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

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

08 Apr '16

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

1 0

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

08 Apr '16

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

1 0

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

05 Apr '16

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

1 0

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

05 Apr '16

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

1 0

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

03 Apr '16

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

1 0

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

01 Apr '16

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

1 0

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

29 Mar '16

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

1 0

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

24 Mar '16

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

1 0

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

16 Mar '16

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

1 0

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

09 Mar '16

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

1 0

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

04 Mar '16

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

1 0

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

04 Mar '16

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

1 0

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

26 Feb '16

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

1 0

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

24 Feb '16

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

1 0

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

20 Feb '16

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

1 0

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

19 Feb '16

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

1 0

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

15 Feb '16

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

1 0

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

12 Feb '16

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

1 0

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

05 Feb '16

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

1 0

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

29 Jan '16

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

1 0

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

28 Jan '16

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

1 0

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

27 Jan '16

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

1 0

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

27 Jan '16

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

1 0

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

25 Jan '16

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

1 1

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

22 Jan '16

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

1 0