January 2016 - compbio-allhands@cgl.ucsf.edu

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

29 Jan '16

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

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

28 Jan '16

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

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

27 Jan '16

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

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

27 Jan '16

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

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[Compbio-allhands] computational jobs at Third Rock startup
by Jacobson, Matt 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

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[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>

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[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.

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

20 Jan '16

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

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

13 Jan '16

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

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

12 Jan '16

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

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compbio-allhands January 2016