- 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 > ____________________ > >

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[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>

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[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

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[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.

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[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

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[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

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[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

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[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/>

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[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

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[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

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[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>

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[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

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[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

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[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 >

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[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

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[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

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[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

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[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. >

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[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

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[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

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[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

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[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

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[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. *** > > > > > > >

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[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

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[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

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[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

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[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

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[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 > ****************************************************************************

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[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

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[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. *** > > > > > > > >

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[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>)

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[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)

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[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 >

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[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…

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[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

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[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

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[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

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[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

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[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

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[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

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[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

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[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

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[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.

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[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

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[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

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[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

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[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

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[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/> >

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[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 > ****************************************************************************

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[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

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