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

[Compbio-allhands] Fwd: Computational Biology Position
by Brian Shoichet 09 Apr '16

09 Apr '16

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

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

08 Apr '16

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

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[Compbio-allhands] Fwd: job opportunity in Seattle area
by Jacobson, Matthew 06 Apr '16

06 Apr '16

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

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

05 Apr '16

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

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

03 Apr '16

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

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

01 Apr '16

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

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

29 Mar '16

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

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

24 Mar '16

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

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

16 Mar '16

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

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

09 Mar '16

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

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[Compbio-allhands] Fwd: Vertex Fellows Program
by Brian Shoichet 05 Mar '16

05 Mar '16

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

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

04 Mar '16

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

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

26 Feb '16

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

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

24 Feb '16

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

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

20 Feb '16

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

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

19 Feb '16

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

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

15 Feb '16

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

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

12 Feb '16

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

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

05 Feb '16

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

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

29 Jan '16

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

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

28 Jan '16

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

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

27 Jan '16

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

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

27 Jan '16

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

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[Compbio-allhands] computational jobs at Third Rock startup
by Jacobson, Matt 26 Jan '16

26 Jan '16

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

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[Compbio-allhands] Fwd: position for biophysicist at Biodesy
by Andrej Sali 23 Jan '16

23 Jan '16

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

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[Compbio-allhands] Fwd: 1/26/16 Seminar with Aled Edwards
by Jacobson, Matt 21 Jan '16

21 Jan '16

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

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

20 Jan '16

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

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

13 Jan '16

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

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

12 Jan '16

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

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

11 Jan '16

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

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

11 Jan '16

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

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[Compbio-allhands] Fwd: Help with a post doc??
by Andrej Sali 24 Dec '15

24 Dec '15

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

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[Compbio-allhands] Fwd: Postdoc merging structure-based drug design with physiologically-based pharmacokinetic simulations
by Jacobson, Matt 12 Dec '15

12 Dec '15

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

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

01 Dec '15

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

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[Compbio-allhands] Fwd: Michael Chimenti Referral
by Jacobson, Matt 26 Nov '15

26 Nov '15

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

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

23 Nov '15

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

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

19 Nov '15

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

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

16 Nov '15

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

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

11 Nov '15

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

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[Compbio-allhands] Job openings at Veracyte, South San Francisco
by Seung Joong Kim 11 Nov '15

11 Nov '15

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

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

09 Nov '15

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

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

06 Nov '15

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

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

30 Oct '15

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

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

30 Oct '15

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

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

30 Oct '15

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

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

29 Oct '15

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

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

28 Oct '15

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

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[Compbio-allhands] Fwd: Tenure-Track Openings in Computational Biology at Carnegie Mellon University
by Jacobson, Matt 26 Oct '15

26 Oct '15

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

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

23 Oct '15

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

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

16 Oct '15

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

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[Compbio-allhands] Fwd: Structural biology faculty positions at CUNY ASRC
by Andrej Sali 16 Oct '15

16 Oct '15

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

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

15 Oct '15

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

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

11 Oct '15

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

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

09 Oct '15

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

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[Compbio-allhands] Fwd: computational scientist at Impossible Foods
by Andrej Sali 03 Oct '15

03 Oct '15

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

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

02 Oct '15

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

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

01 Oct '15

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

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

01 Oct '15

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

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[Compbio-allhands] Fwd: Bioinformatics and Computational Staff Scientists at the University of Oklahoma
by Jacobson, Matt 01 Oct '15

01 Oct '15

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

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

28 Sep '15

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

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

25 Sep '15

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

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

24 Sep '15

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

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

24 Sep '15

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

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

22 Sep '15

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

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

22 Sep '15

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

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

21 Sep '15

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

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

18 Sep '15

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

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

16 Sep '15

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

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

14 Sep '15

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

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

12 Sep '15

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

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

10 Sep '15

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

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

07 Sep '15

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

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[Compbio-allhands] Fwd: Position at Lilly, Please forward to your people who are looking
by Andrej Sali 04 Sep '15

04 Sep '15

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

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

01 Sep '15

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

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

14 Aug '15

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

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

13 Aug '15

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

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[Compbio-allhands] Fwd: Opportunities at the CUNY Graduate Center
by Andrej Sali 11 Aug '15

11 Aug '15

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

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

06 Jul '15

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

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[Compbio-allhands] Fwd: Gladstone Bioinformatics Core Director Position -- please forward
by Scooter Morris 02 Jul '15

02 Jul '15

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

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

01 Jul '15

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

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

23 Jun '15

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

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

22 Jun '15

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

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[Compbio-allhands] Fwd: Temporary position in Novartis Emeryville CADD group
by Jacobson, Matt 18 Jun '15

18 Jun '15

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

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

17 Jun '15

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

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

16 Jun '15

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

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

10 Jun '15

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

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

05 Jun '15

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

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

02 Jun '15

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

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

22 May '15

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

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

21 May '15

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

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

15 May '15

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

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

15 May '15

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

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

08 May '15

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

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

01 May '15

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

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

24 Apr '15

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

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

23 Apr '15

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

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

17 Apr '15

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

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

13 Apr '15

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

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

03 Apr '15

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

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

30 Mar '15

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

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