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

[Compbio-allhands] 4/2/15 Seminar with Jennifer Doudna
by Flowers, Nicole 26 Mar '15

26 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 Signaling pathways in cancer 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

[Compbio-allhands] Fwd: Company looking for a bioinformaticist (or two)
by Tom Ferrin 16 Mar '15

16 Mar '15

-------- Forwarded Message -------- Subject: Company looking for a bioinformaticist (or two) Date: Mon, 16 Mar 2015 14:02:47 +0000 From: Jose Haresco <JHaresco(a)jmpsecurities.com> To: 'tef(a)cgl.ucsf.edu' <tef(a)cgl.ucsf.edu> Hi Tom, It has been quite a while, so I hope this reaches you well. One of the companies I am working with is looking for a bioinformaticist or two. I thought I would pass the job description along in case any of the students or post-docs graduating this year are looking around. Have them contact me if they are interested. Best regards, J ------------------------- Asuragen is seeking an exceptional computational biologist to join its rapidly growing Bioinformatics group. The Sr. Scientist, Computational Biologist will function in a highly interdisciplinary environment, interacting with other Bioinformatics scientists as well as wet bench scientists and the R&D leadership to push the boundaries of diagnostic assay development and overcome computational challenges in data analysis, interpretation and visualization. Specific areas of research and development focus include: ·Application of innovative approaches to identify biomarkers predictive of disease, prognosis, and response to therapy with an emphasis on applications in oncology ·Design of new machine learning and combinatorial optimization algorithms to improve in-silico assay design processes, particularly in the areas of next-generation sequencing and digital PCR ·Development of next-generation sequencing analysis pipelines to take advantage of novel library types and capable of integrating across multiple modalities such as RNA, DNA, and epigenetic modifications. *J.T. Haresco III, Ph.D.* *Managing Director and Senior Equity Analyst*** *Medical Devices / Life Science Tools & Diagnostics* *JMP Securities, LLC* 600 Montgomery Street, Suite 1100 San Francisco, CA 94111 Direct: 415.869.4477 Cell: 415.350.7574 IMPORTANT NOTICE: This message is intended only for the addressee. If you are not the intended recipient, please notify the sender by e-mail reply and delete this message from your computer. You may not copy, disclose, distribute or otherwise make use of this message or its contents for yourself or for any other person, as that action may be unlawful. ORDERS AND INSTRUCTIONS: JMP Securities LLC does not accept action-oriented, time-sensitive instructions or transaction orders via e-mail. JMP Securities LLC will not be responsible for carrying out such instructions or orders, including orders to purchase or sell securities. IMPORTANT DISCLOSURE REGARDING Reg FD AND MATERIAL NON-PUBLIC INFORMATION: JMP Securities LLC maintains strict policies and adherence to all regulatory guidelines and rules pertaining to Reg FD and "material non-public information." Institutional and corporate clients are expected to abide by all similar rules, laws and regulations as they conduct meetings sponsored by JMP Securities LLC. CONFIDENTIALITY AND PRIVACY: JMP Group LLC. reserves the right to monitor and review the content of all e-mail communications sent and/or received by its employees.

1 0

[Compbio-allhands] 3/12/15 BBC Seminar CANCELLED
by Flowers, Nicole 06 Mar '15

06 Mar '15

Please note: There is no BBC Seminar for 3/12/15. 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: Postdoc Positions
by Andrej Sali 04 Mar '15

04 Mar '15

> Begin forwarded message: > > From: "Gregory A. Voth" <gavoth(a)uchicago.edu> > To: "Gregory A. Voth" <gavoth(a)uchicago.edu>, "Voth-Group-Mailing(a)vothgroup.uchicago.edu" <Voth-Group-Mailing(a)vothgroup.uchicago.edu> > Subject: Postdoc Positions > Date: March 4, 2015 at 6:46:41 PM PST > Reply-To: gavoth(a)uchicago.edu > > > Dear Colleague, > > There is the possibility of one or more postdoc position in my group, subject to the qualifications and experience of the applicant as well as > the final availability of funding. For information on my group and our research interests please see my group web page listed below. Interested parties should contact me by email. > > Best wishes, > Greg Voth > > PS-I apologize if you get this email more than once > > __________________________________________________________________ > > Gregory A. Voth, Ph.D. > Haig P. Papazian Distinguished Service Professor > Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, > and Computation Institute > > Department of Chemistry > The University of Chicago > 5735 S. Ellis Avenue > Chicago, Illinois 60637 > Phone: 773-702-9092 > Fax: 773-795-9106 > Administrative Assistant: 773-702-9096 > Email: gavoth(a)uchicago.edu <mailto:gavoth@uchicago.edu> > Group Web Site: vothgroup.uchicago.edu <http://vothgroup.uchicago.edu/> > Office: 231 Searle > Admin Office: 233 Searle > ___________________________________________________________________ > > > _______________________________________________ > Voth-group-mailing mailing list > Voth-group-mailing(a)vothgroup.uchicago.edu > https://vothgroup.uchicago.edu/cgi-bin/mailman/listinfo/voth-group-mailing

1 0

[Compbio-allhands] 3/5/15 Seminar with Ruth Nussinov
by Flowers, Nicole 27 Feb '15

27 Feb '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 Ruth Nussinov NIH Signaling pathways in cancer March 5, 2015 D. Garrido Ruiz, 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] 2/26/15 Seminar with Samie Jaffrey
by Flowers, Nicole 20 Feb '15

20 Feb '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 Samie Jaffrey Cornell Imaging RNA and RNA biology using RNA mimics of green fluorescent protein February 26, 2015 D. Weinberg, 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: Open PhD and Postdoc positions in Bioinformatics in Austria
by Scooter Morris 18 Feb '15

18 Feb '15

-------- Forwarded Message -------- Subject: Open PhD and Postdoc positions in Bioinformatics Date: Wed, 18 Feb 2015 23:11:33 +0100 From: Mario Albrecht <mario.albrecht(a)tugraz.at> To: mario.albrecht(a)tugraz.at Dear colleagues, Please forward these bioinformatics job offers for PhD students and Postdocs to others, thank you much! Kind regards, Mario Albrecht ================================================ Open PhD and Postdoc positions in Bioinformatics ================================================ Deadline: 28 February 2015 Contact: Prof. Dr. Mario Albrecht, Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria, info(a)mario-albrecht.at Further information at http://www.medbioinf.at and below! Note: Please send your application both to info(a)mario-albrecht.at and informatik(a)tugraz.at citing the reference number 7090/15/001. Open full-time paid bioinformatics PhD student position for molecular network research until 28 February 2015, for details see http://wwww.medbioinf.at and as follows: Molecular networks and proteins are involved in many biological processes. Therefore, we aim at the development and application of computational network methods for the analysis and prediction of molecular interactions and their structural and functional changes due to sequence mutations. The mutations might occur in disease genes or bacterial and viral genomes. Based on the analysis results, we also want to develop innovative bioinformatics approaches for modeling pathways and their changes as well as for the design and prioritization of follow-up experiments. Open full-time paid bioinformatics postdoc position for integrative omics research until 28 February 2015, for details see http://bioinf.tugraz.at/images/Postdoc.pdf and as follows: Cancer is the leading cause of death and involves altered lipid metabolism. The rate-limiting enzyme in triacylglyceride degradation, the adipose triglyceride lipase (ATGL), might not participate only in lipid mobilization and degradation, but also in signaling pathways by generating lipid signaling molecules. Therefore, we aim at the large-scale elucidation of the functional role of ATGL in cancer progression using different omics strategies combined with computational approaches. Novel bioinformatics methods are developed for analyzing the data of molecular proteomics and metabolomics networks related to lipolysis in cancer. ________________________________________________________ Prof. Dr. Mario Albrecht http://www.medbioinf.at Institute for Knowledge Discovery Head of Bioinformatics Graz University of Technology Inffeldgasse 13/IV, 8010 Graz, Austria ________________________________________________________

1 0

[Compbio-allhands] 2/19/15 Seminar with Anne-Claude Gingras
by Flowers, Nicole 13 Feb '15

13 Feb '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 Anne-Claude Gingras Lunenfeld Kinase-phosphatase interactomes: a tale of Hippos and mulberries February 19, 2015 R. Levin, 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: MATLAB Seminars Coming to UCSF – Feb 25, 2015]
by Patricia Babbitt 06 Feb '15

06 Feb '15

-- 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 94158-2330, USA (CA 94158 for direct delivery by courier) Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Joslyn Polzien, +1 415-514-1214, 415-514-4861 Joslyn.Polzien(a)ucsf.edu

1 0

[Compbio-allhands] 2/12/15 Seminar with Judith Klinman
by Flowers, Nicole 06 Feb '15

06 Feb '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 Judith Klinman UC Berkeley Moving through Barriers: Unlocking the Mysteries of How Enzymes Really Work February 12, 2015 S. Miller, 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: Open PostDoc position at the Structural Genomics Group (CNAG-CRG, Barcelona)
by Andrej Sali 05 Feb '15

05 Feb '15

Sent from my iPhone Begin forwarded message: > From: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Date: February 5, 2015 at 3:29:51 AM PST > To: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Subject: Open PostDoc position at the Structural Genomics Group (CNAG-CRG, Barcelona) > > Dear friends and colleagues, > > Apologies for the mass posting... > > I would appreciate if you could forward this add to whom may be interested. > > Thanks in advance, > Marc > ... > Marc A. Marti-Renom, ICREA Research Professor > Genome Biology Group Leader - CNAG - Centre Nacional d’Anàlisi Genòmica > Structural Genomics Group Leader - CRG - Centre de Regulació Genòmica > Parc Científic de Barcelona – Torre I (10th floor) > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email mmarti(a)pcb.ub.cat > Web http://marciuslab.org - http://cnag.cat - http://crg.cat > > *** Consider the environment. Print responsibly. *** > > > > > > > > >

1 0

[Compbio-allhands] AZ
by Jacobson, Matt 29 Jan '15

29 Jan '15

From: Dry, Jonathan R Sent: Thursday, January 29, 2015 3:45 PM Cc: Hudson, Kevin Subject: New vacancy in Oncology Bioinformatics - AstraZeneca Cambridge UK Hello Informatics colleagues http://jobs.astrazeneca.com/jobs/details/l1rRD1247-senior-bioinformatics-sc… We have an exciting opportunity for a talented, motivated bioinformatics scientist to join the Oncology Bioinformatics team at AstraZeneca and help with our analyses of clinical NGS data. The career level will be relevant to individuals emerging from a strong PhD, a first post-doctoral role, or equivalent (e.g. a Masters with some experience). I was hoping I might rely on you to reach out to your internal/external informatics network, especially in Cambridge UK and Europe, and highlight this post to relevant individuals. Closing date for applications is 1st March 2015 Many thanks in advance. Jonathan Jonathan R. Dry Bioinformatics discipline lead, Oncology iMED AstraZeneca Boston, Waltham, MA +1 781 839 4845

1 0

[Compbio-allhands] 2/5/15 Seminar with Robert Keenan
by Flowers, Nicole 29 Jan '15

29 Jan '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 Robert Keenan University of Chicago Tail-anchored membrane proteins biogenesis February 5, 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] Fwd: Open position_structure guided protein design
by Andrej Sali 29 Jan '15

29 Jan '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 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 > > > From: HGRQ (Hanne Grøn) [mailto:hgrq@novonordisk.com <mailto:hgrq@novonordisk.com>] > Sent: Tuesday, January 20, 2015 1:50 PM > To: Boris Turk > Subject: Open position_structure guided protein design > > Dear Boris, > > Happy New Year – I hope you are doing well. > > I am writing to you, because we have an open position in my Department for a scientist interested in structure-guided protein design. Unfortunately, Ole Olsen, our very experienced and creative molecular modeler, had decided to retire. Therefore, we are looking to fill his position. The candidate profile is listed in the Job Ad where you can also find a description of our Department (as we see it J). > > I would very much appreciate, if you would please share the link with your network of former students, colleagues, and friends. You can link directly to LinkedIn and other media from the ad: > > http://www.novonordisk.com/careers/job_section/jp.asp?jobid=26462BR&joblng=… <http://www.novonordisk.com/careers/job_section/jp.asp?jobid=26462BR&joblng=…> > > It will be hard to replace Ole, but now the search has started. Please let me know, if I can further elaborate on the Department or the profile of the ideal candidate. > > Kind regards, > Hanne > > Molecular Modelling - Experienced Scientist > Research & Development > > Denmark - Måløv > > The Department of Haemophilia Biochemistry is seeking an experienced scientist for structure-guided protein optimization and design > > About the Department > Haemophilia Biochemistry is an integral part of the Novo Nordisk haemophilia research area in Global Research located in Måløv. We are a diverse department with 22 enthusiastic scientists, research assistants, and students who all support the haemophilia research portfolio through innovation and structure-guided design and development of novel protein-based therapies. The department has a solid base of expertise in haemostasis biology, mode of action studies, protein chemistry, enzyme assays, protein-ligand interaction studies, and molecular modelling. > > The Job > This is a dynamic and challenging position in an innovative discovery department with many cross-functional activities in project teams and focus groups. Ambitious scientific goals will require collaboration with highly specialized colleagues. Your main focus will be structure-guided design and development of novel protein therapeutic candidates as well as proteins with improved biological, formulation, and pharmacological properties. Your responsibilities will include generation of protein homology models, advanced data mining and analysis, and molecular dynamics calculations in interpretation of experimental data (structure and biology). You will have the opportunity to influence your own development and grow into a key role in an exciting and diverse discovery department. > > Qualifications > As a key member of a discovery research team, the ideal candidate has extensive experience in in silico structure-guided design and optimization of protein based therapies, and can combine structural and computational research with experimental data. The candidate holds a PhD and at least three years of documented post-doctoral experience in structural biology or molecular modelling. Experience could include one or more of the following: simulation and visualizing packages, homology modelling, protein-structure prediction, calculation of protein-protein energetics, and/or docking software. Research experience in large-scale data mining and analysis, bioinformatics, and using computational and/or statistical approaches is a plus. The candidate must be fluent in English, have excellent communication skills, a collaborative mind-set, and a passion for innovation. > > Contact > For further information about this position, please contact Hanne Grøn at (+45) 3079 0765 > > Deadline > 15-Feb-2014 > > > ______________________________________ > > Hanne Grøn, Ph.D. > Director of Haemophilia Biochemistry > Biopharmaceutical Research Unit > > Novo Nordisk A/S > Novo Nordisk Park > Room F5.2.11 > DK-2760 Måløv > Denmark > +45 4444 8888 (phone) > +45 3079 0765 (mobile) > hgrq(a)novonordisk.com <mailto:hgrq@novonordisk.com> > > Changing possibilities in haemophilia > Novo Nordisk is focused on the quality of life of people living with haemophilia; for this reason our pipeline continues to evolve, it is why we continue to strengthen our existing formula. Learn more <http://www.novonordisk.com/about_us/improving_haemophilia/ChangingPossibili…> > > This e-mail (including any attachments) is intended for the addressee(s) stated above only and may contain confidential information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information contained herein is strictly prohibited and may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete it immediately hereafter. Thank you. >

1 0

[Compbio-allhands] Tomorrow! ChEMBL: The Organization of Drug Discovery Data - 1:30pm in Byers Hall 212
by Hilary Mahon 29 Jan '15

29 Jan '15

For more information, please see attached. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

1 0

[Compbio-allhands] 1/22/15 Seminar with Barak Cohen
by Flowers, Nicole 16 Jan '15

16 Jan '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 Barak Cohen Washington University in St. Louis Why don’t transcription factors get lost? January 22, 2015 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 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Biophysics Myth-buster Wanted for TV Documentary
by Jacobson, Matt 15 Jan '15

15 Jan '15

definitely one of the more amusing phone calls i've received lately feel free to pass along! Begin forwarded message: From: Poppy Riddle <poppy(a)offthefence.com<mailto:poppy@offthefence.com>> Subject: Biophysics Myth-buster Wanted for TV Documentary Date: January 15, 2015 12:25:55 PM PST To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, I would be incredibly grateful if you could circulate this email amongst your post-grads. I do hope that it pique's someones interest! All the best, Poppy Dear UCSF Students, I am emailing from a TV company based in the United Kingdom called Off the Fence<http://www.offthefence.com/>. We will be flying to California next month to begin filming on a new documentary series looking at extraordinary people with remarkable skills. One of these people is a man called Kanzawa Sensei <https://www.youtube.com/watch?v=vlR15Gnj8wc> - a chi expert from Japan, who claims he has the ability to heal people, and even put animals to sleep by directing 'chi'. The essence of this 'chi' seems to be an "energy" property that he is able to harness and direct at his subjects... We are looking for a post-grad to act as a myth-buster for us for 1 day in February, and perhaps run some basic tests to find out if biophysics can explain what's happening, or if it really is just an elaborate hoax! This programme will be going out internationally and will hopefully prove a fun (possibly enlightening?) experience, so if you think you could handle being on camera and be able to find the time and join us on location, we would love to have you! All the best, Poppy -- Poppy Riddle Researcher and Coordinator Direct: +44 (0)117 909 7561 Off the Fence Productions | 20 Elmdale Road | Tyndalls Park | BS81SG Bristol Tel: +44 (0)117 909 7560 [http://i.imgbox.com/p8RxD9eN.png]<https://twitter.com/PoppyRiddle> [http://i.imgbox.com/Hog3oA2p.png] <https://www.linkedin.com/pub/poppy-riddle/37/49a/4b4> [http://i.imgbox.com/2Nx08TDr.png] <https://plus.google.com/+PoppyRiddle> www.offthefence.com<http://offthefence.com/> [http://i62.tinypic.com/14l3ul4.jpg] Good planets are hard to find - please think of the environment before you print this email.The information in this email including any attachments is confidential and may be legally privileged. If you are not the intended recipient, please advise the sender immediately by return email and then delete this email and any attachment from your system. The unauthorised use, distribution, copying or alteration of this email and any attachments is strictly forbidden. No employee or agent is authorized to conclude any binding agreement on behalf of Off the Fence B.V. with another party by email without a binding written agreement between your company and Off the Fence B.V. Prior to the execution of such agreement, Off the Fence B.V. shall have no obligations with respect to any deal terms discussed and/or agreed to in principle. Any costs/expenses or other activities are incurred at your own cost and risk until full execution of the relevant agreement. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Please forward to interest parties – Postdoc position available
by Andrej Sali 14 Jan '15

14 Jan '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 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 > Begin forwarded message: > > Date: January 14, 2015 at 11:24:59 AM PST > Subject: Fwd: Please forward to interest parties – Postdoc position available > From: Ben Sellers <sellers.benjamin(a)gene.com> > To: Andrej Sali <sali(a)salilab.org> > > > > Hi Andrej > > It was nice speaking with you yesterday. Here is the Stanford/Genentech postdoc position I mentioned. I would appreciate your forwarding it to whomever you see fit. > > Thanks > -Ben > > > > > Stanford‐Genentech > Postdoctoral Research Fellow (Computational) > > We invite interested candidates to apply for this truly unique joint Stanford/Genentech postdoctoral position, co-mentored by Prof. Vijay Pande, PhD (Chemistry, Structural Biology, and Computer Science at Stanford) and Ben Sellers, PhD (Computational Drug Discovery at Genentech). > > The position > We are seeking a highly motivated postdoctoral research fellow to investigate basic function and small molecule modulation of protein receptors using large scale molecular dynamics simulations. Theprimaryaimoftheproposedresearchistopredictmetastablestatesinprotein receptors to identify alternative drug-able conformations. Membrane-bound receptors are of particular interest. > > Who you are > We are looking for a candidate with a PhD in biophysics, theoretical chemistry or related field with a strong background in computational modeling of proteins and small molecules. Expertise in molecular mechanics forcefields, molecular dynamics simulation, and statistics is required. A productive track record and at least one first-author publication in a reputable journal are also required. Programming experience and an ability to analyze massive data sets are also desirable. Most importantly, we seek a driven individual who will lead his/her research independently and communicate frequently and clearly to the field. > > To apply > Please apply to Job# 00436268 on the http://www.gene.com <http://www.gene.com/> website as a preliminary step. Direct Link: http://www.gene.com/careers/detail/00436268 <http://www.gene.com/careers/detail/00436268>/GenentechStanfordPostdoctoralResearchFell owComputationalChemistry > > For more information > > http://pande.stanford.edu/ <http://pande.stanford.edu/> > > http://www.gene.com/careers <http://www.gene.com/careers>/academicprograms/postdocs > > > > > > -- > > Ben Sellers, PhD > Discovery Chemistry > Genentech, Inc. > sellers.benjamin(a)gene.com <mailto:sellers.benjamin@gene.com> > 650-467-3995

1 0

[Compbio-allhands] Reminder -- Tom Blundell Seminar -- Thursday, Jan. 15, 10:30am -- Genentech Hall Auditorium
by Hilary Mahon 13 Jan '15

13 Jan '15

For more information, please see attached. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

1 0

[Compbio-allhands] Fwd: Happy 2015!
by Brian Shoichet 12 Jan '15

12 Jan '15

Anyone interested in a wet-lab position on discovering the MoA of active compounds, and in assay development, this might be a good opportunity. Brian ---------- Forwarded message ---------- From: <federica.morandi(a)emdserono.com> Date: Fri, Jan 9, 2015 at 1:20 PM Subject: Happy 2015! To: bshoichet(a)gmail.com Hi Brian, I wanted to tell you that I have an open position for a PhD Scientist in my team. If there is somebody in your group who is looking for a job in industry I would be happy to consider him/her. It is a lab based position; we develop and run all the biochemical assays for enzyme targets in within the US based therapeutic areas (Immunology and immune oncology). The new hire will also be responsible for studying the MoA of lead compounds and a core member of some of the project teams. I am trying to go through the hiring process as fast as possible because you never know when things will change and the position frozen. Thanks and talk to you soon, Federica This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. -- 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] 1/15/15 Seminar with Edward Marcotte
by Flowers, Nicole 09 Jan '15

09 Jan '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 Edward Marcotte University of Texas at Austin Evolution, the proteome, and disease January 15, 2015 J. Webber, 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 Graduate Program Assistant AMBER Software Administrator 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: postdoc opening
by Jacobson, Matt 08 Jan '15

08 Jan '15

Begin forwarded message: From: "Jansen, Johanna" <johanna.jansen(a)novartis.com<mailto:johanna.jansen@novartis.com>> Subject: postdoc opening Date: January 8, 2015 4:55:49 PM PST To: "'Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>'" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, "shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>" <shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>> Dear Matt & Brian, It was good seeing you at the event today. Below is the summary of the postdoc position that is opening in our group. I will be the mentor and Heinz Moser will be co-mentor. I would appreciate it if you could advertise this at UCSF and I’ll be happy to speak with any interested graduate students to provide further information. Thanks ! Hanneke New in silico descriptors for correlations with biological endpoints and drug design principles: The Computer-Aided Drug Discovery (CADD) group has a strong focus on utilizing the vast Novartis knowledgebase to extract relationships between properties of molecules and their biological activity, and on developing approaches to make predictions based on those relationships using properties calculated from chemical structure (in silico descriptors). We work closely with experimentalists to design the compound sets for measurements of biological and physical properties in an effort to drive drug discovery and determine which molecular properties we can calculate that are predictive of the experimental properties. Two molecular properties that are not well described by the in silico descriptors commonly used in drug discovery are conformational flexibility and hydrogen-bonding strength. These properties play an important role in many biological activities, including various aspects of permeability (entry into mammalian cells, entry into gram-negative pathogens, blood-brain-barrier penetration, and passage across epithelial barriers). In order to better guide chemistry designs in drug discovery, we need better in silico descriptors to capture flexibility and hydrogen bonding strength. Our platform brings together computational, medicinal, and analytical chemistry, with the scientists that measure the relevant physicochemical and biological properties. This environment of experts, software, instruments, and data is particularly suited to develop new approaches for predicting these properties, including creating experimental datasets, and developing and evaluating new in silico descriptors. Applications of such descriptors include selection efforts (archive enhancement, library design, screening set design) as well as prospective chemistry designs during optimization. Qualifications: PhD degree holders, and PhD students within one year of completing of their degrees are eligible to apply. For more information, contact Hanneke Jansen at Johanna.Jansen(a)novartis.com<mailto:Johanna.Jansen@novartis.com>. To download the cover letter template and apply, please visit http://postdoc.nibr.com/ Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Murcko talk at noon
by Jacobson, Matt 08 Jan '15

08 Jan '15

A reminder that Mark Murcko is giving the Kollman lecture today at noon, on free energy calculations in drug discovery. Hope to see a good turnout -- Matt Sent from my iPhone

1 0

[Compbio-allhands] Fwd: Bioinformatics/biostats positions at Roche Sequencing
by Andrej Sali 05 Jan '15

05 Jan '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 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 > Begin forwarded message: > > From: "Chaivorapol, Christina" <christina.chaivorapol(a)roche.com> > Date: January 5, 2015 at 10:59:48 AM PST > Subject: Bioinformatics/biostats positions at Roche Sequencing > To: Andrej Sali <sali(a)salilab.org> > > Hi Andrej, > > Happy new year! I hope things are well with you. I'm not sure if you heard, but I moved to Roche Sequencing to build a bioinformatics group that will focus on developing diagnostics based on NGS technology. I am currently looking to fill a few positions in my group and hope you will be able to forward this to people in your lab and/or at UCSF who might be interested in these jobs. > > Attached are the job postings for the positions in my group. If anyone is interested, please have them apply to the position of interest at the following links: > > Principal Scientist <http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-3017264312&locale=…> > Senior Biostatistican <http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-3017264212&locale=…> > > Thanks, > 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] CheMBL: The Organization of Drug Discovery Data Workshop, January 30, 2015, 1:30pm, Byers Hall 212
by Hilary Mahon 18 Dec '14

18 Dec '14

For more information, please see attached. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

1 0

[Compbio-allhands] Seminar - Tom Blundell/University of Cambridge - Thursday, January 15, 2015 - 10:30am - Genentech Auditorium
by Hilary Mahon 16 Dec '14

16 Dec '14

Please see attached for more information. --- Andrej Sali

1 0

[Compbio-allhands] Fwd: NIST Structure Biology Position
by Andrej Sali 26 Nov '14

26 Nov '14

> Begin forwarded message: > > From: "Marino, John P." <john.marino(a)nist.gov> > To: "sali(a)salilab.org" <sali(a)salilab.org> > Subject: FW: NIST Structure Biology Position > Date: November 25, 2014 at 12:06:33 PM PST > > Dear Andrej, > > I am writing to request your help in identifying outstanding candidates for an Assistant Professor equivalent position in our group at the National Institute of Standards and Technology (NIST) (http://jobs.sciencecareers.org/job/344641/faculty-equivalent-structural-bio…) We are looking for motivated scientists who could establish independent research teams focused on developing new experimental techniques and/or modeling methods to advance protein structure determination. We are particularly interested in applicants whose research will focus on novel ways to combine high resolution structural data (X-ray and NMR) with small angle scattering (SAS) techniques to address important problems in biology and biotechnology. > > This is a federally position with 100% salary support. Base research funds are also provided by NIST, as well as access to state-of-the-art equipment, including high field NMRs (two 600s and a 900 MHz instrument), HDX-MS, X-ray crystallography and SAS facilities (in-house SAXS and internal access to the NIST Center for Neutron Research). Group members can, and are encouraged to, to apply for external funding to expand their program. Moreover, as we are situated in a joint Institute with the University of Maryland, adjunct appointments within UM departments are also possible. > > Our group is currently undergoing a significant expansion and provides an exciting and stimulating environment for cutting edge, collaborative research. We would greatly appreciate it if you could recommend suitable candidates to us and don't hesitate to contact us if there are any questions. > > Note that as this is a federal position, US citizenship is required. > > Best Regards, > John > _______________________________________ > John P. Marino, Ph.D. > Leader, Biomolecular Structure & Function Group > National Institute of Standards and Technology > 9600 Gudelsky Drive, Rockville, MD 20850 > 240-314-6160 [Tel]; 240-314-6255 [Fax] > john.marino(a)nist.gov > -- 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: faculty opening
by Jacobson, Matt 23 Nov '14

23 Nov '14

-- Matt Sent from my iPad Begin forwarded message: From: Emil Alexov <ealexov(a)g.clemson.edu<mailto:ealexov@g.clemson.edu>> Date: November 23, 2014 at 9:58:52 AM PST Cc: Konstantin Kornev <KKORNEV(a)clemson.edu<mailto:KKORNEV@clemson.edu>>, Igor Luzinov <luzinov(a)clemson.edu<mailto:luzinov@clemson.edu>> Subject: faculty opening Colleagues, With this email, I simply would like to bring to your attention a recent ad for a faculty position at Clemson University (including computational/theoretical approaches to bio-materials). See the ad attached. Please, forward the announcement to any interested party. I apologize for multiple copies of this email that you may receive. Thanks, Emil http://www.compbio.clemson.edu

1 0

[Compbio-allhands] Fwd: New position and I'm hiring - any mobile job candiates?
by Andrej Sali 19 Nov '14

19 Nov '14

> Begin forwarded message: > > From: Heidi Imker <hjimker(a)gmail.com> > Date: November 18, 2014 at 8:11:26 PM PST > Subject: New position and I'm hiring - any mobile job candiates? > To: Andrej Sali <sali(a)salilab.org> > > Hi Andrej, > > Hope things going really well in San Francisco! I have a great new position as the director of a campus-wide program for managing and stewarding research data (Research Data Service <http://researchdataservice.illinois.edu/>). I started in May and after getting up to speed, we're ready to to hire. > I’m casting a wide net for 3 new job positions that we’re filling in the data realm. With your group’s expertise and field knowledge, you might know of some great people who are ready to move on to new a position. We’re hiring two data curators (wide open job description - many different skill-sets could be of use) and a data repository developer. Salary will be in the $60K range but our house prices average about $140K. CU is an “easy” place to live. :) > > http://goo.gl/YsBHom <http://goo.gl/YsBHom> (curators) > > http://goo.gl/4vumxA <http://goo.gl/4vumxA> (developer) > > Please pass on to anyone you know who might be interested, and your help is greatly appreciated in getting the word out. > > Do mail back if you get a chance, too – hope to hear things are going great! > > Heidi >

1 0

[Compbio-allhands] 2015 USHUPO conference
by Andrej Sali 16 Nov '14

16 Nov '14

-- 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] 11/20/14 Seminar with Molly Przeworski
by Flowers, Nicole 14 Nov '14

14 Nov '14

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 Molly Przeworski University of Chicago An evolutionary perspective on the human germ line mutation rate November 20, 2014 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 Graduate Program Assistant AMBER Software Administrator 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] SEMINAR ANNOUNCEMENT: Bill Pearson, Nov. 11, 1 pm, BH-212
by Patsy Babbitt 11 Nov '14

11 Nov '14

Seminar notice: Bill Pearson, Univ. of VA School of Medicine Friday, Nov. 14, 1:00 BH-212 Bill works in the areas of computational biology and protein evolution. One of the founders of the field of sequence analysis and its applications for functional inference, he serves on many advisory boards, including that for European Bioinformatics Institute's UniProt, one of the two (with Genbank) primary public database for sequence information and annotation. He wrote the FASTA algorithm, one of the first widely used computer programs for identifying distantly related protein sequences. His approach is widely used to annotate newly sequenced genomes. His current research focuses on improving functional predictions for proteins by integrating annotation and variation information with sequence alignments. Title and abstract: Alignments with Annotations – providing functional information with similarity search Similarity searching with sequence alignment is the most reliable method for characterizing genomes and meta-genomes; sequence alignment algorithms may now be the major consumer of compute cycles in the life sciences. While similarity searching has become dramatically more sensitive over the past 25 years, and the number and diversity of sequences has increased by orders of magnitude, the display of sequence alignments is essentially unchanged. Despite the explosive growth of sequence, variation, and annotation data, and the hyper-connectedness of sequence and annotation databases, popular search programs show the same alignment information that was displayed in 1985. The FASTA search and alignment programs can incorporate functional site annotations, variation data, and domain boundaries Variant annotation allows the alignment score to improve; the domain annotation strategy partitions the alignment score across the annotated domains, reducing the problem of homologous over-extension. Annotation of functional sites allows exploration of the relationship between sequence similarity, active-site conservation, and functional similarity -- 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 94158-2330, USA (CA 94158 for direct delivery by courier) Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Joslyn Polzien, +1 415-514-1214, 415-514-4861 Joslyn.Polzien(a)ucsf.edu

1 0

[Compbio-allhands] 11/13/14 Seminar with Jeff Gore
by Flowers, Nicole 07 Nov '14

07 Nov '14

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 Jeff Gore MIT Cooperation, cheating, and collapse in microbial populations November 13, 2014 M. Thomson, 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 Graduate Program Assistant AMBER Software Administrator 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] 11/6/14 Braisted Lecture with Laura Kiessling
by Flowers, Nicole 06 Nov '14

06 Nov '14

UCSF-UCB Andrew Braisted Award Lectureship Lauraq Kiessling, Ph.D. Professor and MacArthur Foundation Fellow University of Wisconsin-Madison Us Versus Them: Cell Surface Glycans to Distinguish Human and Microbial Cells Thursday, November 6, 2014 4 pm Genentech Hall Byers Auditorium UCSF Mission Bay Campus Simulcast to Parnassus, Room 161 Reception in 1st Floor Atrium following talk Contact: Jim Wells, Charles Craik Sponsor: The Andrew Braisted Lecture Fund Nicole Takesono Flowers BMI, BP, & CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 1

[Compbio-allhands] SAVE THE DATE- PETER KOLLMAN LECTURESHIP- JANUARY 8, 2015
by Flowers, Nicole 04 Nov '14

04 Nov '14

SAVE THE DATE- THURSDAY, January 8, 2015 AT 12:00 PM Mark Murcko Disruptive Biomedical PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS S-161 Reception in Byers Hall 5th Floor Lounge at 3:30 Nicole Takesono Flowers BMI, BP, & CCB Graduate Program Assistant AMBER Software Administrator 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: Faculty search at Ohio State University in theoretical/computational chemistry
by Andrej Sali 04 Nov '14

04 Nov '14

Sent from my iPhone Begin forwarded message: > From: "Herbert, John" <herbert(a)chemistry.ohio-state.edu> > Date: November 4, 2014 at 8:10:10 AM PST > To: "Herbert, John" <herbert(a)chemistry.ohio-state.edu> > Cc: "Herbert, John" <herbert(a)chemistry.ohio-state.edu> > Subject: Faculty search at Ohio State University in theoretical/computational chemistry > Reply-To: "Herbert, John" <herbert(a)chemistry.ohio-state.edu> > > Colleague, > I wish to draw your attention to a theoretical chemistry faculty search in my department, which is part of a larger “Data Analytics” initiative on campus, into which the University has committed significant resources. Because of the broader tie-in and the attendant layers of bureaucracy, the approval to search came relatively late, so I am sending out this blanket email. Please note that we will begin reviewing applications immediately, but the final deadline for applications is Dec. 1. > > The text of the advertisement is pasted at the end of this email. Please forward this email to your postdocs or former students who are looking for academic jobs. > > Thanks in advance, and best regards. > John Herbert > > > ================================== > John M. Herbert, Professor > Dept. of Chemistry & Biochemistry > The Ohio State University > 100 W. 18th Ave., Columbus, OH 43210 > Office: 2114 Newman & Wolfrom > (614) 292-6851 (voice) > (614) 292-1685 (fax) > http://www.chemistry.osu.edu/~herbert > ================================== > > > The College of Arts and Sciences at The Ohio State University seeks applications to fill a tenure-track faculty position in Data Analytics at the Assistant Professor level within the Department of Chemistry and Biochemistry. The successful applicant will develop and apply novel computational methods to guide discovery of new functional materials or molecules, and/or understand the properties of complex systems. The search will consider outstanding candidates in all areas of computational chemistry, but greatest needs exist in either (i) electronic structure theory and dynamics, or (ii) computational structural biology. Ideal candidates in area (i) would address fundamental questions to enable rational design of new materials with possible applications in energy harvesting and storage, novel electronic devices, catalysis, or sensing. The ideal candidate in area (ii) would complement and extend existing and emerging experimental methods in biomolecular structure and function, with possible applications in de novo structure prediction, molecular design, or macromolecule-ligand interactions. Successful candidates will demonstrate the potential to be leaders in methods development, but also have strong ties to experiment. Ohio State has a strong tradition in theoretical and computational chemistry, with access to excellent computing resources through the Ohio Supercomputer Center (www.osc.edu) A doctoral degree in Chemistry or Biochemistry is required at the time of application. This position is partially funded by Ohio State's Discovery Themes Initiative, a significant faculty hiring investment in key thematic areas in which the university can build on its culture of academic collaboration to make a global impact. > > The Ohio State University, Ohio’s flagship institution of higher education, is located in Columbus, a growing and affordable metropolitan area of ~1.5 million people with a stable and diversified economy. Columbus is consistently ranked as one of the most attractive cities in which to live and work. General information about the University, College, and community is available through links at: http://www.osu.edu. A curriculum vitae, a description of research experience and future plans, a description of teaching interests, a list of publications, and 3 letters of recommendation should be submitted to https://academicjobsonline.org/ajo/jobs/5049. Applications will be accepted and reviewed continuously, but to ensure a full review the application materials should be received no later than December 1, 2014. > > The Ohio State University is committed to establishing a culturally and intellectually diverse environment, encouraging all members of our learning community to reach their full potential. We are responsive to dual-career families and strongly promote work-life balance to support our community members through a suite of institutionalized policies. We are an NSF Advance Institution and a member of the Ohio/Western Pennsylvania/West Virginia Higher Education Recruitment Consortium (HERC). > > The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status. Ohio State is an NSF Advance Institution. > > >

1 0

[Compbio-allhands] Fwd: Tenure Track Position in Systems Biology and Microbiology
by Andrej Sali 03 Nov '14

03 Nov '14

-- 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 > Begin forwarded message: > > From: Thibault Mayor <mayor(a)mail.ubc.ca> > Date: November 3, 2014 at 11:14:27 PM PST > Subject: Tenure Track Position in Systems Biology and Microbiology > To: Thibault Mayor <mayor(a)mail.ubc.ca> > > Dear colleague, > > The Centre of High-Throughput Biology and the Department of Microbiology and Immunology of the University of British Columbia are seeking a new Faculty applicant for a tenure-track position. More specifically, we are looking for an applicant with expertise in Microbiology and Systems Biology, and we would be grateful if you could bring this opening to the attention of potential candidates. > > Thank you on the behalf of the Search Committee > > Very Best, > > Thibault > > > Thibault Mayor, Ph.D. > Associate Professor > CHiBi - Centre for High-Throughput Biology > Department of Biochemistry and Molecular Biology > University of British Columbia > 2125 East Mall - Room 306 > Vancouver - BC - V6T 1Z4 - Canada > > office: 604 822 5144 > lab: 604 822 5259 > fax: 604-822-9126 > email: mayor(a)mail.ubc.ca <mailto:mayor@mail.ubc.ca> > web : www.chibi.ubc.ca/faculty/mayor/labhome <http://www.chibi.ubc.ca/faculty/mayor/labhome> > > > > > www.hupo2015.com <http://www.hupo2015.com/> > > > > > > > > > >

1 0

[Compbio-allhands] Fwd: Merck Postdoctoral Research Fellow - Computational Chemistry POS000146
by Jacobson, Matt 03 Nov '14

03 Nov '14

Begin forwarded message: From: "Guo, Zhuyan" <zhuyan.guo(a)merck.com<mailto:zhuyan.guo@merck.com>> Subject: Merck Postdoctoral Research Fellow - Computational Chemistry POS000146 Date: November 3, 2014 8:34:46 AM PST To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Prof. Jacobson, By means of this email, I would like to reach out to you and your group about a postdoc opening in computational chemistry at Merck in New Jersey. The link below will lead directly to the job description on the Merck careers page. If you have students that are finishing up in the next 6 months or postdocs who might be interested in doing a postdoc in pharma for a couple years, please encourage them to apply. Link to the position: https://merck.taleo.net/careersection/merck_external_career_section/jobdeta… I also attached a pdf flyer for general information about the Merck postdoc program. I’ll be happy to answer any questions or provide additional information. So please do not hesitate to contact me. Best regards, Zhuyan Guo, Ph.D Department of Structural Chemistry Merck Research Laboratories Kenilworth, NJ 07033 Tel. 908-740-3796 Email: Zhuyan.Guo(a)merck.com<mailto:Zhuyan.Guo@merck.com> Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), 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. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Postdoctoral opportunities in theoretical biological physics at Princeton University
by Andrej Sali 29 Oct '14

29 Oct '14

> Begin forwarded message: > > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Cc: "Wingreen, Ned S." <wingreen(a)Princeton.EDU> > Subject: Postdoctoral opportunities in theoretical biological physics at Princeton University > Date: October 29, 2014 at 2:17:43 PM EDT > > Dear Colleague, > > We are following up to remind you of the existence at Princeton of several > openings for recent PhDs in theoretical physics who wish to pursue a > career in theoretical biological physics. As we hope you know, we have > been building a group in this area at Princeton over the last decade, and > we now have a robust activity that involves students, postdocs and faculty > from several departments. We are actively recruiting postdocs to join this > group, and we hope that you will urge any outstanding prospective or > recent PhD students of your acquaintance to apply to any of the following > positions for which they might be eligible (please note and do point out that > the mid-October application deadlines for all positions have been extended > to November 15!). > > 1. Postdoctoral Associate in our group. This is a regular Physics > postdoctoral position, but one in which the incumbent has great freedom to > choose projects, and can benefit from the mentorship of any of the senior > members of our group (or linear combinations thereof). Past holders of > this position have had a remarkable record of success in landing > next-level positions in the field of biophysics. Please direct your > students to the following link for more information: > https://www.princeton.edu/physics/about/employment/biophysics/index.xml <https://www.princeton.edu/physics/about/employment/biophysics/index.xml> > > 2. Postdoctoral Fellow of the Princeton Center for Theoretical Science > (PCTS). The PCTS sponsors interdisciplinary research based in theoretical > physics and the PCTS Faculty Fellows select three new Fellows each year > from a pool of candidates in all fields of theory. The PCTS provides a > unique environment for exceptional recent PhDs in theoretical physics, > broadly construed, to broaden their horizons and explore new fields. > Candidates must be nominated by senior scientists. Nominations of > biological physicists are encouraged, and Fellows with such interests > would be welcomed as participants in our group. Appointments to this > position are at the level of Associate Research Scholar. Please consult > 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 (and other) departments, > offers five-year positions at the level of Associate Research Scholar that > carry extra resources and the opportunity to teach in innovative > undergraduate programs. These positions are appropriate for exceptional newly- > minted PhD’s who are ready to lead their own group. LSI Theory Fellows are > selected by the full LSI faculty, but typically work very closely with our > group. Application procedures will be described on the LSI website. Applicants > to (1) who wish to also be considered as Lewis-Sigler Theory Fellows should so > indicate in their cover letter. > > We emphasize that we are interested in applications from students > with exceptional theoretical skills and a strong motivation to use > these skills to pursue biological problems, independent of the depth of their > research experience in biology. Many of our most successful postdocs have > learned their biology "on the job", and we think that we provide an > outstanding environment for such learning. Your assistance in encouraging > strong candidates for any of these positions to apply would 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] Fwd: The Rockefeller University - Fellow Position
by Jacobson, Matt 24 Oct '14

24 Oct '14

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 24, 2014 10:54:48 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 2015. 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 Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] 10/30/14 Seminar with Markus Seeliger
by Flowers, Nicole 24 Oct '14

24 Oct '14

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 Markus Seeliger Stony Brook University Medical School A dynamically coupled allosteric network in the regulation of Src family kinases. October 30, 2014 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 Graduate Program Assistant AMBER Software Administrator 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: post-doc positions available at MD Anderson Cancer Center
by Andrej Sali 23 Oct '14

23 Oct '14

> Begin forwarded message: > > From: "Schlacher,Katharina" <KSchlacher(a)mdanderson.org> > To: "Schlacher,Katharina" <KSchlacher(a)mdanderson.org> > Cc: "Schlacher,Katharina" <KSchlacher(a)mdanderson.org> > Subject: post-doc positions available at MD Anderson Cancer Center > Date: October 23, 2014 at 9:35:55 AM PDT > > Hello! > > We have openings for great post-docs in our group- please see ad below. > > I would very much appreciate it if you could disperse the ad and send interested applicants my way. > > Many thanks! > > > Katharina Schlacher, Ph.D. > > Assistant Professor > > CPRIT Scholar in Cancer Biology > > Department of Cancer Biology > > MD Anderson Cancer Center > > > kschlacher(a)mdanderson.org > > > Office 713-563-2467 > > Lab > > 713-563-0697 > > Fax > > 713-792-8586 > > > 3SCR5.3626 > > 1881 East Road > > Houston TX 77054 > > > -- 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] 10/23/14 Seminar with Gail Fanucci
by Flowers, Nicole 17 Oct '14

17 Oct '14

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 Gail Fanucci University of Florida Mechanisms of Drug Resistance in HIV-1 Protease Explored by EPR and NMR Spectroscopies October 23, 2014 J. Gross, 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 Graduate Program Assistant AMBER Software Administrator 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] 10/16/14 Seminar with Lior Pachter
by Flowers, Nicole 10 Oct '14

10 Oct '14

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 Lior Pachter UC Berkeley Transcriptome genetics. October 16, 2014 D. Himmelstein, 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 Graduate Program Assistant AMBER Software Administrator 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: Faculty Opening in Computational Biochemistry at Michigan State University
by Andrej Sali 07 Oct '14

07 Oct '14

Sent from my iPhone Begin forwarded message: > From: Michael Feig <feig(a)msu.edu> > Date: October 7, 2014 at 10:40:47 PM GMT+1 > To: undisclosed-recipients:; > Subject: Faculty Opening in Computational Biochemistry at Michigan State University > Reply-To: feig(a)msu.edu > > Dear Colleagues, > > I would like to alert you to > > *Two Computational Searches at Michigan State University* > > one each in the departments of Biochemistry & Molecular Biology and Chemistry. Please see attached PDFs for more details. Both are targeted primarily at the junior level. > > Please forward to appropriate candidates > > > Best regards and my apologies if you would have rather not received this email. > > Michael. > > -- > Michael Feig > Professor > Department of Biochemistry & Molecular Biology > Department of Chemistry > Department of Computer Science & Engineering > Michigan State University > > feig(a)msu.edu > (517) 432-7439 > (517) 353-9334 Fax

1 0

[Compbio-allhands] Fwd: Postdoctoral fellow position available
by Andrej Sali 07 Oct '14

07 Oct '14

-- 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 Begin forwarded message: > From: "Steven S. Plotkin" <steve(a)phas.ubc.ca> > Subject: Postdoctoral fellow position available > Date: October 7, 2014 at 6:46:10 AM GMT+1 > To: undisclosed-recipients:; > > Dear Colleague, > > I have opened a search for a postdoctoral fellow in the general area of protein misfolding, with potential applications to ALS and neurodegenerative disease, but I'm worried that I'm not getting many applications from good biophysics/soft-matter people with computational or theoretical experience, and I would like to hire for this position soon. > > Please, if you know of any qualified and motivated grad students or young PDFs in your whereabouts looking for a post-doc position, do refer them to my website, http://www.phas.ubc.ca/~steve/ALS_Canada_PDFposition2014.html , where all the details for applying are given. > > Sincere thanks, > > Steve Plotkin > > -- > Steven S. Plotkin > Associate Professor of Physics > Genome Sciences and Technology Program > University of British Columbia > 6224 Agricultural Road > Vancouver, B.C. V6T 1Z1 > (604)822-8813 > http://www.physics.ubc.ca/~steve

1 0

[Compbio-allhands] 10/9/14 Seminar with Hashim Al-Hashimi
by Flowers, Nicole 03 Oct '14

03 Oct '14

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 Hashim Al-Hashimi Duke Role of Nucleic Acid Dynamics in the Central Dogma of Molecular Biology October 9, 2014 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 Graduate Program Assistant AMBER Software Administrator 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] Martin Karplus Celebration Symposium
by Andrej Sali 30 Sep '14

30 Sep '14

you may wish to attend a series of short talks on molecular simulations this afternoon, from noon to about 5pm, in Helen Diller Cancer Center, Room HD 160: http://martinkarplus.net/content/short-talks -- 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: faculty job opening at MCW
by Brian Shoichet 29 Sep '14

29 Sep '14

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy and OICR, UofT sent from my phone. Please excuse the grammar and spelling ---------- Forwarded message ---------- From: "Brian Volkman" <bvolkman(a)mcw.edu> Date: Sep 29, 2014 8:57 PM Subject: faculty job opening at MCW To: "Brian Shoichet" <bshoichet(a)gmail.com> Cc: Hi Brian, A new MCW faculty position was just posted: http://goo.gl/XrIXtv I am not on the search committee, but at least one of my biochemistry colleagues is. We would welcome applications from candidates with a computational-med chem background. Please share the link with anyone you know who might be interested. Best regards, Brian ___________________________________________________ Brian F. Volkman, PhD, Professor Department of Biochemistry Medical College of Wisconsin 8701 Watertown Plank Rd. Milwaukee, WI 53226 (414)-955-8400(office)/8615(lab)/7363(nmr)/6510(fax) bvolkman(a)gmail.com www.mcw.edu/biochemistry/faculty/Brian_Volkman.htm ___________________________________________________

1 0

[Compbio-allhands] 10/2/14 Seminar with Phil Geissler
by Flowers, Nicole 26 Sep '14

26 Sep '14

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 Phil Geissler UC Berkeley Quantifying the diversity of side-chain fluctuations in folded proteins October 2, 2014 K. Kundert, 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 Graduate Program Assistant AMBER Software Administrator 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: An awesome Data Science and Data Engineering Program
by Jacobson, Matt 25 Sep '14

25 Sep '14

Begin forwarded message: From: Monica Tremont <monica.tremont(a)gmail.com<mailto:monica.tremont@gmail.com>> Subject: An awesome Data Science and Data Engineering Program Date: September 25, 2014 11:22:32 AM PDT To: Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, "Brown, Rebecca" <rebecca.brown3(a)ucsf.edu<mailto:rebecca.brown3@ucsf.edu>> Hi Rebecca and Matt, I hope all is well at UCSF. I wanted to pass along information about the Insight Data Science and Data Engineering Fellows Programs in case you don't have it already. I finished the Data Science program a few months ago, and it was a hugely efficient way of getting into the field. Jerome Nilmeier (also from Matt's group) is currently a fellow in the Data Engineering program. Anyway, the applications are due soon, and I'd be happy to talk to Biophysics or BMI people about the program, the application process and/or working as a Data Scientist. :) Monica ===================== Insight Data Science and Engineering Fellows Programs http://insightdatascience.com http://insightdataengineering.com Applications due soon for January 2015 Silicon Valley and New York programs The demand for data scientists and engineers is increasing rapidly. Companies need to be able to process, query, and make sense of the large volumes of information that are generated each day. The Insight Data Science Fellows Program is a training fellowship for graduate students and postdocs designed to bridge the gap between academia and a career in data science. The Insight Data Engineering Fellows Program is a training fellowship for individuals with software engineering or strong coding backgrounds (no PhD required) who want to work with the latest big data infrastructure and pipeline technologies. Insight highlights: -- 6 week, full-time, data science and engineering training fellowships. -- Dedicated office space, self-directed, project-based learning under the guidance of top industry data professionals. -- Over 100 Insight Fellow alumni are now working at companies like Facebook, Apple, Microsoft, Yelp, Square, AT&T, Twitter, LinkedIn, Airbnb, Palantir, Intuit, Netflix and many startups. -- Interview at top companies in Silicon Valley or New York City immediately following the program. The January 2015 session application deadlines are: October 12 for Data Science - apply at http://insightdatascience.com October 27 for Data Engineering - apply at http://insightdataengineering.com ===================== Please feel free to forward this to any appropriate mailing lists or to anyone who might be a good candidate for the Insight Fellows Program. Questions about the program or application should be directed to info(a)insightdatascience.com or info(a)insightdataengineering.com. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Mobley lab seeking postdoctoral candidates
by Jacobson, Matt 24 Sep '14

24 Sep '14

Begin forwarded message: From: David Mobley <dmobley(a)uci.edu<mailto:dmobley@uci.edu>> Subject: Mobley lab seeking postdoctoral candidates Date: September 24, 2014 3:45:54 PM PDT To: David Mobley <dmobley(a)mobleylab.org<mailto:dmobley@mobleylab.org>> Bcc: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Colleague, I need your help identifying potential candidates for a postdoctoral research position in my group in the Departments of Pharmaceutical Sciences and Chemistry at the University of California, Irvine. If you have suitable candidates with experience in molecular simulations and/or molecular modeling who might be interested, please pass on the below information. Thanks so much for your valuable time. Advertisement: I seek a postdoctoral candidate with experience in molecular simulations or molecular modeling to work on an exciting research project at the interface of molecular modeling and drug discovery. The research will focus on applying molecular modeling techniques - including free energy techniques developed in the lab and elsewhere - to applications in ongoing drug discovery efforts with experimental collaborators. Some of the work may have a methodological focus as well (as has much of our previous work in this area), but this particular position will have a heavy emphasis on applications to pharmaceutically relevant targets. An ideal candidate would have substantial background in molecular modeling, ideally including molecular dynamics simulations and/or Monte Carlo, as well as experience with library search techniques such as docking and potentially informatics-based methods. Experience with free energy techniques is also a plus. Interested applicants should send a cover letter plus a CV to dmobley(a)uci.edu<mailto:dmobley@uci.edu>. Additionally, please have at least three letters of reference sent to the same address as well. All application materials should be received by Oct. 24, 2014. Prospective applicants are welcome to contact me for more information. The exact start date is negotiable, and the position is available immediately. UC Irvine provides exciting opportunities for work in this area. We have a variety of computational groups in several different departments with whom we interact frequently, and groups doing outstanding experimental work in the area as well. Indeed, this project will involve collaborations with at least two different experimental groups at UCI. The area is also renowned for its excellent weather, quality of life, and safety, and, together with the nearby San Diego area, also is home to a fairly wide range of pharmaceutical industry employers. Thank you so much. -- 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 http://www.mobleylab.org<http://www.mobleylab.org/> Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: On Behalf of Taekjip Ha and Klaus Schulten - PLEASE POST AND CIRCULATE
by Andrej Sali 23 Sep '14

23 Sep '14

-- 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 Begin forwarded message: > From: Taekjip Ha <TaekjipHa(a)mx.uillinois.edu> > Subject: On Behalf of Taekjip Ha and Klaus Schulten - PLEASE POST AND CIRCULATE > Date: September 23, 2014 at 8:00:08 AM PDT > > 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" (CPLC), a National Science Foundation Physics Frontier Center at the University of Illinois, Urbana-Champaign. Fellowships are available starting May 2015, 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=840, and should arrive no later thanDecember 1, 2014. 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 . > > Thank you. > > Taekjip Ha and Klaus Schulten > Co-directors, Center for the Physics of Living Cells > director(a)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: Offer of a FPI for the Structural Genomics Group at CNAG and CRG
by Andrej Sali 16 Sep '14

16 Sep '14

Begin forwarded message: > From: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Subject: Offer of a FPI for the Structural Genomics Group at CNAG and CRG > Date: September 16, 2014 at 8:50:16 AM PDT > To: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > > Dear friends and colleagues, > > Could you please forward the add to whom you may believe could be interested in a PhD position in our group (http://marciuslab.org) in Barcelona. The position is a fellowship associated to our project "Determining the three-dimensional structure of genomes and genomic domains" and is open to students with a Master degree. > > The deadline for submitting a CV and a letter of interest is the next 21st of September and should be addressed to my e-mail: mmarti(a)pcb.ub.cat > > Many thanks in advance, > Marc > ... > Marc A. Marti-Renom, ICREA Research Professor > Genome Biology Group Leader - CNAG - Centre Nacional d’Anàlisi Genòmica > Structural Genomics Group Leader - CRG - Centre de Regulació Genòmica > Parc Científic de Barcelona – Torre I > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email mmarti(a)pcb.ub.cat > Web http://marciuslab.org - http://cnag.cat - http://crg.cat > > *** Consider the environment. Print responsibly. *** > > > >

1 0

[Compbio-allhands] Fwd: Faculty position
by Jacobson, Matt 13 Sep '14

13 Sep '14

-- Matt Sent from my iPhone Begin forwarded message: From: "Wei, Guowei" <wei(a)math.msu.edu<mailto:wei@math.msu.edu>> Date: September 12, 2014 at 6:37:20 PM PDT Cc: "ealexov(a)clemson.edu<mailto:ealexov@clemson.edu>" <ealexov(a)clemson.edu<mailto:ealexov@clemson.edu>>, "shs3(a)illinois.edu<mailto:shs3@illinois.edu>" <shs3(a)illinois.edu<mailto:shs3@illinois.edu>>, "warshel(a)usc.edu<mailto:warshel@usc.edu>" <warshel(a)usc.edu<mailto:warshel@usc.edu>>, "alexey(a)cs.vt.edu<mailto:alexey@cs.vt.edu>" <alexey(a)cs.vt.edu<mailto:alexey@cs.vt.edu>>, "s4zhou(a)ucsd.edu<mailto:s4zhou@ucsd.edu>" <s4zhou(a)ucsd.edu<mailto:s4zhou@ucsd.edu>>, "koehl(a)cs.ucdavis.edu<mailto:koehl@cs.ucdavis.edu>" <koehl(a)cs.ucdavis.edu<mailto:koehl@cs.ucdavis.edu>>, "pcb5(a)psu.edu<mailto:pcb5@psu.edu>" <pcb5(a)psu.edu<mailto:pcb5@psu.edu>>, "anna.pyle(a)yale.edu<mailto:anna.pyle@yale.edu>" <anna.pyle(a)yale.edu<mailto:anna.pyle@yale.edu>>, "yzhou(a)math.colostate.edu<mailto:yzhou@math.colostate.edu>" <yzhou(a)math.colostate.edu<mailto:yzhou@math.colostate.edu>>, "stephen.white(a)uci.edu<mailto:stephen.white@uci.edu>" <stephen.white(a)uci.edu<mailto:stephen.white@uci.edu>>, "nussinor(a)helix.nih.gov<mailto:nussinor@helix.nih.gov>" <nussinor(a)helix.nih.gov<mailto:nussinor@helix.nih.gov>>, "mamachuqueiro(a)fc.ul.pt<mailto:mamachuqueiro@fc.ul.pt>" <mamachuqueiro(a)fc.ul.pt<mailto:mamachuqueiro@fc.ul.pt>>, "hdn(a)uci.edu<mailto:hdn@uci.edu>" <hdn(a)uci.edu<mailto:hdn@uci.edu>>, "Nathan.Baker(a)pnnl.gov<mailto:Nathan.Baker@pnnl.gov>" <Nathan.Baker(a)pnnl.gov<mailto:Nathan.Baker@pnnl.gov>>, "Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, "jdmadura(a)me.com<mailto:jdmadura@me.com>" <jdmadura(a)me.com<mailto:jdmadura@me.com>>, "sboxer(a)stanford.edu<mailto:sboxer@stanford.edu>" <sboxer(a)stanford.edu<mailto:sboxer@stanford.edu>>, "lwebb(a)cm.utexas.edu<mailto:lwebb@cm.utexas.edu>" <lwebb(a)cm.utexas.edu<mailto:lwebb@cm.utexas.edu>>, "kubarych(a)umich.edu<mailto:kubarych@umich.edu>" <kubarych(a)umich.edu<mailto:kubarych@umich.edu>>, "shs(a)chem.psu.edu<mailto:shs@chem.psu.edu>" <shs(a)chem.psu.edu<mailto:shs@chem.psu.edu>>, "lli5(a)clemson.edu<mailto:lli5@clemson.edu>" <lli5(a)clemson.edu<mailto:lli5@clemson.edu>>, "brookscl(a)umich.edu<mailto:brookscl@umich.edu>" <brookscl(a)umich.edu<mailto:brookscl@umich.edu>>, "zgw(a)caltech.edu<mailto:zgw@caltech.edu>" <zgw(a)caltech.edu<mailto:zgw@caltech.edu>>, "john.zhang(a)nyu.edu<mailto:john.zhang@nyu.edu>" <john.zhang(a)nyu.edu<mailto:john.zhang@nyu.edu>>, "jwu(a)engr.ucr.edu<mailto:jwu@engr.ucr.edu>" <jwu(a)engr.ucr.edu<mailto:jwu@engr.ucr.edu>>, "dominy(a)clemson.edu<mailto:dominy@clemson.edu>" <dominy(a)clemson.edu<mailto:dominy@clemson.edu>>, "hzhou4(a)fsu.edu<mailto:hzhou4@fsu.edu>" <hzhou4(a)fsu.edu<mailto:hzhou4@fsu.edu>>, "gunner(a)sci.ccny.cuny.edu<mailto:gunner@sci.ccny.cuny.edu>" <gunner(a)sci.ccny.cuny.edu<mailto:gunner@sci.ccny.cuny.edu>>, "mfenley(a)fsu.edu<mailto:mfenley@fsu.edu>" <mfenley(a)fsu.edu<mailto:mfenley@fsu.edu>>, "wcai(a)uncc.edu<mailto:wcai@uncc.edu>" <wcai(a)uncc.edu<mailto:wcai@uncc.edu>>, "czhan6(a)email.uky.edu<mailto:czhan6@email.uky.edu>" <czhan6(a)email.uky.edu<mailto:czhan6@email.uky.edu>>, "fgibou(a)engineering.ucsb.edu<mailto:fgibou@engineering.ucsb.edu>" <fgibou(a)engineering.ucsb.edu<mailto:fgibou@engineering.ucsb.edu>>, "asdis(a)engineering.ucsb.edu<mailto:asdis@engineering.ucsb.edu>" <asdis(a)engineering.ucsb.edu<mailto:asdis@engineering.ucsb.edu>>, "maxime.theillard(a)gmail.com<mailto:maxime.theillard@gmail.com>" <maxime.theillard(a)gmail.com<mailto:maxime.theillard@gmail.com>>, "m.mirzadeh(a)engineering.ucsb.edu<mailto:m.mirzadeh@engineering.ucsb.edu>" <m.mirzadeh(a)engineering.ucsb.edu<mailto:m.mirzadeh@engineering.ucsb.edu>>, "davidboy(a)engineering.ucsb.edu<mailto:davidboy@engineering.ucsb.edu>" <davidboy(a)engineering.ucsb.edu<mailto:davidboy@engineering.ucsb.edu>>, "j.warwicker(a)manchester.ac.uk<mailto:j.warwicker@manchester.ac.uk>" <j.warwicker(a)manchester.ac.uk<mailto:j.warwicker@manchester.ac.uk>>, "ramaro(a)uci.edu<mailto:ramaro@uci.edu>" <ramaro(a)uci.edu<mailto:ramaro@uci.edu>>, "irm2223(a)gmail.com<mailto:irm2223@gmail.com>" <irm2223(a)gmail.com<mailto:irm2223@gmail.com>>, "huang(a)amath.unc.edu<mailto:huang@amath.unc.edu>" <huang(a)amath.unc.edu<mailto:huang@amath.unc.edu>>, "mdate(a)clemson.edu<mailto:mdate@clemson.edu>" <mdate(a)clemson.edu<mailto:mdate@clemson.edu>>, "djacobs1(a)uncc.edu<mailto:djacobs1@uncc.edu>" <djacobs1(a)uncc.edu<mailto:djacobs1@uncc.edu>>, "xsong(a)iastate.edu<mailto:xsong@iastate.edu>" <xsong(a)iastate.edu<mailto:xsong@iastate.edu>>, "abrice(a)clemson.edu<mailto:abrice@clemson.edu>" <abrice(a)clemson.edu<mailto:abrice@clemson.edu>>, "wonglynn2004(a)gmail.com<mailto:wonglynn2004@gmail.com>" <wonglynn2004(a)gmail.com<mailto:wonglynn2004@gmail.com>>, "zz(a)clemson.edu<mailto:zz@clemson.edu>" <zz(a)clemson.edu<mailto:zz@clemson.edu>>, "switham(a)clemson.edu<mailto:switham@clemson.edu>" <switham(a)clemson.edu<mailto:switham@clemson.edu>>, "subhras(a)g.clemson.edu<mailto:subhras@g.clemson.edu>" <subhras(a)g.clemson.edu<mailto:subhras@g.clemson.edu>>, "mzhenir(a)clemson.edu<mailto:mzhenir@clemson.edu>" <mzhenir(a)clemson.edu<mailto:mzhenir@clemson.edu>>, "fhernand(a)accelrys.com<mailto:fhernand@accelrys.com>" <fhernand(a)accelrys.com<mailto:fhernand@accelrys.com>>, "VSpassov(a)accelrys.com<mailto:VSpassov@accelrys.com>" <VSpassov(a)accelrys.com<mailto:VSpassov@accelrys.com>>, "heinemann(a)mdc-berlin.de<mailto:heinemann@mdc-berlin.de>" <heinemann(a)mdc-berlin.de<mailto:heinemann@mdc-berlin.de>>, "nina(a)uaem.mx<mailto:nina@uaem.mx>" <nina(a)uaem.mx<mailto:nina@uaem.mx>>, "dubin(a)chem.umass.edu<mailto:dubin@chem.umass.edu>" <dubin(a)chem.umass.edu<mailto:dubin@chem.umass.edu>>, "ts1(a)haifa.biomath.nyu.edu<mailto:ts1@haifa.biomath.nyu.edu>" <ts1(a)haifa.biomath.nyu.edu<mailto:ts1@haifa.biomath.nyu.edu>>, "newton(a)bnl.gov<mailto:newton@bnl.gov>" <newton(a)bnl.gov<mailto:newton@bnl.gov>>, "judit.fidy(a)eok.sote.hu<mailto:judit.fidy@eok.sote.hu>" <judit.fidy(a)eok.sote.hu<mailto:judit.fidy@eok.sote.hu>>, "sas8(a)columbia.edu<mailto:sas8@columbia.edu>" <sas8(a)columbia.edu<mailto:sas8@columbia.edu>>, "ioerger(a)cs.tamu.edu<mailto:ioerger@cs.tamu.edu>" <ioerger(a)cs.tamu.edu<mailto:ioerger@cs.tamu.edu>>, "gruschus(a)helix.nih.gov<mailto:gruschus@helix.nih.gov>" <gruschus(a)helix.nih.gov<mailto:gruschus@helix.nih.gov>>, "okimoto(a)gsc.riken.jp<mailto:okimoto@gsc.riken.jp>" <okimoto(a)gsc.riken.jp<mailto:okimoto@gsc.riken.jp>>, "pbalbo(a)gate.sinica.edu.tw<mailto:pbalbo@gate.sinica.edu.tw>" <pbalbo(a)gate.sinica.edu.tw<mailto:pbalbo@gate.sinica.edu.tw>>, "vadim.arshavsky(a)duke.edu<mailto:vadim.arshavsky@duke.edu>" <vadim.arshavsky(a)duke.edu<mailto:vadim.arshavsky@duke.edu>>, "lzhou(a)vcu.edu<mailto:lzhou@vcu.edu>" <lzhou(a)vcu.edu<mailto:lzhou@vcu.edu>>, "aqvist(a)xray.bmc.uu.se<mailto:aqvist@xray.bmc.uu.se>" <aqvist(a)xray.bmc.uu.se<mailto:aqvist@xray.bmc.uu.se>>, "amorreale(a)cbm.uam.es<mailto:amorreale@cbm.uam.es>" <amorreale(a)cbm.uam.es<mailto:amorreale@cbm.uam.es>>, "sndatta(a)chem.iitb.ac.in<mailto:sndatta@chem.iitb.ac.in>" <sndatta(a)chem.iitb.ac.in<mailto:sndatta@chem.iitb.ac.in>>, "karchin(a)jhu.edu<mailto:karchin@jhu.edu>" <karchin(a)jhu.edu<mailto:karchin@jhu.edu>>, "eed5(a)cdc.gov<mailto:eed5@cdc.gov>" <eed5(a)cdc.gov<mailto:eed5@cdc.gov>>, "tidor(a)mit.edu<mailto:tidor@mit.edu>" <tidor(a)mit.edu<mailto:tidor@mit.edu>>, "cmstultz(a)csail.mit.edu<mailto:cmstultz@csail.mit.edu>" <cmstultz(a)csail.mit.edu<mailto:cmstultz@csail.mit.edu>>, "mjramos(a)fc.up.pt<mailto:mjramos@fc.up.pt>" <mjramos(a)fc.up.pt<mailto:mjramos@fc.up.pt>>, "chandra(a)bii.a-star.edu.sg<mailto:chandra@bii.a-star.edu.sg>" <chandra(a)bii.a-star.edu.sg<mailto:chandra@bii.a-star.edu.sg>>, "rainer(a)bioinformatik.uni-saarland.de<mailto:rainer@bioinformatik.uni-saarland.de>" <rainer(a)bioinformatik.uni-saarland.de<mailto:rainer@bioinformatik.uni-saarland.de>>, "neshich(a)cbi.cnptia.embrapa.br<mailto:neshich@cbi.cnptia.embrapa.br>" <neshich(a)cbi.cnptia.embrapa.br<mailto:neshich@cbi.cnptia.embrapa.br>>, "the-cherry(a)gsu.edu<mailto:the-cherry@gsu.edu>" <the-cherry(a)gsu.edu<mailto:the-cherry@gsu.edu>>, "gautamda(a)gmail.com<mailto:gautamda@gmail.com>" <gautamda(a)gmail.com<mailto:gautamda@gmail.com>>, "mkubasik(a)mail.fairfield.edu<mailto:mkubasik@mail.fairfield.edu>" <mkubasik(a)mail.fairfield.edu<mailto:mkubasik@mail.fairfield.edu>>, "rku(a)ansto.gov.au<mailto:rku@ansto.gov.au>" <rku(a)ansto.gov.au<mailto:rku@ansto.gov.au>>, "vinay(a)barc.gov.in<mailto:vinay@barc.gov.in>" <vinay(a)barc.gov.in<mailto:vinay@barc.gov.in>>, "mickey.kosloff(a)duke.edu<mailto:mickey.kosloff@duke.edu>" <mickey.kosloff(a)duke.edu<mailto:mickey.kosloff@duke.edu>> Subject: Faculty position Dear Colleagues, Please circulate the enclosed Ad about a faculty position in Theoretical and Computational Chemistry at Michigan State University. Best --------------------------------------------------------------------- Guowei Wei Professor Michigan State University ---------------------------------------------------------------

1 0

[Compbio-allhands] [Fwd: Re: Bioinformatics job openings at Berkeley Lab / NERSC / JGI]
by Patsy Babbitt 28 Aug '14

28 Aug '14

-- 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 94158-2330, USA (CA 94158 for direct delivery by courier) Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Joslyn Polzien, +1 415-514-1214, 415-514-4861 Joslyn.Polzien(a)ucsf.edu

1 0

[Compbio-allhands] Fwd: postdoc positions
by Jacobson, Matt 21 Aug '14

21 Aug '14

Begin forwarded message: From: "Bowman, Greg" <bowman(a)biochem.wustl.edu<mailto:bowman@biochem.wustl.edu>> Subject: postdoc positions Date: August 21, 2014 11:25:53 AM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Dear Matt, Would you mind sharing this brief ad with anyone in your group who might be looking for a postdoctoral position in computational biophysics? I’m currently looking for postdocs who share my passion for understanding the physical mechanisms of protein conformational changes, their role in signaling, and how they are modulated by drugs and mutations. We are currently working to understand and combat the evolution of antibiotic resistance, to understand the phototransduction signaling cascade and the effects of mutations associated with blinding diseases, and to develop new methods for extending the timescales accessible to molecular simulation. Connecting with experiment is a high priority, so much so that we’ll be conducting our own biophysical experiments to test predictions. There is certainly no requirement that everyone do experiments though. We’re located at the medical school at Washington University in St Louis. For those who think this if fly-over territory, I highly recommend you take another look. Forest Park offers amazing science, art, and history museums as well as a zoo and concerts (all of which are free!). We also have an outstanding food scene and the cost of living is a welcome change from other metropolitan areas. Interested candidates should contact me via email at bowman(a)biochem.wustl.edu<mailto:bowman@biochem.wustl.edu> and include their CV and a brief (one page or less) description of a project they might like to pursue in my lab. This research description is meant to give me a sense of your interests and the way you think, it is not a binding commitment to a specific project. Thanks for your time. Greg — Gregory R. Bowman Assistant Professor Department of Biochemistry & Molecular Biophysics Washington University School of Medicine St Louis, Missouri bowman(a)biochem.wustl.edu<mailto:bowman@biochem.wustl.edu> Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Rudolf Mößbauer Tenure Track Assistant Professorships in computational structural biology at TUM
by Andrej Sali 20 Aug '14

20 Aug '14

-- 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 Begin forwarded message: > From: Michael Sattler <michael.sattler(a)tum.de> > Subject: Rudolf Mößbauer Tenure Track Assistant Professorships in computational structural biology at TUM > Date: August 20, 2014 at 2:28:06 PM PDT > To: Michael Nilges <nilges(a)pasteur.fr>, Stephan Grzesiek <stephan.grzesiek(a)unibas.ch>, Bert de Groot <bgroot(a)gwdg.de>, Peter Guentert <guentert(a)em.uni-frankfurt.de>, Martin Blackledge <martin.blackledge(a)ibs.fr>, Bernhard Brutscher <bernhard.brutscher(a)ibs.fr>, Michele Vendruscolo <mv245(a)cam.ac.uk>, "Alexandre M.J.J. Bonvin" <a.m.j.j.bonvin(a)uu.nl>, Wim Vranken <wvranken(a)vub.ac.be>, Elena Conti <conti(a)biochem.mpg.de>, Hartmut Oschkinat <oschkinat(a)fmp-berlin.de>, Wolfgang Baumeister <baumeist(a)biochem.mpg.de>, Harald Schwalbe <schwalbe(a)nmr.uni-frankfurt.de>, Dieter Willbold <d.willbold(a)fz-juelich.de>, Paul Roesch <roesch(a)unibt.de>, Hans-Robert Kalbitzer <hans-robert.kalbitzer(a)biologie.uni-regensburg.de>, Vladimir Sklenar <vladimir.sklenar(a)ceitec.muni.cz>, Frédéric Allain <allain(a)mol.biol.ethz.ch>, Gerhard Wagner <gerhard_wagner(a)hms.harvard.edu>, Ad Bax <bax(a)nih.gov>, Hashim Al-Hashimi <hashimi(a)umich.edu>, Kevin Gardner <Kevin.Gardner(a)utsouthwestern.edu>, "Dinshaw J. Patel" <pateld(a)MSKCC.ORG>, Christian Griesinger <cigr(a)nmr.mpibpc.mpg.de>, Herbert Grubmueller <hgrubmu(a)gwdg.de>, Angela Gronenborn <amg100(a)pitt.edu>, Jens Meiler <jens.meiler(a)vanderbilt.edu>, Andre Sali <sali(a)salilab.org>, David Baker <dabaker(a)u.washington.edu>, David Neuhaus <dn(a)mrc-lmb.cam.ac.uk>, "Vuister, Geerten (Prof.)" <gv29(a)leicester.ac.uk>, Tanja Kortemme <kortemme(a)cgl.ucsf.edu>, Martin Billeter <martin.billeter(a)chem.gu.se>, Xavier Salvatella <xavier.salvatella(a)irbbarcelona.org>, Arthur Palmer <agp6(a)columbia.edu>, Miquel Pons <mpons(a)ub.edu>, Lewis Kay <kay(a)pound.med.utoronto.ca>, Juergen Schleucher <jurgen.schleucher(a)chem.umu.se>, Lucia Banci <banci(a)cerm.unifi.it>, Claudio Luchinat <luchinat(a)cerm.unifi.it> > Cc: Bernd Reif <reif(a)tum.de>, "Prof. Dr. Horst Kessler" <horst.kessler(a)ch.tum.de>, Steffen Glaser <glaser(a)ch.tum.de> > > Dear colleagues > > Please find below an announcement for a tenure-track assistant professorship at TUM. > We would be grateful if you could forward this to suitable potential candidates. > > Thanks, Michael > > --------------------------------------------------------------------------------------------------------------------- > The Technische Universität München (TUM) - Institute for Advanced Studie (IAS) and the Bavarian NMR Centre (http://www.bnmrz.org) is inviting applications for a > > Tenure-track assistant professor (ttW2) > Computational Methods in Integrated Structural Biology > > as Rudolf Mößbauer Tenure Track Assistant Professorships at the TUM Institute for Advanced Study (TUM-IAS). This is under the call topic "Computational Methods for Complex Systems",with application deadline: Sep 22, 2014. > The prospective candidate should have an excellent scientific track record and develop a strong independent research program, complementary to existing activities in the TUM Department of Chemistry and the Bavarian NMR Center. He/she is expected to show interest in local collaborations and commitment to teaching in the TUM Department of Chemistry. > > The research profile should include the development and application of computational methods to combine data from complementary structural biology techniques. I.e. data from solution and solid state NMR, crystallography, SAXS/SANS, EM etc. are combined in integrated structural biology of complex biological macromolecules (i.e. large and dynamic protein complexes and assemblies). > The TUM Department of Chemistry (http://www.ch.tum.de) and the Bavarian NMR Centre (http://www.bnmrz.org) provide an excellent and very well equipped research environment. This includes the installation of a 1.2 GHz NMR Spectrometer at BNMRZ in the near future and access to crystallography, electron microscopy, in-house SAXS, on-site SANS and biophysical techniques. Excellent access to high-performance computing is available at the Leibniz Rechenzentrum on campus. > > Research groups at TUM and in the Munich area provide a unique, collaborative environment where complementary methods and expertise are combined to tackle important and challenging biomolecular systems. The CiPSM Cluster of Excellence and various local network grants SFBs (i.e. SFB1035) and graduate programs provide ample opportunities for support and scientific interactions. > > Candidates must fulfill the mobility requirement for the Marie Curie COFUND program of the EU, i.e., have no more than 12 months residence and/or employment in Germany in the last three years. > Further information is available at http://www.tum-ias.de > > We would be grateful if you could forward this message to potential candidates and colleagues and/or suggest them to us so we can directly contact them. > For inquiries please contact michael.sattler(a)tum.de. > > --------------------------------------------------------------------------------------------------------------------- > > > For the third time, the TUM Institute for Advanced Study (TUM-IAS) invites applications for the prestigious Rudolf Mößbauer Tenure Track Assistant Professorship. > > Within the comprehensive TUM Faculty Tenure Track system, TUM-IAS has hereby created a fellowship offering merit-based academic career options from the appointment as Assistant Professor through a permanent position as Associate Professor and on to Full Professor. > > Rudolf Mößbauer Tenure Track Assistant Professorships are intended for outstanding, high-potential early-career scientists who have already achieved a major scientific or technological breakthrough and who have the ambition of developing a new field of endeavor when joining TUM as a Tenure Track Assistant Professor. > > Applications are invited in the following areas of the TUM research portfolio: > > · Integrated Building Technologies > · Mobility – Sustainable Strategies in Society and Economy > · Data Science and Big Data Mining > · Human Centric Engineering > · Advanced Materials Technology: Polymers and Fibers > · Advanced Materials Technology: Light Metal Engineering > · Cellular Imaging and Quantitative Biology > · Experimental Genomics > · Computational Methods for Complex Systems > > Further information is available here. Applications are to be submitted online by Monday, September 22, 2014 (11:59 a.m. CET). > > Please feel free to forward this announcement to anybody who might be interested in applying, or to publish this announcement in relevant journals or platforms of your research field. > > We are looking forward to receiving excellent applications from all over the world! > > Yours sincerely, > > the TUM-IAS team > > Institute for Advanced Study > Technische Universität München > Lichtenbergstraße 2 a | D-85748 Garching, Germany > > info(a)tum-ias.de > Tel +49 89 | 289 10550 > Fax +49 89 | 289 10699 > > >

1 0

[Compbio-allhands] Fwd: Postdoctoral opportunities in theoretical biological physics at Princeton University
by Andrej Sali 20 Aug '14

20 Aug '14

Sent from my iPhone Begin forwarded message: > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Date: August 20, 2014 at 1:22:37 PM PDT > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Subject: Postdoctoral opportunities in theoretical biological physics at Princeton University > > Dear Colleague, > > We want to bring to your attention the existence at Princeton of several > openings for recent PhDs in theoretical physics who wish to pursue a > career in theoretical biological physics. As we hope you know, we have > been building a group in this area at Princeton over the last decade, and > we now have a robust activity that involves students, postdocs and faculty > from several departments. We are actively recruiting postdocs to join this > group, and we hope that you will urge any outstanding prospective or > recent PhD students of your acquaintance to apply to any of the following > positions for which they might be eligible (do point out that there are mid- > October application deadlines for all of them!). > > 1. Postdoctoral Associate in our group. This is a regular Physics > postdoctoral position, but one in which the incumbent has great freedom to > choose projects, and can benefit from the mentorship of any of the senior > members of our group (or linear combinations thereof). Past holders of > this position have had a remarkable record of success in landing > next-level positions in the field of biophysics. Please direct your > students to the following link for more information: > https://www.princeton.edu/physics/about/employment/biophysics/index.xml > > 2. Postdoctoral Fellow of the Princeton Center for Theoretical Science > (PCTS). The PCTS sponsors interdisciplinary research based in theoretical > physics and the PCTS Faculty Fellows select three new Fellows each year > from a pool of candidates in all fields of theory. The PCTS provides a > unique environment for exceptional recent PhDs in theoretical physics, > broadly construed, to broaden their horizons and explore new fields. > Candidates must be nominated by senior scientists. Nominations of > biological physicists are encouraged, and Fellows with such interests > would be welcomed as participants in our group. Appointments to this > position are at the level of Associate Research Scholar. Please consult > 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 (and other) departments, > offers five-year positions at the level of Associate Research Scholar that > carry extra resources and the opportunity to teach in innovative > undergraduate programs. These positions are appropriate for exceptional newly- > minted PhD’s who are ready to lead their own group. LSI Theory Fellows are > selected by the full LSI faculty, but typically work very closely with our > group. Application procedures will be described on the LSI website. Applicants > to (1) who wish to also be considered as Lewis-Sigler Theory Fellows should so > indicate in their cover letter. > > We emphasize that we are interested in applications from students > with exceptional theoretical skills and a strong motivation to use > these skills to pursue biological problems, independent of the depth of their > research experience in biology. Many of our most successful postdocs have > learned their biology "on the job", and we think that we provide an > outstanding environment for such learning. Your assistance in encouraging > strong candidates for any of these positions to apply would 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] Fwd: Principal Investigator positions
by Brian Shoichet 20 Aug '14

20 Aug '14

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy and OICR, UofT sent from my phone. Please excuse the grammar and spelling ---------- Forwarded message ---------- From: "Giulio Superti-Furga" <GSuperti(a)cemm.oeaw.ac.at> Date: Aug 20, 2014 5:36 AM Subject: Principal Investigator positions To: "Giulio Superti-Furga" <GSuperti(a)cemm.oeaw.ac.at> Cc: Dear Friends CeMM is developing into a really great place for anybody interested in trying to push the boundary between genome-informed biology and medicine. CeMM researchers form a highly dynamic and friendly group, with a familial, super-cooperative mind-set and an already established interface with productive clinicians. It is a great place both to start a group as well as to continue an already established effort. CeMM is looking for PI positions both at starting and level and at consolidation stage. Please find enclosed the advert. Bring this to the attention of anybody who could be interested. It is a unique opportunity Thanks a lot and kind regards Giulio *_________________**_**_______________* *Prof. Dr. Giulio Superti-Furga *Scientific Director *_________________________________* *CeMM* Research Center for Molecular Medicine of the Austrian Academy of Sciences Lazarettgasse 14, AKH BT 25.3 1090 Vienna, Austria Phone +43-1/40160-70 001 Fax +43-1/40160-970 000 Assistant: Dr. Marc Brehme Phone +43 1/40160-70 085 mbrehme(a)cemm.oeaw.ac.at gsuperti(a)cemm.oeaw.ac.at www.cemm.at *_________________________________*

1 0

[Compbio-allhands] Fwd: Postdoc Positions
by Andrej Sali 18 Aug '14

18 Aug '14

-- 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 Begin forwarded message: > From: "Gregory A. Voth" <gavoth(a)uchicago.edu> > Subject: Postdoc Positions > Date: August 18, 2014 at 12:43:48 PM PDT > To: "Voth-Group-Mailing(a)vothgroup.uchicago.edu" <Voth-Group-Mailing(a)vothgroup.uchicago.edu> > Reply-To: gavoth(a)uchicago.edu > > > Dear Colleague, > > There is the possibility of one or more postdoc position in my group, subject to the qualifications and experience of the applicant as well as > the final availability of funding. For information on my group and our research interests please see my group web page listed below. Interested parties should contact me by email. > > Best wishes, > Greg Voth > > PS-I apologize if you get this email more than once > > __________________________________________________________________ > > Gregory A. Voth, Ph.D. > Haig P. Papazian Distinguished Service Professor > Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, > and Computation Institute > Ulam Scholar (2014), Center for Nonlinear Studies, Los Alamos National Laboratory > Senior Scientist, Argonne National Laboratory > > Department of Chemistry > The University of Chicago > 5735 S. Ellis Avenue > Chicago, Illinois 60637 > Phone: 773-702-9092 > Fax: 773-795-9106 > Administrative Assistant: 773-702-9096 > Email: gavoth(a)uchicago.edu > Group Web Site: vothgroup.uchicago.edu > Office: 231 Searle > Admin Office: 233 Searle > ___________________________________________________________________ > > > _______________________________________________ > Voth-group-mailing mailing list > Voth-group-mailing(a)vothgroup.uchicago.edu > https://vothgroup.uchicago.edu/cgi-bin/mailman/listinfo/voth-group-mailing

1 0

[Compbio-allhands] Fwd: PCTS Call for Nominations for Postdoctoral Fellowships is now open- Deadline is Oct. 15
by Andrej Sali 15 Aug '14

15 Aug '14

-- 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 Begin forwarded message: > From: Charlene Borsack <cborsack(a)PRINCETON.EDU> > Subject: PCTS Call for Nominations for Postdoctoral Fellowships is now open- Deadline is Oct. 15 > Date: August 15, 2014 at 7:41:13 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 nominee is October 15, 2014 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 > > and submit the candidate’s name, email address, and a nomination letter. The nominees will then be sent information necessary to complete their application and to submit letters for reference. > > The PCTS Faculty Fellows begin evaluation and invitation to interview on October 15, 2014. (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 > Igor Klebanov, Associate Director klebanov(a)princeton.edu > > Princeton University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, 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: postdoc position
by Jiashun Zheng 14 Aug '14

14 Aug '14

---------- Forwarded message ---------- From: Yang, Qiong <qiongy(a)umich.edu> Date: Thu, Aug 14, 2014 at 11:45 AM Subject: postdoc position To: Jiashun ZHENG <jiashun.zheng(a)gmail.com> Hi Jiashun, It was nice to meet you at the synthetic biology meeting. I'm looking for a postdoctoral fellow in the area of systems biology. I was wondering if you would be willing to forward the attached ad. to your graduate students' list or to anyone who you think might be interested. Thanks a lot! Best, -- Qiong Yang, Ph.D. Assistant Professor of Biophysics University of Michigan Chemistry Building, Room 4019 930 N. University Ave. Ann Arbor, MI 48109-1055 Web: http://www.umich.edu/~qiongy Email: qiongy(a)umich.edu <qiongy(a)umich.edu> Office Phone: 734-764-4669

1 0

[Compbio-allhands] Fwd: Post-doc Opportunity in Colorado
by Hao Li 13 Aug '14

13 Aug '14

-------- Original Message -------- Subject: Post-doc Opportunity in Colorado Date: Wed, 13 Aug 2014 10:55:10 -0600 From: Kechris, Katerina <KATERINA.KECHRIS(a)UCDENVER.EDU> To: hhuang(a)stat.berkeley.edu <hhuang(a)stat.berkeley.edu>, JBBrown(a)lbl.gov <JBBrown(a)lbl.gov>, haoli(a)genome.ucsf.edu <haoli(a)genome.ucsf.edu>, katherine.pollard(a)gladstone.ucsf.edu <katherine.pollard(a)gladstone.ucsf.edu>, elevina(a)umich.edu <elevina(a)umich.edu>, jeff.chuang(a)jax.org <jeff.chuang(a)jax.org>, debra.goldberg(a)colorado.edu <debra.goldberg(a)colorado.edu>, Robin.Dowell(a)Colorado.EDU <Robin.Dowell(a)Colorado.EDU>, wsun(a)bios.unc.edu <wsun(a)bios.unc.edu>, lata(a)uwyo.edu <lata(a)uwyo.edu>, hongyu.zhao(a)yale.edu <hongyu.zhao(a)yale.edu>, huzurbazar(a)samsi.info <huzurbazar(a)samsi.info>, terry(a)wehi.EDU.AU <terry(a)wehi.EDU.AU>, jean.yang(a)sydney.edu.au <jean.yang(a)sydney.edu.au>, keles(a)stat.wisc.edu <keles(a)stat.wisc.edu>, kcli(a)stat.ucla.edu <kcli(a)stat.ucla.edu>, xjzhou(a)dornsife.usc.edu <xjzhou(a)dornsife.usc.edu>, nzh(a)wharton.upenn.edu <nzh(a)wharton.upenn.edu>, asa(a)cs.colostate.edu <asa(a)cs.colostate.edu>, jopsomer(a)stat.colostate.edu <jopsomer(a)stat.colostate.edu>, bickel(a)stat.berkeley.edu <bickel(a)stat.berkeley.edu> CC: Saba, Laura <Laura.Saba(a)ucdenver.edu> Dear Friends, I hope this email finds you well and that you are having a good summer. My apologies for the mass email, as I have been out of touch with some of you for quite a while. However, I'm looking for a post-doctoral fellow in statistical genomics/bioinformatics to be funded by a new NIH grant in my group. If you have any graduating students or a departmental email list, I would be grateful if you could forward this email announcement. There is more information here: https://www.jobsatcu.com/postings/79934 Thank you for the help and best wishes, Katerina ---------------------------------------------------------- Katerina Kechris, PhD Associate Professor Department of Biostatistics and Informatics Colorado School of Public Health University of Colorado Denver Anschutz Medical Campus Building 500, Room W3133 katerina.kechris(a)ucdenver.edu (303) 724-4363 http://csph.ucdenver.edu/Sites/Kechris/ ----------------------------------------------------------

1 0

[Compbio-allhands] Immediately available: Postdoctoral positions in Theoretical and Computational Biophysics
by David Sivak 13 Aug '14

13 Aug '14

Dear friends and colleagues, This fall I start my own research group in the Physics Department at Simon Fraser University in Vancouver, British Columbia (Canada!). In the near future, I hope to hire two exceptional, highly-motivated postdoctoral fellows to work on theoretical and computational biophysics. (I’m also on the lookout for talented undergraduates considering graduate study in biophysics.) Please forward this announcement to any interested parties. My group combines approaches from physics, information theory, and statistics to study the fundamental principles of biomolecular function under strong fluctuations. One postdoctoral position focuses on the design principles for efficient transduction of energy and information in molecular machines; the other opening is for the development of model comparison methods to interpret structural biology experiments, especially X-ray crystallography. Within these broad research thrusts there is ample freedom to pursue particular areas of personal scientific interest. Our theoretical flights of fancy are tethered to reality through close collaborations with experimentalists at SFU, UC Berkeley, and UC San Francisco. Postdoctoral fellows in my group will work in the intellectually-stimulating and interactive biophysics community within SFU Physics, with close ties to the Chemistry and Molecular Biology/Biochemistry departments, and frequent scientific exchange with allied departments at the University of British Columbia. In my own (possibly biased) opinion, the endless all-season outdoors opportunities, mind-blowing food from all ethnicities, and mild weather make Vancouver an enviable place to call home; slightly more objectively, it makes every official top 5 list of most livable cities in the world. The ideal candidate would have experience with computer programming, biomolecular modeling and statistical mechanics, and a PhD in a relevant field (broadly construed: physics, biophysics, chemistry, bio- or chemical-engineering, molecular biology, or relevant areas of statistics, computer science, applied math, etc). But most important is intellectual curiosity, enthusiasm for research in this area, and an excellent track record in whatever field they have pursued. Interested candidates should send me a cover letter and CV (including publication list and contact information for 2-3 references). Further information is available at: http://www.sfu.ca/physics/sivakgroup/ Thank you in advance! David —————————————————————————— David Sivak dsivak(a)sfu.ca http://www.sfu.ca/physics/sivakgroup/ Assistant Professor Dept. of Physics Simon Fraser University 8888 University Drive Burnaby, British Columbia CANADA V5A 1S6

1 0

[Compbio-allhands] Fwd: can you recommend someone for a bioinformatics position?
by Hao Li 07 Aug '14

07 Aug '14

-------- Original Message -------- Subject: can you recommend someone for a bioinformatics position? Date: Tue, 5 Aug 2014 21:37:46 -0700 From: Paul Hartley <paul(a)dovetail-genomics.com> To: haoli(a)genome.ucsf.edu hi Hao, you may remember working with Hiten and me on a project led by Randy Wu a few years ago. I currently work at a startup based out of UCSC and we are looking for a computational biologist with genomics expertise to join our team. Might you review the job ad below and forward it to potential candidates? thanks! Paul Title: Research Bioinformatics Programmer / Analyst Location: Santa Cruz, CA Starting: August 2014 We are a dynamic, early-stage startup company developing new technology for obtaining long-range DNA sequence information. The successful candidate will join a small research team developing and applying software tools for using our new datasets to solve genome assembly, genotyping and other bioinformatics problems, in close collaboration with our wet-lab researchers. Necessary skills and experience: solid bioinformatics programming skills; familiarity with fundamental algorithms on strings, graphs, trees and dynamic programming; experience using standard tools for short-read mapping and variant calling; To apply email your CV and contact information for references to: Brandon Rice <brandon(a)dovetail-genomics.com <mailto:brandon@dovetail-genomics.com>>, CEO.

1 0

[Compbio-allhands] Fwd: Assistant Professor Position in Medicinal Chemistry and Cancer Therapeutics
by Brian Shoichet 06 Aug '14

06 Aug '14

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy and OICR, UofT sent from my phone. Please excuse the grammar and spelling ---------- Forwarded message ---------- From: "Darrell Davis" <darrell.davis(a)utah.edu> Date: Aug 5, 2014 2:40 PM Subject: Assistant Professor Position in Medicinal Chemistry and Cancer Therapeutics To: "Sharma Sunil" <Sunil.Sharma(a)hci.utah.edu> Cc: Dear Colleague: I am requesting your help to identify candidates for an Assistant Professor faculty position working in the area of medicinal chemistry with an emphasis on cancer therapeutic discovery and development. This University of Utah tenure-track faculty position is jointly sponsored by the Department of Medicinal Chemistry, the Huntsman Cancer Institute, and the Department of Medicine. We are searching for talented investigators with the potential to develop outstanding research programs in the area of medicinal chemistry directed toward cancer therapeutic discovery. We will also consider candidates with established independent programs. In addition to their academic interests, the successful candidate is expected to develop programs that will result in new commercial activities. A complete description of the position, highlighting the unique funding source from a Utah State science and technology program and the opportunity to shape drug discovery at the University of Utah is attached. Please forward this information to prospective candidates. Thank you for your attention and assistance. Darrell R. Davis Professor and Chair Department of Medicinal Chemistry University of Utah 30 S. 2000 E. Room 1926 Salt Lake City, UT 84112 801-581-7006 Fax: 801-581-7087

1 0

[Compbio-allhands] [Fwd: Bioinformatics job openings at Berkeley Lab / NERSC / JGI]
by Patsy Babbitt 05 Aug '14

05 Aug '14

-- 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 94158-2330, USA (CA 94158 for direct delivery by courier) Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Joslyn Polzien, +1 415-514-1214, 415-514-4861 Joslyn.Polzien(a)ucsf.edu

1 0

[Compbio-allhands] Fwd: move to Stanford
by Jacobson, Matt 31 Jul '14

31 Jul '14

Ron is a very good scientist Begin forwarded message: From: Ron Dror <rondror(a)stanford.edu<mailto:rondror@stanford.edu>> Subject: move to Stanford Date: July 31, 2014 10:47:07 AM PDT Dear friends and colleagues, After more than eleven years, I left D. E. Shaw Research in March to take a faculty position at Stanford. I'm continuing to work on biomolecular simulation and also exploring some new research directions (with a focus on computational biology, though certain projects may include an experimental component). I hope to hire a couple postdocs in the coming months, so if you know of anyone promising -- particularly with a biomolecular modeling or simulation background -- please send them my way. I've included my new contact information below. Best, Ron -- Ron Dror Associate Professor of Computer Science and, by courtesy, Molecular and Cellular Physiology http://cs.stanford.edu/people/rondror/ E-mail: ron.dror(a)stanford.edu Phone: 650-497-8586 Mailing address: Gates Building 353 Serra Mall Stanford, CA 94305-9025 I'm scheduled to move into a different building (the Bio-X Clark Center) in a few months, so my mailing address will change, but the e-mail and phone above should still work. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Principal Investigator Positions at CeMM, Vienna
by Andrej Sali 31 Jul '14

31 Jul '14

-- 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 Begin forwarded message: > From: Giulio Superti-Furga <GSuperti(a)cemm.oeaw.ac.at> > Subject: Principal Investigator Positions at CeMM, Vienna > Date: July 31, 2014 at 8:39:16 AM PDT > To: Giulio Superti-Furga <GSuperti(a)cemm.oeaw.ac.at> > > Dear Colleague, > > Please find enclosed the announcement for open Principal Investigator positions at CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna. > We are looking for MDs and/or PhD scientists to start in 2015, either at their first independent appointment or already at the consolidation stage to apply their expertise close to a clinical setting in a highly stimulating research environment. > > I kindly ask for your help in distributing this announcement amongst your network of friends and collaborators. > > CeMM is one of the best places candidates should consider to advance their basic, medical-oriented research. > Within our short life, based on our super-cooperative research mode and –omics technologies, we have already identified the missing cancer gene in myeloproliferative neoplasms (Klampfl et al. NEJM 2013), a new cancer pathway with a new drug (Huber et al. Nature 2014), as well as the molecular basis for acute macular degeneration (Weismann et al. Nature 2011). > > For more information about these positions please see the attached announcement or visit the CeMM website http://www.cemm.at. > > Thank you very much for your collaboration! > > Best wishes, > Giulio Superti-Furga > > _________________________________ > > Prof. Dr. Giulio Superti-Furga > Scientific Director > _________________________________ > > CeMM > Research Center for Molecular Medicine > of the Austrian Academy of Sciences > > Lazarettgasse 14, AKH BT 25.3 > 1090 Vienna, Austria > Phone +43-1/40160-70 001 > Fax +43-1/40160-970 000 > > Assistant: Dr. Marc Brehme > Phone +43 1/40160-70 085 > mbrehme(a)cemm.oeaw.ac.at > > gsuperti(a)cemm.oeaw.ac.at > www.cemm.at > _________________________________ > >

1 0

[Compbio-allhands] Fwd: Alternative career path opportunities
by Jacobson, Matt 24 Jul '14

24 Jul '14

I'm not sure if this has gone out to postdoc listservs Begin forwarded message: From: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> Subject: FW: Alternative career path opportunities Date: July 24, 2014 11:19:31 AM PDT To: <BPSTUDENTS(a)LISTSRV.UCSF.EDU<mailto:BPSTUDENTS@LISTSRV.UCSF.EDU>> Reply-To: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> Dear Students, Please see the attached flyer for potential employment opportunities. Nicole Nicole Takesono Flowers BMI, BP, & CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546 From: Keller Brian <Keller.Brian(a)bcg.com<mailto:Keller.Brian@bcg.com>> Date: Thursday, July 24, 2014 at 8:17 AM To: Office 2004 Test Drive User <nicole.flowers(a)ucsf.edu<mailto:nicole.flowers@ucsf.edu>> Subject: Alternative career path opportunities Dear Ms. Flowers, My name is Brian Keller and I'm a Project Leader at The Boston Consulting Group, where we routinely hire Advanced Degree Candidates<http://adc.bcg.com/> (PhDs, Post-Docs, MDs). We are aware that most of your students will go on to careers in academia - and are sensitive to how we position ourselves to you and your students. We see BCG as a career option for those who have decided to seek an alternative career path. We wanted to get your help in distributing the flyer attached, written by one of your alums currently working at BCG, to any PhD students and Post-docs that might be interested. We will be on campus on July 29th to discuss opportunities for students and to help them prepare for the interview process. Our application submission deadline is August 10th. If you have any questions, please feel free to reach out to me and we can schedule some time to speak. Thank you, Brian _____________________________________________________________________________________________________ Brian Keller Project Leader THE BOSTON CONSULTING GROUP Two Embarcadero Center, Suite 2400 San Francisco, California 94111 ▪ United States Tel. +1 415 732 8208 ▪ Mobile +1 415 361 9464 keller.brian(a)bcg.com<mailto:keller.brian@bcg.com> Assistant: Kristy Skelly Tel. +1 415 732 8016 ▪ skelly.kristy(a)bcg.com<mailto:skelly.kristy@bcg.com> _____________________________________________________________________________________________________ Read BCG's latest insights, analysis, and viewpoints at bcgperspectives.com<http://www.bcgperspectives.com/> ________________________________ The Boston Consulting Group, Inc. This e-mail message may contain confidential and/or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BPSTUDENTS&A=1> from this mailing list. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: WINTER SCHOOL IN STRUCTURAL BIOINFORMATICS : MODELING LARGE MACROMOLECULAR ASSEMBLIES
by Hilary Mahon 21 Jul '14

21 Jul '14

Begin forwarded message: > From: Riccardo Pellarin <pellarin.riccardo(a)gmail.com> > Subject: Fwd: WINTER SCHOOL IN STRUCTURAL BIOINFORMATICS : MODELING LARGE MACROMOLECULAR ASSEMBLIES > Date: July 21, 2014 11:46:20 AM PDT > To: Hilary Mahon <hilary(a)salilab.org> > > Hi Hilary, > > can you please forward the announcement > for a winter school in macromolecular modeling below? > > thanks! > > Riccardo > > > %%i%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > WINTER SCHOOL ALGORITHMS IN STRUCTURAL BIOINFORMATICS : > MODELING LARGE MACROMOLECULAR ASSEMBLIES > > 8-12 DECEMBER 2014, INRIA SOPHIA ANTIPOLIS, FRANCE > http://algosb2014.inria.fr/ > %%i%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > We are pleased to announce a one-week school on Algorithms in > Structural Bioinformatics. The aim is to introduce advanced methods in > this domain, giving special attention to interdisciplinary > approaches. The main focus will be on methodological developments > meant to analyze and model large macromolecular assemblies, as well as on > the corresponding software. The following topics will be taught > (details of the lectures at http://algosb2014.inria.fr/lectures.html) > > I. > Modeling of Dynamic Biomolecular Assemblies > Gerhard Hummer, Max Plack Institut fur Biophysik / Theoretical Biophysics > > II. > Small Angle X-ray Scattering from Macromolecular Solutions > Dmitri Svergun, European Molecular Biology Laboratory, Hamburg > > III. > Computational Modeling of large Multimolecular Assemblies based on Multi-resolution Experimental Data > Haim Wolfson, Tel Aviv University > > IV. > Integrative Approaches to Macromolecular Modeling > Riccardo Pellarin, UCSF > > V. > Modeling Contacts in Macromolecular assemblies: from Inference to Assessment > Frederic Cazals, Algorithms-Biology-Structure, Inria Sophia Antipolis > > > Each day's morning session will consist of a lecture, and the > afternoon session will be devoted to a hands-on computer lab on > the participants' laptops. > > > INTENDED AUDIENCE. The school is primarily intended for thirty PhD > students and postdoctoral researchers. A number of slots are also > available for young researchers from academia or industry. > > > DEADLINE FOR APPLICATIONS. A one-page application (pdf format) should > be sent by email to algosb-coordinators(a)inria.fr with Subject "AlgoSB > application", by September 20th, 2014. > > The application should provide a mini-vitae or a pointer to the full > vitae, a brief presentation of the applicant's research interests, and > a few lines commenting on expected synergy between his or her research and > the courses that will be taught. > > Notification of acceptance will be provided by September 30th. It is > expected that all accepted students will participate in the entire > school period. > > VENUE AND PARTICIPATION FEES. The Algorithmics in Structural > Bioinformatics school will take place on the French Riviera, at Inria > Sophia Antipolis - Méditerranée. > > The participation fees will be of 400 euros, which includes lunches, > coffee breaks, and social events. > > The organizers : > Frédéric Cazals, INRIA Sophia Antipolis - Méditerranée > Juan Cortés, LAAS-CNRS, Toulouse > Charles Robert, LBT-CNRS / IBPC, France >

1 0

[Compbio-allhands] Fwd: Opportunity at UCSD Please consider seriously Call me with any questions TQ SKB
by Andrej Sali 18 Jul '14

18 Jul '14

Sent from my iPhone Begin forwarded message: > From: "Stephen K. Burley Rutgers Proteomics" <sburley(a)proteomics.rutgers.edu> > Date: July 18, 2014 at 11:16:55 AM PDT > To: "Dr. Sali" <sali(a)salilab.org> > Subject: Opportunity at UCSD Please consider seriously Call me with any questions TQ SKB > > http://jobs.sciencecareers.org/job/332902/associate-or-full-professor-struc… > > -- > Stephen K. Burley, M.D., D.Phil. (sburley(a)proteomics.rutgers.edu) > Director, Center for Integrative Proteomics Research > Director, RCSB Protein Data Bank > Director, BioMaPS Institute for Quantitative Biology > Distinguished Professor, Department of Chemistry and Chemical Biology > Member, Rutgers Cancer Institute of New Jersey > Rutgers, The State University of New Jersey > 174 Frelinghuysen Road > Piscataway, NJ 08852 > http://rcsb.org

1 0

[Compbio-allhands] Fwd: MGMS - positions available
by Andrej Sali 18 Jul '14

18 Jul '14

-- 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 Begin forwarded message: > From: Elizabeth Yuriev <Elizabeth.Yuriev(a)monash.edu> > Subject: FW: MGMS - positions available > Date: July 18, 2014 at 8:06:54 AM GMT+1 > To: Undisclosed recipients: ; > > FYI > > ************ > Dr Elizabeth Yuriev > 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, Fax: +61 3 9903 9143 > E-mail: elizabeth.yuriev(a)monash.edu > www.pharm.monash.edu.au > > From: Steve Maginn [mailto:maginn@ccdc.cam.ac.uk] > Sent: Friday, 18 July 2014 5:00 PM > To: Steve Maginn > Subject: MGMS - positions available > > Dear Colleague, > > Please find below and attached, information about a postdoctoral position in Phil Biggin’s group at the University of Oxford, and a vacancy at Roche Pharmaceuticals in Basel. > > Best regards, > > Steve Maginn > > > > Postdoctoral Research Associate in Computational Biochemistry > > We are seeking to appoint a Postdoctoral Research Associate in computational biochemistry to investigate the dynamics and explore novel allosteric compounds for a family of ionotropic glutamate receptors. > > Applicants should possess or expect to obtain soon, a PhD in Chemistry, Biochemistry, Physics or a related area and have extensive experience of molecular dynamics simulations, free energy calculations and virtual screening. As the project forms part of a larger ongoing collaboration, excellent communication skills and the ability to interact with people from different scientific backgrounds is an absolute requirement for the post. Experience of high performance computing and some system administration would also be advantageous. > > This full-time post is funded by the MRC for up to 3 years in the first instance and is based in the laboratory of Dr Philip Biggin in the Department of Biochemistry, South Parks Road, Oxford. > > This position is graded on the University’s grade 7 scale, for which the salary range is £29,837 - £36,661 per annum. The actual starting salary offered will be based on qualifications and relevant skills acquired and will also be determined by the funding available. > > For further general information, phone (01865) 613204, quoting reference number (114253) > > Applications for this vacancy are to be made online. > > To apply for this role and for further details, including the job description and selection criteria, please click on the link below: > > www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id… > > The closing date for applications is midday on Friday, 29th August 2014, with interviews for shortlisted candidates as soon as possible thereafter. > > The University of Oxford is a member of the Athena SWAN Charter and holds an institutional Bronze Athena SWAN award. The Department of Biochemistry is strongly committed to equality and valuing diversity and we operate a flexible working policy for all staff. The Department holds a departmental Bronze Athena award in recognition of its efforts to introduce organisational and cultural practices that promote gender equality in SET and create a better working environment for both men and women. > > http://www.bioch.ox.ac.uk/aspsite/index.asp?sectionid=vacancies&job=BR621 > > > > http://careers.roche.com/en/jobs/switzerland/research/2963070709/scientist-… > > … and see attached PDF. > > > > > > > Dr Stephen J. Maginn, > Director of User Services, > Cambridge Crystallographic Data Centre (CCDC), > 12 Union Road, > Cambridge CB2 1EZ, > United Kingdom > > +44 1223 762532 > maginn(a)ccdc.cam.ac.uk > www.ccdc.cam.ac.uk > > > LEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmaster(a)ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ.

1 0

[Compbio-allhands] Fwd: Computer-Aided Drug Design Position at Roche Basel
by Brian Shoichet 17 Jul '14

17 Jul '14

FYI Brian Shoichet Professor sent from my PDA. Please excuse the grammar and spelling ---------- Forwarded message ---------- From: "Hert, Jerome" <jerome.hert(a)roche.com> Date: Jul 17, 2014 6:00 AM Subject: Computer-Aided Drug Design Position at Roche Basel To: Cc: Dear colleague, I would like to inform you of a new job opportunity in our Computer-Aided Drug Design (CADD) team at Roche Basel. Our team is involved in drug discovery projects with the goal of guiding the design of new pharmaceutically active molecules. We are looking for an enthusiastic and talented scientist with 1 to 3 years of industry experience or with no industry experience but an outstanding track record in academia. If you know of any suitable candidate, please let me know. Feel also free to forward this message to anyone who might be interested in this opening. Thank you. Link to the job offer: http://bit.ly/1jB7y9h -- Best regards, Jérôme Hert. T: +41 6168 79639 E: jerome.hert(a)roche.com Section Head, Computer-Aided Drug Design Molecular Design and Chemical Biology F. Hoffmann-La Roche Ltd. -- *Want to know more about Roche?* Explore our marketed products - click here <http://www.roche.com/products/product-list.htm?type=divpharma&id=Pharmaceut…> Have a look at our pipeline - click here <http://www.roche.com/research_and_development/who_we_are_how_we_work/pipeli…> Take a tour of pRED - click here <http://www.youtube.com/watch?v=DVvPCOXdMI0> Hear from one of our scientists - click here <http://www.youtube.com/watch?v=E9TVJ9UZna4> Discover our Brain Shuttle approach - click here <http://www.youtube.com/watch?v=TfJBwoQNaaw>

1 0

[Compbio-allhands] Fwd: 2015 Junior Research Fellowship scheme
by Andrej Sali 09 Jul '14

09 Jul '14

-- 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 Begin forwarded message: > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: FW: 2015 Junior Research Fellowship scheme > Date: July 9, 2014 at 7:54:09 AM PDT > > Dear Colleague > > Could you draw attention to any appropriate postdoctoral researcher about this opportunity for a 3-year JRF at Imperial. This is of course highly competitive and a very strong CV, typically with high impact publications, is essential. > Closing date 15 Sept 2015 > > Anyone interested could e-mail me their CV and I could advise > > Best > > > ******************************************** > 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 > http://www3.imperial.ac.uk/cisbio (CISBIO) > www.sbg.bio.imperial.ac.uk (Group's research) > > Tel +44 (0)20 7594 5212 > > > > We are pleased to announce that the 2015 JRF scheme is now open. Please find attached a Departmental Guidebook, which contains further useful information. Also attached is a poster to advertise this call, which you may wish to use around your Departments. We will also be publishing an external advert shortly. > > Information regarding the scheme can be found on the following website, where interested applicants will also find the application form, guidance document and other information http://www3.imperial.ac.uk/juniorresearchfellowships. >

1 0

[Compbio-allhands] Fwd: San Francisco Career Planning Program (CPP)
by Jacobson, Matt 16 Jun '14

16 Jun '14

Feel free to forward to anyone who might be interested ============================================== Begin forwarded message: From: Kanae Muraiso <kmuraiso(a)cppweb.jp> Subject: San Francisco Career Planning Program (CPP) Date: June 16, 2014 9:40:29 AM PDT To: Matthew Jacobson <matt.jacobson(a)ucsf.edu> Dear Dr. Matthew Jacobson, Greetings, my name is Kanae Muraiso and I am sending this email on behalf of CPP. Career Planning Program (CPP) is a career support program based in Kyoto, Japan, to help graduate students and postdoctoral scholars who aim to succeed in their career paths as scientific researchers. http://cpp.jpn.org/wjs/ The aim of our activity is two-fold: (1) To provide a training venue for researchers to develop essential skills to thrive in social advancement (2) To host career fairs specifically aimed towards scientific researchers who intend to work in industries CPP offers seminars for Japanese research scientists. This year, we are pleased to announce that Takeda Pharmaceutical Company Limited is seeking employees who can work in Japan. This great opportunity is open to anyone, regardless of Japanese skills. We would like to extend our welcome to everyone who is interested to participate in our career fair. Program information is as follows: What: CPP2014 San Francisco Where: DoubleTree by Hilton Hotel San Francisco Airport When: July 5, 2013 Contents: Career fair Participating Companies: Takeda Pharmaceutical, Chiome Bioscience, CPP Personal(as staffing service) ? Companies other than Takeda Pharmaceutical require Japanese speaking skills ? No Japanese skill is required to apply for the position at Takeda Pharmaceutical. Anyone interested is encouraged to bring their applications to Takeda Pharmaceutical on Saturday, July 5th between 9am and 6pm (See Reference). Recruitment information for Takeda Pharmaceutical at CPP2014 San Francisco: http://cpp.jpn.org/wjs/takeda/ Takeda Pharmaceutical Website: http://www.takeda.com/ We are seeking to reach out to the graduate students and postdoctoral scholars overseas who are seeking future employment in Japanese industries. With that said, I am sending this email in hope that you would be able to distribute this information about CPP and the upcoming San Francisco career fair to your graduate students and scholars who may be interested. It is in our best interest to aid them in their career path development. Thank you for your kind assistance and please feel free to contact me with any questions. Sincerely, Kanae Muraiso, Ph.D. ============================== Career Planning Program Kanae Muraiso, Ph.D. CPP LLC. 382 Motohonnohji MB Bdg,Nakagyo Kyoto, Kyoto, Japan 604-8244 TEL +81-50-1349-5842 FAX +81-50-3156-0553 email kmuraiso(a)cppweb.jp URL http://cppweb.jp ============================== Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu jacobsonlab.org

1 0

[Compbio-allhands] Fwd: Call for independent research group leaders
by Andrej Sali 13 Jun '14

13 Jun '14

-- 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 Begin forwarded message: > From: Gene Myers <myers(a)mpi-cbg.de> > Subject: Call for independent research group leaders > Date: June 13, 2014 at 2:06:49 AM PDT > To: Gene Myers <myers(a)mpi-cbg.de> > > Dear ladies and gentlemen, > > The Center for Systems Biology in Dresden is a joint initiative of the MPI-PKS (Max Planck Institute for the Physics of Complex Systems) and the MPI-CBG (Max Planck Institute of Molecular Cell Biology and Genetics). The core of the center is focused on computational biology and theoretical biophysics primarily directed towards questions within cell and developmental biology in tight synchrony and interaction with the various experimental groups of the MPI-CBG. > > We are looking for strong candidates who would like to apply for third party funds in order to set up an > > Independent Research Group > > at our Center for Systems Biology at Dresden (CSBD). Candidates are expected to have an outstanding international research track record in one or several of the research fields that are relevant to the mission of the center, which are: computational biology, biophysics, bioinformatics, genomics and image analysis. To be considered, candidates must (a) satisfy the eligibility criteria of the respective funding programs, (b) have received their PhD in a computational or theoretically oriented discipline, and (c) have published significant research papers recently. Successful candidates will receive mentoring and full support of the MPI-CBG & MPI-PKS to apply for independent group funding. > > > The new research groups will be housed in the new CSBD building currently being built alongside the main building of the MPI-CBG. For further information, please see www.mpg-sysbio.de, www.mpi-cbg.de, and www.pks.mpg.de. > > > Applications should contain: (a) a motivation letter by the applicant, (b) a CV and publication list, (c) a description of past and future research activities, (d) funding history to date. Please arrange for three recommendation letters to be sent directly to visitors(a)pks.mpg.de before the deadline. Women are particularly welcome as candidates. The same applies to disabled people. Dual career applications will be considered. > > > Please see http://mpg-sysbio.de/index.php?id=jobs for how to apply. Closing date is 01.08.2014. > > > Best regards > > Dr. Gene Myers > Director > Tschira Chair of Systems Biology > > Max Planck Institute of > Molecular Cell Biology and Genetics > Pfotenhauerstrasse 108 > 01307 Dresden, Germany > > Tel +49 351 210-1220 > Fax +49 351 210-1209 > E-mail: myers(a)mpi-cbg.de > http://www.mpi-cbg.de > >

1 0

[Compbio-allhands] Fwd: PhD Fellowship program at the Biozentrum Basel
by Andrej Sali 06 Jun '14

06 Jun '14

-- 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 Begin forwarded message: > From: Torsten Schwede <torsten.schwede(a)unibas.ch> > Subject: PhD Fellowship program at the Biozentrum Basel > Date: June 6, 2014 at 10:35:53 AM PDT > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Andrej, > > May I ask you to forward the attached invitation for our PhD Fellowship program to interested students? We are looking for talented Bioinformaticians who would like to do their PhD in Switzerland. Application deadline is June 30. > > Thanks a lot for your help! > > Torsten > > ------------------------------------------------------------------- > > > The Biozentrum of the University of Basel invites talented, ambitious and highly motivated young scientists to apply to the “Fellowships for Excellence” International PhD Program in Molecular Life Sciences. This program offers prestigious PhD fellowships that are awarded on a competitive basis and provide direct entry into the Biozentrum PhD program. > > Opportunities: > • rotation-based selection of research groups > • a lively and interactive educational atmosphere > • competitive salaries > • personal annual research stipend > > For details, please see the attached flyer or the program web site:http://www.biozentrum.unibas.ch/excellence > > Torsten Schwede | Professor | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics > Klingelbergstrasse 50/70 | CH-4056 Basel | Phone: +41 61 267 15 81 | Office: +41 61 267 15 86 > Email: torsten.schwede(a)unibas.ch | www.biozentrum.unibas.ch/schwede/ >

1 0

[Compbio-allhands] Fwd: postdoc postions on computational biology/biophysics
by Jacobson, Matt 06 Jun '14

06 Jun '14

Begin forwarded message: From: "Wei, Guowei" <wei(a)math.msu.edu<mailto:wei@math.msu.edu>> Subject: postdoc postions on computational biology/biophysics Date: June 6, 2014 4:35:10 AM PDT To: "Wei, Guowei" <wei(a)math.msu.edu<mailto:wei@math.msu.edu>> Dear Colleagues, I am looking for postdocs to work on computational biophysics and/or computational biology. An ideal candidate should have a strong background on methodology development. Being good at computer coding is a must. Please encourage your graduating and/or freshly graduated PhD students to apply. Apologies for multiple copies that you may receive. Best regards, Guowei ------------------------------------------------------------- Guowei Wei Professor of Mathematics Professor of Electrical and Computer Engineering Adjunct Professor of Biochemistry and Molecular Biology Michigan State University East Lansing, MI 48824 http://math.msu.edu/~wei ------------------------------------------------------------- Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Data Scientist Position at Quid
by Tom Ferrin 30 May '14

30 May '14

-------- Original Message -------- Subject: Data Scientist Position at Quid Date: Wed, 28 May 2014 11:16:50 -0700 From: Emmanuel Yera <eyera(a)quid.com> To: tef(a)cgl.ucsf.edu Hey Tom, I hope you are doing well. Time passes so quickly, I graduated about a year ago. Work has been going well and have really been enjoying my time at Quid. I wanted to reach out and ask if you knew any students or post-docs interested in Data Science. We just opened a position (https://quid.com/careers?gh_jid=14685) Let me know what you think. Regards, - Emmanuel -- Emmanuel R. Yera, PhD Data Scientist Quid, Inc. 733 Front St, C1A San Francisco, California 94111 Mobile: +1 408 242 7171 www.quid.com <http://www.quid.com/>

1 0

[Compbio-allhands] 5/29/14 Seminar with Johan Paulsson
by Flowers, Nicole 23 May '14

23 May '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus Library 220 Johan Paulsson Harvard Quantifying dynamics in single cells May 29, 2014 G. Heimberg, 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 Graduate Program Assistant AMBER Software Administrator 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: Job Openings at IO
by Jacobson, Matt 15 May '14

15 May '14

Begin forwarded message: From: Patrick Weinkam <pweinkam(a)gmail.com<mailto:pweinkam@gmail.com>> Subject: Job Openings at IO Date: May 15, 2014 2:06:02 PM PDT To: Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>>, Matt Jacobson <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, James Fraser <james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu>>, <tef(a)cgl.ucsf.edu<mailto:tef@cgl.ucsf.edu>> Hi all, In an effort to keep in touch with the good people at UCSF, I am also reaching out because my new company is undergoing a hiring push. We are looking for people with data analysis and programming skills to help us develop the next generation of energy efficient, software controlled data centers. We also have need for people with simulation backgrounds. If you know any good candidates looking for a job, please forward these job descriptions along. Hope you all are doing well! Pat Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] 5/22/14 Seminar with Cliff Brangwynne
by Flowers, Nicole 15 May '14

15 May '14

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 Cliff Brangwynne Princeton Intracellular Phase Transitions and Cell Size May 22, 2014 D. Mullins, 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 Graduate Program Assistant AMBER Software Administrator 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] Informatics Day on June 10 @ Mission Bay
by Patsy Babbitt 13 May '14

13 May '14

Save the Date! Informatics Day at UCSF: Leveraging clinical data for research June 10, 2014, 9:00 am to 5:00 pm Location: Mission Bay Conference Center We are pleased to announce the first UCSF Informatics Day. This event will showcase clinical data sources for use in basic, translational, and clinical research. Over the past few years UCSF has significantly invested in its informatics and IT footprint, providing expanded critical services to support basic, translational, and clinical research. Informatics Day 2014 will give you the opportunity to learn about the systems and tools available to support your research. The day will feature: Keynote Speaker addressing the role of informatics in biomedical research Short presentations highlighting the available systems and tools Scientific presentations by investigators who are utilizing these resources in their own research Hands on demonstrations of tools and resources available at UCSF Opportunities to meet researchers from across the campus using information resources Please join us to see how you can benefit from the expanding informatics infrastructure at UCSF. Sponsored by: CTSI, the Institute for Computational Health Sciences, the Institute for Human Genetics, the UCSF Office of Research, and the UCSF Medical Center Institute for Human Genetics 415-476-2470 http://humangenetics.ucsf.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 94158-2330, USA (CA 94158 for direct delivery by courier) Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Joslyn Polzien, +1 415-514-1214, 415-514-4861 Joslyn.Polzien(a)ucsf.edu

1 0

[Compbio-allhands] CANCELLED- 5/15/14 Seminar with L. Mahadevan- CANCELLED
by Flowers, Nicole 12 May '14

12 May '14

Dr. L. Mahadevan regretfully has to cancel his seminar this Thursday, May 15, 2014. Nicole Takesono Flowers BMI, BP, & CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546 From: <Flowers>, Office 2004 Test Drive User <nicole.flowers(a)ucsf.edu<mailto:nicole.flowers@ucsf.edu>> Date: Friday, May 9, 2014 at 1:05 PM 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>> Subject: 5/15/14 Seminar with L. Mahadevan 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 L. Mahadevan Harvard A physical basis for morphogenesis? May 15, 2014 M. Thomson, 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 Graduate Program Assistant AMBER Software Administrator 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] 5/15/14 Seminar with L. Mahadevan
by Flowers, Nicole 09 May '14

09 May '14

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 L. Mahadevan Harvard A physical basis for morphogenesis? May 15, 2014 M. Thomson, 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 Graduate Program Assistant AMBER Software Administrator 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: Computer-Aided Drug Design Position at Roche Basel
by Brian Shoichet 09 May '14

09 May '14

FYI Brian Shoichet Professor sent from my PDA. Please excuse the grammar and spelling ---------- Forwarded message ---------- From: "Hert, Jerome" <jerome.hert(a)roche.com> Date: May 9, 2014 10:42 AM Subject: Computer-Aided Drug Design Position at Roche Basel To: "Jerome Hert" <jerome.hert(a)roche.com> Cc: Dear colleague, I would like to inform you of a new job opportunity in our Computer-Aided Drug Design (CADD) team at Roche Basel. Our team is involved in drug discovery projects with the goal of guiding the design of new pharmaceutically active molecules. We are looking for an enthusiastic and talented collaborator with industry experience. If you know of any suitable candidate, please let me know. Feel also free to forward this message to anyone who might be interested in this opening. Thank you. Link to the job offer: http://t.co/pnDzkpywo5 -- With best regards, Jérôme Hert. T: +41 6168 79639 E: jerome.hert(a)roche.com Section Head, Computer-Aided Drug Design Molecular Design and Chemical Biology F. Hoffmann-La Roche Ltd. -- *Want to know more about Roche?* Explore our marketed products - click here<http://www.roche.com/products/product-list.htm?type=divpharma&id=Pharmaceut…> Have a look at our pipeline - click here<http://www.roche.com/research_and_development/who_we_are_how_we_work/pipeli…> Take a tour of pRED - click here<http://www.youtube.com/watch?v=DVvPCOXdMI0> Hear from one of our scientists - click here<http://www.youtube.com/watch?v=E9TVJ9UZna4> Discover our Brain Shuttle approach - click here<http://www.youtube.com/watch?v=TfJBwoQNaaw>

1 0

[Compbio-allhands] message from Adrian Roitberg
by Jacobson, Matt 06 May '14

06 May '14

For those of you who do MD simulations: An Overview of AMBER 14 – Creating the World’s Fastest MD Package Date: May 13th, 9am PST Hosted by: Prof. R. Walker, UC San Diego; Prof. A. Roitberg, University of Florida; S. Grand, Amazon Web Services Register at: http://bit.ly/AMBER14<http://www.google.com/url?q=http%3A%2F%2Fbit.ly%2FAMBER14&sa=D&sntz=1&usg=A…> This webinar will provide an overview of new GPU-accelerated features in the recently released AMBER Molecular Dynamics Software package version 14. New features include support for multi–dimensional replica exchange MD and hydrogen mass partitioning. High performance peer–to–peer support and optimizations make version 14 the fastest MD software package on commodity hardware

1 0

Re: [Compbio-allhands] 5/8/14 Seminar with Trey Ideker
by Flowers, Nicole 02 May '14

02 May '14

Hi Everyone, Please note the subject line correction. The talk is definitely with Trey Ideker next week. Thank you, Nicole Nicole Takesono Flowers BMI, BP, & CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546 From: <Flowers>, Office 2004 Test Drive User <nicole.flowers(a)ucsf.edu<mailto:nicole.flowers@ucsf.edu>> Date: Friday, May 2, 2014 at 2:18 PM 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>> Subject: 5/8/14 Seminar with Dorothee Kern 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 Trey Ideker UCSD Siri of the Cell: What Biology Can Learn From The iPhone May 8, 2014 J. Webber, 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 Graduate Program Assistant AMBER Software Administrator 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] 5/8/14 Seminar with Dorothee Kern
by Flowers, Nicole 02 May '14

02 May '14

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 Trey Ideker UCSD Siri of the Cell: What Biology Can Learn From The iPhone May 8, 2014 J. Webber, 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 Graduate Program Assistant AMBER Software Administrator 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] 5/1/14 Seminar with Dorothee Kern
by Flowers, Nicole 25 Apr '14

25 Apr '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus Library 220 Dorothee Kern Brandeis The evolution of kinase dynamics over 1 billion years reveals Gleevec’s selectivity May 1, 2014 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 CCB Graduate Program Assistant AMBER Software Administrator 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] a fellow position at iHuman institute, ShanghaiTech, and UCSF
by Andrej Sali 24 Apr '14

24 Apr '14

We seek a research fellow or assistant professor applicant to engage in an integrative structural biology study of a cellular signaling pathway (e.g., GPCR signaling cascades). The candidate will contribute to the collaboration between the Sali research group at University of California, San Francisco, USA (http://salilab.org) and the Stevens research group at iHuman Institute of ShanghaiTech University, Shanghai, China (http://www.shanghaitech.edu.cn/en/en_iHuman_Overview.asp) The goal will be to develop a spatiotemporal model of the selected system, based on data from a variety of experimental techniques, such as X-ray crystallography, NMR spectroscopy, mass spectrometry, super resolution optical microscopy, and others, generated at iHuman. The prerequisites include a background in computational structural biology, experience with designing and coding computational algorithms, statistical mechanics, and statistics, as well as willingness to learn about integrative structural biology methods and applications in the Sali laboratory. The fellow will spend considerable time initially at UCSF, transitioning into a tenure track faculty position at iHuman. The position will be funded for 5 years at a very competitive international faculty startup level. Please email your cover letter, including a cv and names of at least 3 referees, to Andrej Sali (sali(a)salilab.org) or Ray Stevens (stevens(a)shangaitech.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 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] 4/24/14 Seminar with Alexander Hoffmann
by Flowers, Nicole 18 Apr '14

18 Apr '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Alexander Hoffmann UCSD Network Dynamics as a basis for Specificity April 24, 2014 Hana El Samad, 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 CCB Graduate Program Assistant AMBER Software Administrator 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:
by Jacobson, Matt 15 Apr '14

15 Apr '14

-- Matt Sent from my iPhone Begin forwarded message: From: Olaf Wiest <Olaf.G.Wiest.1(a)nd.edu<mailto:Olaf.G.Wiest.1@nd.edu>> Date: April 15, 2014 at 7:32:14 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Matt I would like to alert you and your students to an opening of one (possibly two) postdoctoral positions in the Computer Aided Molecular Design (CAMD) core facility here at the University of Notre Dame. If you know of suitable candidates from your group or other, please encourage them to apply. I attach the position description, which will also be posted on ccl.net<http://ccl.net> in the next few days. If you have any question, please do not hesitate to contact me at any time. With the best wishes Olaf Wiest Postdoctoral position in the CAMD core at the University of Notre Dame Applications are invited for a postdoctoral position in the Computer Aided Molecular Design core facility at the University of Notre Dame. The successful candidate will work with researchers in the Warren Family Center for Drug Discovery, the Center for Rare and Neglected Diseases, and other researchers at the University of Notre Dame as well as their collaborators to design chemical probes molecules as well as new hit and lead compounds to a treatment of a variety of diseases. Current areas of interest include malaria and other infectious diseases, cancer, and neurodegenerative diseases. The initial appointment will be for one year with additional years, including a possibility to apply for a staff position, available upon mutual agreement. Requirements for the position include: - Ph.D in chemistry, biophysics or other relevant field - documented experience in virtual screening, molecular dynamics simulation of biomolecular systems and/or structure based drug design - ability to support multiple projects simultaneously - ability to work independently and in effective collaborations with medicinal chemists, biochemists and biologists - excellent verbal and written communication skills Previous experience with common programs (Schrödinger Suite, AMBER, G09 etc.), electronic structure calculations, library design, cheminformatics, good programming skills and other aspects of computer aided drug design as well as an understanding of the drug discovery process would be beneficial. To apply, send a CV, statement of research experience and contact addresses of three references to owiest(a)nd.edu<mailto:owiest@nd.edu>. For information on the CAMD core, see http://www3.nd.edu/~camd/.

1 0

[Compbio-allhands] 4/17/14 Seminar with Rama Ranganathan
by Flowers, Nicole 11 Apr '14

11 Apr '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Rama Ranganathan UT Southwestern The evolutionary “design” of proteins April 17, 2014 S. Calhoun & D. Garrdio Ruiz, 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 CCB Graduate Program Assistant AMBER Software Administrator 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: Postdoc opening
by Jacobson, Matt 09 Apr '14

09 Apr '14

I think I may have already sent out a description of this position, but this is much more detailed Begin forwarded message: From: "Xing, Li" <li.xing(a)pfizer.com<mailto:li.xing@pfizer.com>> Subject: Postdoc opening Date: April 9, 2014 6:15:26 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, I am writing to see if you can help me out here. Recently I was fortunate to get an internal Pfizer postdoctoral fellowship funded to investigate PPI targets by molecular dynamics simulations. Specifically, the goals are to expand the current understanding of the complex dynamic phenomena of many biological mechanisms, and to make traditionally difficult targets an increasingly fruitful drug discovery area. I am hoping you may be able to provide suggestions for candidates from your institution or elsewhere where there may be an overlapping interest or experience in this research area. Clearly experience in scientific scripting and programming is essential. The Postdoctoral fellowship is for 2 years with a possible extension to 3 years and is to be focused on generating publishable work (i.e. not constrained by Pfizer drug discovery activities) through internal studies as well as collaborations within and outside of Pfizer. This could be a great opportunity for people who want to gain industrial experience in a real drug discovery setting. I have attached a copy of the recruitment flyer. Online application can be submitted through the link from Pfizer careers website. http://pfizercareers.com/apply Job ID 994031 Any help or guidance that you can provide would be much appreciated. Thanks, Li Li Xing, Ph.D. Pfizer Worldwide Research and Development Cambridge, MA Tel: 617 665 5369 Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] 4/10/14 Seminar with David Baker
by Flowers, Nicole 04 Apr '14

04 Apr '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 David Baker University of Washington Design of protein structures, functions and assemblies April 10, 2014 J. Kung & J. Rettenmaier, 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 CCB Graduate Program Assistant AMBER Software Administrator 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] reminder: Tack Kuntz talking at noon
by Jacobson, Matt 03 Apr '14

03 Apr '14

From: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> Date: March 31, 2014, 10:49:12 AM PDT To: <BBCFACULTY(a)LISTSRV.UCSF.EDU<mailto:BBCFACULTY@LISTSRV.UCSF.EDU>> Subject: PETER A. KOLLMAN LECTURESHIP - April 3, 2014 Reply-To: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> THURSDAY, APRIL 3, 2014 AT 12:00 PM PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS LIBRARY 221 WEBCAST: Reception in Byers Hall 5th Floor Lounge at 3:30 Please see attached flyer. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546 ------------------------------------------------------------------------ Use the following link to unsubscribe from this mailing list: http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BBCFACULTY&A=1 Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: available postdoc position at Pfizer in Cambridge
by Jacobson, Matt 02 Apr '14

02 Apr '14

Begin forwarded message: From: Arjun Narayanan Subject: available postdoc position at Pfizer in Cambridge In our department one of my colleagues is looking for a postdoc candidate to use MD to better understand and predict PPI druggability. Do you know anyone who would be interested? Here is the posting info: Postdoctoral Fellow - Computational Chemistry United States-Massachusetts-Cambridge You can view and apply for this job on our careers website (www.pfizer.com/careers<http://www.pfizer.com/careers>) by searching for the job opening title Postdoctoral Fellow - Computational Chemistry as keywords, or by using the job opening ID 994031 I believe it is a 2 year position. I also believe, unlike some industrial postdocs, there is nothing preventing us from hiring the person at the end of the postdoc (though, of course, there are no guarantees that we will be able to, either). Arjun Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] PETER A. KOLLMAN LECTURESHIP - April 3, 2014
by Flowers, Nicole 01 Apr '14

01 Apr '14

THURSDAY, APRIL 3, 2014 AT 12:00 PM PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS LIBRARY 221 WEBCAST: Reception in Byers Hall 5th Floor Lounge at 3:30 Please see attached flyer. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 1

[Compbio-allhands] Fwd: Job offers at CRG-CNAG
by Tom Ferrin 17 Mar '14

17 Mar '14

-------- Original Message -------- Subject: Job offers at CRG-CNAG Date: Mon, 17 Mar 2014 15:32:34 +0100 From: Marc A. Marti-Renom <mmarti(a)pcb.ub.cat> To: Marc A. Marti-Renom <mmarti(a)pcb.ub.cat> Dear friends and colleagues (apologies for the mass posting), I would appreciate if you pass this e-mail to whom may be interested on working in 4D (structure and dynamics) genomics at the CRG and CNAG in Barcelona. Together with the Beato, Graf and Filion Labs, we have recently opened several positions to work on experimental and computational aspects of our ERC Synergy grant "/4DGenome: Dynamics of human genome architecture in stable and transient gene expression changes/". More details here for the four levels of expertise we seek: Postdocs http://www.nature.com/naturejobs/science/jobs/391399-for-postdoc-position Bioinformaticians http://www.nature.com/naturejobs/science/jobs/391401-for-bioinformatician-p… Technicianshttp://www.nature.com/naturejobs/science/jobs/391403-for-technic… PhDshttp://www.nature.com/naturejobs/science/jobs/391405-for-phd-position Many thanks in advance, Marc ... *Marc A. Marti-Renom, ICREA Research Professor* *Genome Biology Group Leader - CNAG - Centre Nacional d’Anàlisi Genòmica* *Structural Genomics Group Leader - CRG - Centre de Regulació Genòmica* Parc Científic de Barcelona – Torre I Baldiri Reixac, 4, 08028 Barcelona Tel +34 9340 33743 Email _mmarti(a)pcb.ub.cat <mailto:mmarti@pcb.ub.cat>_ Web _http://marciuslab.org_ - _http://cnag.cat_ - _http://crg.cat_ *** Consider the environment. Print responsibly. ***

1 0

[Compbio-allhands] 3/13/14 Seminar with Tim Hughes
by Flowers, Nicole 07 Mar '14

07 Mar '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Tim Hughes University of Toronto Kaleidoscopic evolution of C2H2 zinc finger DNA Binding March 13, 2014 N. Krogan, 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 CCB Graduate Program Assistant AMBER Software Administrator 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: Scientist - Molecular modeller/simulator position at Novozymes
by Jacobson, Matt 06 Mar '14

06 Mar '14

Begin forwarded message: From: "Wittmann, Torsten" <Torsten.Wittmann(a)ucsf.edu<mailto:Torsten.Wittmann@ucsf.edu>> Subject: Fwd: Scientist - Molecular modeller/simulator position at Novozymes Date: March 6, 2014 10:05:51 AM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> In case you have anyone looking for jobs. Sent from my iPhone Begin forwarded message: From: "JEIN (Jens Erik Nielsen)" <JEIN(a)novozymes.com<mailto:JEIN@novozymes.com>> Date: March 6, 2014, 12:27:26 AM PST To: "JEIN (Jens Erik Nielsen)" <JEIN(a)novozymes.com<mailto:JEIN@novozymes.com>> Subject: Scientist - Molecular modeller/simulator position at Novozymes Dear All Please see the job ad below. We are looking for a talented person with a molecular modelling/simulation background who will have a big impact on the protein engineering projects that will develop new products for the world’s largest producer of industrial enzymes. http://novozymes.com/en/careers/jobs/Pages/52705.aspx Best wishes Jens ------------------------------------- Jens Erik Nielsen Senior Manager Novozymes A/S Krogshoejvej 36 2880 Bagsvaerd Denmark Phone: +45 44461692 Mobile: +45 30771692 E-mail: jein(a)novozymes.com<mailto:jein@novozymes.com> Web: www.novozymes.com<http://www.novozymes.com/> Follow Novozymes on: LinkedIn<http://www.linkedin.com/company/novozymes/> | Twitter<https://twitter.com/Novozymes/> Novozymes A/S (reg. no.:10007127). Registered address: Krogshoejvej 36 DK-2880 Bagsvaerd, Denmark This e-mail (including any attachments) is for the intended addressee(s) only and may contain confidential and/or proprietary information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information herein is strictly prohibited. If you are not an intended recipient you should delete this e-mail immediately. Thank you. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Seminar - Friedrich Foerster, Max Planck Institute, March 11, 2014 - 10am - GH S261
by Hilary Mahon 05 Mar '14

05 Mar '14

--- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

1 0

[Compbio-allhands] Fwd: Job Postings for Life Scientists
by Jacobson, Matt 04 Mar '14

04 Mar '14

Begin forwarded message: From: "Lindstaedt, Bill" <Bill.Lindstaedt(a)UCSF.EDU<mailto:Bill.Lindstaedt@UCSF.EDU>> Subject: Job Postings for Life Scientists Date: March 4, 2014 9:52:56 AM PST To: <BPSTUDENTS(a)LISTSRV.UCSF.EDU<mailto:BPSTUDENTS@LISTSRV.UCSF.EDU>> Reply-To: "Lindstaedt, Bill" <Bill.Lindstaedt(a)UCSF.EDU<mailto:Bill.Lindstaedt@UCSF.EDU>> Bio-rad (note: 2 separate positions) (1) Sr. R&D Engineer, Microfluidics department Pleasanton, California Job Description<https://biorad-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.job…> The R&D engineer will design and build new instruments, and develop control and analytical software. You will develop mechatronics and optical systems as well as microfluidic devices. You will have the opportunity to develop these instruments from the research stage through product development. Required Skills • Hands-on working knowledge of microfluidics and automated fluidics instrumentation • Detailed understanding of laminar and liquid-liquid fluid flows • Experience manipulating microliter volumes of fluid • Experience in MEMS and/ or microfluidics fabrication • Proficient with SolidWorks • Proficient in programming in Python, MATLAB or C++ • Capable of developing and executing experimental protocols, and communicating findings clearly and concisely Required Experience • Degree in Mechanical Engineering, Chemical Engineering, or equivalent field • PhD and industrial experience, or MS or BS degree with equivalent research experience --- (2) Staff Scientist, Microfluidics department Pleasanton, California Job Description<https://biorad-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.job…> The staff scientist will help to lead the biology and biochemistry efforts in the group to develop the next generation of products. This is a multidisciplinary group and we will work on a multitude of systems from nucleic acids to proteins and cells. You will devise and develop assays and work intimately with the engineering group developing instrumentation. Finally, we are growing the Digital Biology Center to be the preeminent center for droplet microfluidics research. You will be a foundational member of the group and we look forward to your influence and creativity choosing future research directions. Required Skills • A proven track record of assay design, development and implementation. • Experience with NGS sample preparation methods • Familiarty with ELISA and other protein analysis methods • Experience developing and optimizing nucleic acids protocols, such as PCR. • Experience leading other scientists. • Excellence in written and oral communication. • PhD in biology, biochemistry, Chemical Engineering, or similar field • 3-5+ years experience in industry or academia post PhD or equivalent Apply online or contact Paul Korn paul_korn(a)bio-rad.com<mailto:paul_korn@bio-rad.com> at HR for questions. D. E. Shaw Research Postdoctoral Fellow New York, New York Job Description<https://careers.deshawresearch.com/recruit/JoiningDepartment.html>; or see attachment D. E. Shaw Research is seeking postdoctoral fellows of exceptional ability to join our New York-based team. This is a unique opportunity to develop and work with transformative technology in a dynamic, interdisciplinary environment. Candidates should have expertise in computational chemistry, biology, or physics, or in a relevant area of computer science or applied mathematics. Relevant areas of experience • the study of allosteric interactions or other functionally important conformational changes in biological molecules • structure prediction or design for proteins or RNA • the study of protein–protein or protein–nucleic acid interactions • force field improvement through detailed comparisons of simulation data with NMR measurements • development and implementation of new methodology (e.g., integrators, methods for enhanced sampling or free-energy calculations, or tools to efficiently analyze large simulation datasets). Application URL: http://www.deshawresearch.com/recruit/jobs/Oncampus/UCSF/PF Either apply online or send a CV or resume to Želimir Galjanić at Zelimir.Galjanic(a)career.DEShawResearch.com<mailto:Zelimir.Galjanic@career.DEShawResearch.com>. BioCentury Publications, Inc Senior Writer San Francisco, CA or Chicago, Illinois (See attachment) BioCentury Publications Inc. is widely known as the leading provider of business intelligence about the biotechnology and pharmaceutical industries through its high value-added newsletters, conferences and research services. The company currently has openings for Senior Writers to evaluate scientific developments, clinical research, regulatory and public policy developments for their healthcare, commercial and investment impact and write about them for our publications. Requirements • 4+ years work experience or other credentials to demonstrate advanced knowledge of the topics addressed by the company’s publications and services. • ability to write complex, multi-source articles of up to 3,000 words at least six times a year that identify emerging trends and engage in interpretative, forward-looking thinking. • expected to produce an average of at least two pages of published copy per week. • The ability to write clearly and accurately in English that is correct with respect to grammar, spelling and style, within the company’s deadlines. Fluency in a language other than English is highly desirable. • The ability to think analytically, to be able to evaluate the potential outcomes of actions or events, to communicate this reasoning in writing and, where appropriate, to provide supporting numerical analysis. Experience with financial modeling is highly desirable. • News judgment, i.e., the ability to prioritize news events in order of importance for the company’s audience, and to be able to explain the reasoning behind the ranking. Please contact Susan Morgan,smorgan(a)biocentury.com<mailto:smorgan@biocentury.com> Director of HR, BioCentury Publications, Inc. Bio-rad Scientist, BioEducation R&D Hercules, CA Job Description<https://biorad-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.job…> Bio-Rad believes that the biotechnology industry should play an integral role in supporting education, helping to develop today's students as tomorrow's scientists and problem solvers. Bio-Rad's Biotechnology Explorer program (www.explorer.bio-rad.com<http://www.explorer.bio-rad.com/>) has developed a line of laboratory kits which have provided millions of students around the world the opportunity to explore the fundamental techniques of genetic engineering, DNA fingerprinting, DNA amplification, protein expression and analysis, bioinformatics, and the creation of genetically modified organisms. Required Skills • The primary job responsibility is to develop hands-on biotechnology educational kits and activities for use in teaching labs at the high school, community college and university levels. • Performing the necessary laboratory work required to develop and validate new kits, and managing the project through the new product development process. • Technically support all existing products and be an expert source for technical questions related to all of our products for both internal and external inquiries. • Have an understanding of the education market and US educational system and participate in marketing activities and is expected to interact frequently with teachers and students. • Attend and support training workshops for teachers. The job requires 10-15% time traveling to tradeshows and customer visits. Education: MS (with industry work experience) or PhD in a life science discipline. Engineering, Bioinformatics, chemistry or environmental science background is a plus. The ideal candidate will minimally have completed a life science-based doctoral graduate program or have equivalent work experience. Required Experience • Passion for science education and be excited to work as part of a dynamic, fast paced, and highly motivated team. • Have balanced laboratory skills including molecular biology, protein biochemistry, and bioinformatics analysis. • Broad knowledge base of biology and science in general • Computer programming experience is a plus • Some teaching experience; experience working with teachers to deliver new classroom content are preferred. • Product development experience in industry are highly desirable. Bryony Ruegg, PhD Business Unit Manager Biotechnology Explorer Program Bio-Rad Laboratories, Inc. Email: bryony_ruegg(a)bio-rad.com<mailto:bryony_ruegg@bio-rad.com> Nodality (note: 2 separate positions) Nodality is a start-up biotechnology company with a unique technology that reveals biological function to enable better drug development, diagnostics and patient care. We are seeking qualified applicants for the position of Scientist I/II, Research. The scope of research will address the application of flow cytometric analysis to the interrogation of immune cell signaling in the context of development of therapeutic drugs and diagnostic tests for autoimmune disorders, cancer immunotherapy and hematologic malignancies. (1) Scientist I/II, Research South San Francisco, CA (See attachment) Functions: • Apply and further develop Nodality's SCNP technology to address clinically relevant questions addressing both disease biology and drug development. • Work effectively in multidisciplinary teams including clinical and computational sciences, addressing diverse scientific and clinical questions. • Apply understanding/knowledge of signaling biology to develop SCNP assays for continued expansion of biological scope and disease-based applications. • Effectively operate within multiple projects with varied objectives and timelines. Education and Experience: • PhD in a relevant discipline (or equivalent experience if all other criteria are met);minimal 2 yrs industry experience • Understanding / knowledge of signaling biology is essential and experience in cancer immunotherapy is a plus. • Knowledge of principles of flow cytometry is essential, hands-on experience is highly desirable. • Immunological background is preferred. • Excellent verbal and written communication skills are essential. --- (2) Scientist, Bioinformatics/Data Scientist South San Francisco, CA (See attachment) Responsibilities: • Work with biologists to design experiments to answer complex biological and clinical questions in oncology, autoimmunity, and immunology • Perform a variety of data analysis tasks ranging from exploring biology to developing and validating predictive models for clinical applications • Work in cross-functional teams with research biologists, technology experts, biostatisticians, clinical scientists, and computational scientists • Use your programming skills to efficiently manage experimental data and data workflows • Contribute to development of study protocols, statistical analysis plans and reports • Explore, evaluate, and implement novel approaches and data analysis methods for interpreting biological experiments and improving processes • Present proposals and findings within and beyond your team Job Requirements: • A PhD with strong background in computational biology, biostatistics, bioinformatics, computer science, data science or related field • Knowledge of molecular and cellular biology and experience working with biological data • Knowledge of statistical and machine learning techniques • Proficiency with popular statistical packages such as R • Proficiency with Python • Understanding of database systems (SQL, MongoDB, etc.) • Knowledge of web development languages and packages such as JavaScript, D3.js is a plus Please submit your resume with cover letter to jobs(a)nodalityinc.com<mailto:jobs@nodalityinc.com>. Nodality is an equal opportunity employer. -- Thi Nguyen, PhD Program Director, Career Development Graduate Students and Postdocs Office of Career and Professional Development Student Academic Affairs University of California, San Francisco 1675 Owens St, Ste 310 San Francisco, CA 94143 Phone: 415-514-4750 career.ucsf.edu<http://career.ucsf.edu> Please schedule meetings through Celestine Fry: 415-476-4986, ocpd(a)ucsf.edu<mailto:ocpd@ucsf.edu> --- Bill Lindstaedt, MS Director Office of Career and Professional Development Student Academic Affairs University of California, San Francisco 513 Parnassus Ave., Room S-140 San Francisco, CA 94143 Phone: 415-502-2422 career.ucsf.edu<http://career.ucsf.edu> Please schedule meetings through Celestine Fry: 415-476-4986, ocpd(a)ucsf.edu<mailto:ocpd@ucsf.edu> ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BPSTUDENTS&A=1> from this mailing list. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Postdoc Positions Available
by Jacobson, Matt 26 Feb '14

26 Feb '14

Begin forwarded message: From: Sharon Hammes-Schiffer <shs3(a)illinois.edu<mailto:shs3@illinois.edu>> Subject: Postdoc Positions Available Date: February 26, 2014 4:17:02 PM PST To: undisclosed-recipients:; Dear Colleague, I would appreciate your help in forwarding this e-mail to potential postdoc candidates. Best regards, Sharon POSTDOCTORAL POSITIONS AVAILABLE Several postdoctoral positions are currently available in my group at the University of Illinois at Urbana-Champaign. I am particularly seeking candidates interested in working on biologically oriented projects. These projects are focused on understanding the fundamental principles underlying enzyme and ribozyme catalysis, especially the roles of electrostatics, hydrogen bonding, and protein motion. One of the current projects centers on the use of nitrile probes placed at specific sites within an enzyme to examine the electrostatic and conformational changes along the catalytic cycle via the vibrational frequency shifts. Another current project uses mixed quantum mechanical/molecular mechanical (QM/MM) free energy methods to elucidate the mechanisms of several different ribozymes. Other projects focus on proton-coupled electron transfer (PCET) in enzymes. Two relevant papers are listed below, and additional information can be found on my group web site: http://www.scs.illinois.edu/schiffer/. Interested candidates should send a CV to me at shs3(a)illinois.edu<mailto:shs3@illinois.edu>. J. Layfield and S. Hammes-Schiffer, "Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding," J. Am. Chem. Soc. 135, 717-725 (2013). A. Ganguly, P. Thaplyal, E. Rosta, P. C. Bevilacqua, and S. Hammes-Schiffer, "Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme," J. Am. Chem. Soc. 136, 1483-1496 (2014). -- Sharon Hammes-Schiffer Swanlund Professor of Chemistry Department of Chemistry University of Illinois at Urbana-Champaign A410 Chemical & Life Sciences Laboratory 600 South Mathews Avenue Urbana, IL 61801-3364 Phone: (217) 300-0335 Fax: (217) 244-3186 e-mail: shs3(a)illinois.edu<mailto:shs3@illinois.edu> http://www.scs.illinois.edu/schiffer/ Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Stefan Boresch talk today
by Jacobson, Matt 25 Feb '14

25 Feb '14

Noon, BH212 Stefan Boresch, U. Vienna "Free energy simulations: from boring methodological work to a promising novel approach for QM/MM" http://www.mdy.univie.ac.at/en/people/boresch/boresch.html Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] 2/27/14 Seminar with Bianxiao Cui
by Nicole Takesono Flowers 21 Feb '14

21 Feb '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Bianxiao Cui Stanford Light-controlled intracellular signaling pathways in cell fate determination February 27, 2014 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 CCB Graduate Program Assistant AMBER Software Administrator 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: Cool Kinase Talk (hastily scheduled!) tomorrow (Friday) - 4PM - BH212
by Jacobson, Matt 20 Feb '14

20 Feb '14

-- Matt Sent from my iPad Begin forwarded message: From: James Fraser <jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com>> Date: February 20, 2014 at 6:02:33 PM PST To: "Taunton, Jack (Jack.Taunton(a)ucsf.edu<mailto:Jack.Taunton@ucsf.edu>)" <Jack.Taunton(a)ucsf.edu<mailto:Jack.Taunton@ucsf.edu>>, "Kevan Shokat" <shokat(a)cmp.ucsf.edu<mailto:shokat@cmp.ucsf.edu>>, Natalia Jura <natalia.jura(a)ucsf.edu<mailto:natalia.jura@ucsf.edu>>, "Michael Grabe" <mdgrabe(a)pitt.edu<mailto:mdgrabe@pitt.edu>>, David Sivak <david.sivak(a)gmail.com<mailto:david.sivak@gmail.com>>, "Matthew Jacobson" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>>, Jim Wells <Jim.Wells(a)ucsf.edu<mailto:Jim.Wells@ucsf.edu>>, "Lim, Wendell" <Wendell.Lim(a)ucsf.edu<mailto:Wendell.Lim@ucsf.edu>>, Tanja Kortemme <kortemme(a)cgl.ucsf.edu<mailto:kortemme@cgl.ucsf.edu>>, "Fujimori, Danica" <Danica.Fujimori(a)ucsf.edu<mailto:Danica.Fujimori@ucsf.edu>>, Fletterick Robert <flett(a)msg.ucsf.edu<mailto:flett@msg.ucsf.edu>>, Agard Dave <agard(a)msg.ucsf.edu<mailto:agard@msg.ucsf.edu>>, Robert Stroud <stroud(a)msg.ucsf.edu<mailto:stroud@msg.ucsf.edu>>, Trever Bivona <TBivona(a)medicine.ucsf.edu<mailto:TBivona@medicine.ucsf.edu>>, Mark von Zastrow <vonzastrow(a)gmail.com<mailto:vonzastrow@gmail.com>>, "Jeff Cox" <jeffery.cox(a)ucsf.edu<mailto:jeffery.cox@ucsf.edu>> Subject: Cool Kinase Talk (hastily scheduled!) tomorrow (Friday) - 4PM - BH212 Matthew Young (Prof at UMichigan, was a postdoc once upon a time with John Kuriyan) was in town for BPS. He has some cool new mechanistic stories on Kinase regulation (and also some new directions on deubiquitinase inhibitors) that you all might be interested in! The seminar will be at 4PM Friday (tomorrow) in BH212. Please forward to your labs! https://dl.dropboxusercontent.com/u/7403581/matt_young.pdf If you want to meet with Matt, let me know, he'll get to campus around 2:30-3 and be free until 4. I'm happy to direct him your way - first come first served! The plan was to grab a beer after the talk at Terzetto, to which everyone is invited. Hope to see you there! And apologies for the last minute nature of the invite, Jaime ABSTRACT: Matthew Young - University of Michigan Allosteric Regulation Of Protein Kinase Enzymes Via An Electrostatic Switch That Modulates Active Site Dynamics Protein kinase (PK) enzymes are a large family of signaling proteins that play a central role in signal transduction pathways. Robust regulation of their catalytic activity is critical, and many oncogenes harbor mutations that result in misregulated PK activity. The chemical basis for how some PK regulatory factors ultimately affect the rate of chemistry is still not completely understood. We have identified a long-range electrostatic switch that we believe is used by allosteric PK regulatory factors to modulate the rate of chemistry by tuning active-site dynamics. We applied a combination of crystallography, kinetics, and molecular dynamics to determine the chemical kinetic basis for how this electrostatic switch, toggled by regulatory subunit binding, affects each step of the catalytic cycle of CDK2 kinase. We engineered point mutants to deconstruct the kinetic, dynamic, and thermodynamic consequences of the switch. We also evaluated other PKs and find that, although it has evolved to be triggered in different ways by diverse PK regulatory factors, the mechanics of this switch can be conserved. We demonstrate that a key component of the switch is that it affects a significant change in the electrostatic potential within the ATP*Mg binding site of the enzyme. This electrostatic effect is propagated through the low-dielectric protein interior and directly affects the two dominant rate-determining steps of catalysis: attenuating both the recruitment of catalytically essential Mg cofactors (affecting both kcat and KM) as well as the release of the ADP product. Conclusion: We present a chemical hypothesis that provides a mechanistic explanation for one way that a large-scale conformation transition, observed in diverse PK family members, is able to significantly affect the rate of chemistry by acting at a distance from the active site. -- -- James Fraser, PhD Assistant Professor Department of Bioengineering and Therapeutic Sciences Office: N212C Genentech Hall, Lab: N216 Genentech Hall james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu> // jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com> (415) 493-8421 http://www.fraserlab.com

1 0

[Compbio-allhands] Biomolecular Discovery Dome - TODAY ONLY 11:30-1:30 Byers Hall 2nd floor atrium
by Tom Ferrin 20 Feb '14

20 Feb '14

If you didn't get a chance to experience the 3D Biomolecular Discovery Dome this week at the Biophysical Society annual meeting, you've still got a chance to see it. The dome will be running in the 1st floor atrium area of Genentech Hall TODAY Feb 20th between noon and 3pm. Short videos that examine macromolecular complexes and explore datasets from electron microscopy will be shown. Co-sponsored by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI).

1 2

[Compbio-allhands] 2/20/14 Seminar with Claudio Joazeiro
by Nicole Takesono Flowers 14 Feb '14

14 Feb '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Claudio Joazeiro Scripps Listerin/Ltn1 links Co-translational Protein Quality Control and Neurodegeneration. February 20, 2014 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 CCB Graduate Program Assistant AMBER Software Administrator 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: Postdoc opportunity: design of HIV entry inhibitors
by Andrej Sali 31 Jan '14

31 Jan '14

-- 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 Begin forwarded message: > From: Cameron Abrams <cfa22(a)drexel.edu> > Subject: Postdoc opportunity: design of HIV entry inhibitors > Date: January 31, 2014 at 7:49:20 AM PST > To: sali(a)salilab.org > > Dear Andrej, > > My name is Cameron Abrams and I am the director of the computational core of an NIH-P01 program project entitled "Structure-based antagonism of HIV-1 envelope function in cell entry". I have immediate need to hire a postdoc with experience in docking calculations and molecular dynamics. I have attached a description of the position to this email. I would very much appreciate it if you could let me know if any members of your group would be interested in learning more about this position. > > Thanks in advance, > Cameron > ---- > Cameron F Abrams, Professor > Department of Chemical and Biological Engineering > Drexel University, Philadelphia, Pennsylvania > t 215-895-2231

1 0

[Compbio-allhands] 2/13/14 Seminar with Benjamin Cravatt
by Nicole Takesono Flowers 31 Jan '14

31 Jan '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Benjamin Cravatt Scripps Activity-based proteomics- applications for enzyme and inhibitor discovery. February 13, 2014 C. Fitzsimmons & R. Levin, 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 CCB Graduate Program Assistant AMBER Software Administrator 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: Astex Postdoctoral Training Program
by Brian Shoichet 29 Jan '14

29 Jan '14

FYI ---------- Forwarded message ---------- From: Marcel Verdonk <Marcel.Verdonk(a)astx.com> Date: Wed, Jan 29, 2014 at 10:48 AM Subject: Astex Postdoctoral Training Program To: "bshoichet(a)gmail.com" <bshoichet(a)gmail.com> Dear Brian, I hope you are well! I wanted to bring to your attention that Astex is starting a Postdoctoral Training Program this year. This will involve a number of postdocs each year, working in and across a range of disciplines, doing cutting edge science. These are fully industrial postdocs, based at the Astex site in Cambridge, UK, with supervision provided by Astex scientists. Assuming we can get a candidate of high enough calibre, one of these postdocs will be working with me in the Astex Computational Chemistry group. We have posted an advert on the CCL web site describing the Postdoctoral Training Program, and a little bit about a possible project in computational structure-based design: http://www.ccl.net/cca/jobs/joblist/mess0028548.shtml We are looking for outstanding young scientists with a background in computational chemistry, preferably with an expertise in structure-based methods. Given your outstanding work in Computational Chemistry I wondered if you were aware of a potential candidate in your group or department who might be suitable, and to whom you could pass on this message? Best wishes, Marcel _______________________________ *Marcel Verdonk, PhD* Director, Computational Chemistry & Informatics Astex Pharmaceuticals 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 226206 Fax: +44(0)1223 226201 marcel.verdonk(a)astx.com <m.verdonk(a)astex-therapeutics.com> www.astx.com <http://www.astex-therapeutics.com> _______________________________ This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. -- Brian Shoichet, Professor http://www.uoft.bkslab.org/ University of Toronto, Leslie Dan Faculty of Pharmacy Donnelly Centre Room 604 (416) 978-7224 University of California, San Francisco Dept. of Pharmaceutical Chemistry

1 0

[Compbio-allhands] Fwd: Group leader search FMI
by Jacobson, Matt 28 Jan '14

28 Jan '14

Begin forwarded message: From: "Gasser, Susan" <susan.gasser(a)fmi.ch<mailto:susan.gasser@fmi.ch>> Subject: Group leader search FMI Date: January 28, 2014 6:28:00 AM PST To: "'matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>'" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Cc: _DS directors office <directors.office(a)fmi.ch<mailto:directors.office@fmi.ch>> Dear Matthew, I am writing to ask your help in identifying promising candidates for tenure-track group leader positions at the Friedrich Miescher Institute in Basel, Switzerland. As you know, the FMI pursues biomedical research of a basic nature, being particularly strong in the study of neuronal circuits, epigenetics (both chromatin and small RNAs) and in mechanisms that signal and determine cell fate. With the impending retirements of two senior scientists, we have decided to expand into a new area – that of quantitative cell biology. This means we are looking for individuals trained in either physics, math or computational sciences, who address basic biological questions both computationally and experimentally. Of course, we also accept applications from biologists, but we are particularly interested in attracting persons who will probe cell physiology quantitatively, such that they can propose and test models of complex cell and/or organismal function. The research environment at the FMI is outstanding. Young group leaders are given up to 6 years before tenure evaluation, and they have a large range of efficient core facilities at their disposal. They will have sufficient funding to run a group of 4-5 scientists without raising external support. The language of the institute is English and Basel has a lively biomedical research community. The exact research topic is less critical than the energy and enthusiasm with which the candidates address their question, and their willingness to interact with other FMI research teams. The deadline for application is April 15, 2014. Applications should be submitted online at www.fmi.ch/gl_search<http://www.fmi.ch/gl_search> and enquiries can be sent to Dirk Schuebeler (dirk(a)fmi.ch<mailto:dirk@fmi.ch>) or to me. We would be grateful if you could distribute the attached flyer in your institute and among promising scientists in your field. Best wishes, Susan Professor S. M. Gasser Director of the Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 CH-4058 Basel Switzerland tel +41 61 697 7255 (assistant) tel +41 61 697 5025 (direct) fax +41 61 697 3976 susan.gasser(a)fmi.ch<mailto:susan.gasser@fmi.ch> http://www.fmi.ch/<http://www.fmi.ch%3chttp:/www.fmi.ch/> Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] 1/30/14 Seminar with Kate Carroll
by Nicole Takesono Flowers 24 Jan '14

24 Jan '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursday, 1 pm CVRI 159 **PLEASE NOTE THE TIME AND ROOM CHANGE** Kate Carroll Scripps Painting the Cysteine Chapel: New Tools to Probe Oxidation Biology January 30, 2014 B. DeGrado, Host **PLEASE NOTE THE TIME AND ROOM CHANGE** This seminar is sponsored by Novartis. BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Grabe lab post-doc candidate
by Jacobson, Matt 22 Jan '14

22 Jan '14

-- Matt Sent from my iPhone Begin forwarded message: From: "Grabe, Michael" <Michael.Grabe(a)ucsf.edu<mailto:Michael.Grabe@ucsf.edu>> Date: January 22, 2014, 4:02:52 PM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: Grabe lab post-doc candidate Hi Matt, I have a post-doc candidate, David Argudo, interviewing this Friday from Penn. His background is in the mechanical behavior of DNA under force. Please feel free to share the information on his talk with your group - they are more than welcome to attemd if the topic is of any interest. Cheers, Michael Speaker: David Argudo, University of Pennsylvania, Department of Mechanical Engineering (post-doc candidate in Grabe Lab) Presentation Title : "The Mechanical Response of DNA: Twisting the Molecule" Time: 10:30 am Friday January 24th, 2014 Room: 342 Smith Building (3rd floor) Abstract: Since the structure of double stranded DNA was discovered about six decades ago, there have been great developments in the fields of biology, genetic engineering, molecular biology, biophysics and numerous others. It is the objective of our work to carry on with these developments by providing new insights and understanding of DNA behavior/function using mechanics as our primary tool. To achieve this goal we focus on building analytical models for DNA molecules using rod theory and statistical mechanics. We model a key experiment in which a tensile force is applied on the DNA while simultaneously twisting it using optical or magnetic tweezers. In these experiments, DNA has been seen to form helical structures (supercoils), collapse into tightly condensed structures (toroids) and undergo structural changes (phase transitions). Our work focuses on studying all these phenomena by accounting for DNA elasticity, entropic effects due to thermal fluctuations and electrostatics. ------------------------------------------------------------------- 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

1 0

[Compbio-allhands] Fwd: 5 year post-doctoral fellowship in Medical Image Analysis
by Tom Ferrin 21 Jan '14

21 Jan '14

-------- Original Message -------- Subject: 5 year post-doctoral fellowship in Medical Image Analysis Date: Tue, 21 Jan 2014 23:58:17 +0000 From: Bob Fisher <rbf(a)inf.ed.ac.uk> To: tef(a)cgl.ucsf.edu 5 year post-doctoral fellowship in Medical Image Analysis The University of Edinburgh is advertising a number of 5 year fellowships that are expected to evolve into open ended tenured positions. Of particular interest to this email are applicants in Medical Image Analysis However, the School of Informatics is also looking for applicants in Algorithms for Big Data and distributed Systems, Cryptography, Automated reasoning, Cyber-security, Robotic hardware control, Geo-location and modelling of natural systems, Data-intensive biomedicine, Analysis of gene regulation data and data-driven modelling of gene networks controlling neural development, Design with data, Data-intensive social systems The advertisement is below. Closing date 7 February 2014 (5pm). Candidates likely to be considered for interview will already have a PhD and several publications in quality journals or top conferences. Best wishes, Bob ================================================================ Chancellor's Fellowships: Informatics University of Edinburgh - School of Informatics 37,756 - 45,053 GBP College of Science and Engineering The University of Edinburgh, a global top 20 University located in one of the world`s finest cities, continues to invest in the future of its academic staff with the appointment of a cohort of 50 tenure-track Chancellor's Fellowships across all disciplines. These 5-year Fellowships are intended to support candidates at the start of their independent academic careers. Subject to satisfactory review at the end of year 3, the Fellow will then move to a standard University academic open-ended contract. It is anticipated that most appointees will be successful in obtaining an open ended contract. Our people have been making their mark on the world for more than four centuries. They've explored space, revolutionised surgery, won Nobel Prizes, published era-defining books, paved the way for life-saving medical breakthroughs and laid the foundations for solving the mysteries of the universe. We are looking for highly talented academics who will contribute to our continued achievement of excellence in research. Colleagues addressing data intensive research are encouraged. You will already be working in an independent research capacity and will be developing your reputation for high quality research. Chancellor's Fellows also make an important contribution to enriching student learning experiences through their research, teaching and personal tutoring. You will concentrate on research initially, but will be trained in teaching skills and progressively take up this core academic activity. As we are a global University, we are interested in candidates from any location and we can offer relocation support. The culture of the University is open and diverse and we strive to replicate that in our appointments. Whilst we are proud of our rich heritage, we are a University that looks to the future. We are a global University with world leading interdisciplinary research capability, ideal for collaborative work as required. By joining our research-led community of international academics you will enjoy excellent career opportunities and support. Appointment will normally be made on the Grade 8 Academic scale (37,756-45,053 GBP), dependent on experience. In exceptional circumstances a more senior appointment may be made. This is an excellent opportunity to be part of one of the world's top Universities where you will develop your career in a stimulating, friendly and diverse environment that nurtures talent and rewards success. We welcome applications from everyone irrespective of gender or ethnic group. As women and members of ethnic minorities are currently under-represented in posts at this level we particularly encourage applications from members of these groups. For more information visit our website https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.disp… Closing date: 7 February 2014 (5pm). Committed to Equality and Diversity The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

1 0

[Compbio-allhands] Fwd: Novartis Symposium on Novel Approaches to Therapeutics and Targets - January 30th
by Jacobson, Matt 21 Jan '14

21 Jan '14

-- Matt Sent from my iPhone Begin forwarded message: From: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Date: January 21, 2014, 11:55:41 AM PST To: <BBCFACULTY(a)LISTSRV.UCSF.EDU<mailto:BBCFACULTY@LISTSRV.UCSF.EDU>> Subject: Novartis Symposium on Novel Approaches to Therapeutics and Targets - January 30th Reply-To: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Please join us for the Novartis Symposium on Novel Approaches to Therapeutics and Targets. Speakers include Eric Martin and Cindy Shafer of Novartis and Kate Carroll from the Scripps Research Institute. See the attached flyer for more details. Thursday, January 30th 9:00 am - 2:00 pm Smith Cardiovascular Research Building Room 159 **Please note, Kate Carroll’s BBC Seminar Series talk will be from 1-2pm in CVRI Rm 159 and NOT in Byers Auditorium at 12pm. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ About the invited speakers: Eric Martin is Director of Computational Chemistry at Novartis. He is credited with having started the field of combinatorial library design in the early 90s. Over the past 25 years he has worked in computational chemistry, analytical instrument development, environmental-fate modeling, drug design and herbicide design. His recent research includes the development of three novel kinase virtual screening methods, which he has combined with experimental IC50 and structural data to screen 4 million compounds across the entire kinome achieving unprecedented speed and accuracy. Cindy Shafer is a Project Leader in the Global Discovery Chemistry Group at Novartis. While at Novartis, she has worked on oncology, diabetes and anti-viral programs from the hit-to-lead stage through lead optimization. Several of these programs have progressed to the clinic including TKI258/dovitinib (Ph III), HSP990 and the mutant-b-Raf inhibitors RAF265 and LGX818 (Ph III). In addition, she has led several early stage programs to develop tool compounds to further elucidate the biological relevance in oncology settings. Kate Carroll is an Associate Professor of Chemistry at The Scripps Research Institute, Florida Campus. Her research focuses on the role of oxidative thiol modifications in the dynamic regulation of signaling pathways and physiological processes. Her work includes the development of chemical probes and proteomic technologies for the dissection of redox signaling pathways. Recently she has applied these tools to the global analysis of sulfenic acid modified proteins for the identification of signaling networks regulated by cysteine oxidation. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We thank Novartis, CVRI and UCSF BBC Graduate Groups for their participation and generous financial support. Julia Molla UC San Francisco Program Coordinator, Biological& Medical Informatics and Chemistry& Chemical Biology 600-16th St. MC2280 San Francisco, CA 94158-2517 415-476-1914 phone ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BBCFACULTY&A=1> from this mailing list.

1 0

[Compbio-allhands] Fwd: Post-doc with Rhoades and Miranker
by Andrej Sali 20 Jan '14

20 Jan '14

-- 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 Begin forwarded message: > From: Andrew Miranker <Andrew.Miranker(a)YALE.EDU> > Subject: Post-doc with Rhoades and Miranker > Date: January 20, 2014 at 8:37:04 AM PST > To: Andrej Sali <sali(a)salilab.org> > > Dear Andrej, > > I am looking to recruit a post-doc in the near future for a position joint between myself and the lab of > Prof Liz Rhoades. I've attached a job-ad below. > Please encourage your graduating students to send me an application and/or come find Prof Rhoades > or myself at the Biophysical Society Meeting next month. > > Sincerely, > > Andrew > > > Andrew Miranker > Professor | Office: (203) 432-8954 > Dept of Molecular Biophysics & Biochemistry | Lab: (203) 432-5563 > Yale University | Assistant: (203) 432-5708 > 266 Whitney Avenue / Bass 318 | Fax: (203) 432-8492 > PO Box 208114 | Email: andrew.miranker(a)yale.edu > New Haven, CT 06520-8114 | Web: www.yale.edu/miranker/ > > **Please note. This is my professional email address and as such is read and > managed by my assistant, Lisa Adams (lisa.adams(a)yale.edu) >

1 0

[Compbio-allhands] postdoc jobs ad in Singapore
by Andrej Sali 17 Jan '14

17 Jan '14

-- 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: Reminder for TDT competition
by Jacobson, Matt 12 Jan '14

12 Jan '14

-- Matt Sent from my iPhone Begin forwarded message: From: Hanneke Jansen <hanneke(a)tdti.org<mailto:hanneke@tdti.org>> Date: January 12, 2014, 3:10:08 PM PST To: "'Jacobson, Matt'" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: Reminder for TDT competition Dear Matt, A quick reminder that the deadline for the second round of the TDT competition is coming up! There are four exciting challenges that focus on developing and disseminating computational workflows for drug discovery of neglected diseases with a premium on reproducibility (use freely available software tools!). Note that one of these challenges is an open innovation challenge which is a great place to submit truly novel workflows that can be exemplified on any publicly available dataset. The other three challenges are structured around specific questions with held-out test data to compare across the various submissions. Three cash prizes - plus partial reimbursement of travel - will be awarded! Winners are required to present their work at the TDT Award symposium during the Fall 2014 ACS National Meeting in San Francisco, California. Detailed information about the 2014 Competition can be found here: http://www.TDTproject.org/2014-competition.html Submissions deadline is February 3, 2014. Please remind people in your group and let me know if there are any questions. Ciao, Hanneke ++++++++++++++++++++++++++ Hanneke Jansen Hanneke(a)TDTi.org<mailto:Hanneke@TDTi.org> 415.336.3036 (cell)

1 0

[Compbio-allhands] 1/16/14 Seminar with Kevin Healy
by Flowers, Nicole 10 Jan '14

10 Jan '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Kevin Healy UC Berkeley Disease-Specifric Microphysiological Human Organ Models: the Future of Personalized Medicine? January 16, 2014 B. Conklin, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Very Exciting Postdoctoral Position Available
by Andrej Sali 09 Jan '14

09 Jan '14

Sent from my iPhone Begin forwarded message: > From: Klaus Schulten <kschulte(a)ks.uiuc.edu> > Date: January 9, 2014 at 1:25:50 PM PST > To: mike.himmel(a)nrel.gov, michael.crowley(a)nrel.gov, smithjc(a)ornl.gov, rwoods(a)ccrc.uga.edu, fsl+3(a)psu.edu, skaf(a)iqm.unicamp.br, ipolikarpov(a)ifsc.usp.br, pascutti(a)biof.ufrj.br, olson(a)scripps.edu, ramaro(a)ucsd.edu, jmccammon(a)ucsd.edu, sali(a)salilab.org, daggett(a)uw.edu, jonuchic(a)rice.edu, tolya(a)rice.edu, jpma(a)bcm.tmc.edu, cecilia(a)rice.edu, mpettitt(a)utmb.edu, brookscl(a)umich.edu, brb(a)mail.nih.gov, feig(a)msu.edu, tom.cheatham(a)pharm.utah.edu, case(a)biomaps.rutgers.edu, mlklein(a)temple.edu, twoolf(a)jhu.edu, thirum(a)umd.edu, pande(a)stanford.edu, haw2002(a)med.cornell.edu, Elizabeth.rhoades(a)yale.edu, tieleman(a)ucalgary.ca, treptow(a)unb.br, s.j.marrink(a)rug.nl, mv245(a)cam.ac.uk, g-schatz(a)northwestern.edu, bahar(a)pitt.edu, jerome.henin(a)ibpc.fr, david.perahia(a)lbpa.ens-cachan.fr, grace.brannigan(a)rutgers.edu, matteo.dalperaro(a)epfl.ch, wah(a)bcm.edu, roberto.lins(a)ufpe.br, thereza.soares(a)ufpe.br, mark.sansom(a)bioch.ox.ac.uk, cui(a)chem.wisc.edu, hgrubmu(a)gwdg.de, laio(a)sissa.it, dennis.salahub(a)ucalgary.ca, modesto.orozco(a)irbbarcelona.org, straub(a)bu.edu, itamar(a)ime.eb.br, schlick(a)nyu.edu, amackere(a)rx.umaryland.edu, rbb24(a)cam.ac.uk, pastorr(a)nhlbi.nih.gov, ddmmzz(a)pitt.edu, andricio(a)umich.edu, cbp(a)purdue.edu, roux(a)uchicago.edu, dinner(a)uchicago.edu, gavoth(a)uchicago.edu, vandervaart(a)asu.edu, chapmami(a)ohsu.edu, dabaker(a)uw.edu, gianni.defabritiis(a)upf.edu, p.g.bolhuis(a)uva.nl, christoph.dellago(a)univie.ac.at, erik.lindahl(a)scilifelab.se, Lennart.Nilsson(a)ki.se, stefan.fischer(a)iwr.uni-heidelberg.de, bgroot(a)gwdg.de, gerhard.hummer(a)biophys.mpg.de, caflisch(a)bioc.uzh.ch, takada(a)biophys.kyoto-u.ac.jp > Subject: Very Exciting Postdoctoral Position Available > > Dear Colleagues, > > > The Theoretical and Computational Biophysics Group of the University of Illinois is seeking applications for a postdoctoral research associate position in theoretical biophysics. > > The position is funded by the Energy Biosciences Institute (www.energybiosciencesinstitute.org) to guide through molecular dynamics simulations the development of enzymes needed in second generation biofuel production. These biofuels are made from degradation of agricultural waste, e.g., of wood chips, a process which involves use of redesigned bacterial enzymes. The redesign aims at preventing inhibition of the used enzymes by process products and at enhancing efficiency. The work will be performed in collaboration with experimentalists both at the University of California – Berkeley and at the University of Illinois Urbana-Champaign. The postdoc will interact with first rate researchers in polymer science, bacteriology, plant science and bioengineering and be involved in starting an exciting, completely new research area. Pursuing in connection with biofuel studies bacterial degradation of biomass in general will be encouraged. The new postdoc will join another Energy Biosciences Institute postdoc in my group and will enjoy a well equipped research laboratory and intense research team. > > More information is available in our website (http://tcbg.illinois.edu) and also in the attached announcement. > > Please feel free to share this announcement. > > Best regards, > > Klaus Schulten >

1 0

[Compbio-allhands] Fwd: Happy New Year and hiring at new company
by Jacobson, Matt 09 Jan '14

09 Jan '14

Job opportunity ... Begin forwarded message: I’ve recently moved from Amazon because this is a compelling opportunity. IO is the global leader in software-defined data centers, and has pioneered the next-generation of data center infrastructure technology and Intelligent Control. We are a mature startup with over 600 clients, including for example Goldman Sachs. The Applied Intelligence team in San Francisco uses predictive modeling, analytics and simulation to impact both design and intelligent control. Are there any great people that spring to mind? I will attach the two job descriptions and may I ask you to let people know about the opportunity? Thank you and I’d love to catch up soon, Jim James Arnold, Ph.D. | Director Applied Intelligence Software M +1.415.216.5655 E jarnold(a)io.com<mailto:jarnold@io.com> | www.io.com<http://www.io.com> The communication contained in this e-mail is confidential and is intended only for the named recipient(s) and may contain information that is privileged, proprietary, attorney work product or exempt from disclosure under applicable law. If you have received this message in error, or are not the named recipient(s), please note that any form of distribution, copying or use of this communication or the information in it is strictly prohibited and may be unlawful. Please immediately notify the sender of the error, and delete this communication including any attached files from your system. Thank you for your cooperation. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Lunenfeld Tanenbaum Research Institute PI Search
by Andrej Sali 08 Jan '14

08 Jan '14

-- 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 Begin forwarded message: > From: Donna Doherty <doherty(a)lunenfeld.ca> > Subject: Lunenfeld Tanenbaum Research Institute PI Search > Date: January 8, 2014 at 11:30:30 AM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Professor Sali, > > Please find enclosed information related to recruitment of scientists at the Lunenfeld Tanenbaum Research Institute at Mt. Sinai Hospital. Please feel free to forward this information to your colleagues. > > Sincerely, > > > Donna Doherty on behalf of Professors Jim Woodgett, Dan Durocher, and Daniel Drucker >

1 0

[Compbio-allhands] 1/9/14 Seminar with Wah Chiu
by Nicole Takesono Flowers 06 Jan '14

06 Jan '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Wah Chiu Baylor College of Medicine Structures of Viruses Inside and Outside the Host Cells January 9, 2014 Y. Cheng, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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] Mini-course: Information Theory and Biology
by David Sivak 03 Jan '14

03 Jan '14

Hi. You ever noticed how people around here use the word "Information" like it's going out of style? You ever wondered what's the big deal? We (David Sivak, Raj Bhatnagar, Michael Chevalier) plan on getting to the heart of all that in a mini-course at Mission Bay this spring on "Information Theory and Biology." If you have any interest in possibly taking this mini-course, please help us get a sense of numbers and backgrounds by sharing a little information [sorry] about yourself at: https://docs.google.com/forms/d/1HtENxOKiXyZXyzq9-4zoK0qWpTklQHLPpZC-UKqQYA… Feel free to pass along to other interested parties. Apologies for any mailing list duplication... Thanks, David -- David Sivak Systems Biology Fellow University of California, San Francisco david.sivak(a)gmail.com davidsivak.com 510-541-9006

1 0

[Compbio-allhands] SAVE THE DATE- PETER A. KOLLMAN LECTURESHIP - April 3, 2014
by Nicole Takesono Flowers 20 Dec '13

20 Dec '13

SAVE THE DATE- THURSDAY, APRIL 3, 2014 AT 12:00 PM PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS LIBRARY 221 Reception in Byers Hall 5th Floor Lounge at 3:30 Please see attached flyer. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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] Peter Kolb Seminar - Thursday, Dec. 12 - 10am - Byers Hall 212
by Hilary Mahon 10 Dec '13

10 Dec '13

Please see attached. Thank you. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

1 0

[Compbio-allhands] BBC Seminar Speaker David Allis Talk CANCELLED
by Nicole Takesono Flowers 05 Dec '13

05 Dec '13

Please note that Dr. Allis had to cancel his previously scheduled talk (1/16/14) for the BBC Seminar Series. Thank you, Nicole Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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] Janet Thornton Seminar: Thurs., Dec. 5
by Patsy Babbitt 01 Dec '13

01 Dec '13

Please add to your calendars a special seminar by Janet Thornton: "The Evolution of Enzyme Mechanisms and Functional Diversity" Thursday, December 5th, 2013 3:00 – 4:00 PM Genentech Hall Auditorium Professor Dame Janet Thornton is the Director of the European Molecular Biology Laboratory — European Bioinformatics Institute (EMBL-EBI). She has been a leader in computational biology and bioinformatics throughout her career and has be awarded many honors, among them her election as a Fellow of the Royal Society and as a foreign associate of the National Academy of Sciences. >From her biography on Wikipedia, she is rightfully described as "one of the world’s leading researchers in structural bioinformatics, using computational methods to understand protein structure and function." Don't miss it! (Hosted by Patsy Babbitt) -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94158-2330, USA (CA 94158 for direct delivery by courier) Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Joslyn Polzien, +1 415-514-1214, 415-514-4861 Joslyn.Polzien(a)ucsf.edu

1 0

[Compbio-allhands] Fwd: Faculty positions in computational biology at the University of Rochester
by Jacobson, Matt 23 Nov '13

23 Nov '13

-- Matt Sent from my iPad Begin forwarded message: From: Sina Ghaemmaghami <sghaemma(a)bio.rochester.edu<mailto:sghaemma@bio.rochester.edu>> Date: November 22, 2013 9:18:43 AM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: Faculty positions in computational biology at the University of Rochester Dear Matt, I hope everything is going well with you. At the University of Rochester, we have undertaken a Data Science initiative. As part of that initiative, we are having tenure track job searches this year for individuals using computational approaches to investigate cross-disciplinary topics. One of the identified target areas is Computational Biology and Computational Bioengineering, e.g. functional and evolutionary genomics, proteomics and protein folding, systems biology, multi-scale modeling in bioengineering, or multimodal bio-imaging informatics. I am contacting you to see if you know of candidates on the job market (e.g. promising postdocs or already established researchers) who you could recommend, or let them know about this job search. An emphasis here would be on individuals for whom computational approaches are a key part of their research. Attached is the job description with information on how to apply, and please feel free to circulate this among your colleagues. Further information on the Data Science initiative and instructions for this search can be found at: http://www.rochester.edu/rocdata/recruit/interdisciplinary.html. The search is open to senior level candidates. So, if you know of someone who may be interested, please let me know. Sincerely, Sina Ghaemmaghami Department of Biology, University of Rochester 326 Hutchison Hall Rochester NY 14627 Tel (office): 585-275-4829 Tel (cell): 415-992-2594

1 0

[Compbio-allhands] from Hanneke Jansen
by Jacobson, Matt 20 Nov '13

20 Nov '13

Forwarding ... ------------ Teach-Discover-Treat (TDT) is excited to announce our 2014 Competition. We have four exciting challenges that focus on developing and disseminating computational workflows for drug discovery of neglected diseases with a premium on reproducibility. Three cash prizes - plus partial reimbursement of travel - will be awarded! Winners are required to present their work at the TDT Award symposium during the Fall 2014 ACS National Meeting in San Francisco, California. Create and submit computational workflows that inspire drug discovery activities using freely available software tools. Detailed information about the 2014 Competition can be found here: http://www.TDTproject.org/2014-competition.html Submissions deadline is February 3, 2014. The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell, Patrick Walters and Emilio Xavier Esposito www.TDTproject.org<http://www.tdtproject.org/> twitter.com/TeachDiscoTreat<http://twitter.com/TeachDiscoTreat>

1 0

[Compbio-allhands] Fwd: FINAL CALL: Faculty positions in Bioinformatics/Computational Biology in the Crick at LRI
by Andrej Sali 17 Nov '13

17 Nov '13

-- 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 Begin forwarded message: > From: Nicholas Luscombe <nick(a)valleyofpigs.org> > Subject: FINAL CALL: Faculty positions in Bioinformatics/Computational Biology in the Crick at LRI > Date: November 15, 2013 at 2:40:52 AM PST > To: Paul Nurse <paul.nurse(a)royalsociety.org> > Cc: Richard Treisman <richard.treisman(a)cancer.org.uk>, Jim Smith <director(a)nimr.mrc.ac.uk>, Paul Nurse <paul.nurse(a)royalsociety.org> > > Dear Colleagues, > > Thank you for your help in circulating information about the Bioinformatics/Computational Biology position at the Crick@LRI. We’ve had a lot of interest and we’re hoping that many will result in applications! > > I would like to remind you that the deadline is 22 November 2013; I should be grateful if you would continue to spread the word. > > With many thanks for your support, > > Nick Luscombe > > > Website: http://tinyurl.com/ohgnxw8 > Application deadline: 22 November 2013 > Informal enquiries may be made by e-mail to nicholas.luscombe(a)cancer.org.uk > > --- > > Faculty positions for Bioinformatics and Computational Biology > Francis Crick Institute group leaders at the CRUK London Research Institute > > An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis. > > The Francis Crick Institute http://www.crick.ac.uk > The Francis Crick Institute will open at St Pancras in central London in 2015. Its research will use interdisciplinary approaches to investigate the biology of human health and disease, supported by core funding from CRUK, the MRC, and the Wellcome Trust, and by grants from UK and international funding agencies. > > The Crick is expanding Computational Biology research as a key component of its scientific strategy. The institute will offer an outstanding environment for computational research, with excellent opportunities for wet/dry collaborations across the range of biomedical and clinical research disciplines, supported by a strategic alliance with the Wellcome Trust Sanger Institute. The new Crick laboratories will feature excellent computational facilities including a state-of-the-art data centre. > > The London Research Institute http://www.london-research-institute.org.uk > The London Research Institute (LRI) is the largest Cancer Research UK research institute, with 40 research groups focusing on fundamental cancer biology. The Institute is based in well-equipped laboratories at Lincoln's Inn Fields in central London, and at Clare Hall in Hertfordshire. > > Computational Biology in Cancer http://tinyurl.com/ohgnxw8 > An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis. The LRI recruitment process for 2013 will carried out jointly with the Crick Institute. We shall appoint outstanding scientists seeking to establish independent and innovative research programmes focussed on: > > Newly appointed group leaders will receive core funding for research personnel, travel and consumables, and access to the Institute's comprehensive computational core facilities, backed by competitive employment terms. The new group leaders will move to the Crick laboratories in 2015. > > Website: http://tinyurl.com/ohgnxw8 > Application deadline: 22 November 2013 > Informal enquiries may be made by e-mail to nicholas.luscombe(a)cancer.org.uk > > > --- > Check out our new website: www.luscombelab.org > > Nicholas M LUSCOMBE, Professor of Computational Biology > > University College London (joint appointment) > UCL Genetics Institute, Dept of Genetics, Evolution & Environment, > University College London, Gower Street, London WC1E 6BT, UK > > Cancer Research UK London Research Institute (joint appointment) > 44 Lincoln's Inn Fields, London WC2A 3LY, UK > > Okinawa Institute of Science & Technology (adjunct faculty) > 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan > > > > > >

1 0

[Compbio-allhands] 11/21/13 Seminar with Dana Pe'er
by Nicole Takesono Flowers 15 Nov '13

15 Nov '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Dana Pe'er Columbia What can you do with 40 dimensions in single cells, mapping development, signal processing and disease? November 21, 2013 W. Lim, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Computational and Systems Biology Positions at the Genome Institute of Singapore
by Tom Ferrin 14 Nov '13

14 Nov '13

-------- Original Message -------- Subject: Computational and Systems Biology Positions at the Genome Institute of Singapore Date: Thu, 14 Nov 2013 19:15:30 +0800 From: Tara Leah HUBER (GIS) <hubertl(a)gis.a-star.edu.sg> CC: Shyam PRABHAKAR (GIS) <prabhakars(a)gis.a-star.edu.sg>, Niranjan NAGARAJAN (GIS) <nagarajann(a)gis.a-star.edu.sg> Dear Colleague, We have some immediate Faculty openings in Computational and Systems biology at the Genome Institute of Singapore. Applicants with computational expertise in all areas and at all levels are welcome; areas of particular interest include: Regulatory Genomics and Epigenomics, Microbial Evolution and Metagenomics, Systems Biology and Cancer Genomics. Applicants should submit a CV, a statement of research interests and the names of three references by email (with job code "CSB-I" in the subject line) to: gisrecruit(a)gis.a-star.edu.sg <mailto:gisrecruit@gis.a-star.edu.sg> We are seeking outstanding researchers with the potential to establish impactful, independent and creative research programs at the GIS. Candidates are expected to have significant experience in the analysis of genome-wide/cell-wide biological datasets and to have demonstrated exceptional originality and excellence in their work. We would appreciate if you would share this information with your colleagues and bring it to the attention of any qualified candidate for these positions. With best regards, Niranjan and Shyam Niranjan Nagarajan Group Leader Associate Director, Computational and Systems Biology Shyam Prabhakar Group Leader Associate Director, Integrative Genomics Genome Institute of Singapore 60 Biopolis Street, #02-01 Genome, Singapore 138672 Tel: +65 6808 8071 (Niranjan Nagarajan) +65 6808 8046 (Shyam Prabhakar) http://www.gis.a-star.edu.sg ------------------------------- This e-mail and any attachments are only for the use of the intended recipient and may be confidential and/or privileged. If you are not the recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person as it may be an offence under the Official Secrets Act. -------------------------------

1 0

[Compbio-allhands] Fwd: Institute for Genomic Biology Fellowship
by Andrej Sali 13 Nov '13

13 Nov '13

Begin forwarded message: > From: Taekjip Ha <TaekjipHa(a)mx.uillinois.edu> > Subject: Institute for Genomic Biology Fellowship > Date: November 13, 2013 at 10:03:13 AM PST > > > Dear colleagues, > > I wanted to bring to your attention an exciting postdoctoral fellows program at the University of Illinois at Urbana-Champaign. The Institute of Genomic Biology (IGB) opened its $70 M building in 2007 and is research home to dozens of world-class scientists. The IGB Fellows program appoints several new fellows each year through theme-based competition. For the Cellular Decision Making in Cancer Theme that I am involved with, the first two fellows became professors in Princeton and UIUC, both winning the NIH new innovators awards, just to give you some examples of the excellence of the program. This year’s application deadline is December 1st and I am attaching an ad that ran on Science magazine. The link below points to the application site which also shows a nice video about the virtue of living in Champaign-Urbana among other things. Please share this exciting opportunity with your young colleagues. > > http://www.igb.illinois.edu/education/igb-fellows > > Best wishes, > Taekjip Ha

1 0

[Compbio-allhands] Fwd: Two junior group leader positions at the CRG (Barcelona)
by Andrej Sali 09 Nov '13

09 Nov '13

Sent from my iPhone Begin forwarded message: > From: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Date: November 9, 2013 at 8:11:26 AM PST > To: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Cc: Juan Valcarcel Juarez <juan.valcarcel(a)crg.eu> > Subject: Two junior group leader positions at the CRG (Barcelona) > > Dear friends, > > I would appreciate if you could forward this e-mail to whom you may think could be interested in a Junior Group Leader position at CRG in Barcelona. > > Additional information in the attached PDF. > > Many thanks in advance, > Marc > > > > ... > Marc A. Marti-Renom, ICREA Research Professor > Genome Biology Group Leader - CNAG - Centre Nacional d’Anàlisi Genòmica > Structural Genomics Group Leader - CRG - Centre de Regulació Genòmica > Parc Científic de Barcelona – Torre I > Baldiri Reixac, 4 > 08028 Barcelona > Tel +34 9340 33743 > Email mmarti(a)pcb.ub.cat > Web http://marciuslab.org - http://cnag.cat - http://crg.cat > > *** Consider the environment. Print responsibly. *** >

1 0

[Compbio-allhands] Fwd: Postdoctoral opportunities at Princeton
by Andrej Sali 07 Nov '13

07 Nov '13

Sent from my iPhone Begin forwarded message: > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Date: November 7, 2013 at 1:47:15 PM PST > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Subject: Postdoctoral opportunities at Princeton > > Dear Colleagues, > > In an effort to attract the strongest possible candidates, we are extending our annual search for young theorists interested in problems at the interface of physics and biology, broadly interpreted. Princeton offers a very interactive community, with a nearly unique combination of theoretical mentors and friendly experimental collaborators. We have been fortunate so far in attracting a steady stream of wonderful postdoctoral scholars. We would like to continue this pattern, and ask for your further help in pointing a few more excellent new candidates in our direction. Thank you in advance for your willingness to contribute to this effort. > > We have extended the deadline for applications and letters another week, to November 15th. > > For more details, please see http://www.princeton.edu/physics/about/employment/biophysics/index.xml > > Best wishes, > > William Bialek > Chase Broedersz > Curtis Callan > Benjamin Machta > 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] Fwd: POSTDOCTORAL POSITION IN COMPUTATIONAL NEUROSCIENCE AT ENS, PARIS
by Andrej Sali 07 Nov '13

07 Nov '13

Sent from my iPhone Begin forwarded message: > From: "Rava A. da Silveira" <rava(a)ens.fr> > Date: November 6, 2013 at 9:27:17 PM CST > To: "Rava A. da Silveira (Me)" <rava(a)ens.fr> > Subject: POSTDOCTORAL POSITION IN COMPUTATIONAL NEUROSCIENCE AT ENS, PARIS > > Dear colleague, > > Would you be so kind as to forward the postdoc ad pasted below to > potential candidates? > > Many thanks, and best regards, > > Rava > (Apologies for multiple postings.) > > ********* > > POSTDOCTORAL POSITION available in the group of RAVA AZEREDO DA > SILVEIRA at the ECOLE NORMALE SUPERIEURE, Paris > > This position will be devoted, in part, to the analysis and modeling > of exciting retina data sets from the labs of Botond Roska (FMI) and > Andreas Hierlemann (ETH). Experience with data analysis and > proficiency with numerical methods and programming, in addition to > familiarity with neuroscience topics and mathematical and statistical > methods, are desirable. In addition, research may be pursued on > problems of single-cell and network dynamics, neural coding, or > cognitive and behavioral modeling (inference, sensory integration, > decision making, etc), with more or less connection with data > depending upon the specific problem. Thus, a spirit of intellectual > adventure and eagerness is at least as desirable. > > The ENS, together with a number of neighboring institutions (College > de France, Institut Curie, ESPCI, Universités Paris 5, 6, and 7, and > Institut Pasteur), offers a rich scientific and intellectual > environment, with a strong representation in computational > neuroscience and related fields. Furthermore, as far as cities go, > Paris is not bad. > > The postdoctoral salary will be supplemented by travel and equipment funds. > > To apply, please send a letter of motivation and statement of > research, a curriculum vitae, a list of publication, and arrange for > three letters of recommendations to be sent, to rava(a)ens.fr. Reviewing > of the applications with start on 25 November 2013.

1 0

[Compbio-allhands] Fwd: opening at Principia Biopharma
by Jacobson, Matt 05 Nov '13

05 Nov '13

Begin forwarded message: From: Ken Brameld <ken.brameld(a)principiabio.com<mailto:ken.brameld@principiabio.com>> Subject: opening at Principia Biopharma Date: November 5, 2013 10:31:24 AM PST To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, We met briefly at the Frontiers in Medicinal Chemistry meeting this past June. Things continue to go will at Principia and we are expanding. I have an opening for a recent PhD or postdoc in comp chem/chem informatics. The ideal candidate will be an enthusiastic and self-motivated individual who is seeking a position with the potential to broadly influence the efficiency and outcome of discovery research at Principia. The job description is attached. Would you mind circulating this to your group or to anyone you feel may be interested and qualified? Kind regards, -Ken Ken Brameld, Ph.D. Executive Dir., Research Technologies Principia Biopharma 650-416-7714 ken.brameld(a)principiabio.com<mailto:ken.brameld@principiabio.com> This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Dr. James Petersson Talk, 11/5/13 10:00 am
by Flowers, Nicole 04 Nov '13

04 Nov '13

Dr. James Petersson, University of Pennsylvania, Department of Chemistry Tuesday, November 5 – 10 AM, RH-102, Pottruck Auditorium Thioamides: Minimalist chromophores for monitoring protein folding and stability Abstract: Our laboratory is developing new tools to understand protein folding, conformational changes, and proteolysis. We have recently shown that the thioamide - a single-atom substitution of the peptide backbone - can be used as a probe to monitor structural changes in proteins by quenching fluorophores, including the natural amino acids tryptophan and tyrosine, and several unnatural amino acids. We have developed methods for incorporating the thioamides into full-sized proteins by chemically synthesizing peptides containing the thioamides, and ligating them to proteins expressed in E. coli cells. Donor fluorophores can be incorporated into the cellularly-expressed fragment using unnatural amino acid mutagenesis or post-expression labeling, so that double-labeled proteins can be generated with a minimum of unnecessary peptide synthesis. Development of these methods allows us to begin study of the role of protein motion in processes such as cell signaling and amyloid diseases. We have alsoadapted our fluorophore/thioamide pairs to make probes of proteolysis, using the minimally-perturbing nature of the thioamide to investigate cleavage at specific sequences. We have used these tools in vitro, and we are working to extend them to use in lysates and living cells. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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] FREE Laser Toner Cartridges
by babbitt 28 Oct '13

28 Oct '13

The Babbitt lab is giving away four unused toner cartridges: HP-96A (part #C4096A). These cartridges fit HP LaserJet Series 2100/2200* (really old) printers. Please contact Joslyn Polzien atjoslyn.polzien(a)ucsf.edu<mailto:%20joslyn.polzien@ucsf.edu> if you are interested in some or all of them. *2100, 2100EP, 2100M, 2100SE, 2100TN, 2100XI, 2200, 2200D, 2200DN, 2200DT, 2200DSE, 2200DTN -- Patricia Babbitt, Professor Dept. of Bioengineering & Therapeutic Sciences 1700 4th Street, MC2550 University of California San Francisco, CA 94158 Phone: 1-415-476-3784 Email: babbitt(a)cgl.ucsf.edu Assistant: Ms. Joslyn Polzien Email: Joslyn.Polzien(a)ucsf.edu 8 AM – 12 PM: (415) 514-1214 1 PM – 5 PM: (415) 514-4861

1 0

[Compbio-allhands] Fwd: ignite Bay Area (protein) Dynamics - November 5th
by Flowers, Nicole 28 Oct '13

28 Oct '13

Want to get together and talk science with other Bay Area researchers interested in the ways macromolecules move? Come to ignite Bay Area Dynamics (iBAD) on November 5th. Absolutely everyone is invited, from student to professor and academia to industry. Hear the latest work on dynamics in a fast, pithy form: Ignite talks are only five minutes apiece, with auto-advancing slides! Refreshments are provided and there will be plenty of time to chat with colleagues and speakers. Speakers: Susan Marqusee (Berkeley) Vijay Pande (Stanford) Jacob Corn (Genentech) Gira Bhabha (UCSF) November 5th, 2013 - 7 PM UCSF - Mission Bay Campus Byers Hall 212 More info: http://www.fraserlab.com/ibad or email Jaime Fraser (james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu>) or Jacob Corn (corn.jacob(a)gene.com<mailto:corn.jacob@gene.com>) Sponsored by the Protein Society (Society membership not required to attend). James Fraser, PhD Assistant Professor Department of Bioengineering and Therapeutic Sciences Office: N212C Genentech Hall, Lab: N216 Genentech Hall james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu> // jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com> (415) 493-8421 http://www.fraserlab.com Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Protein Society Sponsored Dynamics Meeting - Tuesday November 5th 7PM at UCSF
by Jacobson, Matt 27 Oct '13

27 Oct '13

-- Matt Sent from my iPad Begin forwarded message: From: James Fraser <jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com>> Date: October 27, 2013 12:58:39 PM PDT To: Mark Kelly <mark.kelly(a)ucsf.edu<mailto:mark.kelly@ucsf.edu>>, Tanja Kortemme <kortemme(a)cgl.ucsf.edu<mailto:kortemme@cgl.ucsf.edu>>, Agard Dave <agard(a)msg.ucsf.edu<mailto:agard@msg.ucsf.edu>>, Robert Stroud <stroud(a)msg.ucsf.edu<mailto:stroud@msg.ucsf.edu>>, Fletterick Robert <flett(a)msg.ucsf.edu<mailto:flett@msg.ucsf.edu>>, Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>>, Jim Wells <Jim.Wells(a)ucsf.edu<mailto:Jim.Wells@ucsf.edu>>, Jack Taunton <taunton(a)cmp.ucsf.edu<mailto:taunton@cmp.ucsf.edu>>, Patsy Babbitt <babbitt(a)cgl.ucsf.edu<mailto:babbitt@cgl.ucsf.edu>>, Charles Craik <Charles.Craik(a)ucsf.edu<mailto:Charles.Craik@ucsf.edu>>, "Danica Fujimori" <fujimori(a)cmp.ucsf.edu<mailto:fujimori@cmp.ucsf.edu>>, Natalia Jura <natalia.jura(a)ucsf.edu<mailto:natalia.jura@ucsf.edu>>, "Degrado, William" <Bill.DegRado(a)ucsf.edu<mailto:Bill.DegRado@ucsf.edu>>, "England, Pamela" <Pamela.England(a)ucsf.edu<mailto:Pamela.England@ucsf.edu>>, John Gross <jdgross(a)cgl.ucsf.edu<mailto:jdgross@cgl.ucsf.edu>>, Bo Huang <bo.huang(a)ucsf.edu<mailto:bo.huang@ucsf.edu>>, Xiaokun Shu <xiaokun.shu(a)ucsf.edu<mailto:xiaokun.shu@ucsf.edu>>, Susan Miller <smiller(a)cgl.ucsf.edu<mailto:smiller@cgl.ucsf.edu>>, "Gestwicki, Jason" <Jason.Gestwicki(a)ucsf.edu<mailto:Jason.Gestwicki@ucsf.edu>>, "Cheng, Yifan" <YCheng(a)ucsf.edu<mailto:YCheng@ucsf.edu>>, Alan Frankel <frankel(a)cgl.ucsf.edu<mailto:frankel@cgl.ucsf.edu>>, "Narlikar, Geeta" <geeta.narlikar(a)ucsf.edu<mailto:geeta.narlikar@ucsf.edu>>, "Lim, Wendell" <Wendell.Lim(a)ucsf.edu<mailto:Wendell.Lim@ucsf.edu>>, <Shawn.Douglas(a)ucsf.edu<mailto:Shawn.Douglas@ucsf.edu>>, Chris Waddling <waddling(a)msg.ucsf.edu<mailto:waddling@msg.ucsf.edu>>, Ajay Jain <ajain(a)jainlab.org<mailto:ajain@jainlab.org>>, Adam Abate <arabate(a)gmail.com<mailto:arabate@gmail.com>>, Michael Fischbach <fischbach(a)fischbachgroup.org<mailto:fischbach@fischbachgroup.org>>, "John Kuriyan" <kuriyan(a)berkeley.edu<mailto:kuriyan@berkeley.edu>>, Jamie Cate <jcate(a)lbl.gov<mailto:jcate@lbl.gov>>, <doudna(a)berkeley.edu<mailto:doudna@berkeley.edu>>, Bryan Krantz <bakrantz(a)berkeley.edu<mailto:bakrantz@berkeley.edu>>, David Wemmer <DEWemmer(a)lbl.gov<mailto:DEWemmer@lbl.gov>>, Andreas Martin <a.martin(a)berkeley.edu<mailto:a.martin@berkeley.edu>>, Judith Klinman <klinman(a)berkeley.edu<mailto:klinman@berkeley.edu>>, <jfkirsch(a)berkeley.edu<mailto:jfkirsch@berkeley.edu>>, Ron Vale <vale(a)cmp.ucsf.edu<mailto:vale@cmp.ucsf.edu>>, James Partridge <partridge.james(a)gmail.com<mailto:partridge.james@gmail.com>>, David Sivak <david.sivak(a)gmail.com<mailto:david.sivak@gmail.com>> Cc: Jacob Corn <corn.jacob(a)gene.com<mailto:corn.jacob@gene.com>> Subject: Protein Society Sponsored Dynamics Meeting - Tuesday November 5th 7PM at UCSF Want to get together and talk science with other Bay Area researchers interested in the ways macromolecules move? Come to ignite Bay Area Dynamics (iBAD) on November 5th. Absolutely everyone is invited, from student to professor and academia to industry. Hear the latest work on dynamics in a fast, pithy form: Ignite talks are only five minutes apiece, with auto-advancing slides! Refreshments are provided and there will be plenty of time to chat with colleagues and speakers. Speakers: Susan Marqusee (Berkeley) Vijay Pande (Stanford) Jacob Corn (Genentech) Gira Bhabha (UCSF) November 5th, 2013 - 7 PM UCSF - Mission Bay Campus Byers Hall 212 More info: http://www.fraserlab.com/ibad or email Jaime Fraser (james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu>) or Jacob Corn (corn.jacob(a)gene.com<mailto:corn.jacob@gene.com>) Sponsored by the Protein Society (Society membership not required to attend). -- -- James Fraser, PhD Assistant Professor Department of Bioengineering and Therapeutic Sciences Office: N212C Genentech Hall, Lab: N216 Genentech Hall james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu> // jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com> (415) 493-8421 http://www.fraserlab.com

1 0

[Compbio-allhands] Fwd: Postdoctoral Fellow Position - The Rockefeller University
by Jacobson, Matt 25 Oct '13

25 Oct '13

-- Matt Sent from my iPad Begin forwarded message: From: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Date: October 25, 2013 11:17:43 AM PDT To: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Subject: Postdoctoral Fellow Position - The Rockefeller University We would greatly appreciate sharing the attached position within your graduate students and postdocs. Best regards, Melanie J. Lee Administrative Assistant Center for Studies in Physics and Biology The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: 212-327-8636 Fax: 212-327-8544 http://www.rockefeller.edu/research/intercenter/cenphysics

1 0

[Compbio-allhands] 10/31/13 Seminar with Erin Carlson
by Nicole Takesono Flowers 24 Oct '13

24 Oct '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Erin Carlson Indiana Chemical Probes to Explore and Inhibit Bacterial Pathogenesis October 31, 2013 D. Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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] 10/24/13 Seminar with David Bartel
by Nicole Takesono Flowers 18 Oct '13

18 Oct '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 David Bartel MIT MicroRNAs and a developmental switch in the nature of translational control. October 24, 2013 H. Madhani, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Dr. Nicholas Furnham Seminar -- Thursday, October 24th
by Flowers, Nicole 17 Oct '13

17 Oct '13

Please join Patsy Babbitt on Thursday, October 24th, 2013 3:00 – 4:00 PM Byers Hall, Room BH-215 for a talk by visiting speaker Nick Furnham, PhD Postdoctoral Fellow, Thornton Research Group EMBL-EBI (European Molecular Biology Laboratory — European Bioinformatics Institute) on Automatically Cataloguing Changes in Enzyme Chemistry with Changes in Protein Evolution for 380 Domain Superfamilies --- Joslyn Polzien Assistant to Drs. Patricia Babbitt & Tanja Kortemme Dept. of Bioengineering & Therapeutic Sciences University of California, San Francisco 8 AM – 12 PM: (415) 514-1214 1 PM – 5 PM: (415) 514-4861 joslyn.polzien(a)ucsf.edu<mailto:joslyn.polzien@ucsf.edu> Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Assistant Professor Position in Biochemistry CU Boulder
by Brian Shoichet 14 Oct '13

14 Oct '13

---------- Forwarded message ---------- From: Brian Shoichet <bshoichet(a)gmail.com> Date: Mon, Oct 14, 2013 at 11:56 AM Subject: Fwd: Assistant Professor Position in Biochemistry CU Boulder To: Ryan Coleman <ryan.g.coleman(a)gmail.com> FYI. Brian ---------- Forwarded message ---------- From: Amy E Palmer <amy.palmer(a)colorado.edu> Date: Mon, Oct 14, 2013 at 11:45 AM Subject: Assistant Professor Position in Biochemistry CU Boulder To: Amy E Palmer <amy.palmer(a)colorado.edu> Dear Colleagues I am writing to request your help in identifying candidates for a *faculty position in Biochemistry at the Assistant Professor* level at the *University of Colorado, Boulder*. In addition to establishing a vigorous research program, the new faculty will participate in teaching biochemistry or chemistry at the undergraduate and graduate levels. Candidates working in all areas of research will be considered. We have a healthy graduate program with each faculty member taking about one new graduate student a year, as well as excellent support facilities and a large amount of shared research equipment. Because the Biochemistry Program is situated within the Department of Chemistry & Biochemistry, there are many opportunities to interact with chemistry faculty, some of whom have considerable interest in biochemistry. We also have a joint graduate program with the Department of Molecular, Cellular, and Developmental Biology, located on campus, thus there are excellent interactions with molecular biologists and geneticists. There are strong connections between biochemistry and the physical sciences, and these connections are supported by an NIH-funded training program in Biophysics. Finally, we moved into a new state of the art Jennie Smoley Caruthers Biotechnology Building about 1 year ago which also houses the Department of Chemical and Biological Engineering and the BioFrontiers Institute, providing ample opportunity for cross-disciplinary and interdisciplinary interactions. The University has a strong interest in recruiting minority and women for faculty positions. There is a general feeling that simply stating in advertisements that "The University of Colorado is an Affirmative Action/Equal Opportunity Institution" is not enough. We would like to maximize chances of identifying all minorities and women who would be appropriate candidates for present and future openings in the Biochemistry Program. We would greatly appreciate it if you would bring this opening to the attention of candidates you feel are suitable. Enclosed is a copy of our position announcement. The position is advertised in Sciencejobs and Naturejobs.**** Sincerely,**** Amy Palmer ************************************ Associate Professor Department of Chemistry and Biochemistry BioFrontiers Institute UCB 596 3415 Colorado Ave Univesity of Colorado Boulder, CO 80303 303-492-1945 http:/Chem.colorado.edu/palmergroup -- Brian Shoichet, Professor http://www.uoft.bkslab.org/ University of Toronto, Leslie Dan Faculty of Pharmacy Donnelly Centre Room 604 (416) 978-7224 University of California, San Francisco Dept. of Pharmaceutical Chemistry -- Brian Shoichet, Professor http://www.uoft.bkslab.org/ University of Toronto, Leslie Dan Faculty of Pharmacy Donnelly Centre Room 604 (416) 978-7224 University of California, San Francisco Dept. of Pharmaceutical Chemistry

1 0

[Compbio-allhands] 10/17/13 Seminar with Richard Bonneau
by Nicole Takesono Flowers 11 Oct '13

11 Oct '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Richard Bonneau NYU Integrative computational methods for learning dynamic regulatory models: application to T-cell differentiation and function October 17, 2013 A. Sczesnak, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Group leader in Computational Biology at EMBL Heidelberg
by Andrej Sali 10 Oct '13

10 Oct '13

Sent from my iPhone Begin forwarded message: > From: Christoph Mueller <cmueller(a)embl.de> > Date: October 10, 2013 at 6:30:23 AM PDT > To: sali(a)salilab.org > Subject: Group leader in Computational Biology at EMBL Heidelberg > > Dear Andrej, > > We are seeking to recruit a group leader/teamleader in Computational Biology/Bioinformatics at EMBL Heidelberg. > > Although the call is deliberately broad structural bioinformatics (e.g. modelling of protein complexes and their interactions and/or dynamics in a cellular context), image analysis/visualisation (e.g. reading out data from GFP screens, E-tomograms or visualising a virtual cell atlas) is one of the topics. I would be grateful if you could forward the attached advert to suitable candidates! > > Thanks for your help! > Christoph > -- > ---------------------------------------------------------------------------- > Dr. Christoph W. Müller > Joint Head of Structural and Computational Biology Unit > > EMBL > Meyerhofstrasse 1 > 69117 Heidelberg, Germany > > email: cmueller(a)embl.de > phone: 0049-6221-387-8320 > fax: 0049-6221-387-519 > http://www.embl.de > ----------------------------------------------------------------------------- > > > >

1 0

[Compbio-allhands] Fwd: Listservs: Business Careers for Scientists: considering the options
by Jacobson, Matt 07 Oct '13

07 Oct '13

Begin forwarded message: From: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Subject: Fwd: Listservs: Business Careers for Scientists: considering the options Date: October 7, 2013 10:45:48 AM PDT To: <BPSTUDENTS(a)LISTSRV.UCSF.EDU<mailto:BPSTUDENTS@LISTSRV.UCSF.EDU>> Reply-To: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Hi everyone, The Business Club at UCSF invites you to our first event this academic year, Business Careers for Scientists: Considering the Options. Dr. Jenny Rooke will give an overview of business careers for scientists from her own experience. Dr. Jenny Rooke drives innovation in the life sciences through investing and business building around brilliant scientists and engineers with novel technologies. Her investing experience includes roles at the Bill & Melinda Gates Foundation and at Fidelity Biosciences, a healthcare venture capital firm. Dr. Rooke held multiple executive roles at U.S. Genomics, a venture-backed biotech start-up advancing single molecule detection technologies for diagnostics, biodefense, and research tools. Previously, Dr. Rooke was a management consultant with McKinsey & Co., where she advised leading pharmaceutical and biotech companies on business strategy. Dr. Rooke earned her PhD in genetics from Yale University and her BS in physics from Georgia Tech. When: 5:30PM, 10/9/2013 Where: Byer Hall 212, UCSF Mission Bay Campus --------------------------------------------------------------- Business Club at UCSF<http://www.businessatucsf.org/>, join us on LinkedIn<http://www.linkedin.com/groups?gid=4111410> Julia Molla UC San Francisco Program Coordinator, Biological& Medical Informatics and Chemistry& Chemical Biology 600-16th St. MC2280 San Francisco, CA 94158-2517 415-476-1914 phone ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BPSTUDENTS&A=1> from this mailing list. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: FACULTY POSITIONS OPEN--Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
by Jacobson, Matt 03 Oct '13

03 Oct '13

Begin forwarded message: From: imbwww <imbwww(a)imb.sinica.edu.tw<mailto:imbwww@imb.sinica.edu.tw>> Subject: FACULTY POSITIONS OPEN--Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan Date: October 2, 2013 6:26:31 PM PDT To: Undisclosed recipients:; Dear colleagues, The Institute of Molecular Biology (Academia Sinica, Taiwan) is recruiting young and talented faculty to join the research groups. We would like to seek your help in distributing this advertisement to potential candidates in your laboratory or to those who you think might be interested in. Your kind assistance is highly appreciated. Best regards, ************************ The recruitment committee Institute of Molecular Biology Academia Sinica, Taipei, Taiwan Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Opportunity at start up
by Jacobson, Matt 26 Sep '13

26 Sep '13

-- Matt Sent from my iPhone Begin forwarded message: From: Kathy Young <kathy(a)hertzfoundation.org<mailto:kathy@hertzfoundation.org>> Date: September 26, 2013, 2:04:55 PM PDT To: Katherine Young <kathy(a)hertzfoundation.org<mailto:kathy@hertzfoundation.org>> Subject: Opportunity at start up We are passing this opportunity along on behalf of Hertz Fellow Michael Schnall-Levin in case you, or someone you know, are interested in this opportunity. If this doesn't apply to you, please disregard. Thanks, Kathy Young Chief Operating Officer Fannie & John Hertz Foundation Dear Hertz Fellows and Alumni, We are an early-stage startup located in the SF bay area building a really exciting technology to revolutionize Next Generation Sequencing. Our company is truly multidisciplinary- together we have backgrounds in biochemistry, chemistry, microfluidics, engineering and computational biology. We are a young company but we are very ambitious and our leadership includes founders of the some of the biggest companies in Biotech. We are currently looking for a superstar in Computational Biology (see the attached job description), but are always interested in meeting talented people in any discipline. If you or anyone you know is interested, please reach out to me at mike(a)10xtechnologies.com<mailto:mike@10xtechnologies.com>. Michael Schnall-Levin (Hertz Fellow 2006 - 2011)

1 0

[Compbio-allhands] Fwd: computational chemistry position for your students
by Brian Shoichet 24 Sep '13

24 Sep '13

FYI ---------- Forwarded message ---------- From: Kerry Boehner <kerry(a)kobsolutions.com> Date: Tue, Sep 24, 2013 at 11:03 AM Subject: computational chemistry position for your students To: bshoichet(a)gmail.com Hi Brian, My name is Kerry Boehner, and I’m a recruiter in the pharmaceutical and biotechnology fields. I’m recruiting for a Computational Chemist for a client in China & I thought one of your post-docs or students might be interested. I’ve included the description below. They are open to scientists coming straight from academia, as well as industry. My client offers a great compensation package, including relocation. Please don't hesitate to contact me if you need anything, and I appreciate your assistance! Kerry Kerry Boehner KOB Solutions, Inc. 412-851-9696 kerry(a)kobsolutions.com www.kobsolutions.com *Recruiting Solutions for Pharma, Biotech & Med Device* My client seeks a Computational Chemist for Computer-Aided Drug Design – the ideal candidate will take on the following responsibilities: --structure-based drug design --target identification and lead generation --assist project teams to answer key issues during hit-to-lead and lead optimization through techniques like protein/ligand analysis and simulation using MD and molecular docking. Requirements: --Ph.D. degree in computational chemistry, computational biology or a related field. --Familiarity with up-to-date biological screening paradigms. --A proven track record in leveraging in silico techniques to drive basic science projects or in impacting hit finding activities in a drug discovery environment. --Demonstrate the ability to work independently as effectively as being able to collaborate in multidisciplinary teams. --Strong analytical and problem-solving skills and scientific creativity are essential. --Excellent oral and written communication skills and organizational skills are required. -- Brian Shoichet, Professor http://www.uoft.bkslab.org/ University of Toronto, Leslie Dan Faculty of Pharmacy Donnelly Centre Room 604 (416) 978-7224 University of California, San Francisco Dept. of Pharmaceutical Chemistry

1 0

[Compbio-allhands] Fwd: Attractive Statistical Genomics Faculty Position in Vancouver
by Andrej Sali 23 Sep '13

23 Sep '13

-- 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 Begin forwarded message: > From: Jennifer Bryan <jenny(a)stat.ubc.ca> > Subject: Attractive Statistical Genomics Faculty Position in Vancouver > Date: September 23, 2013 4:54:11 PM PDT > To: Jennifer Bryan <jenny(a)stat.ubc.ca> > > The University of British Columbia has an exceptional opportunity for > a highly qualified researcher in the broad domain of statistical > genomics to launch a career as an Assistant Professor. As described > in the attached advertisement, this position is backed by a Canada > Research Chair for the early career, and is supported as a hard-money > position afterwards. The position is jointly backed by the > Departments of Statistics and Medical Genetics at UBC, and the > research would be based at the successful Centre for Molecular > Medicine and Therapeutics - a centre based on interdisciplinary > research collaboration. > > The search is open, with flexibility for the top candidate to build a > successful research program in the area of their interest. Research > space, training programs and computational resources are in place, > allowing the recruit to move rapidly. > > In short, this is a great position. We hope you will pass this > information along within the broad biostatistics community and > encourage top candidates to apply. > > I would be pleased to communicate with anyone having questions about > the position. > > Regards, > > Jenny Bryan > jenny(a)stat.ubc.ca > > P.S .The criteria for the Canada Research Chair restricts eligibility > to scientists within 10 years of receiving a Ph.D. As the position > will include some teaching within the Department of Statistics, > applications must indicate formal training in a field of statistics. > > Jennifer Bryan > Associate Professor > Department of Statistics and > the Michael Smith Laboratories > University of British Columbia > Vancouver, BC Canada >

1 0

[Compbio-allhands] 9/26/13 Seminar with Laura Lavery
by Nicole Takesono Flowers 20 Sep '13

20 Sep '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Laura Lavery Clements Lecture Molecular asymmetry provides new insights into Hsp90 mechanism September 26, 2013 D. Agard, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Faculty position in Theoretical Soft/Bio Physics
by Andrej Sali 20 Sep '13

20 Sep '13

-- 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 Begin forwarded message: > From: "Mossman, Kaspar" <kaspar.mossman(a)qb3.org> > Subject: FW: Faculty position in Theoretical Soft/Bio Physics > Date: September 20, 2013 12:02:52 PM PDT > To: "SALI, ANDREJ" <sali(a)salilab.org> > > Hi Andrej, could you forward this to anyone who might be interested? and maybe if you know of relevant faculty w/ similar labs to yours, you could tell me who they might be? > > Thanks! > > Kaspar > > -----Original Message----- > From: Nancy Forde [mailto:nforde@sfu.ca] > Sent: Friday, September 20, 2013 11:37 AM > To: Mossman, Kaspar > Subject: Faculty position in Theoretical Soft/Bio Physics > > Dear Kaspar, > > I hope this message finds you well. If you are able to pass on this message and attached ad for a faculty position here at SFU to interested parties (i.e., theorists) at QB3, that would be great. > > SFU Physics is hiring a theorist in soft condensed matter or biological Physics. We are excited to be growing our complement of researchers in this area, and to further strengthen our already strong international reputation. Please help us to find the best candidate possible by forwarding the attached ad to outstanding theorists who would be interested in moving to beautiful Vancouver, British Columbia! Details are also available online at http://www.physics.sfu.ca/news/newsitem?id=79. > > Best wishes, > Nancy > > > -- > Nancy Forde > Associate Professor > Department of Physics > Simon Fraser University > 8888 University Dr. > Burnaby, BC V5A 1S6 > -- > nforde(a)sfu.ca > 778-782-3161; 778-782-3592 (fax) > http://www.sfu.ca/fordelab >

1 0

[Compbio-allhands] Monica's thesis talk
by Jacobson, Matt 13 Sep '13

13 Sep '13

Reminder: Please join for Monica's Thesis Seminar! Monica Tremont (Jacobson Lab) Multiscale Models for Microtubule Assembly and Cytoplasmic Crowding Friday Sept 13, 2pm in GH Auditorium

1 0

[Compbio-allhands] Fwd: POSTDOC OPPORTUNITY-PLEASE DISTRIBUTE
by Jacobson, Matt 05 Sep '13

05 Sep '13

Begin forwarded message: From: "Zachow, Christine A." <zachow2(a)llnl.gov<mailto:zachow2@llnl.gov>> Subject: POSTDOC OPPORTUNITY-PLEASE DISTRIBUTE Date: September 4, 2013 11:31:45 AM 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, 2013. 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 Lawrence Fellow & Lawrence Scholar Programs Lawrence Livermore National Laboratory 7000 East Ave. L-19 Livermore, CA 94550 925-423-0633 -- Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Job Description
by Andrej Sali 12 Aug '13

12 Aug '13

-- 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 Begin forwarded message: > From: "Mark Smythe" <m.smythe(a)protagonist-inc.com> > Subject: Job Description > Date: August 8, 2013 10:23:35 PM PDT > To: "'Andrej Sali'" <sali(a)salilab.org>, "'Charles Craik'" <Charles.Craik(a)ucsf.edu> > > Hi Andrej and Charly > Attached is the job description with a shorter version embeeded in this email. > If you have any comments/ammendments please let me know. > I will submit it to the web sites Andrej mentioned. > Please feel free to distribute. > Thanks for your help. > Mark > > Protagonist Therapeutics - Molecular Modeller /Computational Chemist / Bioinformatician > > Organisational Environment > Protagonist Therapeutics (www.protagonist-inc.com) is a US biotechnology company dedicated to the discovery of disulfide-rich peptides as well differentiated orally active peptides against those targets/diseases for which suitable small molecule or biologic options are not available. > > The work will be carried out at Menlo Park, California, USA. > > DUTY STATEMENT > > Primary Purpose of Position > Protagonist Therapeutics is seeking a talented and highly motivated scientist to join the drug design group. The candidate will use proprietary molecular modeling tools in combination with existing commercial software packages to design new compounds and optimize existing compounds. Protagonist is pursing the development of orally stable peptide derivatives for gastrointestinal diseases. > > The successful candidate will have a PhD in computational chemistry, bioinformatics or related discipline. The candidate will have previous involvement in all elements of molecular design impacting on IND candidate generation and proven ability to enhance peptide stability and permeability. In addition, the candidate will be familiar with molecular recognition and improving potency, be familiar with accessing public domain sequence, function, and structural information, has knowledge of disulfide rich peptides, macrocyles, clustering algorithm, molecular modeling packages, scripting/programming languages, with a preference for C++ and has worked in a Linux environment. The candidate well versed of the relevant literature, and have demonstrated hands on experience in structure based design. At least three years of industry experience is desirable. > > Duties > Duties and responsibilities include, but are not to: > • To be responsible for the structure-based drug design of one or more targets > • To optimize affinity of peptide-derivatives whilst maintaining and optimizing oral stability features > • To have up to date knowledge of the literature of one or more target > • The use of drug-design tools such as database searching, docking, scoring etc for the structure-based design of biologically active molecules > • To interpret and to use structural data, biological assay data, stability data, mutagenesis data, sequencing data, pharmacological data etc in the design of biological active molecules > > Reporting Relationships > The position reports to Dr Mark Smythe, VP Technology and Alliances for Protagonist Therapeutics. > > SELECTION CRITERIA > > Qualifications > The candidate will hold a Ph.D. in bioinformatics, computational chemistry or molecular modelling or related discipline, with significant research experience. Experiences in enhancing peptide affinity, stability and oral stability are essential. Project planning and meeting deadlines is an absolute advantage. Moreover, proven capacity and knowledge in deriving SAR of hit and lead candidates is highly desirable. > > Knowledge and Skills/Experience > Essential > • PhD in computational chemistry, bioinformatics or related discipline is required > • Proven translational experience towards IND candidates > • Knowledge of disulfide rich peptides and macrocycles > • Knowledge and practical experience in improving stability of peptides and macrocyles > • Previous experience in clustering > • Ability to program, preferably in C/C++ > • Working experience with pharmacophores > • Previous experience in structure-based drug design > • Thorough understanding of molecular recognition > • Thorough understanding of the drug design literature > • To have experience in scaffold hopping and peptide/protein engineering > • Develop and maintain integrated chemoinformatic database/registry > > Desirable > • Previous experience in database searching and docking > • Understanding of scoring functions > • Understanding of sequence search/alignment (Blast) > • Knowledge of SQL and Oracle Database > > Personal Qualities > Essential > • Ability to work in an efficient and well organized manner > • Ability to work collaboratively with internal and external team colleagues > • Ability to work with minimal supervision > • Ability to adhere to specific work schedules and meet deadlines > • Methodical approach to problem solving > • Excellent written and verbal communication skills > • Excellent interpersonal skills > • Sound problem-solving skills > > Remuneration: Protagonist Therapeutics provides competitive salary packages commensurate to experience to ensure that we are able to hire the best people from around the world. > > Closing Date: 21st August, 2013 > > Applications are to be sent to: > Human Resource Consultant > Email: hr(a)protagonist-inc.com > > >

1 0

[Compbio-allhands] Fwd: 3 postdoc positions available immediately
by Jacobson, Matt 07 Aug '13

07 Aug '13

Begin forwarded message: From: <ealexov(a)clemson.edu<mailto:ealexov@clemson.edu>> Subject: 3 postdoc positions available immediately Date: August 7, 2013 6:18:02 AM PDT To: Undisclosed recipients:; Dear Colleagues, Just a quick announcement: 3 postdoctoral fellowships are immediately available here in Clemson (see below and the attached PDF file). Please, forward the announcement to all interested parties. I apologize to multiple copies of the ad that you may receive. Thank you in advance, Emil ================== Three post-doctoral fellowships in Biology of Human Diseases The Departments of Biological Sciences, Genetics and Biochemistry, and Physics at Clemson University are seeking three exceptionally talented new investigators, who hold a PhD in relevant fields. This unique opportunity exists for PhD graduates and postdoctoral fellows with a special interest in "The biology of human diseases: mechanisms, diagnosis, and personalized medicine", who aspire to become tenure track faculty in the near future. The fellows will be mentored by NIH funded researchers and trained in writing successful research grants, management of budgets and running a laboratory. We are especially looking for a computational biophysicist (3D structure modeling, energy calculations, MD and in silico virtual screening), an experimental biochemist (molecular cloning and protein purification, protein stability, enzyme activity, binding efficiency, enzyme kinetics, and structural determination) and an experimental biologist (cell and molecular biology/zebrafish model). These positions are part of the "Biology of Human Diseases" initiative at Clemson University to understand the molecular basis of human diseases and will provide the opportunity to development a pipe-line for diagnostics and treatment of genetic disorders. Postdoctoral fellows will have access to excellent experimental facilities and a supercomputer cluster. These positions are intended to act as a springboard for fast-track tenure track faculty positions and accepted post-doctoral fellows are required to submit a NIH Pathway to Independence Award (K99/R00). The positions are for an initial period of one year with possible appointment for an additional two years depending on satisfactory progress. The postdoctoral fellows will also help to train students in the participating departments. A competitive stipend inclusive of benefits and funding for research are offered according to field and experience. Interested candidates should send their CV, a statement of research and career objectives, and the names of at least three references in a single PDF to the following faculty: 1) Computational Biophysicist: Prof. Emil Alexov (ealexov(a)clemson.edu<mailto:ealexov@clemson.edu>) 2) Experimental Biochemist: Prof. Weiguo Cao (wgc(a)clemson.edu<mailto:wgc@clemson.edu>) 3) Experimental Biologist: Prof. Susan Chapman (SCHAPM2(a)clemson.edu<mailto:SCHAPM2@clemson.edu>) All application material received by September 1, 2013 will receive guaranteed consideration; however, applications will be accepted and evaluated until the positions are filled. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Postdoc in Computational GPCR Ligand Design
by Brian Shoichet 28 Jun '13

28 Jun '13

FYI ---------- Forwarded message ---------- From: "David E. Gloriam" <david.gloriam(a)sund.ku.dk> Date: Jun 28, 2013 5:13 AM Subject: Postdoc in Computational GPCR Ligand Design To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu> Dear Brian, I have a computational chemistry postdoc opening in my group ( http://ccl.net/cca/jobs/joblist/mess0027098.shtml) I would be most grateful if you could please forward this mail to any interested person in your own group or network, that you think may be interested in a GPCR ligand design postdoc in Europe. Best Regards, David David Gloriam | Associate Professor Department of Drug Design and Pharmacology Faculty of Health And Medical Sciences University of Copenhagen T +45 35 33 61 62 | M +46 70 31 48 390

1 0

[Compbio-allhands] Fwd: Job Opening for a Computational Chemist
by Jacobson, Matt 14 Jun '13

14 Jun '13

-- Matt Sent from my iPhone Begin forwarded message: From: "Demeter, David (DA)" <dademeter(a)dow.com<mailto:dademeter@dow.com>> Date: June 14, 2013, 12:44:50 PM PDT To: "kschulte(a)ks.uiuc.edu<mailto:kschulte@ks.uiuc.edu>" <kschulte(a)ks.uiuc.edu<mailto:kschulte@ks.uiuc.edu>>, "rod(a)ysbl.york.ac.uk<mailto:rod@ysbl.york.ac.uk>" <rod(a)ysbl.york.ac.uk<mailto:rod@ysbl.york.ac.uk>>, "brookscl(a)umich.edu<mailto:brookscl@umich.edu>" <brookscl(a)umich.edu<mailto:brookscl@umich.edu>>, "william.jorgensen(a)yale.edu<mailto:william.jorgensen@yale.edu>" <william.jorgensen(a)yale.edu<mailto:william.jorgensen@yale.edu>>, "shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>" <shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>>, "alex_tropsha(a)unc.edu<mailto:alex_tropsha@unc.edu>" <alex_tropsha(a)unc.edu<mailto:alex_tropsha@unc.edu>>, "pearlman(a)mail.utexas.edu<mailto:pearlman@mail.utexas.edu>" <pearlman(a)mail.utexas.edu<mailto:pearlman@mail.utexas.edu>>, "toprea(a)salud.unm.edu<mailto:toprea@salud.unm.edu>" <toprea(a)salud.unm.edu<mailto:toprea@salud.unm.edu>>, "carlos.simmerling(a)sunysb.edu<mailto:carlos.simmerling@sunysb.edu>" <carlos.simmerling(a)sunysb.edu<mailto:carlos.simmerling@sunysb.edu>>, "merz(a)qtp.ufl.edu<mailto:merz@qtp.ufl.edu>" <merz(a)qtp.ufl.edu<mailto:merz@qtp.ufl.edu>>, "nathan.baker(a)pnnl.gov<mailto:nathan.baker@pnnl.gov>" <nathan.baker(a)pnnl.gov<mailto:nathan.baker@pnnl.gov>>, "maxb(a)unc.edu<mailto:maxb@unc.edu>" <maxb(a)unc.edu<mailto:maxb@unc.edu>>, "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, "fetrowjs(a)wfu.edu<mailto:fetrowjs@wfu.edu>" <fetrowjs(a)wfu.edu<mailto:fetrowjs@wfu.edu>>, "ajain(a)jainlab.org<mailto:ajain@jainlab.org>" <ajain(a)jainlab.org<mailto:ajain@jainlab.org>>, "mgilson(a)ucsd.edu<mailto:mgilson@ucsd.edu>" <mgilson(a)ucsd.edu<mailto:mgilson@ucsd.edu>>, "jbriggs(a)uh.edu<mailto:jbriggs@uh.edu>" <jbriggs(a)uh.edu<mailto:jbriggs@uh.edu>>, "flbrown(a)chem.ucsb.edu<mailto:flbrown@chem.ucsb.edu>" <flbrown(a)chem.ucsb.edu<mailto:flbrown@chem.ucsb.edu>>, "carlsonh(a)umich.edu<mailto:carlsonh@umich.edu>" <carlsonh(a)umich.edu<mailto:carlsonh@umich.edu>>, "lybrand(a)structbio.vanderbilt.edu<mailto:lybrand@structbio.vanderbilt.edu>" <lybrand(a)structbio.vanderbilt.edu<mailto:lybrand@structbio.vanderbilt.edu>>, "madura(a)mail.cc.duq.edu<mailto:madura@mail.cc.duq.edu>" <madura(a)mail.cc.duq.edu<mailto:madura@mail.cc.duq.edu>>, "dmorikis(a)engr.ucr.edu<mailto:dmorikis@engr.ucr.edu>" <dmorikis(a)engr.ucr.edu<mailto:dmorikis@engr.ucr.edu>>, "pomes(a)sickkids.on.ca<mailto:pomes@sickkids.on.ca>" <pomes(a)sickkids.on.ca<mailto:pomes@sickkids.on.ca>>, "tps(a)pnl.gov<mailto:tps@pnl.gov>" <tps(a)pnl.gov<mailto:tps@pnl.gov>>, "Celia.Schiffer(a)umassmed.edu<mailto:Celia.Schiffer@umassmed.edu>" <Celia.Schiffer(a)umassmed.edu<mailto:Celia.Schiffer@umassmed.edu>>, "case(a)biomaps.rutgers.edu<mailto:case@biomaps.rutgers.edu>" <case(a)biomaps.rutgers.edu<mailto:case@biomaps.rutgers.edu>>, "pap4(a)uic.edu<mailto:pap4@uic.edu>" <pap4(a)uic.edu<mailto:pap4@uic.edu>>, "ramaro(a)mccammon.ucsd.edu<mailto:ramaro@mccammon.ucsd.edu>" <ramaro(a)mccammon.ucsd.edu<mailto:ramaro@mccammon.ucsd.edu>> Subject: Job Opening for a Computational Chemist Ladies & Gentlemen, Dow AgroSciences currently has a job opening for a Ph.D. computational chemist. An additional 2-5 years of post-doctoral and/or industrial experience in molecular modeling is preferred. If you know of anyone who is currently seeking such a position, I would appreciate it if you would pass along this information. We are currently collecting resume’s and would like to start phone interviews by mid July. A link to the job posting is included below. Thank you for your time. http://careers.dowagro.com/job/Indianapolis-Computational-Chemist-Discovery… Sincerely, David A. Demeter, Ph.D. Senior Research Scientist, R&D Chemistry / CAMD Dow AgroSciences LLC 9330 Zionsville Road, Bldg 306/D2-884 Indianapolis, IN 46268 Voice: 317-337-3413 Fax: 317-337-3215 E-mail: dademeter(a)dow.com<mailto:dademeter@dow.com> NOTICE: This e-mail message (including all attachments) from Dow AgroSciences LLC is for the sole use of the intended recipient(s). Any unauthorized review, use, disclosure or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message and any attachments.

1 0

[Compbio-allhands] Dan Tawfik Seminar Announcement
by Flowers, Nicole 11 Jun '13

11 Jun '13

Please join Patsy Babbitt and Jaime Fraser on Thursday, June 20, 2013 12:00 – 1:00 PM Byers Auditorium, Genentech Hall for a talk by visiting seminar speaker Dan Tawfik, PhD Professor, Weizmann Institute of Science, Israel Department of Biological Chemistry on Enzyme Mechanism and Evolution --- Joslyn Polzien Assistant to Drs. Patricia Babbitt & Tanja Kortemme Dept. of Bioengineering & Therapeutic Sciences University of California, San Francisco 8 AM – 12 PM: (415) 514-1214 1 PM – 5 PM: (415) 514-4861 joslyn.polzien(a)ucsf.edu<mailto:joslyn.polzien@ucsf.edu> Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Available Postdoctoral Positions in Computational Chemical Biology
by Jacobson, Matt 04 Jun '13

04 Jun '13

Begin forwarded message: From: David Minh <dminh(a)iit.edu<mailto:dminh@iit.edu>> Subject: Available Postdoctoral Positions in Computational Chemical Biology Date: June 4, 2013 9:40:56 AM PDT To: Undisclosed recipients:; Dear Colleagues, I am accepting applications for postdoctoral positions in my new research group at the Illinois Institute of Technology, located in Chicago. Please encourage interested and suitable candidates to apply. One position is available in Fall 2013 and potentially another in Summer 2014. Research will focus on developing and applying molecular docking algorithms based on implicit ligand theory, a new theoretical framework for binding free energies based on rigid receptor configurations (http://dx.doi.org/10.1063/1.4751284<http://link.aip.org/link/doi/10.1063/1.4751284>). Ideal candidates will have strong computer programming skills, a background in computational/theoretical chemistry or physics (especially statistical mechanics), and interest in chemical biology and drug discovery. A PhD is required prior to the start date. Interested candidates should submit a cover letter, CV, and contact information for 2-3 references to david.minh(a)iit.edu<mailto:david.minh@iit.edu>. For more information, see http://mccammon.ucsd.edu/~dminh/ Best regards, David Minh Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: superior CADD candidates
by Brian Shoichet 22 May '13

22 May '13

Dear Colleagues, This may interest some of you. Brian ---------- Forwarded message ---------- From: Herbertz, Torsten <therbertz(a)formatherapeutics.com> Date: Wed, May 22, 2013 at 12:51 PM Subject: superior CADD candidates To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu>, " klebe(a)staff.uni-marburg.de" <klebe(a)staff.uni-marburg.de>, " klebe(a)mailer.uni-marburg.de" <klebe(a)mailer.uni-marburg.de> Dear Prof. Shoichet & Klebe,**** ** ** I am reaching out to ask for your help in identifying exceptional candidates for open CADD positions at Forma Therapeutics ( http://formatherapeutics.com/) in the Boston area & making you aware that we would consider highly recommended post-docs in your labs.**** I made your acquaintance all the way back in 2002 at the Erice Gene-to-drugs xray crystallography conference and we have encountered each other on numerous occasions like the CADD GRC. Furthermore, I have been following your published work with much interest. Your laboratories produce very important results and insights that I attempt to apply & adapt to my own work, particularly here at Forma, where I have the privilege of leading a growing CompChem group (with 5 current members).**** We are mostly interested in candidates who have demonstrated small molecule drug discovery experience, a very sound understanding of medicinal chemistry and how to work with medchemists. Furthermore, good organic chemistry & biophysical chemistry are more important than method development, chemoinformatics, ….**** Forma is an oncology-focused relatively young (~5 years) and small (~110 people) company located in Watertown, MA.**** We are interested in many molecular target classes relevant to cancer biology, including cancer metabolism, epigenetics, protein-protein interactions and protein homeostasis to name a few.**** Computational chemistry is an integral part of our discovery paradigm; we generally only work on structure-enabled targets. Every project team includes a compchemists, who is invested as much as medicinal chemists, biologist and biochemists. In general, we follow two strategies in parallel: lead identification and chemical biology - in essence finding a tool compound for target validation. The hope is to push interesting chemical matter as far as we can toward pre-clinical development.**** This is a brief & simplified introduction to Forma and I hope that it convinces you that Forma is an exciting place to do drug discovery.**** I hope that you can provide interesting candidate leads for me to follow up. **** Any assistance that you can extend is deeply appreciated.**** ** ** Best regards,**** ** ** Torsten Herbertz, PhD**** Principal Scientist**** ** ** Forma Therapeutics, Inc.**** 500 Arsenal Street, Suite 100**** Watertown, MA 02472**** Email: therbertz(a)formatherapeutics.com <dmillan(a)formatherapeutics.com>**** Office: +1-857-209-2327**** www.formatherapeutics.com**** [image: Description: cid:image001.jpg@01CA92A2.4F452810]**** ** ** -- Brian Shoichet Professor University of California, San Francisco Dept. of Pharmaceutical Chemistry phone: 415-514-4126; fax: 415-514-4260 http://shoichetlab.compbio.ucsf.edu

1 0

[Compbio-allhands] Fwd: UT Southwestern Seeks Research Scientists for Bioinformatics Initiative
by Tom Ferrin 21 May '13

21 May '13

-------- Original Message -------- Subject: UT Southwestern Seeks Research Scientists for Bioinformatics Initiative Date: Wed, 15 May 2013 19:37:33 +0000 From: Mack Dressler <Mack.Dressler(a)UTSouthwestern.edu> To: tef(a)cgl.ucsf.edu <tef(a)cgl.ucsf.edu> Dear Dr. Ferrin The Department of Clinical Sciences at the University of Texas Southwestern Medical Center is recruiting for its newly launched Translational Bioinformatics Initiative (http://tinyurl.com/UTSW-TBI) The Initiative is recruiting full-time bioinformatics researchers at all levels, including postdoctoral researchers and research scientists. Successful candidates will join an active and expanding bioinformatics research effort and will have the opportunity to collaborate with experimental and clinical researchers throughout UT Southwestern, the Department of Computer Science at UT Dallas, and the Texas Advanced Computing Center at UT Austin. Please share the attached posting with colleagues who might know of potential candidates, graduating students, and your institution’s career guidance center. Thank you for your consideration. If you would like additional information please contact me via e-mail or telephone (see below.) Sincerely, Lindsay G. Cowell, PhD Division of Biomedical Informatics Department of Clinical Sciences University of Texas Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-9066 phone: 214-648-2289 fax: 214-648-2064 Lindsay.Cowell(a)utsouthwestern.edu <mailto:Lindsay.Cowell@utsouthwestern.edu> ------------------------------------------------------------------------ UT Southwestern Medical Center The future of medicine, today.

1 0

[Compbio-allhands] Fwd: Consulting Panel
by Jacobson, Matt 13 May '13

13 May '13

Begin forwarded message: From: "Brown, Rebecca" <Rebecca.Brown3(a)UCSF.EDU<mailto:Rebecca.Brown3@UCSF.EDU>> Subject: Consulting Panel Date: May 13, 2013 3:41:32 PM PDT To: <BPSTUDENTS(a)LISTSRV.UCSF.EDU<mailto:BPSTUDENTS@LISTSRV.UCSF.EDU>> Reply-To: "Brown, Rebecca" <Rebecca.Brown3(a)UCSF.EDU<mailto:Rebecca.Brown3@UCSF.EDU>> ----- Hi everyone, Are you interested in a career in consulting? The 2013 Consulting Panel is tomorrow! The panelists are: Cory Blaiss, Ph.D., Analyst at Kantar Health Leslie Waite, Ph.D., Senior Clinical Trainer at Genentech Neil Sheehy, Ph.D., Analyst at Prescient Life Sciences Networking reception afterward where the people can mingle and network. Time: 5/14/2013, 5:30PM Location: Mission Bay Helen Diller 160 For more information on the panelists, go to http://www.businessatucsf.org/<https://mail.ucsf.edu/owa/redir.aspx?C=Z06Py7uo7EelPdTT0oztNUEDQkWzI9AI17UG…> --------------------------------------------------------------- Business Club at UCSF<https://mail.ucsf.edu/owa/redir.aspx?C=Z06Py7uo7EelPdTT0oztNUEDQkWzI9AI17UG…>, join us on LinkedIn<https://mail.ucsf.edu/owa/redir.aspx?C=Z06Py7uo7EelPdTT0oztNUEDQkWzI9AI17UG…> and Consulting Club at UCSF<https://mail.ucsf.edu/owa/redir.aspx?C=Z06Py7uo7EelPdTT0oztNUEDQkWzI9AI17UG…> ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BMI_STUDENTS&A=1> from this mailing list. Rebecca Brown Biophysics Graduate Program Coordinator Genentech Hall S-406 600 16th St. Box 2240 University of California San Francisco San Francisco, CA 94158-2517 (415) 476-6671 (p) (415) 476-1902 (f) ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BPSTUDENTS&A=1> from this mailing list. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Fwd: Bill Eaton Visit today -- Seminar Room Change -- now in GH-N114
by Jacobson, Matt 09 May '13

09 May '13

Bill Eaton Seminar – “Transition paths in protein folding from theory, molecular dynamics simulations and single molecule fluorescence experiments" 1:30 PM, now in N114 Begin forwarded message: Hi all, Please see updated schedule for Bill. I would appreciate if you could forward to your labs -- the lunch with students and postdocs will still be in GH - S261, just the seminar room has changed. Thanks ! Hilary Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] 5/16/13 Seminar with Jeffrey Skolnick
by Nicole Takesono Flowers 09 May '13

09 May '13

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 Jeffrey Skolnick Georgia Tech Interplay of physics and evolution in the likely origin of protein biochemical function May 16, 2013 P. Cimermancic, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Editorial position
by Brian Shoichet 29 Apr '13

29 Apr '13

For those interested in editor positions, this is a good group -- ---------- Forwarded message ---------- From: Sheppard, Terry <t.sheppard(a)us.nature.com> Date: Mon, Apr 29, 2013 at 9:40 AM Subject: Editorial position To: Brian Shoichet <shoichet(a)cgl.ucsf.edu> Hi Brian,**** I hope that you are well and that your transition to your new digs is proceeding smoothly.**** ** ** We are hiring a new Assistant Editor at *Nature Chemical Biology* and seek your help in getting the word out. You can see the advertisement here: http://www.nature.com/naturejobs/science/jobs/318829-Assistant-Editor. **** ** ** Please pass it along to colleagues and to any of your research associates who may be interested in applying. We have a slight preference for candidates whose backgrounds fall more on the biological side of chemical biology, but we are happy to see applications from scientists with training in any area of chemical biology.**** ** ** Many thanks,**** Terry**** ** ** Terry L. Sheppard, Ph.D.**** Editor, *Nature Chemical Biology***** ** ** -- Brian Shoichet Professor University of California, San Francisco Dept. of Pharmaceutical Chemistry phone: 415-514-4126; fax: 415-514-4260 http://shoichetlab.compbio.ucsf.edu

1 0

[Compbio-allhands] 5/2/13 Seminar with Laura Kiessling
by Nicole Takesono Flowers 26 Apr '13

26 Apr '13

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 Laura Kiessling University of Wisconsin-Madison Probing and Perturbing the Cell's Glycan Coat May 2, 2013 K. Shokat, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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] 5/2/13 Seminar with Laura Kiessling
by Nicole Takesono Flowers 26 Apr '13

26 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus HSW 303 Laura Kiessling University of Wisconsin-Madison Probing and Perturbing the Cell's Glycan Coat May 2, 2013 K. Shokat, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: postdoc ad
by Tom Ferrin 23 Apr '13

23 Apr '13

Postdoc opportunity... -------- Original Message -------- Subject: postdoc ad Date: Sun, 21 Apr 2013 16:22:56 -0400 (EDT) From: Sarah Tishkoff <tishkoff(a)mail.med.upenn.edu> To: <tef(a)cgl.ucsf.edu> Dear Dr. Ferrin, I am currently advertising for postdoc position and would be very appreciative if you could send out this postdoc ad to graduate students in the bioinformatics program at UCSF. We have a FANTASTIC opportunity for creative and independent postdocs to work on some one-of-a-kind datasets that we are generating in the next year. There will definitely be opportunities for developing/applying novel methodology and for publishing high profile papers Thanks very much in advance. Best Regards, Sarah Sarah Tishkoff, Ph.D. David and Lyn Silfen University Professor Departments of Genetics and Biology University of Pennsylvania Tel: 215-746-2670 tishkoff(a)mail.med.upenn.edu http://www.med.upenn.edu/tishkoff/

1 0

[Compbio-allhands] Fwd: Bioinformatics Summer Intern Posting_Ltr(2).docx
by Andrej Sali 23 Apr '13

23 Apr '13

-- 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 Begin forwarded message: > From: Dan Hostetter <dan(a)cytomx.com> > Subject: Bioinformatics Summer Intern Posting_Ltr(2).docx > Date: April 22, 2013 4:29:09 PM PDT > To: Dave Barkan <davebarkan(a)gmail.com>, "sali(a)salilab.org" <sali(a)salilab.org> > Cc: Luc Desnoyers <luc(a)cytomx.com> > > Hi Dave and Andrej, > > Hope you are both doing really well! > > I’ve been having a great time applying my protease knowledge at CytomX . We have started our very first summer internship program and need bioinformatics expertise. I thought both of you would be a great resource for recommendations. > > CytomX has applied the pro-drug concept to antibody therapeutics to address toxicities that occur when antibodies bind to target in healthy tissue. We call our protease activated antibodies “Probodies”. Our technology leverages protease activity that is present in tumor tissue and not healthy tissue to activate our Probodies. We would love to mine RNA expression databases for targets that fit certain criteria such as (1) extracellular and therefore accessible to an antibody therapeutic and (2) a protease that can cleave our Probody is also expressed. The ideal candidate would be comfortable working with RNA expression databases and able to create filters based on the needs of our Probody platform. I’ve attached a description of the intern position to this email as a Word document. > > I’m copying Luc Desnoyers on this email. Luc is the head of our cell biology group and is a great mentor. The student intern would be working with Luc and someone in the cell biology group. I can vouch that everyone in Luc’s group is nice and all of them are patient teachers. > > If you have anyone in mind that would be a good fit, please let us know. I’m confident they would have a great experience at CytomX. > > Thanks guys! > > Best, > Dan

1 0

[Compbio-allhands] 4/18/13 Seminar with Adrian Keatinge-Clay
by Nicole Takesono Flowers 19 Apr '13

19 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus HSW 303 Former Biophysics Student and Stroud Lab Post-doc, Adrian Keatinge-Clay University of Texas Visualizing and harnessing polyketide assembly lines April 25, 2013 R. Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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] 4/18/13 Seminar with Garry Nolan
by Nicole Takesono Flowers 19 Apr '13

19 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus HSW 303 Former Biophysics Student and Stroud Lab Post-doc, Adrian Keatinge-Clay University of Texas Visualizing and harnessing polyketide assembly lines April 25, 2013 R. Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Computational biologist position at Monsanto
by Jacobson, Matt 16 Apr '13

16 Apr '13

Begin forwarded message: From: "Groban, Eli" <EGroban(a)intrexon.com<mailto:EGroban@intrexon.com>> Subject: FW: Computational biologist position at Monsanto Date: April 16, 2013 11:33:58 AM PDT To: "matt(a)cgl.ucsf.edu<mailto:matt@cgl.ucsf.edu>" <matt(a)cgl.ucsf.edu<mailto:matt@cgl.ucsf.edu>> FYI. Thank you, Eli Groban, PhD Director, Metabolic Engineering and Systems Biology Industrial Products Division Intrexon Corporation 201 Industrial, Suite 450, San Carlos, CA 94070 p: 650.597.4026 | m: 415.971.7517 | egroban(a)intrexon.com<mailto:name@intrexon.com> www.dna.com<http://www.dna.com/> From: Kevin Costa <kcosta(a)berkeley.edu<mailto:kcosta@berkeley.edu>> Date: Tuesday, April 16, 2013 11:19 AM To: "all(a)synberc.org<mailto:all@synberc.org>" <all(a)synberc.org<mailto:all@synberc.org>> Subject: Computational biologist position at Monsanto Monsanto seeks a creative, mathematically-minded Computational Biologist to help us transform big data into higher yielding crops. In this role you role will support research across Monsanto Technology by integrating, modeling, and interpreting unprecedented genomic, transcriptomic, metabolic, phenotypic, population genetic, and geospatial data, all with the goal of driving interpretation into practical use. We aim to help feed the mid-21st century world using less water, less fertilizer, and less pesticide. https://monsanto.taleo.net/careersection/2/jobdetail.ftl?job=262740&lang=en… -- [cid:part2.03050501.00000805@berkeley.edu]<http://synberc.org/> Kevin Costa Administrative Director SynBERC - Synthetic Biology Engineering Research Center University of California, Berkeley 5885 Hollis Street, Room 4214, Mailcode 3224 Emeryville, CA 94608-2015 510-486-7568 510-432-7568 (cell) 510-486-4252 (fax) kcosta(a)berkeley.edu<mailto:kcosta@berkeley.edu> www.synberc.org<http://www.synberc.org/> ________________________________ CONFIDENTIAL TRANSMISSION - This message, including any attachments, is confidential and may be privileged. If you are not the intended recipient, please delete it without further distribution and reply to the sender that you have received the message in error. [cid:part2.03050501.00000805@berkeley.edu] Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] 4/18/13 Seminar with Garry Nolan
by Nicole Takesono Flowers 12 Apr '13

12 Apr '13

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 Garry Nolan Stanford A structure for cancer and immunity at the single cell level by mass cytometry April 18, 2013 J. Rettenmaier, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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] 4/11/13 Seminar with Brenda Schulman
by Nicole Takesono Flowers 04 Apr '13

04 Apr '13

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 Brenda Schulman St. Jude Children's Research Hospital Twists and Turns in Ubiquitin Conjugation Cascades April 11, 2013 J. Gross, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: A summer intern position opening in computational chemistry at GlaxoSmithKline
by Jacobson, Matt 02 Apr '13

02 Apr '13

Begin forwarded message: From: Xuan Hong <xuan.2.hong(a)gsk.com<mailto:xuan.2.hong@gsk.com>> Subject: A summer intern position opening in computational chemistry at GlaxoSmithKline Date: April 2, 2013 8:21:56 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Matt, I am a computational chemist in GlaxoSmithKline and am based in the Upper Merion, PA site. I have a summer intern position open (June 3rd to August 31st). The intern would be looking into strengths and weaknesses of loop sampling methods. I am wondering if you know any students who might be interested? (Interested students could directly email their CVs to me.) Thank you so much. Kind regards, Xuan Xuan Hong, PhD Computational & Structural Chemistry GlaxoSmithKline Pharmaceuticals 709 Swedeland Road King of Prussia, PA 19406 Office: 610-270-5013 Email: Xuan.2.Hong(a)gsk.com<mailto:Xuan.2.Hong@gsk.com> Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] Seminar - Bill Eaton, NIH-Biophysical Chemistry Section - May 9, 2013, GH - S261
by Hilary Mahon 01 Apr '13

01 Apr '13

Please see attached. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

1 0

[Compbio-allhands] 3/14/13 Seminar with Celeste Nelson
by Nicole Takesono Flowers 07 Mar '13

07 Mar '13

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 Celeste Nelson Princeton Physical control of tissue morphogenesis March 14, 2013 Z. Gartner, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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] 3/7/13 Seminar with Michael Laub
by Nicole Takesono Flowers 04 Mar '13

04 Mar '13

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 Laub MIT Specificity and evolution of bacterial signaling pathways March 7, 2013 A. Shiver, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: University of Calgary, Canada Research Chair-II Chair in Computational NanoBioMedicine
by Andrej Sali 28 Feb '13

28 Feb '13

-- 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 Begin forwarded message: > From: Peter Tieleman <tieleman(a)ucalgary.ca> > Subject: University of Calgary, Canada Research Chair-II Chair in Computational NanoBioMedicine > Date: February 28, 2013 6:07:27 PM PST > To: "Prof. J. Andrew McCammon" <jmccammon(a)mail.ucsd.edu>, Ken Dill <dill(a)laufercenter.org>, "\"\"\"\"jonuchic\"@rice. edu"@guitar.compbio.ucsf.edu, "'Hue Sun Chan'" <chan(a)arrhenius.med.utoronto.ca>, Régis Pomès <pomes(a)sickkids.ca>, "'Gilles H. Peslherbe'\"" <Gilles.Peslherbe\"@Concordia.ca>, mgilson(a)ucsd.edu, mlklein(a)temple.edu, hgrubmu@��gwdg.de, Bert de Groot <bgroot(a)gwdg.de>, Erik Lindahl <lindahl(a)cbr.su.se>, Qiang Cui <cui(a)chem.wisc.edu>, Arun Yethiraj <yethiraj(a)chem.wisc.edu>, Marc Baaden <baaden(a)smplinux.de>, David Spoel <spoel(a)xray.bmc.uu.se>, Benoit Roux <roux(a)uchicago.edu>, g.gompper(a)fz-juelich.de, Sandeep Patel <spatel(a)mail.chem.udel.edu>, Edward Lyman <elyman(a)udel.edu>, sali(a)salilab.org, Mark Sansom <mark.sansom(a)bioch.ox.ac.uk>, Michael Feig <feig(a)msu.edu>, "Baker,"Nathan <Nathan.Baker"@pnnl.gov>, David Sept <dsept(a)umich.edu>, David Shaw <David.Shaw(a)DEShawResearch.com>, Simon Bernèche <simon.berneche(a)unibas.ch>, bb8(a)columbia.edu, amackere(a)rx.umaryland.edu, Thomas Cheatham III <tec3(a)utah.edu>, Ross Walker <ross(a)rosswalker.co.uk>, Bernard.Brooks2(a)nih.hhs.gov, Wilfred F. van Gunsteren <wfvgn(a)igc.phys.chem.ethz.ch>, Siewert Jan Marrink <S.J.Marrink(a)rug.nl>, hummer(a)helix.nih.gov, Christine Peter <peter(a)mpip-mainz.mpg.de>, "> > > Dear colleagues, > > Please bring the attached ad to the attention of potential candidates. We think this is a great opportunity for excellent younger scholars. > > With best regards, > > Peter > > -- > Dr. D. Peter Tieleman, Professor, AIHS Scientist > AITF Strategic Chair in (Bio)Molecular Simulation > Department of Biological Sciences, University of Calgary

1 0

[Compbio-allhands] Invitae hiring multiple bioinformatics positions
by Alexandra Schnoes 28 Feb '13

28 Feb '13

BMI alum Lawrence Lee is now at Invitae and looking for multiple bioinformaticists (among other positions). Link to job postings below. Alex ---------- Forwarded message ---------- From: Lawrence Lee via LinkedIn <member(a)linkedin.com> Date: Thu, Feb 28, 2013 at 11:32 AM Subject: Lawrence shared a link with you To: Alexandra Schnoes <schnoes(a)gmail.com> LinkedIn MESSAGES *Lawrence Lee wrote:* Hey Alex! Hope all is well. We are hiring a lot of bioinformaticists right now. Perhaps you can pass this job posting along to near and recent grads? Thanks, Lawrence *Careers*<http://www.linkedin.com/e/63rla0-hdqb8faj-38/YpT4cyzc6TmEskh6Y1GeBi3Jj0B_/b…> invitae.com InVitae offers competitive compensation and full health benefits to our staff. If you are interested in applying to any of the following positions, please contact: InVitae-jobs(a)InVitae.com Customer Success (Client Services):... (See more articles »<http://www.linkedin.com/e/63rla0-hdqb8faj-38/tod/-1/INDUSTRY/industryNews/E…> ) View Article<http://www.linkedin.com/e/63rla0-hdqb8faj-38/YpT4cyzc6TmEskh6Y1GeBi3Jj0B_/b…>| -- Alexandra Schnoes schnoes(a)gmail.com

1 0

[Compbio-allhands] 2/28/13 Seminar with David Liu
by Nicole Takesono Flowers 22 Feb '13

22 Feb '13

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 Liu Harvard Small-molecule and macromolecule discovery driven by evolution February 28, 2013 Z. Gartner, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: bioinformatics/programmer opening for BindingDB project
by John Irwin 21 Feb '13

21 Feb '13

FYI ---------- Forwarded message ---------- From: Michael K. Gilson <mgilson(a)ucsd.edu> Date: Fri, Feb 15, 2013 at 1:26 PM Subject: bioinformatics/programmer opening for BindingDB project To: John Irwin <jji(a)cgl.ucsf.edu> Dear John, I would be grateful if you could bring the following opportunity to the attention of suitable individuals who may be interested. Due to renewed NIH funding, the BindingDB project (www.bindingdb.org) has opportunities at the postdoctoral or staff levels, depending upon background and interests, to further the development and application of BindingDB. Potential directions included inventing, implementing and deploying new BindingDB functionalities; and making new scientific connections between BindingDB data and structural, genomic, pathway and/or clinical data. Relevant background and expertise includes chemistry, chemical informatics, biochemistry, systems biology, genomics, web application development (Java, Javascript, HTML 5, CSS, XML), IT (Tomcat, Apache, sysadmin), and relational databases. Contact: Mike Gilson, mgilson(a)ucsd.edu Please feel free to contact me if you have any questions. Thanks and best regards, Mike P.S. Are you staying at UCSF? -- Michael K. Gilson, M.D., Ph.D. Professor, Skaggs School of Pharmacy and Pharmaceutical Sciences Director, UCSD Drug Discovery Institute U. C. San Diego 9500 Gilman Drive Pharmaceutical Sciences Building, Room 3224 La Jolla, CA 92093-0736 Voice: 858-822-0622 Fax: 858-822-7726http://gilson.ucsd.eduhttp://www.bindingdb.orghttp://drugdiscov…

1 0

[Compbio-allhands] Fwd: recruitment letter...
by Andrej Sali 21 Feb '13

21 Feb '13

Begin forwarded message: > From: Ram Samudrala <ram(a)compbio.washington.edu> > Subject: recruitment letter... > Date: February 21, 2013 4:31:36 PM PST > To: sali(a)salilab.org > Reply-To: ram(a)compbio.washington.edu > > Hi Andrej, I hope you are well. I am wondering if you could forward > this email around to your local CompBio groups? Thanks. > > --Ram > > > Postdoctoral opportunity in Translational Research Project at the Samudrala > Group in University of Washington, Seattle > > -- > > The Samudrala group at the University of Washington in Seattle is > seeking to recruit 2-3 postdoctoral fellows to work on the > Computational Analysis of Noval Drug Opportunities (CANDO) drug > discovery project funded by a 2012 NIH Director's Pioneer Award > (http://cando.compbio.washington.edu) The project goals are to screen > all human ingestible compounds against all proteins (primarily solved > protein structures) computationally to identify new uses for existing > drug compounds. Computational hits/leads are verified in vitro quickly > followed by clinical studies (since all compounds studied initially > are FDA approved drugs) for more than 30 indications with the aid of > numerous collaborations. > > The project has just begin its 3rd year, and an initial version of the > compound-protein matrix covering several thousand drugs (mostly FDA > approved drugs) vs. ~40,000 protein structures has been > completed. Bench studies are underway for two of the initial > indications we are going after (beta thalessemia major and multi-drug > resistant tuberculosis) and numerous other bench studies are soon to > follow. This is based on the multitargeting idea of how one compound > (or more) interacts with multiple proteins (all structures and > homologues) in a given system to produce a desired outcome (which is > how it happens in nature). More importantly, anything we find can be > directly evaluated by quick clinical study to demonstrate efficacy > since everything we'll initially focus on would've made it clinical > trials or through phase 2 testing at least. > > We are looking for individuals with the passion and skill set to help > us complete and deploy the pipeline for maximal benefit. Particularly > we are interested in a pipeline developer who would ideally be an > expert on machine learning techniques that will help integrate the > chem- and bioinformatic data with docking simulations, i.e., create a > more robust and automated pipeline that is adaptable to individual > indications and genotypes. We are also interested in a docking code > developer that will help implement the third version of the > fragment-based docking with dynamics protocol we have developed and > integrate the pipeline and docking methodology as a systems-based drug > discovery product. Another role which is part of the developer job > description is to work on a web application that can handle > personalisation and integrate it with our in-house cando database > API. This will finally give one-stop-shop-software to find putative > drugs for a particular indication of interest done using all the > proteins of the related organisms. So the final output of our > methodology is a drug-disease network which is linked back to > protein-compounds network, i.e. an atomistic description of all > existing and new drug prediction we are making. > > Gaurav Chopra, one of my postdocs and the overall project manager of > CANDO, will be attending CASP10 and is the person who you'd closely > work with should you accept this position. So please talk to him and > if you're interested in this position, and if you feel the project is > a good fit for you, send us both your CV and a brief statement of > interest to gaurav(a)compbio.washington.edu and > ram(a)compbio.washington.edu > > -- > > -- > > --- > You received this message because you are subscribed to the Google Groups "samudrala-compbio" group. > To unsubscribe from this group and stop receiving emails from it, send an email to samudrala-compbio+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > > > > --20cf306f722a5dcabe04d6442e13 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Hi = > George,<div> =3D"arial,helvetica,sans-serif"> </div><div> olor=3D"#000000">Here is th= > e email we sent out for CASP when I met people there. Please change as need= > ed and spread the word for recruiting two postdocs!</d= > iv> > > <div> "> </div><div> ace=3D"arial,helvetica,sans-serif">Thanks,</div><div><= > font color=3D"#000000">Gaur= > av</div> > > <div> "> </div><div> =3D"arial, helvetica, sans-serif">--</div><div> style-span" face=3D"arial, helvetica, sans-serif"> e-span" style=3D"border-collapse:collapse;color:rgb(34,34,34);font-family:a= > rial,sans-serif;font-size:13px"> > > Postdoctoral opportunity in Translational Research Project at the Samudrala= > Group in University of Washington, Seattle -- The Samudrala = > group at the University of Washington in Seattle is seeking to recruit 2= > -3 postdoctoral fellows to work on the > > Computational Analysis of Noval Drug Opportunities (CANDO) drug discover= > y project funded by a 2012 NIH Director's Pioneer Award (<a href=3D"= > http://cando.compbio.washington.edu/" target=3D"_blank" style=3D"color:rgb(= > 17,85,204)">http://cando.compbio.washington.edu</a>). The project goals are= > to screen > > all human ingestible compounds against all proteins (primarily solved pr= > otein structures) computationally to identify new uses for existing drug= > compounds. Computational hits/leads are verified in vitro quickly > followed by clinical studies (since all compounds studied initially > are FDA approved drugs) for more than 30 indications with the aid of num= > erous collaborations. The project has just begin its 3rd year, and a= > n initial version of the compound-protein matrix covering several thousa= > nd drugs (mostly FDA > > approved drugs) vs. ~40,000 protein structures has been completed. Bench= > studies are underway for two of the initial indications we are going af= > ter (beta thalessemia major and multi-drug resistant tuberculosis) and n= > umerous other bench studies are soon to > > follow. =A0This is based on the multitargeting idea of how one compound = > (or more) interacts with multiple proteins (all structures and homologue= > s) in a given system to produce a desired outcome (which is how it happe= > ns in nature). More importantly, anything we find can be > > directly evaluated by quick clinical study to demonstrate efficacy since= > everything we'll initially focus on would've made it clinical t= > rials or through phase 2 testing at least. We are looking for indivi= > duals with the passion and skill set to help > > us complete and deploy the pipeline for maximal benefit. Particularly we= > are interested in a pipeline developer who would ideally be an expert o= > n machine learning techniques that will help integrate the chem- and bio= > informatic data with docking simulations, i.e., create a > > more robust and automated pipeline that is adaptable to individual indic= > ations and genotypes. We are also interested in a docking code developer= > that will help implement the third version of the fragment-based dockin= > g with dynamics protocol we have developed and > > integrate the pipeline and docking methodology as a systems-based drug d= > iscovery product. Another role which is part of the developer job descri= > ption is to work on a web application that can handle personalisation an= > d integrate it with our in-house cando database > > API. This will finally give one-stop-shop-software to find putative drug= > s for a particular indication of interest done using all the proteins of= > the related organisms. So the final output of our methodology is a drug= > -disease network which is linked back to > > protein-compounds network, i.e. an atomistic description of all existing= > and new drug prediction we are making. Gaurav Chopra, one of my pos= > tdocs and the overall project manager of CANDO, will be attending CASP10= > and is the person who you'd closely > > work with should you accept this position. So please talk to him and if = > you're interested in this position, and if you feel the project is a= > good fit for you, send us both your CV and a brief statement of interes= > t to=A0<a href=3D"mailto:gaurav@compbio.washington.edu" style=3D"color:rgb(= > 17,85,204)">gaurav(a)compbio.washington.edu</a>=A0and > > <a href=3D"mailto:ram@compbio.washington.edu" style=3D"color:rgb(17,85,204)= > ">ram(a)compbio.washington.edu</a></div><div></div><div> lass=3D"Apple-style-span" color=3D"#222222" face=3D"arial, sans-serif"><spa= > n class=3D"Apple-style-span" style=3D"border-collapse:collapse"> > > </div><div> lvetica, sans-serif">--</div> > > > > -- >   > --- > You received this message because you are subscribed to the Google Groups &= > quot;samudrala-compbio" group. > To unsubscribe from this group and stop receiving emails from it, send an e= > mail to samudrala-compbio+unsubscribe(a)googlegroups.com. > For more options, visit <a href=3D"https://groups.google.com/groups/opt_out= > ">https://groups.google.com/groups/opt_out</a>. >   >   > > --20cf306f722a5dcabe04d6442e13-- -- 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] 2/21/13 Seminar with Bridget Carragher
by Nicole Takesono Flowers 15 Feb '13

15 Feb '13

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 Bridget Carragher Scripps Investigating the dynamics of nanomachines using automated electron microscopy February 21, 2013 R. Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Informatics Positions at Janssen
by Andrej Sali 15 Feb '13

15 Feb '13

Sent from my iPhone Begin forwarded message: > From: "Stephens, Susan [JRDUS]" <sstephens1(a)its.jnj.com> > Date: February 15, 2013, 11:31:33 AM EST > To: "Stephens, Susan [JRDUS]" <sstephens1(a)its.jnj.com> > Subject: Informatics Positions at Janssen > > Janssen has a number of excellent positions open for individuals with strong informatics skills. The positions are within therapeutic areas, so individuals will have the ability to strongly impact the portfolio of drugs that we bring to market. > > Interested individuals should apply on J&J’s job Web site. > > Susie > > ___________________________________________________________________________________________ > 1088130206 PRINCIPAL SCIENTIST, COMPUTATIONAL BIOLOGIST - http://jobs.jnj.com/s/uNXQ58#.URkufVX9Qks.email > 1063130206 SENIOR SCIENTIST, COMPUTATIONAL BIOLOGIST - http://jobs.jnj.com/s/oAdSR4#.URkxIA12K8Y.email > 1339130206 SENIOR SCIENTIST, COMPUTATIONAL BIOLOGIST - http://jobs.jnj.com/s/OOTkcD#.URlfw9kwEto.email > 1302130206 SCIENTIST, COMPUTATIONAL BIOLOGIST - http://jobs.jnj.com/s/eQ7P7N#.URkv71XYu-0.email > 2216121206 SENIOR SCIENTIST, BIOMARKERS - http://jobs.jnj.com/job/Spring-House-SENIOR-SCIENTIST%2C-BIOMARKERS-Job-PA-… > >

1 0

[Compbio-allhands] QB3 Informal Seminar: Dr. Jon Mason
by Yvonne Y. Munchua 14 Feb '13

14 Feb '13

Hello, everyone. Dr. Brian Shoichet will be hosting a QB3 Informal Seminar to be given by Dr. Jon Mason, Senior Research Fellow/Head of Computational Chemistry at Heptares Therapeutics. The event will be held tomorrow, Friday, February 15, from 9:30 am - 11:00 am RH-102 - Rock Hall Auditorium (please see attached flyer). The title of the presentation is, "SBDD for GPCRs: Driving druggability assessment, lead identification & optimization for potency & kinetics with receptor structure, including the use of new water network energetic analyses." Thank you, Yvonne Y. Munchua Asst. to Dr. Brian Shoichet UCSF Dept. of Pharm. Chem. 1700 4th Street, BH-508, Box 2550 San Francisco, CA 94158 P: (415) 514-4261 F: (415) 514-4260 yvonne.munchua(a)ucsf.edu

1 0

[Compbio-allhands] Fwd: Open Positions: ELBE Postdoc Program in Dresden
by Andrej Sali 14 Feb '13

14 Feb '13

Begin forwarded message: > From: Gene Myers <myers(a)mpi-cbg.de> > Subject: Open Positions: ELBE Postdoc Program in Dresden > Date: February 14, 2013 7:48:29 AM PST > To: undisclosed-recipients:; > > Dear colleague, > > The Max-Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG) and the MPI for the Physics of Complex Systems (MPI-PKS) in Dresden have formed a new Systems Biology Center that is particularly focused on combining genomics, image-based, and bio-physical approaches. > We are beginning the next cycle of a fully-funded postdoctoral program and are seeking applicants. > > We kindly ask you to bring the attached one-page announcement to the attention of your students. > > Best regards, > Gene Myers > Founding Director, The Systems Biology Center at Dresden > > > Dr. Gene Myers, Director > Tschira Chair of Systems Biology > Max-Planck Institute of > Molecular Cell Biology & Genetics > Pfotenhauerstr. 108 > 01307 Dresden > > Tel: +49 351 210-1220 > Fax: +49 351 210-1209 > -- 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: Job Openings with the RCSB PDB in San Diego
by Andrej Sali 09 Feb '13

09 Feb '13

Sent from my iPhone Begin forwarded message: > From: Philip Bourne <bourne(a)sdsc.edu> > Date: February 9, 2013, 3:47:59 PM PST > To: Philip Bourne <bourne(a)sdsc.edu> > Cc: Philip Bourne <bourne(a)sdsc.edu> > Subject: Job Openings with the RCSB PDB in San Diego > > Folks: > > Excuse the intrusion, but I would very much appreciate you passing on the job opportunities (attached) with our group here in San Diego. In a nutshell we are looking for: > An outstanding Web developer to work on the next generation RCSB PDB interface > An outstanding database programmer to work on the next generation PDB RCSB data model and data warehouse > Thanks. > > Sincerely, > Phil > > Philip E. Bourne, Ph.D. > Associate Vice Chancellor for Innovation and Industrial Alliances, UCSD > Professor of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD > Associate Director, RCSB Protein Data Bank > Founding Editor in Chief, PLoS Computational Biology > Co-founder, SciVee Inc. www.scivee.tv > www.sdsc.edu/pb > +1 858 354 8301

1 0

[Compbio-allhands] Peter A. Kollman Lectureship with Michael Levitt - February 14, 2013
by Nicole Takesono Flowers 08 Feb '13

08 Feb '13

Peter A. Kollman Lectureship Michael Levitt, Ph.D. Stanford Combinatorial Methods Solve a Difficult Structural Problem to Reveal How Chaperonins Work in Eukaryotes Thursday, February 14, 2013 12:00 PM J. Gross, Host Genentech Hall Byers Auditorium UCSF Mission Bay Campus Simulcast to Parnassus. Room S161 Reception in Byers Hall 5th Floor Lounge at 3:30 Sponsor: The Peter Kollman Fund Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator 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: Post-doctoral positions available
by Andrej Sali 07 Feb '13

07 Feb '13

-- 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 Begin forwarded message: > From: "Alan E. Mark" <a.e.mark(a)uq.edu.au> > Subject: Re: Post-doctoral positions available > Date: February 7, 2013 5:29:40 PM PST > To: Robert Best <robertbe(a)helix.nih.gov> > Cc: mlklein(a)temple.edu, dietmar.paschek(a)uni-rostock.de, marrink(a)chem.rug.nl, Ron Elber <ron(a)ices.utexas.edu>, jernigan(a)iastate.edu, dmz(a)ccbb.pitt.edu, Richard Lavery <richard.lavery(a)ibcp.fr>, kremer(a)mpip-mainz.mpg.de, Cecilia Clementi <cecilia(a)rice.edu>, Juan J de Pablo <depablo(a)engr.wisc.edu>, ftama(a)u.arizona.edu, Bruce Berne <bb8(a)columbia.edu>, David Coker <coker(a)chem.bu.edu>, Peter Rossky <rossky(a)mail.utexas.edu>, Dmitry Matyushov <dmitrym(a)asu.edu>, Kenneth Jordan <ken(a)visual1.chem.pitt.edu>, Doug Tobias <dtobias(a)uci.edu>, "Richard A. Friesner" <rich(a)chem.columbia.edu>, Bernhardt Trout <trout(a)mit.edu>, Karl Freed <k-freed(a)uchicago.edu>, Ken Dill <dill(a)maxwell.compbio.ucsf.edu>, David Reichman <reichman(a)chem.columbia.edu>, Jonathan Essex <J.W.Essex(a)soton.ac.uk>, bbagchi(a)sscu.iisc.ernet.in, gardes(a)rpi.edu, Jay Ponder <ponder(a)dasher.wustl.edu>, skolnick(a)gatech.edu, Andrei Tokmakoff <tokmakof(a)mit.edu>, Mark E Tuckerman <mark.tuckerman(a)nyu.edu>, pdebene(a)Princeton.EDU, william.jorgensen(a)yale.edu, lpratt(a)tulane.edu, aluzar(a)vcu.edu, bertil.halle(a)bpc.lu.se, Berend Smit <Berend-Smit(a)Berkeley.edu>, truskett(a)che.utexas.edu, Alexander Grosberg <ayg1(a)nyu.edu>, Barry Honig <bh6(a)columbia.edu>, Christopher Jarzynski <cjarzyns(a)umd.edu>, Eric Vanden-Eijnden <eve2(a)cims.nyu.edu>, Eugene Stanley <hes(a)bu.edu>, Felix Ritort <ritort(a)ffn.ub.es>, George Oster <goster(a)nature.berkeley.edu>, Hank Ashbaugh <hanka(a)tulane.edu>, Leonid Mirny <leonid(a)mit.edu>, Massimo Marchi <marchi(a)dsi.unimi.it>, Michael Shirts <michael.shirts(a)virginia.edu>, Michelle Parrinello <parrinello(a)phys.chem.ethz.ch>, Nicolae-Viorel Buchete <buchete(a)ucd.ie>, PieterRein tenWolde <tenwolde(a)amolf.nl>, Terry Hwa <hwa(a)ucsd.edu>, Thomas Miller <tfm(a)caltech.edu>, William Swope <swope(a)almaden.ibm.com>, "Wilfred F. van Gunsteren" <wfvgn(a)igc.phys.chem.ethz.ch>, "Alexandre M.J.J. Bonvin" <a.m.j.j.bonvin(a)uu.nl>, Xavier Daura <Xavier.Daura(a)uab.cat>, Helmut Grubmüller <hgrubmu(a)gwdg.de>, Daan Geerke <d.p.geerke(a)vu.nl>, David Smith <dsmith(a)irb.hr>, Christine Peter <peter(a)mpip-mainz.mpg.de>, Peter Tieleman <tieleman(a)ucalgary.ca>, "Megan O'Mara" <m.omara(a)uq.edu.au>, Alan Mark <a.e.mark(a)uq.edu.au>, David Fairlie <d.fairlie(a)imb.uq.edu.au>, Jennifer Martin <j.martin(a)imb.uq.edu.au>, Ricardo Mancera <R.Mancera(a)curtin.edu.au>, Durba Sengupta <d.sengupta(a)ncl.res.in>, Julian Gale <julian(a)ivec.org>, Irene Yarovsky <irene.yarovsky(a)rmit.edu.au>, jill.gready(a)anu.edu.au, Shin-Ho Chung <shin-ho.chung(a)anu.edu.au>, pande(a)stanford.edu, Ken Merz <merz(a)qtp.ufl.edu>, sali(a)salilab.org, Nilges Michael <nilges(a)pasteur.fr>, giorgio colombo <g.colombo(a)icrm.cnr.it>, lucy.forrest(a)biophys.mpg.de, ben.corry(a)anu.edu.au, Toby Allen <e88304(a)ems.rmit.edu.au>, dominik.marx(a)theochem.ruhr-uni-bochum.de, brookscl(a)umich.edu, roux(a)uchicago.edu, Rebecca Wade <rebecca.wade(a)h-its.org>, "michael.shirts(a)virginia.edu" <michael.shirts(a)virginia.edu>, Chandra Verma <chandra(a)bii.a-star.edu.sg>, "Dr M. Vendruscolo" <mv245(a)cus.cam.ac.uk>, Emanuele Paci <e.paci(a)leeds.ac.uk>, Chris Oostenbrink <chris.oostenbrink(a)boku.ac.at>, Bojan Zagrovic <bojan.zagrovic(a)univie.ac.at> > > Dear All, > > I would greatly appreciate it if you could pass the attached advertisement onto suitable post-doctoral candidates. I currently have two post-doctoral positions available funded by the Australian Health and Medical Research council (NHMRC) in my group at the University of Queensland, Australia. > > The specific projects focus on the use of molecular dynamics simulations to investigate the mechanism of action of ABC transporters and cytokine receptors as well as the interaction of small molecules and antimicrobial peptides with lipid bilayers. Applicants should hold or have recently submitted a PhD in computational chemistry or biophysics, or a related discipline. Experience in molecular dynamics simulations or related computational techniques, strong computational and programming skills are essential. Prior experience in free energy simulation techniques, simulations of membrane protein systems, or forcefield parameterisation will be an advantage. The University of Queensland (UQ) is located in sub tropical Brisbane on the east coast of Australia. UQ is one of the top research Universities in the Country and is consistently ranked within the top 50 Universities world wide. UQ was also one one of only two Institutions to receive a top ranking on Computational Chemistry in the most recent national research assessment. > > Interested applicants must apply online according to the instructions given in the attached file or see http://uqjobs.uq.edu.au/jobDetails.asp?sJobIDs=494312. > > If applicants have specific questions they can also contact me <a.e.mark(a)uq.edu.au> or Megan O'Mara <m.omara(a)uq.edu.au> directly. >> > Best wishes, > > Alan Mark > -- > -------------------------------------------------------------------- > This message was composed using voice recognition software. Please forgive any strange words I fail to correct. > ____________________________________________________________________ > Prof. Alan E. Mark > > BRISBANE > Molecular Dynamics Group > School of Chemistry and Molecular Biosciences (SCMB) > University of Queensland > Brisbane, QLD 4072, > Australia > > http://scmb.uq.edu.au/staff/alan-mark > http://compbio.biosci.uq.edu.au > > Physical address: > Rm 331 Level 3, Molecular Biosciences Building (#76) > > Email a.e.mark(a)uq.edu.au > Secretary: md.secretary(a)uq.edu.au > Phone: +61-7-3365 4180 > FAX: +61-7-3365 3872 > Secr: +61-7-3365 3821 > > Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland

1 0