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

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

20 Jan '16

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

1 0

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

20 Jan '16

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

2 1

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

13 Jan '16

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

1 0

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

12 Jan '16

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

1 0

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

11 Jan '16

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

1 0

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

11 Jan '16

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

1 0

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

23 Dec '15

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

1 0

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

11 Dec '15

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

1 0

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

01 Dec '15

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

1 0

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

25 Nov '15

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

1 0

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

23 Nov '15

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

1 0

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

19 Nov '15

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

1 0

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

16 Nov '15

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

1 0

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

11 Nov '15

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

1 0

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

10 Nov '15

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

1 0

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

09 Nov '15

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

1 0

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

06 Nov '15

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

1 0

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

30 Oct '15

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

1 0

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

30 Oct '15

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

1 0

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

30 Oct '15

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

1 0

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

29 Oct '15

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

1 0

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

28 Oct '15

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

1 0

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

25 Oct '15

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

1 0

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

23 Oct '15

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

1 0

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

16 Oct '15

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

1 0