structbio.asrc.cuny.edu/>http://structbio.asrc.cuny.edu <http://structbio.asrc.cuny.edu/> and <http://asrc.cuny.edu/>http://asrc.cuny.edu <http://asrc.cuny.edu/> or contact me at StructuralBiology.Jobs(a)asrc.cuny.edu <mailto:StructuralBiology.Jobs@asrc.cuny.edu>. > > The City University of New York (CUNY) is committed to enhancing our diverse academic community by actively encouraging people with disabilities, minorities, veterans, and women to apply. We take pride in our pluralistic community and continue to seek excellence through diversity and inclusion. EO/AA Employer. > > Best regards, > Kevin > > > — > Kevin H. Gardner, Ph.D. > Director, Structural Biology Initiative, CUNY Advanced Science Research Center > Professor of Chemistry and Biochemistry, City College of New York > Kevin.Gardner(a)asrc.cuny.edu <https://urldefense.proofpoint.com/v1/url?u=http://mailto:Kevin.Gardner%40as…> http://asrc.cuny.edu <http://asrc.cuny.edu/> > phone: 212-413-3220 <tel://212-413-3220> >

1 0

[Compbio-allhands] Fwd: Medicinal Chemistry Informatics Expert Position at Roche Basel
by Michael Keiser 15 Oct '15

15 Oct '15

-------- Forwarded Message -------- Subject: Medicinal Chemistry Informatics Expert Position at Roche Basel Date: Thu, 15 Oct 2015 16:38:57 +0200 From: Hert, Jerome <jerome.hert(a)roche.com> Dear colleague, I would like to inform you of a new job opportunity in the Small Molecule Discovery Workflows group in Pharma Research and Early Development Informatics department. The opening calls for a PhD level scientist who will develop and/or support applications for medicinal chemists requiring an excellent understanding of their ways of working and some agile development skills. Additional details about the opening can be found at http://goo.gl/YWDiQ2 Feel free to forward this message to anyone who might be interested. For additional information, please contact the hiring manager Dr. Roman Affentrager (roman.affentranger(a)roche.com <mailto:roman.affentranger@roche.com>). -- With best regards, Jérôme Hert. -- Section Head, Computer-Aided Drug Design Small Molecule Research, Molecular Design & Chemical Biology Roche Pharmaceutical Research and Early Development Roche Innovation Center Basel F. Hoffmann-La Roche Ltd T: +41 6168 79639 E: jerome.hert(a)roche.com <mailto:jerome.hert@roche.com> -- *Want to know more about Roche?* Roche at a glance <https://www.youtube.com/watch?v=A4fDD8ByyrE>. Explore our marketed products <http://www.roche.com/products/product-list.htm?type=divpharma&id=Pharmaceut…>. Have a look at our pipeline <http://www.roche.com/research_and_development/who_we_are_how_we_work/pipeli…>. Take a tour of pRED <https://www.youtube.com/watch?v=DVvPCOXdMI0>. See what it's like to work at Roche <https://www.youtube.com/playlist?list=PL4610DC508842D098>.

1 0

[Compbio-allhands] Fwd: position for upcoming graduates/postdocs @Dow
by Andrej Sali 11 Oct '15

11 Oct '15

> Begin forwarded message: > > From: "John, Bino (B)" <bjohn1(a)dow.com> > Date: October 10, 2015 at 2:45:57 PM PDT > To: "Andrej Sali (sali(a)salilab.org)" <sali(a)salilab.org> > Subject: position for upcoming graduates/postdocs @Dow > > Job Description > Dow AgroSciences seeks an innovative Computational Biologist for genetic, genomic, proteomic, and phenotypic data analysis. The successful candidate will join the Data Analysis Department within R&D and will interface with scientists across Dow AgroSciences R&D. The candidate will use computational approaches spanning genetic, genomic, phenotype, and protein sequence data to drive hypothesis generation and enable automated computing systems. > > Key job responsibilities are: > > - Develop innovative automated computing platforms for integrating genetic, genomic, and phenotype data to enable R&D decisions > - Enable hypothesis generation using genomic and proteomics data analysis spanning sequence (gene, RNA, protein) and protein structure analysis. > - Monitor emerging computational and data analysis technologies to accelerate program objectives and translate leads into actionable research activities. > > This position is located at Dow AgroSciences’ world headquarters in Indianapolis, IN, USA on its modern and expanding campus. Domestic relocation support is provided for this position. > > Qualifications > > - Doctoral degree in computational biology or closely related field > - Demonstrated experience in multiple areas of the following data types: DNA, RNA, protein, pathway, and phenotype > - Demonstrated experience in working in a high-performance computing environment > - Demonstrated experience in computing software (MATLAB or similar), compiled programming languages (Java or similar) and database programming languages (e.g. SQL or similar) > > Basic qualifications > > - Doctoral degree in computational biology or closely related field > > About Dow AgroSciences > Dow AgroSciences discovers, develops, and brings to market crop protection and plant biotechnology solutions for the growing world. Based in Indianapolis, Indiana, USA, Dow AgroSciences is a wholly owned subsidiary of The Dow Chemical Company and had annual global sales of $7.3 billion in 2014. Learn more at www.dowagro.com <http://www.dowagro.com/>. Follow Dow AgroSciences on Facebook, Twitter, LinkedIn, and Google+, or subscribe to our News Release RSS Feed. > > Dow AgroSciences offers: > > - Competitive salaries and comprehensive benefits > - An annual variable pay program that rewards team and individual performance while sharing success across the company > - Employee stock ownership - and the commitment to long-term success that it brings > - On-going learning opportunities within a diverse, inclusive and rewarding work environment > - Career experiences that can span different Dow businesses and functions with opportunities for personal and professional growth > - The chance to work within a global company and interact with colleagues from around the world > - Opportunities that spark your imagination and ignite your passion to help others > > Primary Location: North America-USA-Indiana-Indianapolis > Schedule: Full-time > Apply now : http://careers.dowagro.com/talentcommunity/apply/300576800 <http://careers.dowagro.com/talentcommunity/apply/300576800> > Visa: H1B sponsorship available > > > > > > > Bino John > Computational Biology Group Leader > Dow AgroSciences LLC > 9330 Zionsville Road > Indianapolis, IN 46268 > O:317-337-5325, C:917-6640462 > bjohn1(a)dow.com <mailto:bjohn1@dow.com>

1 0

[Compbio-allhands] 10/15/15 Seminar with Timothy Lu
by Flowers, Nicole 09 Oct '15

09 Oct '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Timothy Lu MIT Programming Cells for Human Health Applications October 15, 2015 H. El-Samad, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: computational scientist at Impossible Foods
by Andrej Sali 02 Oct '15

02 Oct '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Michael Eisen <mbeisen(a)gmail.com> > Date: October 2, 2015 at 6:17:35 AM GMT+9 > To: Michael Eisen <mbeisen(a)gmail.com> > Subject: computational scientist at Impossible Foods > > Colleagues- > > Sorry for the blast email. > > As most of you know I've been helping Pat Brown out with Impossible Foods, the company he founded to create plant-based alternatives to meat and other animal products, with the goal of ending the world's most destructive industry (animal farming). As part of this effort we have been generating a lot of very interesting data on the identity and properties of plant proteins, on various plant-based materials, on small molecules present in uncooking, cooking and cooked foods, on microbes used in cheesemaking, and how all of the various properties of animal products and the products we are making influence how they're perceived by consumers. > > With all this data, we are now in great need of a smart scientists to do interesting things with it. Pat and I have been doing a lot of this ourselves, but we just can't keep up. So if you know anyone really good, who wants to work in a fun and exciting startup with a important mission (our goal is to change the way the Earth looks from space) please send them my way. > > Here's our website: www.impossiblefoods.com <http://www.impossiblefoods.com/> > > And a job description: http://impossiblefoods.com/jobs/?gh_jid=98307 <http://impossiblefoods.com/jobs/?gh_jid=98307> > > Let me know if you have any questions. > > -Mike > > -- > Michael Eisen, Ph.D. > Investigator, Howard Hughes Medical Institute > Professor of Genetics, Genomics and Development > Department of Molecular and Cell Biology > University of California, Berkeley

1 0

[Compbio-allhands] 10/8/15 Seminar with Eric Siggia
by Flowers, Nicole 02 Oct '15

02 Oct '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Eric Siggia Rockefeller Differentiation of micropatterned human embryonic stem cell colonies recapitulates the early embryo October 8, 2015 M. Thompson, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: 2016 Postdoc in Computational Protein Design Job Posting
by Jacobson, Matt 01 Oct '15

01 Oct '15

-- Matt Sent from my iPhone Begin forwarded message: From: "Lexa, Katrina W" <katrina.lexa(a)merck.com<mailto:katrina.lexa@merck.com>> Date: October 1, 2015 at 10:43:57 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: FW: 2016 Postdoc in Computational Protein Design Job Posting Hi Matt, Passing along a computational postdoc posting, for people who might be interested. ------------- Katrina From: Crespo, Alejandro Sent: Friday, September 25, 2015 10:35 AM To: MRL Process Chemistry - Truppo Subject: 2016 Postdoc in Computational Protein Design Job Posting Hello Chemical Biotechnology, As you may know, we are looking for candidates for the 2016 postdoc in computational protein design. I would appreciate if you could forward the job posting link below to your scientific academic network so we can capture the best candidates. https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft… FYI the full advertisement is due to be published in the October 16th edition of Science. Thank you Regards Alejandro Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

1 0

[Compbio-allhands] Fwd: Job offer for a programmer in Barcelona
by Andrej Sali 01 Oct '15

01 Oct '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > Date: October 1, 2015 at 7:33:34 AM PDT > To: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > Subject: Job offer for a programmer in Barcelona > > Dear Friends and Colleagues, > > Apologies for the mass posting. > > Please, forward that e-mail to whom you believe could be interested in a Programmer position in our group to work on developing tools for modeling and visualizing 3D genomes. > > More information here http://recruitment.crg.eu/content/jobs/position/programmer <http://recruitment.crg.eu/content/jobs/position/programmer> as well as in the attached PDF. > > Deadline 19th of October. > > All the best, > Marc > ... > Marc A. Marti-Renom, ICREA Research Professor > Structural Genomics Group Leader > Centre Nacional d’Anàlisi Genòmica - Centre de Regulació Genòmica (CNAG-CRG) > Parc Científic de Barcelona – Torre I (10th floor) > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email: martirenom(a)cnag.crg.eu <mailto:martirenom@cnag.crg.eu> > Web: http://marciuslab.org <http://marciuslab.org/> · http://cnag.crg.eu <http://cnag.crg.eu/> · http://crg.cat <http://crg.cat/> > > *** Consider the environment. Print responsibly. *** > > > > > > > > > > > > >

1 0

[Compbio-allhands] Fwd: Bioinformatics and Computational Staff Scientists at the University of Oklahoma
by Jacobson, Matt 30 Sep '15

30 Sep '15

-- Matt Sent from my iPhone Begin forwarded message: From: <jzhoulab(a)gmail.com<mailto:jzhoulab@gmail.com>> Date: September 30, 2015 at 8:20:26 AM HST To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Bioinformatics and Computational Staff Scientists at the University of Oklahoma Dear Dr. Matthew Jacobson We have two positions in bioinformatics and computational biology available at the Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA. We are looking for highly motivated computational scientists and bioinformaticians with strong background and experience in computation, bioinformatics, mathematics, statistics, environmental engineering, and theoretical ecology, and the development and/or applications of new algorithms and methods for big microbiome data analysis. Both positions are permanent, 12-month appointments supported by the University funds. Both positions will be focused on microbiome studies related to bioenergy, climate change, environmental science and human health. Individuals in both positions will participate in grant proposal writing as a PI, or Co-PI, and may hold adjunct faculty positions at relevant academic departments such as Microbiology and Computer Science (See attachment fo r details). I will appreciate greatly that you can pass this announcement on to any potential candidates that you know. Please feel free to post the announcement or forward it to any colleagues who may know of potential candidates. Thanks for your kind assistance! Yours sincerely Joe Jizhong Zhou, Ph.D George Lynn Cross Research Professor, Department of Microbiology and Plant Biology Director, Institute for Environmental Genomics (IEG) University of Oklahoma 101 David L. Boren Blvd. Norman, OK, 73072 Phone: 205-325-6073 Fax: 405-325-7552 E-mail jzhoulab(a)gmail.com<mailto:jzhoulab@gmail.com> Website: http://ieg.ou.edu

1 0

[Compbio-allhands] Fwd: Princeton University postdoctoral opportunities in theoretical biological physics
by Andrej Sali 28 Sep '15

28 Sep '15

> Begin forwarded message: > > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Subject: Princeton University postdoctoral opportunities in theoretical biological physics > Date: September 28, 2015 at 1:27:55 PM PDT > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Cc: "Curtis G. Callan Jr." <ccallan(a)Princeton.EDU>, William Bialek <wbialek(a)Princeton.EDU>, "Wingreen, Ned S." <wingreen(a)Princeton.EDU> > > Dear Colleague, > > We want to bring to your attention the existence at Princeton ofseveral openings for recent PhDs in theoretical physics who wishto pursue a career in theoretical biological physics. As we hopeyou know, we have been building a group in this area at Princetonover the last decade, and we now have a robust activity thatinvolves students, postdocs and faculty from several departments.We are actively recruiting postdocs to join this group, and wehope that you will urge any outstanding prospective or recent PhDstudents of your acquaintance to apply to any of the following > positions for which they might be eligible (do point out that there aremid-‐ October application deadlines for all of them!). > > 1. Postdoctoral Associate in our group. This is a regular Physicspostdoctoral position, but one in which the incumbent has greatfreedom to choose projects, and can benefit from the mentorship ofany of the senior members of our group (or linear combinationsthereof). Past holders of this position have had a remarkablerecord of success in landing > next-‐level positions in the field of biophysics. Please direct yourstudents to the following link for more information: https://www.princeton.edu/physics/about/employment/biophysics/index.xml <http://www.princeton.edu/physics/about/employment/biophysics/index.xml> > > 2. Postdoctoral Fellow of the Princeton Center for TheoreticalScience (PCTS). The PCTS sponsors interdisciplinary research basedin theoretical physics and the PCTS Faculty Fellows select threenew Fellows each year from a pool of candidates in all fields oftheory. The PCTS provides a unique environment for exceptionalrecent PhDs in theoretical physics, broadly construed, to broadentheir horizons and explore new fields. Candidates must benominated by senior scientists. Nominations of biologicalphysicists are encouraged, and Fellows with such interests wouldbe welcomed as participants in our group. Appointments to thisposition are at the level of Associate Research Scholar. Pleaseconsult http://pcts.princeton.edu/pcts <http://pcts.princeton.edu/pcts>for more information. > > 3. Lewis-‐Sigler Theory Fellow. The Lewis-‐Sigler Institute (LSI),a joint venture of the Physics and Molecular Biology (andother) departments, offers positions at the level of AssociateResearch Scholar that > carry extra resources and the opportunity to teach in innovativeundergraduate programs. These positions are appropriate forexceptional newly-‐ minted PhD’s who areready to lead their own group. LSI Theory Fellows are selected bythe full LSI faculty, but typically work very closely with ourgroup. Application procedures will be described on the LSI website.Applicants to (1) who wish to also be considered as Lewis-‐SiglerTheory Fellows should so indicate in their cover letter. > > We emphasize that we are interested in applications fromstudents with exceptional theoretical skills and a strongmotivation to use > these skills to pursue biological problems, independent of the depth oftheir research experience in biology. Many of our most successfulpostdocs have learned their biology "on the job", and we think that weprovide an outstanding environment for such learning. Your assistancein encouraging strong candidates for any of these positions to applywould be appreciated. > > Bill Bialek, Curt Callan and Ned Wingreen > > Lee Morgan > 257 Carl Icahn Laboratory > Lewis-Sigler Institute of Integrative Genomics > Princeton University > Princeton, NJ 08544 > 609-258-0859

1 0

[Compbio-allhands] 10/1/15 Seminar with David Burkhardt
by Flowers, Nicole 25 Sep '15

25 Sep '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 David Burkhardt Clements Lecture Operon mRNAs are organized into ORF-centric structures that specify translation efficiency October 1, 2015 D. Agard, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: On Behalf of Yann Chemla and Klaus Schulten - PLEASE POST AND CIRCULATE
by Andrej Sali 24 Sep '15

24 Sep '15

> Begin forwarded message: > > From: "Chemla, Yann Robert" <ychemla(a)illinois.edu> > Subject: On Behalf of Yann Chemla and Klaus Schulten - PLEASE POST AND CIRCULATE > Date: September 24, 2015 at 12:51:55 PM PDT > Cc: "Chemla, Yann Robert" <ychemla(a)illinois.edu>, "Schulten, Klaus J" <schulten(a)illinois.edu> > > Dear Colleagues, > We are writing to inform you of several postdoctoral fellowship opportunities in experimental and theoretical biophysics in the "Center for the Physics of Living Cells <http://www.cplc.illinois.edu/>" (CPLC), a National Science Foundation Physics Frontier Center at the University of Illinois, Urbana-Champaign. Fellowships are available starting May 2016, and will normally last a minimum of two years. > > Research in the Center falls in four themes: > (1) Single-molecule biophysics at the molecular-cellular interface; > (2) Maximizing information content of single cell experiments; > (3) Collective dynamics: from cell-cell interaction to multicellular organisms; > (4) Increasing biological realism in theory and computation. > Fellows will use state-of-the-art experimental and theoretical biophysical tools to accomplish these goals: optical tweezers, single-molecule and super-resolution fluorescence microscopy, fabrication of synthetic nanostructures, live cell imaging, chemical biology and genomic biology tools, classical and quantum mechanical molecular simulations, stochastic modeling, whole cell simulations, as well as the standard methods of molecular and cellular biology and genetics. Research will involve both the development and improvement of experimental and computational techniques and the application of these techniques to particular biological processes such as replication, transcription, translation, cell transport, cellular mechanics signaling, and motility. As projects are collaborative endeavors between several labs, the Fellows will have the opportunity to be jointly advised by two or more faculty members of the Center. Fellows will also be expected to participate in education and outreach activities of the Center. > Candidates for this postdoctoral position must have a Ph.D. in the physical sciences, life science, or related disciplines, and must be highly qualified in one of the experimental or theoretical areas. Excellent oral- and written-communication skills are required for this position. The University of Illinois is an equal opportunity/affirmative action employer, and welcomes applications from minority and women candidates. > > Applications for this position (and other positions available in the Physics Department) may be submitted electronically via https://my.physics.illinois.edu/submit/go.asp?id=945 <https://my.physics.illinois.edu/submit/go.asp?id=945>, and should arrive no later than November 1, 2015. Applications received after the deadline may not be considered. These applications should include, in PDF format: > (1) A cover letter > (2) A curriculum vitae > (3) A research statement not exceeding three pages, summarizing your past and ongoing research, > (4) A publications list, including papers and preprints with their URLs. For any papers or preprints that are not readily available via the internet, applicants may wish to upload electronic copies via the "supporting document" channel. > > Please post and circulate the attached announcement or if interested, apply accordingly. > > For more information about CPLC, please visit http://cplc.illinois.edu <http://cplc.illinois.edu/> . > > Thank you. > > Yann Chemla and Klaus Schulten > Co-directors, Center for the Physics of Living Cells > <>director(a)cplc.illinois.edu <mailto:director@cplc.illinois.edu> > http://cplc.illinois.edu <http://cplc.illinois.edu/> > University of Illinois at Urbana-Champaign > 1110 West Green Street, MC 704 > Urbana, IL 61801-3080, USA > > >

1 0

[Compbio-allhands] Fwd: POSTDOC OPPORTUNITY-PLEASE DISTRIBUTE
by Jacobson, Matt 24 Sep '15

24 Sep '15

- Matt Begin forwarded message: From: "Zachow, Christine A." <zachow2(a)llnl.gov<mailto:zachow2@llnl.gov>> Subject: POSTDOC OPPORTUNITY-PLEASE DISTRIBUTE Date: September 24, 2015 at 12:48:45 PM PDT To: Undisclosed recipients:; POSTDOC OPPORTUNITY-PLEASE DISTRIBUTE Lawrence Livermore National Laboratory is currently accepting applications for its prestigious Lawrence Fellowship. Applications can be submitted through our website: https://fellowship.llnl.gov/ They must be completed no later than November 1, 2015. The Lawrence Livermore National Laboratory’s prestigious Lawrence Fellowship is once again soliciting applications from your most promising rising postdocs. The fellowship was established to provide outstanding postdocs an opportunity to pursue cutting-edge science and stimulate cross-fertilization of ideas. The successful candidates have freedom to pursue world-class research with ample resources to support their efforts. The Fellows will interact with scientists with a wide range of expertise. The Laboratory is committed to making their experience at LLNL positive and rewarding. This three-year fellowship is awarded only to candidates with exceptional talent, credentials, scientific track records, and potential for significant achievements. Typically, two to four awards are given each year. After their three-year term, the Fellows may consider any career options, including employment at the Laboratory. Fellows will propose original and independent research in one or more aspects of science relevant to the mission and goals of LLNL. Research areas may include: * Atmospheric Science * Engineering * Biology * Environmental Science * Chemistry * Geoscience * Applied Mathematics * Lasers * Computer Science * Materials Science * Energy * Physics Further information is available at https://fellowship.llnl.gov/. You may contact me at zachow2(a)llnl.gov<x-msg://70/zachow2@llnl.gov> if you have any questions. Christine Zachow Program Administrator Institutional Postdoc, Lawrence Fellow & Livermore Graduate Scholar Programs Lawrence Livermore National Laboratory 7000 East Ave. L-19 Livermore, CA 94550 925-423-0633 --

1 0

[Compbio-allhands] Fwd: postdoctoral position in the MacCallum lab at the University of Calgary
by Jacobson, Matt 22 Sep '15

22 Sep '15

- Matt Begin forwarded message: From: Justin MacCallum <justin.maccallum(a)ucalgary.ca<mailto:justin.maccallum@ucalgary.ca>> Subject: postdoctoral position in the MacCallum lab at the University of Calgary Date: September 22, 2015 at 4:51:50 PM PDT To: Justin MacCallum <justin.maccallum(a)ucalgary.ca<mailto:justin.maccallum@ucalgary.ca>> Dear Colleague, I have a postdoctoral position available in my lab at the University of Calgary (www.maccallumlab.org<http://www.maccallumlab.org/>). The details are below. I would appreciate your help in filling this position, so please pass this message along to any suitable candidates. Thank you for your time. Regards, Justin Postdoctoral Fellowship at the University of Calgary I am recruiting a talented, motivated postdoc to join my lab at the University of Calgary. Candidates should have a strong computational background and will work at the interface between computational modeling, biophysics, and structural biology. Research in this position will focus on the design of molecular interactions, specifically the development of protein-based sensors for small molecules, including drugs, toxins, and metabolites. We will use a combination of computational tools, including Rosetta, molecular dynamics simulations, and free energy calculations to design binding proteins and to understand the driving forces behind binding. The most promising designs will then be validated and characterized experimentally. For this position, I am looking for someone with a strong background in computational chemistry, biophysics, structural biology, or a related field. Experience with free energy calculations, umbrella sampling, Rosetta, or related tools is a strong asset. Depending on the interests of the applicant, there could also be an opportunity to gain wet lab experience, but this is not required. The University of Calgary is one of Canada’s top research institutions. Calgary routinely ranks as one of the most livable cities in the world and is only an hour from the Canadian Rockies—one of the world’s most spectacular outdoor playgrounds. The stipend is $50,000/year for two years, plus benefits. The start date is negotiable, but must be no later than spring 2016. To apply, please send a CV and a brief (4–5 sentences maximum) statement of interest to justin.maccallum(a)ucalgary.ca<mailto:justin.maccallum@ucalgary.ca>. I will begin reviewing applications immediately. -- Justin MacCallum - Assistant Professor Canada Research Chair in Biomolecular Structure and Design Department of Chemistry University of Calgary justin.maccallum(a)ucalgary.ca<mailto:justin.maccallum@ucalgary.ca> http://maccallumlab.org<http://maccallumlab.org/>

1 0

[Compbio-allhands] Fwd: Chair, Department of Pharmaceutical Sciences, University of Tennessee College of Pharmacy
by Andrej Sali 22 Sep '15

22 Sep '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Nolly, Robert J" <rnolly(a)uthsc.edu> > Subject: Chair, Department of Pharmaceutical Sciences, University of Tennessee College of Pharmacy > Date: September 22, 2015 at 9:43:57 AM PDT > To: "sali(a)salilab.org" <sali(a)salilab.org> > > College of Pharmacy Faculty Member, > > I am contacting you to make you aware of a full-time, tenure-track faculty position at the University of Tennessee College of Pharmacy. Perhaps someone you know may be interested in pursuing this opportunity. The position is at the level of Full Professor and will serve as Chair of the Department of Pharmaceutical Sciences. The Department of Pharmaceutical Sciences is one of two departments within the College of Pharmacy. Our faculty members are engaged in competitive research and the education and training of professional and graduate students, fellows, and post-doctoral fellows. > > The successful candidate will have a PhD in pharmaceutical sciences, medicinal chemistry or related biomedical sciences, excellent interpersonal skills and evidence of strong leadership and management skills. The candidate will have academic credentials sufficient to meet the rank of Professor, an outstanding established and ongoing research record, which includes a track record of extramural funding and proven abilities to foster pharmaceutical and biomedical research. > > The Chair of the Department of Pharmaceutical Sciences is responsible for the Department’s strategic planning, budget, fiscal management, policies and procedures, communications, recruitment, and faculty and staff annual performance and development. Additionally, the Chair is responsible for ensuring faculty contributions to teaching, University/College/Department service, and research. > > The University of Tennessee Health Science Center is located in Memphis, TN, an economically vibrant center, with a metropolitan population of more than 1.3 million, reflecting the richness along the bluffs of the mighty Mississippi River. The College of Pharmacy is ranked among the top 20 colleges of pharmacy in the country by US News and World Report. The College of Pharmacy’s Memphis Campus is located in a new 184,000 square-foot building on the Health Science Center complex with additional campuses in Nashville and Knoxville. For further information regarding the College of Pharmacy, please see the College’s web site at http://www.uthsc.edu/pharmacy <http://www.uthsc.edu/pharmacy>. > > This position is available immediately, but the start date is negotiable. Salary is competitive and commensurate with experience. The combination of the Van Vleet Endowed Professorship and Chair position is also negotiable. Review of applications will start immediately and will continue until the position is filled. Interested applicants should submit by email a cover letter, curriculum vitae, research statement, and a list of three references to: > > Robert J. Nolly, MS, D.Ph. > Search Committee Chair > Professor, Pharmaceutical Sciences > University of Tennessee College of Pharmacy > rnolly(a)uthsc.edu <mailto:rnolly@uthsc.edu> > > Should you have any questions or desire additional information, please do not hesitate to contact me at 901-448-1144 or by email. Thank you for considering sharing this opportunity with colleagues who may be looking for a chair leadership position within a college of pharmacy. > > Sincerely, > > Robert J. Nolly > Robert J. Nolly, MS., D.Ph. > Chair, Pharmaceutical Sciences Search Committee > Professor, Department of Pharmaceutical Sciences > UT College of Pharmacy > 881 Madison Avenue, Office 452 > Memphis, TN 38163 > Phone: 901-448-1144 > Email: RNolly(a)uthsc.edu <mailto:RNolly@uthsc.edu>

1 0

[Compbio-allhands] Fwd: genomic data sets
by Jacobson, Matt 21 Sep '15

21 Sep '15

- Matt Begin forwarded message: From: Zia Joseph <ziajoseph(a)magnusinformatics.com<mailto:ziajoseph@magnusinformatics.com>> Subject: genomic data sets Date: September 21, 2015 at 9:20:31 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Matt I was told to contact you for dept distribution if you are willing: -- My name is Zia Joseph and I consult nationally in genomic bioinformatics. I’m expanding a bioinformatics team developing NGS-based NIPT & oncogenic diagnostics. Would you know PhD’s interested? Requirements: 3+ years: DNA Seq (NGS) 3+ years: mySQL 3+ years: Python 3+ years: R 3+ years: Perl 1+ years: C/C++/C# Happy coding! Zia Zia Joseph Business Development Genomics/Bioinformatics c: 619.764.8431 Zia Joseph Business Development Genomics/Bioinformatics c: 619.764.8431

1 0

[Compbio-allhands] 9/24/15 Seminar with Hiro Furukawa
by Flowers, Nicole 18 Sep '15

18 Sep '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Hiro Furukawa Cold Spring Harbor Laboratory Structure and Biology of NMDA receptor ion channels September 24, 2015 D. Minor, Host This seminar is co-sponsored by the PSPG/BioE Seminar Series BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Harvard Medical School, Chemical Biology Faculty Position
by Brian Shoichet 16 Sep '15

16 Sep '15

FYI. Brian ---------- Forwarded message ---------- From: Parker, Kristen M <Kristen_Parker(a)hms.harvard.edu> Date: Wed, Sep 16, 2015 at 12:17 PM Subject: Harvard Medical School, Chemical Biology Faculty Position To: "bshoichet(a)gmail.com" <bshoichet(a)gmail.com> [image: Description: Macintosh HD:Users:kristen:Desktop:HMS_Biochem&MolPhamH.jpg] September 16, 2015 Dear Dr. Shoichet, The Biological Chemistry and Molecular Pharmacology Department at Harvard Medical School has initiated a search for tenure-track junior faculty position at the rank of Assistant or Associate Professor, and we are writing to seek your help in identifying outstanding candidates for this position. We are interested in identifying junior faculty candidates with significant accomplishments and promise at the interface of chemistry, biology, and medicine. The candidate’s overall originality and promise are more important than the area of specialization. Additional details about the position can be found in the attached advertisement. We would greatly appreciate your bringing this opportunity to the attention of postdoctoral fellows, former graduate students, and others who might be interested. Women and minority candidates are strongly encouraged to apply. Applicants should apply online at http://academicpositions.harvard.edu/postings/6328 Applications will be considered starting November 1, 2015 Thank you. Jon Clardy, PhD Hsien Wu & Daisy Yen Wu Professor Biological Chemistry & Molecular Pharmacology Harvard Medical School Phone: 617-432-2845 Email: jon_clardy(a)hms.harvard.edu Nathanael Gray, PhD Professor Biological Chemistry & Molecular Pharmacology, HMS Professor, Cancer Biology, Systems Biology, Dana-Farber Cancer Institute Phone: 617-582-8590 Email: nathanael_gray(a)dfci.harvard.edu <jdubois(a)stanford.edu> *Thank you,* *Kristen* Kristen Parker | Senior Research Administration Coordinator 240 Longwood Avenue, C-213 B | Boston, MA 02115 Tel: 617-432-5620 | Email: kristen_parker(a)hms.harvard.edu -- Brian Shoichet, Professor, UCSF http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 Dept. of Pharmaceutical Chemistry By Courtesy: Univ. of Toronto, Fac. of Pharmacy

1 0

[Compbio-allhands] Fwd: Faraldo-Gomez Seminar Monday 9/14 at noon
by Jacobson, Matt 14 Sep '15

14 Sep '15

Please note this CVRI seminar hosted by MIchael, likely of interest to some of you - Matt Begin forwarded message: From: "Grabe, Michael" <Michael.Grabe(a)ucsf.edu<mailto:Michael.Grabe@ucsf.edu>> Subject: Faraldo-Gomez Seminar Monday 9/14 at noon I have a guest, José Faraldo-Gomez, speaking tomorrow (Monday) in the CVRI/Gladstone Seminar series. He will present simulations as well as new structures on the sodium-calcium exchanger. Please feel free to share this with your lab and encourage anyone that is interested to attend (it is in the Gladstone). Thanks Michael ---------------------------------------------------------- Michael Grabe Associate Professor University of California, San Francisco Cardiovascular Research Institute Department of Pharmaceutical Chemistry 555 Mission Bay Blvd South, Room 452T, MC 3122 San Francisco, California 94158-9001 415-502-2874 (office) 415-476-8173 (fax)

1 0

[Compbio-allhands] Fwd: 30th Annual Johnson Symposium in Organic Chemistry | Friday, October 9, 2015 - Stanford University
by Jacobson, Matt 12 Sep '15

12 Sep '15

-- Matt Sent from my iPad Begin forwarded message: From: Siejen Yin-Stevenson <siejeny(a)stanford.edu<mailto:siejeny@stanford.edu>> Date: September 11, 2015 at 5:25:57 PM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Cc: Chemchair <chemchair(a)stanford.edu<mailto:chemchair@stanford.edu>>, Paul A Wender <wenderp(a)stanford.edu<mailto:wenderp@stanford.edu>>, Barry M Trost <bmtrost(a)stanford.edu<mailto:bmtrost@stanford.edu>>, Chaitan Khosla <khosla(a)stanford.edu<mailto:khosla@stanford.edu>>, Robert M Waymouth <waymouth(a)stanford.edu<mailto:waymouth@stanford.edu>> Subject: 30th Annual Johnson Symposium in Organic Chemistry | Friday, October 9, 2015 - Stanford University

1 0

[Compbio-allhands] Fwd: com chem candidates
by Brian Shoichet 10 Sep '15

10 Sep '15

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "Christoph Dehnhardt" <cdehnhardt(a)xenon-pharma.com> Date: Sep 10, 2015 7:19 AM Subject: com chem candidates To: "Brian Shoichet" <shoichet(a)cgl.ucsf.edu> Cc: Hi Brian, my name Christoph Dehnhardt and I am contacting you following Dan Ortwine's suggestion. I have an opening for a computational chemist in my group and I was wondering if you know a graduate/ postdoc in your group that is looking for a position in Canada. If so please let me know. Thanks Christoph http://www.xenon-pharma.com/2015/05/principal-scientist-computational-chemi… -- Christoph M. Dehnhardt, PhD Director Chemistry Xenon Pharmaceuticals 3650 Gilmore Way Burnaby, BC Canada, V5G 4W8 phone 604-484-3336 fax 604-484-3450 cdehnhardt(a)xenon-pharma.com This email message is confidential and may contain privileged information. Any unauthorized dissemination or copying is strictly prohibited. If you have received this message in error, please delete it and notify us (*Xenon*) immediately.

1 0

[Compbio-allhands] Fwd: Technion - President’s Interdisciplinary Faculty Hiring Initiative
by Andrej Sali 07 Sep '15

07 Sep '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Roy Kishony <rkishony(a)technion.ac.il> > Subject: Technion - President’s Interdisciplinary Faculty Hiring Initiative > Date: September 7, 2015 at 4:23:05 AM PDT > To: Roy Kishony <rkishony(a)techunix.technion.ac.il> > > > Dear colleague, > > The Technion is seeking exceptional faculty candidates for tenure-track / tenured positions as part of our newly announced President’s Interdisciplinary Faculty Hiring Initiative. We are looking for exceptional interdisciplinary candidates who bridge across disciplines, combining new approaches from Physics, Chemistry, Materials, Computer Sciences or Mathematics to bear upon fundamental questions in Biology and Medicine. > > Please see attached ad as advertised in Nature and Science. > > We would appreciate it if you could kindly recommend suitable candidates and/or bring this search to their attention. > > Thank you on the behalf of the Search Committee. > > Best regards, > Roy Kishony > > Chair, President’s Interdisciplinary Search Committee > Marilyn and Henry Taub Professor of Life Sciences > Faculty of Biology and Faculty of Computer Science > Technion - Israel Institute of Technology > > > > > >> >> >> >> >> >> >

1 0

[Compbio-allhands] Fwd: Position at Lilly, Please forward to your people who are looking
by Andrej Sali 03 Sep '15

03 Sep '15

> Begin forwarded message: > > From: Michal Vieth <vieth_michal(a)lilly.com> > Subject: Position at Lilly, Please forward to your people who are looking > Date: September 3, 2015 at 1:06:44 PM PDT > To: Andrej Sali <sali(a)salilab.org> > > > We have the position open in the lilly.com <http://lilly.com/> now. You can find the detail throughhttps://careers.lilly.com/job/indianapolis/computational-chemist-che… <https://careers.lilly.com/job/indianapolis/computational-chemist-cheminform…>. > Please forward this to your contacts as you see fit. We want to recruit top talents to increase both the capacity and capability of our global computational chemistry and cheminformatics group. > > Best, > Michal > > Sent from my iPad

1 0

[Compbio-allhands] Fwd: Stanford Bioengineering, Jr. Faculty Search Announcement
by Andrej Sali 01 Sep '15

01 Sep '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Jessica J Negrette <bussey(a)stanford.edu> > Subject: Stanford Bioengineering, Jr. Faculty Search Announcement > Date: September 1, 2015 at 11:48:48 AM PDT > To: "bioefacultysearch(a)stanford.edu" <bioefacultysearch(a)stanford.edu> > > Hello, > > Please see the attached solicitation from Prof. Markus Covert regarding an open search for a faculty member in the Dept. of Bioengineering at Stanford University. We have recently launched a broad area search, open to faculty at the Assistant and Untenured Associate Professor level. Details and application instructions can be found in the enclosed announcements, as well as our departmental website. https://bioengineering.stanford.edu/about/open-faculty-positions <https://bioengineering.stanford.edu/about/open-faculty-positions> > > > Best, > Jessica > > --- > Jessica Negrette > Faculty Affairs Officer > Shriram Center, Room 119D > 443 Via Ortega > MC: 4245 > Stanford, CA 94305-4125 > (650) 725-7583 > jnegrette(a)stanford.edu > >

1 0

[Compbio-allhands] Fwd: PCTS Call for nomination of postdoctoral fellows--eadline October 15, 2015
by Andrej Sali 14 Aug '15

14 Aug '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Charlene Borsack <cborsack(a)PRINCETON.EDU> > Subject: PCTS Call for nomination of postdoctoral fellows--eadline October 15, 2015 > Date: August 14, 2015 at 6:50:49 AM PDT > To: pcts_nominators(a)PRINCETON.EDU > Reply-To: Charlene Borsack <cborsack(a)PRINCETON.EDU> > > Dear Colleague, > > We are writing to encourage you to submit nominations for the Princeton Center for Theoretical Science Postdoctoral Fellowships. > > Center Postdoctoral Fellowships are the most prestigious postdoctoral positions offered in the theoretical sciences at Princeton. They are intended for early-career theoretical scientists, broadly construed, including the fields of astrophysics, biology, chemistry, geosciences, physics, and engineering. The nominees should be individuals with outstanding talent and accomplishment who are eager to broaden their scientific horizons. We particularly encourage nominations of qualified candidates who are women or members of other groups that are underrepresented in the theoretical sciences. Fellows receive a three-year appointment in the Center fully supported by Center funds, an office in the Center facility, and have full freedom to develop their scientific interests with the support and mentoring of the senior Faculty Fellows. It is our intention that the Center experience will have a profound impact on the scientific development and future careers of the Fellows. > > The deadline for receipt of the Postdoctoral nomination, reference letters, and supporting materials from the candidate is October 15, 2015 so it is important for you to submit your nomination as soon as possible to give your candidate and their references time to complete their parts. > > The nomination process is very simple: go to our website > http://pcts.princeton.edu/pcts <http://pcts.princeton.edu/pcts> > > and submit the candidate’s name, email address, and a nomination letter. The candidates will then be sent information necessary to complete their application and to submit letters of reference. (Please note, this is a new nomination site, so please use this link to make sure you get to the correct page.) > > The PCTS Faculty Fellows begin evaluation and invitation to interview on October 15, 2015. (The website will continue to accept late nominations and applications, but there can be no assurance they will be considered.) > > The mission of the Center is to foster interaction and collaboration between theorists across the natural sciences at Princeton to enhance research and education. We pursue this goal through our Center Postdoctoral Fellowships and our sponsorship of focused programs of study in frontier areas in theoretical science that cut across traditional disciplinary boundaries. A group of Senior Faculty Fellows, coming from a broad range of disciplines and departments, take active responsibility for guiding the intellectual life of the Center. > > Sincerely, > > Paul Steinhardt, Director steinh(a)princeton.edu <mailto:steinh@princeton.edu> > Igor Klebanov, Associate Director klebanov(a)princeton.edu <mailto:klebanov@princeton.edu> > > Princeton University is an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, protected veteran status, or any other characteristic protected by law. This position is subject to the University’s background check policy. > >

1 0

[Compbio-allhands] Fwd: SAVE-THE-DATE: UCSF-AMGEN SYMPOSIUM - Saturday, October 10, 2015
by Andrej Sali 13 Aug '15

13 Aug '15

Sent from my iPhone Begin forwarded message: > From: UCSF Biotech Symposium <biotechsymposium(a)ucsf.edu> > Date: August 13, 2015 at 2:34:16 PM PDT > To: Pharm Chem - Adjuncts <PCAdjuncts(a)ucsf.edu>, Pharm Chem - All Staff <PCAllstaff(a)ucsf.edu>, Pharm Chem - Emeritus Faculty <PCEmeritusFAC(a)ucsf.edu>, Pharm Chem - Joint Faculty <PCJointFAC(a)ucsf.edu>, Pharm Chem - NMR <nmr(a)ucsf.edu>, Pharm Chem - Recall <PCRecall(a)ucsf.edu>, Pharm Chem Faculty <pcfac(a)ucsf.edu> > Subject: SAVE-THE-DATE: UCSF-AMGEN SYMPOSIUM - Saturday, October 10, 2015 > > >

1 0

[Compbio-allhands] Fwd: Opportunities at the CUNY Graduate Center
by Andrej Sali 10 Aug '15

10 Aug '15

> Begin forwarded message: > > From: "Bialek, William" <WBialek(a)gc.cuny.edu> > Subject: Opportunities at the CUNY Graduate Center > Date: August 10, 2015 at 7:25:49 PM PDT > To: Mike DeWeese <deweese(a)berkeley.edu>, Oskar Hallatschek <ohallats(a)berkeley.edu>, "dsrokhsar(a)lbl.gov" <dsrokhsar(a)lbl.gov>, "goster(a)nature.berkeley.edu" <goster(a)nature.berkeley.edu>, "pande(a)stanford.edu" <pande(a)stanford.edu>, "GECrooks(a)lbl.gov" <GECrooks(a)lbl.gov>, "SXDWC(a)SLAC.Stanford.Edu" <SXDWC(a)SLAC.Stanford.Edu>, "Daniel S. Fisher" <dsfisher(a)stanford.edu>, "kchuang(a)stanford.edu" <kchuang(a)stanford.edu>, Surya Ganguli <sganguli(a)stanford.edu>, "steven.altschuler(a)ucsf.edu" <steven.altschuler(a)ucsf.edu>, "haoli(a)genome.ucsf.edu" <haoli(a)genome.ucsf.edu>, "sali(a)salilab.org" <sali(a)salilab.org>, "leor.weinberger(a)gladstone.ucsf.edu" <leor.weinberger(a)gladstone.ucsf.edu>, "lani.wu(a)ucsf.edu" <lani.wu(a)ucsf.edu> > Cc: "Balasubramanian, Vijay" <vbalasubramanian(a)gc.cuny.edu> > > Dear colleagues, > > As you may know, the Graduate Center of the City University of New York has launched an Initiative for the Theoretical Sciences. For the past several years, the efforts of ITS have included seminars, workshops, public lectures, and visiting faculty. I have had the pleasure of being involved in this from the start, as a visitor and adviser to the administration. > > The time has now come to search systematically for permanent faculty. > > The President of the Graduate Center is committed to growing ITS into a vibrant community of 8-10 permanent faculty exploring theoretical problems across a range of traditional disciplines. It is expected that there will be communal support for postdoctoral fellows and visitors, and the activities of ITS will continue to be supplemented by the involvement of faculty from the CUNY colleges. There are many steps involved making this work, but we need to start by recruiting an initial cluster of faculty. > > We have decided that our first search will be for theorists interested in biological problems, whose methods and intellectual style are grounded in theoretical physics and applied mathematics. We take these definitions broadly, and emphasize that part of the job for the first group of faculty will be to help in the recruiting of others, who will share their intellectual style but certainly have interests in very different problems. While many institutions can offer to embed theorists into a large (and perhaps even overwhelming) community of experimental biologists, few can offer the opportunity to have theorizing about biological systems at the core of a larger theoretical effort. > > The Graduate Center is not a place with a great tradition in the natural sciences. On the other hand, it is more nearly a tabula rasa, and offers an almost unique chance to build a community from the ground up, including space for novel educational programs. We have shown, I think, that we can attract world class visitors, and with a critical mass of faculty this should be even easier. And, of course, being in New York is just plain fun. > > Just so you know, although I have no intention of leaving Princeton, I do plan to continue spending a fraction of my time at The Graduate Center. I have had a wonderful time really working at ITS, where discussions at the blackboard seem to come very easily, and I am committed to helping with the transition to a permanent community. > > We would appreciate your bringing this opportunity to the attention of appropriate candidates. While the Graduate Center has a preference for making senior appointments, we will consider junior candidates as well. > > Interested candidates can navigate the application procedure starting at the website cuny.jobs, and entering the Job ID “13244" under “What.” The nominal deadline is soon. Of course, you can also point me to people I should contact directly. > > With best wishes, > > Bill > > William Bialek > Visiting Presidential Professor of Physics > The Graduate Center, City University of New York > John Archibald Wheeler/Battelle Professor in Physics, and > Lewis-Sigler Institute for Integrative Genomics > Princeton University > > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: assistant(a)salilab.org, Tel +1 (415) 514-4228 Email sali(a)salilab.org; Web http://salilab.org

1 0

[Compbio-allhands] Fwd: bioinformatics position at Haifa University
by Andrej Sali 06 Jul '15

06 Jul '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: assistant(a)salilab.org, Tel +1 (415) 514-4228 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Leonid Brodsky" <lbrodsky(a)research.haifa.ac.il> > Subject: bioinformatics position at Haifa University > Date: July 5, 2015 at 9:39:35 PM PDT > To: "'Raul Andino'" <Raul.Andino(a)ucsf.edu>, "'Judith Frydman'" <jfrydman(a)stanford.edu>, <sali(a)salilab.org>, "'Krogan, Nevan'" <Nevan.Krogan(a)ucsf.edu>, "Gudkov, Andrei" <Andrei.Gudkov(a)RoswellPark.org>, "'Andrea Gamarnik'" <AGamarnik(a)leloir.org.ar>, "'Cattaneo, Roberto, Ph.D.'" <Cattaneo.Roberto(a)mayo.edu>, "'Sesma, Ana'" <ana.sesma(a)mssm.edu>, "'Ashley Acevedo'" <acevedo.ashley(a)gmail.com>, "'Asaph Aharoni'" <Asaph.Aharoni(a)weizmann.ac.il>, "Avi Levy" <avi.levy(a)weizmann.ac.il>, "Chernova, Olga" <ochernova(a)tartiscorp.com>, "Dina Schneidman" <duhovka(a)gmail.com>, "Leonid A Mirny" <leonid(a)MIT.EDU>, "Nelson Lau" <nlau(a)brandeis.edu>, "Orr Dunkelman" <orrd(a)cs.haifa.ac.il>, "Richard Borowsky" <rborowsky(a)nyu.edu>, "rosbash" <rosbash(a)brandeis.edu>, "Shtutman, Michael" <shtutmanm(a)sccp.sc.edu>, "rosbash" <rosbash(a)brandeis.edu>, <walter.bodmer(a)hertford.ox.ac.uk>, <pinter(a)cs.technion.ac.il>, <apurmal(a)cbiolabs.com>, <azlotnic(a)indiana.edu>, <alan.schulman(a)helsinki.fi> > > > Dear All, > > Perhaps you know someone in Israel or abroad who might be interested at the position below? > > Many thanks, > Leonid > > > Recruitment in Israel: Tauber Bioinformatics Research Center, University of Haifa > > Available position: > Chief Bioinformatician (PhD): University of Haifa Researcher > Analysis of High-throughput Omics Data: participation in algorithm development, Bioinformatics, biological interpretation of results > Salary $70,000 per annum including all benefits. > Fixed-term for 3 years > > General Information > The Tauber Bioinformatics Research Center at the University of Haifa conducts research in bioinformatics of the high-throughput omics data (NGS, Mass-spec, structural data) by developing algorithms and scaled hardware/software solutions for data analysis and data integration. The Center participates at high-profile medical data analysis/integration projects in Israel and abroad. > > Job Description > • Take part in the development of computer applications in the area of omics analysis and data integration > • Focus on cutting edge algorithms in several areas of computational biology. > • Develop and perform automated and manual tests to ensure the quality of the bioinformatics algorithms. > • Biological interpretation of the bioinformatics analysis results. > • Become part of an international development team. > > Job Requirements > • A PHD in Genomics, Genetics, Computational Biology, Computer Science, Mathematics (or similar), and a passion for problem solving > • Required skills: > o Experience in biology/bioinformatics and the area of omics analyses – must > o Algorithms development experience - an advantage. > o Good knowledge of mathematics, machine learning, and statistics - an advantage. > o Good written and verbal English. > o Proven independent working style, technical problem solving, data analysis and generation of novel ideas. > • Experience: more than 2 years working experience in algorithms and bioinformatics applications. > > Please include a covering letter and CV with your application. > > Leonid Brodsky, Director > Email: lbrodsky(a)research.haifa.ac.il <mailto:lbrodsky@research.haifa.ac.il>

1 0

[Compbio-allhands] Fwd: Gladstone Bioinformatics Core Director Position -- please forward
by Scooter Morris 01 Jul '15

01 Jul '15

-------- Forwarded Message -------- Subject: Gladstone Bioinformatics Core Director Position -- please forward Date: Wed, 1 Jul 2015 17:33:59 -0700 From: Alexander Pico <apico(a)gladstone.ucsf.edu> To: Alexander Pico <apico(a)gladstone.ucsf.edu> Hi all, We’ve got a Bioinformatics Core Director position open here at Gladstone and are eager to find a good match. They will be working with me as the Associate Director and Katie Pollard as the Faculty Advisor. It’s an exciting time for the core as Gladstone has just launched a new initiative to promote technology, innovation and computational biology, and we’ll be at the center of it. It should be a very dynamic and fun effort to join. Please feel free to forward this email, the link, the text below and/or the attached PDF. https://careers-gladstoneinstitutes.icims.com/jobs/1125/job Thanks! - Alex ---------------------------------------- Alexander Pico, PhD NRNB Executive Director Bioinformatics Assoc. Director Gladstone Institutes http://nrnb.org http://gladstoneinstitutes.org ----------------------------------------

1 0

[Compbio-allhands] Fwd: Recommendations for Physics-Based Lead Optimization at Schrödinger
by Jacobson, Matt 01 Jul '15

01 Jul '15

- Matt Begin forwarded message: From: Josh Akin <josh.akin(a)schrodinger.com<mailto:josh.akin@schrodinger.com>> Subject: Recommendations for Physics-Based Lead Optimization at Schrödinger Date: July 1, 2015 at 2:45:54 PM PDT To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Dr. Jacobson, My name is Josh Akin, and I'm a Strategic Growth Associate at Schrödinger in New York City. We have an opening for a Physics-Based Lead Optimization role, and the team suggested I might get in touch with you regarding possible candidates. Do you know of anyone who might possibly be interested in applying? Here is the job description: https://www.schrodinger.com/careers/description/218 If you do know of anyone, feel free to either have them contact me directly or apply through the link. Please let me know if you have any questions and/or concerns. Thank you so much for your help in advance, and I hope all is well! Best Regards, Josh -- Josh Akin Associate, Strategic Growth Schrödinger, Inc. 120 West 45th Street, 17th floor New York, NY 10036 (770) 328-6319 josh.akin(a)schrodinger.com<mailto:josh.akin@schrodinger.com> skype: josh.e.akin www.linkedin.com/in/joshakin<http://www.linkedin.com/in/joshakin>

1 0

[Compbio-allhands] Fwd: Positions at Lilly
by Jacobson, Matt 23 Jun '15

23 Jun '15

This is an interesting group in that it is focused specifically on computational ADME, supporting projects from early stages through to pre-clinical development and also phase 1, I think. Job ad attached - Matt Begin forwarded message: Subject: Positions at Lilly Date: June 23, 2015 at 7:02:52 AM PDT To: "Jacobson, Matt (Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>)" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Dear Matt: I hope this message finds you well. Our computational groups are continuing to press the science forward and work hard to enhance the discovery projects. This is to inform you that we have another opening in the CADME group (see the attached flyer with details). We might also get an additional opening in the general area of molecular modeling and design in the near future, in Christine’s group. If you know of any talented candidates please don’t hesitate to let them know and have them contact either one of us. Best regards, Prashant ______________________________________ Prashant Desai, PhD Principal Research Scientist Computational ADME Drug Disposition Lilly Corporate Center Indianapolis, IN 46285 Tel: 317-651-4086 Fax: 317-276-7040 _____________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

1 0

[Compbio-allhands] Fwd: NIST/NRC Postdoctoral Research--hydrogen/deuterium exchange MS
by Andrej Sali 22 Jun '15

22 Jun '15

Sent from my iPhone Begin forwarded message: > From: "Hudgens, Jeffrey W" <jeffrey.hudgens(a)nist.gov> > Date: June 22, 2015 at 7:57:23 AM PDT > To: "Hudgens, Jeffrey W" <jeffrey.hudgens(a)nist.gov> > Subject: NIST/NRC Postdoctoral Research--hydrogen/deuterium exchange MS > > Dear Colleague, > > INVITATION: I wish to invite applications for postdoctoral research at NIST. My laboratory program focuses on topics involving hydrogen/deuterium exchange mass spectrometry (HDX-MS) of proteins and biological drugs; however, the applicant needs no prior experience in this area. Please forward this e-mail to any candidates who can benefit from this opportunity. > > BACKGROUND: Through a head-to-head competition administered by the National Research Council of the National Academy of Sciences, NIST awards approximately 60 new fellowships to recent PhD recipients in sciences, mathematics, and engineering. The competition is judged from each applicant’s research proposal, letters of reference, transcripts, and publications. Appointments are for two years at an annual stipend of $66,919 per year, plus moving expenses, an allowance for professional expenses and travel, and cost-shared health insurance. Applicants must be U.S. citizens. > > Associateships are awarded to persons who have held the doctorate for less than five years at the time of application. (Candidates may apply before their PhD degree is conferred.) Electronic applications for the next competition are due on 1 AUG (5:00 PM EST), and supporting documents (e.g., letters, transcripts) must be received by 15 AUG (5:00 PM EST). Postdoctoral appointments are usually announced in late SEP for start dates beginning in JAN-JUN 2016 (sometimes earlier). Also, NIST/NRC will conduct a second competition with an application deadline of 1 FEB 2016 for start dates between JUN-DEC 2016. > > THE PROPOSAL: The application includes a proposal describing research that the candidate will conduct during his/her tenure. My interests are quite broad and afford much creativity to the candidate: > · H/D exchange mass spectrometry (HDX-MS) for biopharmaceutical analysis > · Expanding the application of HDX-MS to new protein types (e.g., trans-membrane proteins), > · Studies of protein-protein and protein-ligand interactions, and > · Enhancing HDX-MS resolution and dynamic range. > > Candidates should contact me to discuss their project and proposal preparation. The formal description of the HDX-MS research opportunity is available at the NRC website. > > Helpful NIST and NRC web-links are: > My Website: http://go.usa.gov/YD9d > My HDX-MS Opportunity: http://nrc58.nas.edu/RAPLab10/Opportunity/Opportunity.aspx?LabCode=50&ROPCD… > NIST Announcement: http://www.nist.gov/iaao/postdoc.cfm > NRC E-Application: http://sites.nationalacademies.org/PGA/RAP/PGA_046398 > > From personal experience I can testify that the NIST/NRC program is a terrific opportunity that enables emergent scientists to jumpstart their careers. I encourage potential candidates to contact me today. > > Best wishes, > > Dr. Jeffrey W. Hudgens (hudgens(a)NIST.gov) > Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD 20850 > Tel. 240-314-6485 Fax. 240-314-6255

1 0

[Compbio-allhands] Fwd: Temporary position in Novartis Emeryville CADD group
by Jacobson, Matt 17 Jun '15

17 Jun '15

- Matt Begin forwarded message: From: "Jansen, Johanna" <johanna.jansen(a)novartis.com<mailto:johanna.jansen@novartis.com>> Subject: Temporary position in Novartis Emeryville CADD group Date: June 17, 2015 at 5:48:58 PM PDT To: "Brian Shoichet (bshoichet(a)gmail.com<mailto:bshoichet@gmail.com>)" <bshoichet(a)gmail.com<mailto:bshoichet@gmail.com>>, "'Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>'" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, "michael.grabe(a)ucsf.edu<mailto:michael.grabe@ucsf.edu>" <michael.grabe(a)ucsf.edu<mailto:michael.grabe@ucsf.edu>> Cc: "Xu, Yongjin" <yongjin.xu(a)novartis.com<mailto:yongjin.xu@novartis.com>> Dear Brian, Matt & Michael, I hope this message finds you well. I wanted to alert you to a temporary position in our group which may be of interest to current or recently graduated students looking for some industry experience. We are looking for a commitment of 6 months to ensure we get good productivity. We would really appreciate it if you circulate the job description below through your UCSF and other relevant networks. Applicants can send their resumes to either me or Yongjin. Thanks, Hanneke Computational Chemistry Research Scientist (MS) Computer-Aided Drug Discovery (CADD) Group Novartis Institutes for BioMedical Research, Emeryville This is a temporary position (6 months) for a computational chemist or computer scientist, with experience equivalent to an MS in chemistry or computer science plus a few years’ experience in a research-based environment or alternatively, a newly graduated PhD with relevant research experience. A basic knowledge of chemistry is required as well as programming skills in python and java. Scripting skills in a Linux environment and web development experience are desirable. Knowledge of at least some of the following tools or scientific technologies is important: molecular modeling, cheminformatics, machine learning, KNIME. The position requires a highly motivated, self-directed individual with excellent communication and collaboration skills. The primary responsibility will be to create and validate high quality computational tools and workflows in collaboration with members of the CADD group. Research areas will include data analysis, data mining & data visualization, (Q)SAR modeling, virtual screening, hit list triaging, and library design. The successful candidate will also apply these tools and workflows in collaboration with other chemistry colleagues in multidisciplinary drug discovery teams. Contact for further information or to submit resume: Yongjin Xu, Yongjin.xu(a)novartis.com<mailto:Yongjin.xu@novartis.com>

1 0

[Compbio-allhands] Fwd: Insight Data Science Program
by Jacobson, Matt 17 Jun '15

17 Jun '15

Feel free to forward - Matt Begin forwarded message: From: John Joo <john(a)insightdatascience.com<mailto:john@insightdatascience.com>> Subject: Re: Insight Data Science Program Date: June 12, 2015 at 5:59:09 PM PDT To: Jerome Nilmeier <nilmeier(a)gmail.com<mailto:nilmeier@gmail.com>> Cc: Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, Alexandra Schnoes <aschnoe(a)itsa.ucsf.edu<mailto:aschnoe@itsa.ucsf.edu>> Jerome -- thanks for the intro! Hi Matthew and Aleksandra, I'm the Director of Product at Insight Data Science. We've been around for 3 years and have help over 250 alumni transition from academia to full-time roles in data science. We have had 5 Fellows who have gone through the program from UCSF, including Jerome and Monica Hsu, who now have data science or data engineering roles at IBM, Intuit, Counsyl, and Athos. We'd love to help more UCSF alumni make that transition. Would you be willing to spread the word by forwarding the announcement below to your various email lists? Let me know if there are any questions you have or if there's anything we can do to help. Best, John ===================== Insight Data Science Fellows Program http://insightdatascience.com<http://insightdatascience.com/?fid=15C> Now accepting applications for the September 2015 sessions in New York City and Silicon Valley - application deadline: June 29. Top companies are hiring data scientists to help them glean insights from the terabytes of data that they collect every day. The Insight Data Science Fellows Program<http://t.signauxsix.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XZs2zGp0…> is a training fellowship for graduate students and postdocs designed to bridge the gap between academia and a career in data science. Insight program overview: * 7 week, full-time, tuition-free postdoctoral data science training fellowship. Need-based scholarships available to help cover living costs. * Dedicated office space; self-directed, project-based learning under the guidance of top industry data scientists. * 250+ Insight alumni are now data scientists at Facebook, LinkedIn, Airbnb, Apple, Netflix, Twitter, Uber, etc. in Silicon Valley, and New York Times, Memorial Sloan Kettering Cancer Center, Wall Street Journal, Bloomberg, NBC, ZocDoc, Oscar Health, etc. in New York City, and 100+ other top companies. The application deadline for the September 2015 session of Insight is Monday, June 29. For more information and to apply, please visit: http://insightdatascience.com<http://insightdatascience.com/?fid=15C> Applications are also open for our Data Engineering programs in New York City and Silicon Valley. If you are more interested in Data Engineering, please check out our Insight Data Engineering website<http://t.signauxsix.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XZs2zGp0…>. ==================== On Fri, Jun 12, 2015 at 3:17 PM, Jerome Nilmeier <nilmeier(a)gmail.com<mailto:nilmeier@gmail.com>> wrote: Hello: I would like to forward you a posting for the Insight Data Science Fellows program....it is a great for those looking for industry positions in data science. Cheers, Jerome ===================== Insight Data Science Fellows Program http://insightdatascience.com<http://insightdatascience.com/?fid=15C> Now accepting applications for the September 2015 sessions in New York City and Silicon Valley - application deadline: June 29. Top companies are hiring data scientists to help them glean insights from the terabytes of data that they collect every day. The Insight Data Science Fellows Program<http://t.signauxsix.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XZs2zGp0…> is a training fellowship for graduate students and postdocs designed to bridge the gap between academia and a career in data science. Insight program overview: * 7 week, full-time, tuition-free postdoctoral data science training fellowship. Need-based scholarships available to help cover living costs. * Dedicated office space; self-directed, project-based learning under the guidance of top industry data scientists. * 250+ Insight alumni are now data scientists at Facebook, LinkedIn, Airbnb, Apple, Netflix, Twitter, Uber, etc. in Silicon Valley, and New York Times, Memorial Sloan Kettering Cancer Center, Wall Street Journal, Bloomberg, NBC, ZocDoc, Oscar Health, etc. in New York City, and 100+ other top companies. The application deadline for the September 2015 session of Insight is Monday, June 29. For more information and to apply, please visit: http://insightdatascience.com<http://insightdatascience.com/?fid=15C> Applications are also open for our Data Engineering programs in New York City and Silicon Valley. If you are more interested in Data Engineering, please check out our Insight Data Engineering website<http://t.signauxsix.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XZs2zGp0…>. ==================== -- Jerome Nilmeier, PhD Cell: 510-325-8695<tel:510-325-8695> Home: 925-292-5321<tel:925-292-5321>

1 0

[Compbio-allhands] Fwd: Bioinformatics job opening: please post
by Andrej Sali 16 Jun '15

16 Jun '15

Sent from my iPhone Begin forwarded message: > From: Antitsa Stoycheva <astoycheva(a)aliosbiopharma.com> > Date: June 16, 2015 at 3:49:39 PM PDT > To: "agard(a)msg.ucsf.edu" <agard(a)msg.ucsf.edu>, "nadav.ahituv(a)ucsf.edu" <nadav.ahituv(a)ucsf.edu>, "steven.altschuler(a)ucsf.edu" <steven.altschuler(a)ucsf.edu>, "babbitt(a)cgl.ucsf.edu" <babbitt(a)cgl.ucsf.edu>, "bandyopadhyays(a)cc.ucsf.edu" <bandyopadhyays(a)cc.ucsf.edu>, "sebaran(a)cgl.ucsf.edu" <sebaran(a)cgl.ucsf.edu>, "brenner(a)compbio.berkeley.edu" <brenner(a)compbio.berkeley.edu>, "atul.butte(a)ucsf.edu" <atul.butte(a)ucsf.edu>, "bconklin(a)gladstone.ucsf.edu" <bconklin(a)gladstone.ucsf.edu>, "joe(a)derisilab.ucsf.edu" <joe(a)derisilab.ucsf.edu>, "hana.el-samad(a)ucsf.edu" <hana.el-samad(a)ucsf.edu>, "tef(a)cgl.ucsf.edu" <tef(a)cgl.ucsf.edu>, "fischbach(a)fischbachgroup.org" <fischbach(a)fischbachgroup.org>, "kathy.giacomini(a)ucsf.edu" <kathy.giacomini(a)ucsf.edu>, "ryan.hernandez(a)ucsf.edu" <ryan.hernandez(a)ucsf.edu>, "matt(a)cgl.ucsf.edu" <matt(a)cgl.ucsf.edu>, "ajain(a)jainlab.org" <ajain(a)jainlab.org>, "ajohnson(a)cgl.ucsf.edu" <ajohnson(a)cgl.ucsf.edu>, "michael.keiser(a)ucsf.edu" <michael.keiser(a)ucsf.edu>, "kortemme(a)cgl.ucsf.edu" <kortemme(a)cgl.ucsf.edu>, "nevan.krogan(a)ucsf.edu" <nevan.krogan(a)ucsf.edu>, "haoli(a)genome.ucsf.edu" <haoli(a)genome.ucsf.edu>, "lim(a)cmp.ucsf.edu" <lim(a)cmp.ucsf.edu>, "hitenmadhani(a)gmail.com" <hitenmadhani(a)gmail.com>, "mmcmanus(a)diabetes.ucsf.edu" <mmcmanus(a)diabetes.ucsf.edu>, "kpollard(a)gladstone.ucsf.edu" <kpollard(a)gladstone.ucsf.edu>, "rischn(a)humgen.ucsf.edu" <rischn(a)humgen.ucsf.edu>, "sali(a)salilab.org" <sali(a)salilab.org>, "mark(a)biostat.ucsf.edu" <mark(a)biostat.ucsf.edu>, "mark.seielstad(a)ucsf.edu" <mark.seielstad(a)ucsf.edu>, "sen(a)biostat.ucsf.edu" <sen(a)biostat.ucsf.edu>, "bshoichet(a)gmail.com" <bshoichet(a)gmail.com>, "peter.turnbaugh(a)ucsf.edu" <peter.turnbaugh(a)ucsf.edu>, "wallj(a)humgen.ucsf.edu" <wallj(a)humgen.ucsf.edu>, "leor.weinberger(a)gladstone.ucsf.edu" <leor.weinberger(a)gladstone.ucsf.edu>, "weissman(a)cmp.ucsf.edu" <weissman(a)cmp.ucsf.edu>, "wittej(a)humgen.ucsf.edu" <wittej(a)humgen.ucsf.edu>, "lani.wu(a)ucsf.edu" <lani.wu(a)ucsf.edu>, "jimmie.ye(a)ucsf.edu" <jimmie.ye(a)ucsf.edu>, "noah.zaitlen(a)ucsf.edu" <noah.zaitlen(a)ucsf.edu> > Cc: Antitsa Stoycheva <astoycheva(a)aliosbiopharma.com> > Subject: Bioinformatics job opening: please post > > Dear Bioinformatics Faculty at UCSF, > > Alios BioPharma, Inc., a Johnson & Johnson company, is recruiting for an entry Ph. D. level bioinformatics job opening. This is an excellent opportunity for a Ph. D. scientist with 2+ years of relevant post-doctoral experience who seeks to join a dynamic interdisciplinary team of dedicated researchers in a biotech setting. > > Would you please forward the attached announcement to qualified candidates who might be interested in this opportunity? We’d like to reach as many outstanding applicants as possible, so please feel free to pass on to other research groups. > > With appreciation, > Antitsa Stoycheva > > Antitsa D. Stoycheva, Ph. D. > Group Leader, Computational Chemistry & Bioinformatics > Alios BioPharma > 260 E. Grand Ave., 2nd Floor > South San Francisco, CA 94080 > astoycheva(a)aliosbiopharma.com > Phone: (650) 635-5513 > Fax: (650) 872-0584 > > > Job description follows: > > Scientist/Senior Scientist, Bioinformatics > Description > Alios BioPharma, Inc, a member of Johnson & Johnson's Family of Companies, is recruiting for a Scientist/Senior Scientist, Bioinformatics to be located in South San Francisco, CA. > > Alios BioPharma, Inc of Johnson & Johnson are dedicated to addressing and solving the most important unmet medical needs of our time, including in oncology, immunology, neuroscience, infectious disease, and cardiovascular and metabolic diseases. Driven by our commitment to patients, we develop sustainable, integrated healthcare solutions by working side-by-side with healthcare stakeholders, based on partnerships of trust and transparency. > > Thriving on a diverse company culture, celebrating the uniqueness of our employees and committed to inclusion. Proud to be an equal opportunity employer. > Summary/Scope: > We seek an exceptional candidate to join the Computational Chemistry and Bioinformatics group at Alios BioPharma. The candidate must be a highly motivated self-starter and team player who performs well in a fast-paced, multidisciplinary team environment. The candidate will report to the Group Leader, Computational Chemistry and Bioinformatics, and their main responsibility will be to conduct a comprehensive scope of bioinformatics and computational activities supporting discovery and development stage oligonucleotide therapeutics projects. Hands-on experience with data mining, sequence processing, in silico design, structure prediction and free energy calculation for nucleic acid constructs is required. Expert knowledge of Unix/Linux, Perl/Python, vi, sed, object-oriented programming language(s), leading-edge software packages relevant to the nucleic acids field, as well as the ability to create custom code to address specific research tasks is a must. Experience with database management, SQL, and Linux system administration is a plus. Advanced understanding of biological pathways relevant to oligonucleotide therapeutics is highly desirable. Ability to initiate and carry out project-driven research with minimal supervision, as well as accomplished communication skills, including clear and efficient presentation of their own work to a diverse group of experts is required. Proven productivity track record in an academic or industrial setting is expected. > > Qualifications: > > Ph.D. in bioinformatics/cheminformatics, theoretical or computational chemistry, or a related field with 2+ years of relevant post-doctoral experience in an academic or industrial setting is required. Publication/patent record backing up a productive research track is a definite plus. > > > > > > > > > This message (including any attachments) is intended only for the use of the individual or entity to which it is addressed and may contain > information that is non-public, proprietary, privileged, confidential, and exempt from disclosure under applicable law or may constitute as attorney > work product. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this communication > is strictly prohibited. If you have received this communication in error, notify us immediately by telephone (650-635-5500) or delete this message immediately. > Thank you.

1 0

[Compbio-allhands] Fwd: Bayer Mission Bay Job Description to circulate
by Andrej Sali 10 Jun '15

10 Jun '15

Sent from my iPhone Begin forwarded message: > From: Fred Aswad <fred.aswad(a)bayer.com> > Date: June 10, 2015 at 6:40:41 PM GMT+2 > To: "Andrej Sali (sali(a)salilab.org)" <sali(a)salilab.org>, "Allan.Balmain(a)ucsf.edu" <Allan.Balmain(a)ucsf.edu>, Charles Craik <Charles.Craik(a)ucsf.edu>, "'Lewis.Lanier(a)ucsf.edu'" <Lewis.Lanier(a)ucsf.edu> > Subject: FW: Bayer Mission Bay Job Description to circulate > > Dear Andrej, Allan, Charlie and Lewis, > > We have a couple of positions open in Mission Bay and I wanted to share with you the position descriptions in case you think there are candidates that you feel may be a good fit. > > Thank you for any help with this! > > Cheers, > Fred > > The information contained in this e-mail is for the exclusive use of the intended recipient(s) and may be confidential, proprietary, and/or legally privileged. Inadvertent disclosure of this message does not constitute a waiver of any privilege. If you receive this message in error, please do not directly or indirectly use, print, copy, forward, or disclose any part of this message. Please also delete this e-mail and all copies and notify the sender. Thank you. > > For alternate languages please go to http://bayerdisclaimer.bayerweb.com > >

1 0

[Compbio-allhands] Fwd: Research positions in IRB Barcelona
by Brian Shoichet 05 Jun '15

05 Jun '15

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF ---------- Forwarded message ---------- From: "Patrick Aloy" <paloy(a)irbbarcelona.org> Date: Jun 5, 2015 8:20 AM Subject: Research positions in IRB Barcelona To: Cc: Dear Friends and Colleagues, just a quick message to let you know that we currently have two open positions in the lab (Postdoc in network biology and Research Associate in structural bioinformatics), and I should be grateful if you could forward this message to people that might be interested. Please, find the two job adverts attached. Thanks for your help !! Best, PTCK. -- Patrick Aloy, ICREA Research Professor Structural Bioinformatics & Network Biology Institute for Research in Biomedicine - Barcelona Science Park c/ Baldiri i Reixac 10-12, 08028 Barcelona, Spain Email: patrick.aloy(a)irbbarcelona.org http://sbnb.irbbarcelona.org Tel : +34 93 4039690 Fax : +34 93 4039954

1 0

[Compbio-allhands] Fwd: Bayer Fellwoship: Invitation to Apply (350,000€)
by Andrej Sali 02 Jun '15

02 Jun '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: assistant(a)salilab.org, Tel +1 (415) 514-4228 Email sali(a)salilab.org; Web http://salilab.org > > > ---------- Forwarded message ---------- > From: Bayer Fellowship <bayer.fellowship(a)bayer.com <mailto:bayer.fellowship@bayer.com>> > Date: Tue, Jun 2, 2015 at 10:15 AM > Subject: Bayer Fellwoship: Invitation to Apply (350,000€) > To: Bayer Fellowship <bayer.fellowship(a)bayer.com <mailto:bayer.fellowship@bayer.com>> > > > Bayer Fellowship: Invitation to Apply > EUR 350,000 for study and research projects for students and young professionals > Dear Fellows or Friends of Bayer Foundation: > > The application window 2015/2016 for the Bayer Fellowship Program is about to be opening. > > The program offers individual financial support for international talents (students up to PhD level and young professionals up to 2ys after graduation) who intend to go from Germany abroad (or from abroad to Germany) for an individual study or research project in the following areas: > > · Biology and molecular biology > · Biotechnology, bio-engineering, bio-informatics > > · Chemistry and biochemistry > > · Medicinal sciences and medicine, veterinary medicine, public health > > · Agricultural sciences, agronomy, green biotechnology > > · STEM Education (science teachers) > > Further selection criteria include good study grades, a concrete project plan and a passion for progress in science and society. > > Applications are now being accepted online until July 10, 2015 (application form here <https://secure.bayer.com/foundations/BewerbungStipendium.aspx?lang=en>). > > The foundation in Leverkusen (Germany) is happy to support with any queries at +49 214 30 41111. > > We are much looking forward to receiving applications from you (or your students)! > > Kind regards > > Thimo V. Schmitt-Lord, MBE > > Head Foundation & Donations Management > > Executive Director of Bayer Foundations > > _________________________________ > > Bayer Science & Education Foundation > > Kaiser-Wilhelm-Allee 1 > > 51373 Leverkusen > > Germany > > > > Fon: +49 (0) 214 30 41 111 <tel:%2B49%20%280%29%20214%2030%2041%20111> > Fax: +49 (0) 214 30 34 893 <tel:%2B49%20%280%29%20214%2030%2034%20893> > > > bayer.fellowship(a)bayer.com <mailto:bayer.fellowship@bayer.com> > www.bayer-stiftungen.de <http://www.bayer-stiftungen.de/> > > > Vorstand: Kemal Malik | Thimo V. Schmitt-Lord > > Vorsitzender des Kuratoriums: Prof. Dr. Ernst-Ludwig Winnacker > > > > Sitz der Stiftung: Leverkusen > >

1 0

[Compbio-allhands] Fwd: Postdoc – Biomolecular Modeling at IBM Research
by Jacobson, Matt 22 May '15

22 May '15

— Matt Begin forwarded message: From: Ruhong Zhou <ruhongz(a)us.ibm.com<mailto:ruhongz@us.ibm.com>> Subject: Postdoc – Biomolecular Modeling at IBM Research Date: May 22, 2015 at 1:08:22 PM EDT To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Matt How are you? Hope this email finds you well. I have several immediate postdoc position openings in my group. If you have good graduate students or current postdocs who would like to work at IBM Research, it might be a great opportunity for them. We do pay postdocs very nicely (>= $100K) in addition to a very academic like research environment. Feel free to forward this job post (https://jobs3.netmedia1.com/cp/faces/job_summary?job_id=RES-0731149) to other students you think appropriate as well. Thanks. Best, Ruhong ======================================================================= Postdoc – Biomolecular Modeling IBM Thomas J. Watson Research Center located in Yorktown Heights, NY expects to hire three Postdocs in the Soft Matter Science Group, Computational Biology Center. The position will involve contributing to ongoing research program in high performance computing (HPC), parallel programming, and biomolecular modeling. We are interested in candidates with deep theoretical or technical knowledge in relevant aspects of computational biology and bioinformatics, including but not limited to novel computational algorithms and methods, large scale biomolecular simulations, parallel programming, multiscale modeling, and data analysis. Outstanding communication skills, ability to interact with a technically diverse team and excellent publication record are critical. For more information, please visit our group page (http://researcher.watson.ibm.com/researcher/view_project.php?id=961) Required Doctorate Degree At least 2 years experience in biomolecular modeling At least 2 years experience in programming English: Intermediate Preferred Doctorate Degree in Chemistry, Physics or Biology A strong track record of publications Huntington disease (HD) related modeling a plus English : Fluent ================================================================================ Ruhong Zhou, PhD Distinguished Research Staff Member (DRSM) Manager, Soft Matter Science Group Computational Biology Center IBM Thomas J. Watson Research Center Yorktown Heights, NY 10598 Tel: (914) 945-3591, eFax: (845) 489-9512 researcher.ibm.com/researcher/view.php?person=us-ruhongz<http://researcher.ibm.com/researcher/view.php?person=us-ruhongz>

1 0

[Compbio-allhands] 5/28/15 Seminar with Michael Elowitz
by Flowers, Nicole 21 May '15

21 May '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Michael Elowitz CalTech A design-based view of signaling and memory circuits in mammalian cells May 28, 2015 B. Sharon, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Schrodinger UGM in SF
by Jacobson, Matt 15 May '15

15 May '15

— Matt Begin forwarded message: From: Woody Sherman <woody.sherman(a)schrodinger.com<mailto:woody.sherman@schrodinger.com>> Subject: Schrodinger UGM in SF Date: May 15, 2015 at 6:38:05 PM GMT+1 To: Matthew Jacobson <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, Our SF UGM is next Wed, and there is a workshop on Tues. Feel free to invite anyone from your lab, or anyone else from UCSF: http://www.schrodinger.com/events/502/ best Woody -- Woody Sherman, Vice President Applications Science, Schrodinger, Inc. ......................................................................... Mobile: 617-306-2050 ; Work: 413-835-0752 WebEx: 408-792-6300 ; WebEx PIN: 68104781# Uber: 857-216-5680 ; Uber PIN: 59858# ......................................................................... Knowledge Base: http://schrodinger.com/kb/ Citations: http://schrodinger.com/citations/ Linkedin: http://www.linkedin.com/in/woodysherman/ Publications: http://scholar.google.com/citations?user=54rCpTkAAAAJ

1 0

[Compbio-allhands] 5/21/15 Seminar with Ming Hammond
by Flowers, Nicole 15 May '15

15 May '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Ming Hammond UC Berkeley Riboswitches as privileged scaffolds for in vivo sensing, directed evolution, and targeting May 21, 2015 D. Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 5/14/15 Seminar with Evgeny Nudler
by Flowers, Nicole 08 May '15

08 May '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Evgeny Nudler NYU Medical Center Molecular Trafficking in Gene Control and DNA Maintenance. May 14, 2015 L. Gendelev, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 5/7/15 Seminar with Jennifer Prescher
by Flowers, Nicole 01 May '15

01 May '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Jennifer Prescher UC Irvine Expanding the imaging toolbox May 7, 2015 Z. Gartner, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 4/30/15 Seminar with Vlad Denic
by Flowers, Nicole 24 Apr '15

24 Apr '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Vlad Denic Harvard Activation of Atg1 kinase by receptor-bound targets initiates selective autophagy. April 30, 2015 J. Weissman, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: New open bioinformatics/CS position
by Andrej Sali 23 Apr '15

23 Apr '15

> Begin forwarded message: > > From: "Chaivorapol, Christina" <christina.chaivorapol(a)roche.com> > Subject: New open bioinformatics/CS position > Date: April 23, 2015 at 10:17:42 AM PDT > To: undisclosed-recipients:; > > Hi, > > I am recruiting for a new position on my team that just opened up. Do you know of any bioinformatician with more of a CS background who is looking for a position? This person will mainly work within the bioinformatics group and with external software partners. I would appreciate it if you could post this to the appropriate distribution lists and send it to people you think might be interested. Please have people who are interested send their CVs to christina.chaivorapol(a)roche.com <mailto:christina.chaivorapol@roche.com>. > > Thanks in advance for your help. > > Best regards, > Christina > -- > Christina Chaivorapol, Ph.D. > Research Leader, Bioinformatics > > Roche Sequencing > Bioinformatics > 4300 Hacienda Dr. > Pleasanton, CA 94588 > Email: christina.chaivorapol(a)roche.com <mailto:christina.chaivorapol@roche.com> > Phone: +1 925-474-7343 > Fax: +1 925-730-8988 > > Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. >

1 0

[Compbio-allhands] 4/23/15 Seminar with Jeffery Hubbell
by Flowers, Nicole 17 Apr '15

17 Apr '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Jeffery Hubbell University of Chicago Engineering antigen presentation in immunity and tolerance April 23, 2015 T. Desai, Host This seminar is co-sponsored by the PSPG/BioE Seminar Series BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 4/16/15 Seminar with Ron Raines
by Flowers, Nicole 13 Apr '15

13 Apr '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Ron Raines University of Wisconsin-Madison Ribonuclease: From kcat/KM to the Clinic April 16, 2015 C. Fitzsimmons, A. Martinko, S. Pollock, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 4/9/15 Seminar with Dewey McCafferty
by Flowers, Nicole 03 Apr '15

03 Apr '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Dewey McCafferty Duke Lysine-Specific Histone Demethylase LSD1: Mechanism, Biology, and Emerging Role in Breast Cancer April 9, 2015 B. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] 4/2/15 Seminar with Jennifer Doudna (Title Correction)
by Flowers, Nicole 30 Mar '15

30 Mar '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Jennifer Doudna UC Berkeley CRISPR Biology: From Discovery to Application April 2, 2015 B. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0