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

[Compbio-allhands] Seminar, Jan Ellenberg, “Imaging the assembly of protein complexes and the dynamics of protein networks in dividing human cells”
by Andrej Sali 14 Oct '16

14 Oct '16

Wed, Oct 19, 12-1pm, MH-1406 -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] 10/20/16 Seminar with Yong Xiong
by Flowers, Nicole 14 Oct '16

14 Oct '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.) Yong Xiong Yale HIV Capsid Pattern Sensing by the Host October 20, 2016 J. Gross, Host This seminar is sponsored by the HARC Center BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Following up: recruiting postdoc for GROMACS improvements and development
by Jacobson, Matt 12 Oct '16

12 Oct '16

- Matt Begin forwarded message: From: Michael R Shirts <Michael.Shirts(a)Colorado.EDU<mailto:Michael.Shirts@Colorado.EDU>> Subject: Following up: recruiting postdoc for GROMACS improvements and development Date: October 12, 2016 at 4:18:09 PM PDT To: Michael R Shirts <Michael.Shirts(a)Colorado.EDU<mailto:Michael.Shirts@Colorado.EDU>> Cc: Peter Kasson <kasson(a)virginia.edu<mailto:kasson@virginia.edu>> Hi, all- Thanks very much for the responses to my previous email. We have hired one postdoc (located at the U. of Virginia) on the NIH-sponsored collaborative project to improve GROMACS robustness and functionality I emailed you about before. However, I am still recruiting one postdoctoral researcher to join my group here at CU Boulder. Perhaps you knew someone for whom this fall was not a good starting time, but January might be; we’d love to hear from them. As discussed before, the work on the Colorado side involves statistical physics to test and diagnose simulation validity, improving the testing framework, and new Monte Carlo methods. Strong software engineering skills are a must, and we would particularly appreciate active members of the molecular simulation development community. As always, members of groups under-represented in the molecular simulation field are especially encouraged to apply. Please refer anyone you think appropriate or have them apply at the link below. The Shirts research group in the Department of Chemical and Biological Engineering is hiring a highly capable research associate to help develop the GROMACS molecular simulation package. GROMACS is an open-source project with a strong international development community as well as a 10,000+ user base. This position is part of a new NIH funded collaborative effort between the Shirts group and the Kasson group (at the University of Virginia) to improve the robustness, functionality, and usability of GROMACS, offering the candidate the opportunity to positively affect the work of thousands of researchers across the globe. Candidates will have the opportunity to learn state-of-the-art simulation methodology and work collaboratively with a global team of developers. This position requires a Ph.D. in Chemistry, Chemical Engineering, Physics, Computer Science or a related field. It requires very strong statistical mechanical, molecular simulation and theoretical skills, as well as significant software engineering experience and ability. Experience in C++ and Python is preferred, as well as experience with version control, code review systems, and team-oriented software development. Competitive candidates will have a track record of scientific success in graduate study with a strong publication record. Apply at https://cu.taleo.net/careersection/2/jobdetail.ftl?job=05979&lang=en&sns_id… ~~~~~~~~~~~~~~~~ Michael Shirts Associate Professor michael.shirts(a)colorado.edu<mailto:michael.shirts@colorado.edu> http://www.colorado.edu/lab/shirtsgroup/ Phone: (303) 735-7860 Office: JSCBB C123 Department of Chemical and Biological Engineering University of Colorado Boulder

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[Compbio-allhands] 10/13/16 Seminar with Eckhard Jankowsky
by Flowers, Nicole 07 Oct '16

07 Oct '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.) Eckhard Jankowsky Case Western RNA helicases in translation initiation and granule formation. October 13, 2016 J. Gross & D. Weinberg, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 10/6/16 Seminar with Jonathan Gable
by Flowers, Nicole 06 Oct '16

06 Oct '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.) Jonathan Gable Clements Lecture Targeting a Dynamic Protein-Protein Interface to Inhibit a Critical Herpesvirus Enzyme October 6, 2016 D. Agard, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 10/4/16 Seminar with Ruth Ley
by Flowers, Nicole 04 Oct '16

04 Oct '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Tuesday, 12 Noon Genentech Hall Auditorium NO SIMULCAST Ruth Ley Max Planck Institute Tübingen Genetic determinants of the gut micro biome and links to phenotype October 4, 2016 S. Lyalina, 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] Knapp Seminar (Monday October 3rd 2:30 pm, CVRI 441)
by Grabe, Michael 02 Oct '16

02 Oct '16

Hi everyone, I wanted to remind you of the following lecture tomorrow: Walter Knapp Free University of Berlin Computing pKa values in proteins Smith CVRI Building 4th floor Room 441 Monday October 3rd 2:30 pm Walter’s website can be found here: http://agknapp.chemie.fu-berlin.de/agknapp/ Please share this posting with interested members of your lab. Best Michael PS - I apologize if you get this email twice. ---------------------------------------------------------- Michael Grabe Associate Professor University of California, San Francisco Cardiovascular Research Institute Department of Pharmaceutical Chemistry 555 Mission Bay Blvd South, Room 452T, MC 3122 San Francisco, California 94143 415-502-2874 (office) 415-476-8173 (fax)

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[Compbio-allhands] Seminar in CVRI (Walter Knapp)
by Grabe, Michael 27 Sep '16

27 Sep '16

Hi everyone, Walter Knapp from the Free University of Berlin will be visiting my lab next Monday October 3rd and giving a seminar in CVRI titled: Computing pKa values in proteins Smith CVRI Building 4th floor Room 441 Monday October 3rd 2:30 pm Walter’s website can be found here: http://agknapp.chemie.fu-berlin.de/agknapp/ Please share this posting with anyone that may be interested, and let me know if you want to meet with him during the day. Best Michael l---------------------------------------------------------- Michael Grabe Associate Professor University of California, San Francisco Cardiovascular Research Institute Department of Pharmaceutical Chemistry 555 Mission Bay Blvd South, Room 452T, MC 3122 San Francisco, California 94143 415-502-2874 (office) 415-476-8173 (fax)

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[Compbio-allhands] Fwd: Faculty position openings
by Jacobson, Matt 25 Sep '16

25 Sep '16

Not sure which lists this has gone out to so apologies if it’s a duplicate - Matt Begin forwarded message: From: Talent Project <talents(a)cuhk.edu.cn<mailto:talents@cuhk.edu.cn>> Subject: Faculty position openings Date: September 25, 2016 at 5:25:03 PM PDT To: Talent Project <talents(a)cuhk.edu.cn<mailto:talents@cuhk.edu.cn>> Dear Colleague, We have the pleasure to announce an ambitious hiring plan for faculty members at all ranks in areas of Science and Engineering at The Chinese University of Hong Kong, Shenzhen [CUHK(SZ)]. CUHK(SZ) is a research intensive University executed with the highest international standards and traditions. English is the official language. The University extends the core values and educational philosophy of The Chinese University of Hong Kong, Hong Kong. Operated under a modern and transparent management system that values academic freedom, CUHK(SZ) contributes to higher education by nurturing graduates at all levels with broad international outlook, sound scholarship and commitment to society. Besides education, the University also contributes to the long-term prosperity of Shenzhen and China by its leading work in research and entrepreneurship. The campus (http://www.cuhk.edu.cn/en/index.html) is located in a picturesque area of Shenzhen (http://www.eyeshenzhen.com/, http://v.qq.com/x/page/m0308sptsyb.html) one of the fastest growing communities in the World. The University offers the right candidate an excellent salary package, competitive startup funds and space. The City and Longang Municipal District also offer generous signing bonuses and financial incentives (http://www.cuhk.edu.cn/UploadFiles/TalentsProgramOutline.pdf) While the University welcomes applicants from all areas of expertise, current strengths include Computer Science and Engineering, Electronic Information Engineering, Robotics and Control, New Energy Science and Engineering, Statistics and Data Science, Mathematics and Applied Mathematics, Bioinformatics, Biological Sciences and Biomedical Engineering, Design and Manufacturing Systems, Physics, Chemistry, and Materials Science. A number of multi-million dollar research centers have already been set up. Cluster hiring for the right groups are also considered. The University expects to hire 150 to 200 new faculty in the next five years. By joining us, the person will become a member of one of the best run educational and research institutions in the world. We should be much obliged if you would kindly broadcast this information to those who might be interested in this announcement. For interested individuals, please send CV and/or inquiries to talents4sse(a)cuhk.edu.cn<mailto:talents4sse@cuhk.edu.cn>. Sincerely, S Y Tong (David) Director, President’s Special Unit in Faculty Recruitment The Chinese University of Hong Kong, Shenzhen

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[Compbio-allhands] 9/29/16 Seminar with Jennifer Cochran
by Flowers, Nicole 22 Sep '16

22 Sep '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.) Jennifer Cochran Stanford Engineered Proteins for Visualizing and Treating Cancer September 29, 2016 B. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 9/22/16 Seminar with Grant Jensen- NOTE ROOM
by Flowers, Nicole 22 Sep '16

22 Sep '16

Just a reminder that today’s BBC Seminar will be in Mission Hall 1400. Thank you, Nicole 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 From: Nicole Flowers <nicole.flowers(a)ucsf.edu<mailto:nicole.flowers@ucsf.edu>> Date: Friday, September 16, 2016 at 9:44 AM To: CCB Student List <CCB_STUDENTS(a)LISTSRV.UCSF.EDU<mailto:CCB_STUDENTS@LISTSRV.UCSF.EDU>>, BMI Students List <BMI_STUDENTS(a)LISTSRV.UCSF.EDU<mailto:BMI_STUDENTS@LISTSRV.UCSF.EDU>>, "bpstudents(a)listserv.ucsf.edu<mailto:bpstudents@listserv.ucsf.edu>" <bpstudents(a)listserv.ucsf.edu<mailto:bpstudents@listserv.ucsf.edu>>, "BBCFACULTY(a)LISTSRV.UCSF.EDU<mailto:BBCFACULTY@LISTSRV.UCSF.EDU>" <BBCFACULTY(a)LISTSRV.UCSF.EDU<mailto:BBCFACULTY@LISTSRV.UCSF.EDU>> Cc: "Alvarez-Buylla, Arturo" <AlvarezBuyllaA(a)ucsf.edu<mailto:AlvarezBuyllaA@ucsf.edu>>, "abul.abbas(a)ucsf.edu<mailto:abul.abbas@ucsf.edu>" <abul.abbas(a)ucsf.edu<mailto:abul.abbas@ucsf.edu>>, "adam.gazzaley(a)ucsf.edu<mailto:adam.gazzaley@ucsf.edu>" <adam.gazzaley(a)ucsf.edu<mailto:adam.gazzaley@ucsf.edu>>, "allan.basbaum(a)ucsf.edu<mailto:allan.basbaum@ucsf.edu>" <allan.basbaum(a)ucsf.edu<mailto:allan.basbaum@ucsf.edu>>, "Butte, Atul" <Atul.Butte(a)ucsf.edu<mailto:Atul.Butte@ucsf.edu>>, "brian.black(a)ucsf.edu<mailto:brian.black@ucsf.edu>" <brian.black(a)ucsf.edu<mailto:brian.black@ucsf.edu>>, "Hueschen, Christina" <Christina.Hueschen(a)ucsf.edu<mailto:Christina.Hueschen@ucsf.edu>>, "Cunha, Gerald" <gerald.cunha(a)ucsf.edu<mailto:gerald.cunha@ucsf.edu>>, "david.erle(a)ucsf.edu<mailto:david.erle@ucsf.edu>" <david.erle(a)ucsf.edu<mailto:david.erle@ucsf.edu>>, David Morgan <david.morgan(a)ucsf.edu<mailto:david.morgan@ucsf.edu>>, Deanna Kroetz <deanna.kroetz(a)ucsf.edu<mailto:deanna.kroetz@ucsf.edu>>, "edward.goetzl(a)ucsf.edu<mailto:edward.goetzl@ucsf.edu>" <edward.goetzl(a)ucsf.edu<mailto:edward.goetzl@ucsf.edu>>, "Gupta, Nalin" <Nalin.Gupta(a)ucsf.edu<mailto:Nalin.Gupta@ucsf.edu>>, "hal.chapman(a)ucsf.edu<mailto:hal.chapman@ucsf.edu>" <hal.chapman(a)ucsf.edu<mailto:hal.chapman@ucsf.edu>>, "Bourne, Henry" <Henry.Bourne(a)ucsf.edu<mailto:Henry.Bourne@ucsf.edu>>, "jason.cyster(a)ucsf.edu<mailto:jason.cyster@ucsf.edu>" <jason.cyster(a)ucsf.edu<mailto:jason.cyster@ucsf.edu>>, "Chang, Jeremy" <Jeremy.Chang(a)ucsf.edu<mailto:Jeremy.Chang@ucsf.edu>>, "Ye, Chun" <Jimmie.Ye(a)ucsf.edu<mailto:Jimmie.Ye@ucsf.edu>>, Joachim Li <joachim.li(a)ucsf.edu<mailto:joachim.li@ucsf.edu>>, "john.rubenstein(a)ucsf.edu<mailto:john.rubenstein@ucsf.edu>" <john.rubenstein(a)ucsf.edu<mailto:john.rubenstein@ucsf.edu>>, "jon.levine(a)ucsf.edu<mailto:jon.levine@ucsf.edu>" <jon.levine(a)ucsf.edu<mailto:jon.levine@ucsf.edu>>, "Thompson-Peer, Katherine" <Katherine.Thompson-Peer(a)ucsf.edu<mailto:Katherine.Thompson-Peer@ucsf.edu>>, Keith Mostov <keith.mostov(a)ucsf.edu<mailto:keith.mostov@ucsf.edu>>, "Kriegstein, Arnold" <Arnold.Kriegstein(a)ucsf.edu<mailto:Arnold.Kriegstein@ucsf.edu>>, "larry.tecott(a)ucsf.edu<mailto:larry.tecott@ucsf.edu>" <larry.tecott(a)ucsf.edu<mailto:larry.tecott@ucsf.edu>>, "Lowenstein, Daniel" <Lowenstein(a)ucsf.edu<mailto:Lowenstein@ucsf.edu>>, "Lee-Baird, Marissa" <Marissa.Lee-Baird(a)ucsf.edu<mailto:Marissa.Lee-Baird@ucsf.edu>>, "mary.dallman(a)ucsf.edu<mailto:mary.dallman@ucsf.edu>" <mary.dallman(a)ucsf.edu<mailto:mary.dallman@ucsf.edu>>, "mary.elting(a)ucsf.edu<mailto:mary.elting@ucsf.edu>" <mary.elting(a)ucsf.edu<mailto:mary.elting@ucsf.edu>>, "Matija.Peterlin(a)ucsf.edu<mailto:Matija.Peterlin@ucsf.edu>" <Matija.Peterlin(a)ucsf.edu<mailto:Matija.Peterlin@ucsf.edu>>, Melissa Paraiso <Melissa.Paraiso(a)ucsf.edu<mailto:Melissa.Paraiso@ucsf.edu>>, Mike Wilson <Michael.A.Wilson(a)nasa.gov<mailto:Michael.A.Wilson@nasa.gov>>, "michael.lazarus(a)ucsf.edu<mailto:michael.lazarus@ucsf.edu>" <michael.lazarus(a)ucsf.edu<mailto:michael.lazarus@ucsf.edu>>, "millo.pasquini(a)ucsf.edu<mailto:millo.pasquini@ucsf.edu>" <millo.pasquini(a)ucsf.edu<mailto:millo.pasquini@ucsf.edu>>, Noleine Blizzard <Noleine.Blizzard(a)ucsf.edu<mailto:Noleine.Blizzard@ucsf.edu>>, "pao-tien.chuang(a)ucsf.edu<mailto:pao-tien.chuang@ucsf.edu>" <pao-tien.chuang(a)ucsf.edu<mailto:pao-tien.chuang@ucsf.edu>>, Peter Sargent <peter.sargent(a)ucsf.edu<mailto:peter.sargent@ucsf.edu>>, "Philip.Coffino(a)ucsf.edu<mailto:Philip.Coffino@ucsf.edu>" <Philip.Coffino(a)ucsf.edu<mailto:Philip.Coffino@ucsf.edu>>, "Philippe.Gascard(a)ucsf.edu<mailto:Philippe.Gascard@ucsf.edu>" <Philippe.Gascard(a)ucsf.edu<mailto:Philippe.Gascard@ucsf.edu>>, "pui.kwok(a)ucsf.edu<mailto:pui.kwok@ucsf.edu>" <pui.kwok(a)ucsf.edu<mailto:pui.kwok@ucsf.edu>>, Raul Andino <Raul.Andino(a)ucsf.edu<mailto:Raul.Andino@ucsf.edu>>, "rik.derynck(a)ucsf.edu<mailto:rik.derynck@ucsf.edu>" <rik.derynck(a)ucsf.edu<mailto:rik.derynck@ucsf.edu>>, "Nicoll, Roger" <Roger.Nicoll(a)ucsf.edu<mailto:Roger.Nicoll@ucsf.edu>>, "Packman, Seymour" <Seymour.Packman(a)ucsf.edu<mailto:Seymour.Packman@ucsf.edu>>, "Sam.Pleasure(a)ucsf.edu<mailto:Sam.Pleasure@ucsf.edu>" <Sam.Pleasure(a)ucsf.edu<mailto:Sam.Pleasure@ucsf.edu>>, "Scott.Baraban(a)ucsf.edu<mailto:Scott.Baraban@ucsf.edu>" <Scott.Baraban(a)ucsf.edu<mailto:Scott.Baraban@ucsf.edu>>, "Hickey, Scott" <Scott.Hickey(a)ucsf.edu<mailto:Scott.Hickey@ucsf.edu>>, "shaun.coughlin(a)ucsf.edu<mailto:shaun.coughlin@ucsf.edu>" <shaun.coughlin(a)ucsf.edu<mailto:shaun.coughlin@ucsf.edu>>, "Sretavan, David" <David.Sretavan(a)ucsf.edu<mailto:David.Sretavan@ucsf.edu>>, "takashi.mikawa(a)ucsf.edu<mailto:takashi.mikawa@ucsf.edu>" <takashi.mikawa(a)ucsf.edu<mailto:takashi.mikawa@ucsf.edu>>, Thanh Lam <thanh.lam(a)ucsf.edu<mailto:thanh.lam@ucsf.edu>>, "thea.tlsty(a)ucsf.edu<mailto:thea.tlsty@ucsf.edu>" <thea.tlsty(a)ucsf.edu<mailto:thea.tlsty@ucsf.edu>>, "Ullian, Erik" <Erik.Ullian(a)ucsf.edu<mailto:Erik.Ullian@ucsf.edu>>, "Yee, Laura" <Laura.Yee2(a)ucsf.edu<mailto:Laura.Yee2@ucsf.edu>>, "Shen, Yin" <Yin.Shen(a)ucsf.edu<mailto:Yin.Shen@ucsf.edu>>, "ying-hui.fu(a)ucsf.edu<mailto:ying-hui.fu@ucsf.edu>" <ying-hui.fu(a)ucsf.edu<mailto:ying-hui.fu@ucsf.edu>>, "YuhNung.Jan(a)ucsf.edu<mailto:YuhNung.Jan@ucsf.edu>" <YuhNung.Jan(a)ucsf.edu<mailto:YuhNung.Jan@ucsf.edu>>, "Balmain, Allan" <Allan.Balmain(a)ucsf.edu<mailto:Allan.Balmain@ucsf.edu>>, "akreitzer(a)gladstone.ucsf.edu<mailto:akreitzer@gladstone.ucsf.edu>" <akreitzer(a)gladstone.ucsf.edu<mailto:akreitzer@gladstone.ucsf.edu>>, "Albertson, Donna" <Donna.albertson(a)ucsf.edu<mailto:Donna.albertson@ucsf.edu>>, "allhands(a)compbio.ucsf.edu<mailto:allhands@compbio.ucsf.edu>" <allhands(a)compbio.ucsf.edu<mailto:allhands@compbio.ucsf.edu>>, "Weiss, Art" <Art.Weiss(a)ucsf.edu<mailto:Art.Weiss@ucsf.edu>>, "barondes(a)cgl.ucsf.edu<mailto:barondes@cgl.ucsf.edu>" <barondes(a)cgl.ucsf.edu<mailto:barondes@cgl.ucsf.edu>>, "Cheyette, Ben" <bc(a)ucsf.edu<mailto:bc@ucsf.edu>>, "Bhatnagar, Rajendr" <Rajendr.Bhatnagar(a)ucsf.edu<mailto:Rajendr.Bhatnagar@ucsf.edu>>, "bishop(a)cgl.ucsf.edu<mailto:bishop@cgl.ucsf.edu>" <bishop(a)cgl.ucsf.edu<mailto:bishop@cgl.ucsf.edu>>, Jeff Blaney <blaney.jeff(a)gene.com<mailto:blaney.jeff@gene.com>>, "Seaman, William" <William.Seaman(a)ucsf.edu<mailto:William.Seaman@ucsf.edu>>, Robert Chalkley <chalkley(a)cgl.ucsf.edu<mailto:chalkley@cgl.ucsf.edu>>, "charles.ordahl(a)ucsf.edu<mailto:charles.ordahl@ucsf.edu>" <charles.ordahl(a)ucsf.edu<mailto:charles.ordahl@ucsf.edu>>, "chris(a)phy.ucsf.edu<mailto:chris@phy.ucsf.edu>" <chris(a)phy.ucsf.edu<mailto:chris@phy.ucsf.edu>>, "Cleaver, James" <James.Cleaver(a)ucsf.edu<mailto:James.Cleaver@ucsf.edu>>, "clifford.lowell(a)ucsf.edu<mailto:clifford.lowell@ucsf.edu>" <clifford.lowell(a)ucsf.edu<mailto:clifford.lowell@ucsf.edu>>, "cope(a)phy.ucsf.edu<mailto:cope@phy.ucsf.edu>" <cope(a)phy.ucsf.edu<mailto:cope@phy.ucsf.edu>>, "damsky(a)cgl.ucsf.edu<mailto:damsky@cgl.ucsf.edu>" <damsky(a)cgl.ucsf.edu<mailto:damsky@cgl.ucsf.edu>>, "david.wofsy(a)ucsf.edu<mailto:david.wofsy@ucsf.edu>" <david.wofsy(a)ucsf.edu<mailto:david.wofsy@ucsf.edu>>, "Sheppard, Dean" <Dean.Sheppard(a)ucsf.edu<mailto:Dean.Sheppard@ucsf.edu>>, "defranco(a)cgl.ucsf.edu<mailto:defranco@cgl.ucsf.edu>" <defranco(a)cgl.ucsf.edu<mailto:defranco@cgl.ucsf.edu>>, "Hanahan, Doug" <Doug.Hanahan(a)ucsf.edu<mailto:Doug.Hanahan@ucsf.edu>>, "dieter.gruenert(a)ucsf.edu<mailto:dieter.gruenert@ucsf.edu>" <dieter.gruenert(a)ucsf.edu<mailto:dieter.gruenert@ucsf.edu>>, Dirk Bussiere <dirksen.bussiere(a)novartis.com<mailto:dirksen.bussiere@novartis.com>>, "Ron, Dorit" <Dorit.Ron(a)ucsf.edu<mailto:Dorit.Ron@ucsf.edu>>, "dsrivastava(a)gladstone.ucsf.edu<mailto:dsrivastava@gladstone.ucsf.edu>" <dsrivastava(a)gladstone.ucsf.edu<mailto:dsrivastava@gladstone.ucsf.edu>>, Erin Simonds <erin.simonds(a)gmail.com<mailto:erin.simonds@gmail.com>>, "fathi.karouia(a)nasa.gov<mailto:fathi.karouia@nasa.gov>" <fathi.karouia(a)nasa.gov<mailto:fathi.karouia@nasa.gov>>, "Brodsky, Frances" <Frances.Brodsky(a)ucsf.edu<mailto:Frances.Brodsky@ucsf.edu>>, Kati Medzihradszky <folkl(a)cgl.ucsf.edu<mailto:folkl@cgl.ucsf.edu>>, "gail.r.martin(a)ucsf.edu<mailto:gail.r.martin@ucsf.edu>" <gail.r.martin(a)ucsf.edu<mailto:gail.r.martin@ucsf.edu>>, "Davis, Graeme" <Graeme.Davis(a)ucsf.edu<mailto:Graeme.Davis@ucsf.edu>>, "gevan(a)cc.ucsf.edu<mailto:gevan@cc.ucsf.edu>" <gevan(a)cc.ucsf.edu<mailto:gevan@cc.ucsf.edu>>, "Jan , Lily" <Lily.Jan(a)ucsf.edu<mailto:Lily.Jan@ucsf.edu>>, "Guo, Su" <Su.Guo(a)ucsf.edu<mailto:Su.Guo@ucsf.edu>>, Christine Guthrie <guthrie(a)cgl.ucsf.edu<mailto:guthrie@cgl.ucsf.edu>>, "heberleinu(a)janelia.hhmi.org<mailto:heberleinu@janelia.hhmi.org>" <heberleinu(a)janelia.hhmi.org<mailto:heberleinu@janelia.hhmi.org>>, "hjr(a)phy.ucsf.edu<mailto:hjr@phy.ucsf.edu>" <hjr(a)phy.ucsf.edu<mailto:hjr@phy.ucsf.edu>>, "Horton, Jonathan" <Jonathan.Horton(a)ucsf.edu<mailto:Jonathan.Horton@ucsf.edu>>, "hypusine(a)gmail.com<mailto:hypusine@gmail.com>" <hypusine(a)gmail.com<mailto:hypusine@gmail.com>>, "Bluestone, Jeffrey (Private)" <Jeff.Bluestone(a)ucsf.edu<mailto:Jeff.Bluestone@ucsf.edu>>, "Lansman, Jeffry" <jeff.lansman(a)ucsf.edu<mailto:jeff.lansman@ucsf.edu>>, "Engel, Joanne" <Joanne.Engel(a)ucsf.edu<mailto:Joanne.Engel@ucsf.edu>>, "Fike, John" <John.Fike(a)ucsf.edu<mailto:John.Fike@ucsf.edu>>, "Imboden, John" <john.imboden(a)ucsf.edu<mailto:john.imboden@ucsf.edu>>, "jlee111(a)mac.com<mailto:jlee111@mac.com>" <jlee111(a)mac.com<mailto:jlee111@mac.com>>, "johanna.jansen(a)novartis.com<mailto:johanna.jansen@novartis.com>" <johanna.jansen(a)novartis.com<mailto:johanna.jansen@novartis.com>>, J Gray <jwgray(a)lbl.gov<mailto:jwgray@lbl.gov>>, Kim Osborn <kim.osborn(a)gladstone.ucsf.edu<mailto:kim.osborn@gladstone.ucsf.edu>>, "knudsen(a)cgl.ucsf.edu<mailto:knudsen@cgl.ucsf.edu>" <knudsen(a)cgl.ucsf.edu<mailto:knudsen@cgl.ucsf.edu>>, Irwin Kuntz <kuntz(a)cgl.ucsf.edu<mailto:kuntz@cgl.ucsf.edu>>, "LaVail, Jennifer" <Jennifer.LaVail(a)ucsf.edu<mailto:Jennifer.LaVail@ucsf.edu>>, "Li, Lili" <Lili.Li(a)ucsf.edu<mailto:Lili.Li@ucsf.edu>>, "ljp(a)ucsf.edu<mailto:ljp@ucsf.edu>" <ljp(a)ucsf.edu<mailto:ljp@ucsf.edu>>, "lmucke(a)gladstone.ucsf.edu<mailto:lmucke@gladstone.ucsf.edu>" <lmucke(a)gladstone.ucsf.edu<mailto:lmucke@gladstone.ucsf.edu>>, "Locksley, Richard" <Richard.Locksley(a)ucsf.edu<mailto:Richard.Locksley@ucsf.edu>>, "loren(a)phy.ucsf.edu<mailto:loren@phy.ucsf.edu>" <loren(a)phy.ucsf.edu<mailto:loren@phy.ucsf.edu>>, "Correia, Maria" <almira.correia(a)ucsf.edu<mailto:almira.correia@ucsf.edu>>, Mark Von Zastrow <mark.vonzastrow(a)ucsf.edu<mailto:mark.vonzastrow@ucsf.edu>>, "McCormick, Frank" <Frank.mccormick(a)ucsf.edu<mailto:Frank.mccormick@ucsf.edu>>, "merz(a)phy.ucsf.edu<mailto:merz@phy.ucsf.edu>" <merz(a)phy.ucsf.edu<mailto:merz@phy.ucsf.edu>>, "Hebrok, Matthias" <Matthias.Hebrok(a)ucsf.edu<mailto:Matthias.Hebrok@ucsf.edu>>, "mike.mccune(a)ucsf.edu<mailto:mike.mccune@ucsf.edu>" <mike.mccune(a)ucsf.edu<mailto:mike.mccune@ucsf.edu>>, "msb(a)phy.ucsf.edu<mailto:msb@phy.ucsf.edu>" <msb(a)phy.ucsf.edu<mailto:msb@phy.ucsf.edu>>, "Wabl, Matthias" <Matthias.Wabl(a)ucsf.edu<mailto:Matthias.Wabl@ucsf.edu>>, "nms(a)ucsf.edu<mailto:nms@ucsf.edu>" <nms(a)ucsf.edu<mailto:nms@ucsf.edu>>, Patrick O'farrell <ofarrell(a)cgl.ucsf.edu<mailto:ofarrell@cgl.ucsf.edu>>, "olivijuly(a)gmail.com<mailto:olivijuly@gmail.com>" <olivijuly(a)gmail.com<mailto:olivijuly@gmail.com>>, "Oppenheimer, Norman" <Norman.Oppenheimer(a)ucsf.edu<mailto:Norman.Oppenheimer@ucsf.edu>>, "peter.ohara(a)ucsf.edu<mailto:peter.ohara@ucsf.edu>" <peter.ohara(a)ucsf.edu<mailto:peter.ohara@ucsf.edu>>, Peter Sargent <peter.sargent(a)ucsf.edu<mailto:peter.sargent@ucsf.edu>>, "Pinkel, Dan" <Dan.pinkel(a)ucsf.edu<mailto:Dan.pinkel@ucsf.edu>>, "R.A. Bradshaw" <rablab(a)uci.edu<mailto:rablab@uci.edu>>, "richard.m.lawn(a)gmail.com<mailto:richard.m.lawn@gmail.com>" <richard.m.lawn(a)gmail.com<mailto:richard.m.lawn@gmail.com>>, "Kelly, Regis" <Regis.Kelly(a)qb3.org<mailto:Regis.Kelly@qb3.org>>, "sbaekkeskov(a)ucsf.edu<mailto:sbaekkeskov@ucsf.edu>" <sbaekkeskov(a)ucsf.edu<mailto:sbaekkeskov@ucsf.edu>>, "scoyle79(a)gmail.com<mailto:scoyle79@gmail.com>" <scoyle79(a)gmail.com<mailto:scoyle79@gmail.com>>, "sfinkbeiner(a)gladstone.ucsf.edu<mailto:sfinkbeiner@gladstone.ucsf.edu>" <sfinkbeiner(a)gladstone.ucsf.edu<mailto:sfinkbeiner@gladstone.ucsf.edu>>, "sgl(a)phy.ucsf.edu<mailto:sgl@phy.ucsf.edu>" <sgl(a)phy.ucsf.edu<mailto:sgl@phy.ucsf.edu>>, Martin Shetlar <shetlar(a)cgl.ucsf.edu<mailto:shetlar@cgl.ucsf.edu>>, Anita Sil <sil(a)cgl.ucsf.edu<mailto:sil@cgl.ucsf.edu>>, "Prusiner, Stanley" <Stanley.Prusiner(a)ucsf.edu<mailto:Stanley.Prusiner@ucsf.edu>>, "steven.rosen(a)ucsf.edu<mailto:steven.rosen@ucsf.edu>" <steven.rosen(a)ucsf.edu<mailto:steven.rosen@ucsf.edu>>, "stimulusartifact(a)gmail.com<mailto:stimulusartifact@gmail.com>" <stimulusartifact(a)gmail.com<mailto:stimulusartifact@gmail.com>>, "stryker(a)phy.ucsf.edu<mailto:stryker@phy.ucsf.edu>" <stryker(a)phy.ucsf.edu<mailto:stryker@phy.ucsf.edu>>, "Kornberg, Tom" <Tom.Kornberg(a)ucsf.edu<mailto:Tom.Kornberg@ucsf.edu>>, Jon Trinidad <trinidad(a)cgl.ucsf.edu<mailto:trinidad@cgl.ucsf.edu>>, "vincent514(a)gmail.com<mailto:vincent514@gmail.com>" <vincent514(a)gmail.com<mailto:vincent514@gmail.com>>, "vlingappa(a)prosetta.com<mailto:vlingappa@prosetta.com>" <vlingappa(a)prosetta.com<mailto:vlingappa@prosetta.com>>, William Weiss <waweiss(a)gmail.com<mailto:waweiss@gmail.com>>, "wgreene(a)gladstone.ucsf.edu<mailto:wgreene@gladstone.ucsf.edu>" <wgreene(a)gladstone.ucsf.edu<mailto:wgreene@gladstone.ucsf.edu>>, "yinshen2000(a)gmail.com<mailto:yinshen2000@gmail.com>" <yinshen2000(a)gmail.com<mailto:yinshen2000@gmail.com>>, "yw.kan(a)ucsf.edu<mailto:yw.kan@ucsf.edu>" <yw.kan(a)ucsf.edu<mailto:yw.kan@ucsf.edu>>, "zena.werb(a)ucsf.edu<mailto:zena.werb@ucsf.edu>" <zena.werb(a)ucsf.edu<mailto:zena.werb@ucsf.edu>>, "Kanter, Joan" <Joan.Kanter(a)ucsf.edu<mailto:Joan.Kanter@ucsf.edu>>, "Donnella, Hayley" <Hayley.Donnella(a)ucsf.edu<mailto:Hayley.Donnella@ucsf.edu>>, "Titus, Erron" <Erron.Titus(a)ucsf.edu<mailto:Erron.Titus@ucsf.edu>> Subject: 9/22/16 Seminar with Grant Jensen BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Mission Hall 1400 Livestream: https://lecture.ucsf.edu/ets/Catalog/Full/f94c469bb908465691ec810f578ecbb221 Grant Jensen CalTech Structural biology in vivo through electron cryotomography September 22, 2016 B. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Two open positions on molecule visualization and virtual reality in Paris
by Tom Ferrin 21 Sep '16

21 Sep '16

FYI... -------- Forwarded Message -------- Subject: Two open positions on molecule visualization and virtual reality in Paris Date: Thu, 22 Sep 2016 01:03:38 +0200 From: baaden(a)smplinux.de To: tef(a)cgl.ucsf.edu Dear Colleague, It's already 2,5 years since Faraday discussion #169. I hope this message finds you well. Because of your interest for molecular visualization, I thought I share the following in the hope you can circulate it, or even direct candidates towards me :) Thanks in advance! We have two open positions in Paris, France, both relating to molecule and network visualization developments in Unity3D, and one specifically to VR. We are looking to hire ASAP and funds are available. The first position is for a postdoc on Development and Application of a Virtual Reality Immersive Modelling Platform for Enabling Drug Discovery. You can find an html version at [1] and PDF at [2]. The second position is for an engineer (or postdoc) on Computational Analysis, Visualization and Modeling of Redox Signaling Networks. You can find an html version at [3] and PDF at [4]. Thank you, Marc [1] http://www.baaden.ibpc.fr/ns16/pdoc1.html [2] http://www.baaden.ibpc.fr/ns16/pdoc1.pdf [3] http://www.baaden.ibpc.fr/ns16/inge1.html [4] http://www.baaden.ibpc.fr/ns16/inge1.pdf -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217

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[Compbio-allhands] Fwd: Computational Biology faculty search at USC
by Andrej Sali 20 Sep '16

20 Sep '16

Sent from my iPhone Begin forwarded message: > From: Frank Uwe Alber <alber(a)usc.edu> > Date: September 20, 2016 at 7:42:19 AM PDT > To: Andrej Sali <sali(a)salilab.org> > Subject: Computational Biology faculty search at USC > > Hi Andrej, > > I just wanted to let you know that we are having a faculty search for one (or two) open rank positions, in case you know people who would like to apply. > > Here is the link: https://jobs.usc.edu/postings/74647 > > Best wishes, > Frank > > > ----------- > https://jobs.usc.edu/postings/74647 > > Requisition ID > 2002954 > Position ID > P01473861 > Academic Title > Assistant, Associate or Full Professor in Computational Biology > Department > Biological Sciences > Location > University Park Campus > Employment Type > Full-Time > > > The Department of Biological Sciences in the Dana and David Dornsife College of Letters, Arts and Sciences at the University of Southern California invites applications for Open Rank tenured Associate or Full Professor or tenure-track Assistant Professor positions in the broad area of Computational Biology. Applicants will be evaluated based on the overall originality of their work and promise for establishing a strong independent research program. > > Successful candidates will join the Molecular and Computational Biology section within Biological Sciences at USC, located in Los Angeles, California. We have a robust Ph.D. program in Computational Biology and Bioinformatics, which emphasizes both rigorous mathematical training and immersive co-localization with experimental biologists. The anticipated start date is August 16, 2017, and applicants must have received a Ph.D. (or equivalent) degree by time of appointment. > > Review of applications will begin November 1st, 2016 and continue until the position is filled. In order to be considered for this position, all candidates must apply via the “CLICK HERE” link at the top or bottom of this page. Please submit, in a single PDF file, a curriculum vita, a cover letter, a statement of research accomplishments and future research plans, and the contact information of at least three references. Please direct inquiries to: oginskis(a)usc.edu . > > USC is an equal-opportunity educator and employer, proudly pluralistic and firmly committed to providing equal opportunity for outstanding persons of every race, gender, creed and background. The University particularly encourages women, members of underrepresented groups, veterans and individuals with disabilities to apply. USC will make reasonable accommodations for qualified individuals with known disabilities unless doing so would result in an undue hardship. Further information is available by contacting uschr(a)usc.edu. > >

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[Compbio-allhands] Fwd: Group Leader Position at EMBL
by Andrej Sali 19 Sep '16

19 Sep '16

> Begin forwarded message: > > From: "Jan Ellenberg" <jan.ellenberg(a)embl.de> > Subject: Group Leader Position at EMBL > Date: September 19, 2016 at 12:39:55 AM PDT > To: sali(a)salilab.org > > Dear Andrej, > > I would like to draw your attention to two openings for a group leader position in the Cell Biology and Biophysics Unit at EMBL Heidelberg, as recently advertised in Nature and Science. > > We are looking for outstanding junior scientists with a background in biology, physics, chemistry or mathematics that want to pursue original and interdisciplinary research in cutting edge molecular cell biology, especially also in the areas of chemical biology and fluorescent probe development, image analysis and/bioimage informatics and computational modelling of complex dynamic biological processes. > > We generally hire group leaders early in their careers, often after their first postdoc and sometimes immediately after their PhD, and provide them with very generous internal support and a highly collaborative environment for their first independent position. We therefore strongly encourage highly promising young male and especially also female candidates to apply. > > I would very much appreciate if you could bring the attached advertisement to the attention of suitable candidates or let me know if I should contact them personally. > > Thanks so much for help with this recruitment, > All the best, > Jan > > Jan Ellenberg > Cell Biology and Biophysics Unit > European Molecular Biology Laboratory (EMBL) > Meyerhofstr. 1 > D-69117 Heidelberg > Germany > > T +49-6221-3878328 > F +49-6221-3878512 > jan.ellenberg(a)embl.de <mailto:jan.ellenberg@embl.de> > www.embl.de/research/units/cbb/ellenberg/index.html <http://www.embl.de/research/units/cbb/ellenberg/index.html> > > > >

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[Compbio-allhands] 9/22/16 Seminar with Grant Jensen
by Flowers, Nicole 16 Sep '16

16 Sep '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Mission Hall 1400 Livestream: https://lecture.ucsf.edu/ets/Catalog/Full/f94c469bb908465691ec810f578ecbb221 Grant Jensen CalTech Structural biology in vivo through electron cryotomography September 22, 2016 B. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Greg Landrum will talk about RDKit Tomorrow Tues Sept 13 10am in BH313
by John Irwin 12 Sep '16

12 Sep '16

Greg Landrum will be talking about his toolkit RDKit tomorrow. Tues Sept 13 10am in BH313 Over the past 5 years or so, RDKit had changed the landscape of chemoinformatics and has had a huge impact on our research. John

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[Compbio-allhands] Fwd: Faculty opening in Computational Biology
by Andrej Sali 12 Sep '16

12 Sep '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: Ilya Vakser <vakser(a)ku.edu> > Subject: Faculty opening in Computational Biology > Date: September 12, 2016 at 10:14:21 AM PDT > To: Ilya Vakser <vakser(a)ku.edu> > > Dear Colleagues, > We would highly appreciate if you attract attention of qualified individuals to a tenure-track faculty opening in Computational Biology at The University of Kansas - see the ad attached. > Thank you very much! > Ilya > > ------ > Ilya Vakser > Professor and Director > Computational Biology Program and Center for Computational Biology > Professor > Department of Molecular Biosciences > The University of Kansas > 2030 Becker Dr. > Lawrence, KS 66045 > vakser(a)ku.edu <mailto:vakser@ku.edu>, +1-785-864-1057 > www.compbio.ku.edu <http://www.compbio.ku.edu/> > >

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[Compbio-allhands] Fwd: PhD and postdoc positions avaiable
by Andrej Sali 06 Sep '16

06 Sep '16

> Begin forwarded message: > > From: Kresten Lindorff-Larsen <lindorff(a)bio.ku.dk> > Subject: PhD and postdoc positions avaiable > Date: September 6, 2016 at 11:15:31 AM PDT > To: Kresten Lindorff-Larsen <lindorff(a)bio.ku.dk> > > Dear colleagues > > We're looking to hire several postdocs and a ph.d. student working on various aspects of computational biology and integrative structural biology. If you know of any strong candidates that are looking for positions, I would appreciate it if you would pass on the adverts on to them, or have them contact me directly. > > For the postdoc positions, we are looking for people with a strong background in molecular dynamics simulations as well as people with hands on experience interpreting experimental data using computational simulation methods. > > Postdoc positions (deadline for applications Sept 15th): > http://employment.ku.dk/faculty/?show=850415 <http://employment.ku.dk/faculty/?show=850415> > Ph.d. position (deadline for applications Sept 16th): > http://employment.ku.dk/phd/?show=851613 <http://employment.ku.dk/phd/?show=851613> > > The positions advertised above have starting dates between now and february, but we will also be hiring 1-2 additional people over the next year, so if you know of candidates who have a longer timeframe, that is also of interest. > > > Regards > Kresten > > > > > -- > Prof. Kresten Lindorff-Larsen > Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science > Department of Biology, University of Copenhagen > Rm. 3.2.11, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark > Mobile: +45 4267 0074 ; Office: +45 3532 2027 > > >

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[Compbio-allhands] Fwd: Comp Chem open position at Biogen
by Jacobson, Matt 26 Aug '16

26 Aug '16

- Matt Begin forwarded message: From: Govinda Bhisetti <govinda.bhisetti(a)biogen.com<mailto:govinda.bhisetti@biogen.com>> Subject: Comp Chem open position at Biogen Date: August 26, 2016 at 9:05:02 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Prof. Jacobson I have an open position in my group. Likely to have one more next year. Please see the attachment for the job description. Mark Murcko suggested that I contact you to find post-docs in your group with suitable training/experience who might be interested to work at Biogen. Please ask interested candidates to contact me. Thanks and regards. -Govinda Govinda Rao Bhisetti, PhD Principal Investigator and Head of Computational Chemistry Chem & Mol Therapeutics Biogen | 225 Binney Street | Cambridge, MA | 02142 Email: govinda.bhisetti(a)biogen.com<mailto:john.smith@biogen.com>| Direct: 617 914 7273 | Mobile: 781 325 6029 [cid:d748c923-d57c-4042-af36-219dd386c41c@ucsf.edu]

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[Compbio-allhands] Fwd: Comp Chem open position at Biogen
by Brian Shoichet 26 Aug '16

26 Aug '16

---------- Forwarded message ---------- From: Govinda Bhisetti <govinda.bhisetti(a)biogen.com> Date: Fri, Aug 26, 2016 at 8:40 AM Subject: Comp Chem open position at Biogen To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu> Hi Brian, I have an open position in my group. Likely to have one more next year. Please see the attachment for the job description. Please let me know if you have anyone suitable for this position in your group who would be interested to work at Biogen. Regards. -Govinda *Govinda Rao Bhisetti, PhD* Principal Investigator and Head of Computational Chemistry Chem & Mol Therapeutics Biogen | 225 Binney Street | Cambridge, MA | 02142 Email: govinda.bhisetti(a)biogen.com <john.smith(a)biogen.com>| Direct: 617 914 7273 | Mobile: 781 325 6029 [image: unknown.png] -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

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[Compbio-allhands] Fwd: WANTED: Talented computational chemists
by Jacobson, Matt 26 Aug '16

26 Aug '16

- Matt Begin forwarded message: Subject: WANTED: Talented computational chemists Date: August 26, 2016 at 7:54:50 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Matt, The Modeling and Informatics group at Merck is seeking creative, self-motivated entry level PhD computational chemists with exceptional interpersonal and problem solving skills to join our scientific teams in Boston, MA or West Point, PA. If you have (or know of) any talented students who might be interested, could you please ask them to apply online here<https://merck.taleo.net/careersection/int_merckunitedstates_10880_en/jobdet…>? The job code is CHE004912. And thanks for already sending along Katrina. She’s great! - Kate M. Katharine Holloway, Ph.D. | Senior Principal Scientist | Structural Chemistry | Merck & Co WP14-1101 | 215-652-7425 (Office) |

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[Compbio-allhands] Fwd: job opportunity: computational epidemiology
by Jacobson, Matt 09 Aug '16

09 Aug '16

- Matt Begin forwarded message: From: Jaline Gerardin <jgerardin(a)idmod.org<mailto:jgerardin@idmod.org>> Subject: job opportunity: computational epidemiology Date: August 9, 2016 at 2:26:39 PM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, "rebecca.brown3(a)ucsf.edu<mailto:rebecca.brown3@ucsf.edu>" <rebecca.brown3(a)ucsf.edu<mailto:rebecca.brown3@ucsf.edu>> Hi Matt and Rebecca, Would you mind recirculating our job posting to the compbio/iPQB listservs? We’re looking for someone with a strong quantitative background and a couple years of experience with coding/scripting. Previous knowledge of malaria and disease modeling are absolutely not required. The pay is competitive for Research Scientist positions, and Seattle is a great place to live! Thanks, and hope this finds you well. Jaline jgerardin(a)idmod.org<mailto:jgerardin@idmod.org> ________________________________ TITLE: Research Scientist – Malaria LOCATION: Bellevue, WA, USA The Institute for Disease Modeling (IDM) team is composed of research scientists and software professionals who focus on creating powerful and innovative disease modeling and data analysis tools to help researchers and policy makers understand diseases, their causes, the way they spread, and the best types of interventions to use for the particular situation faced. IDM partners with selected universities, NGOs, government ministries, and other research and public health institutions focused on researching new ways to understand and combat diseases both locally and globally. We seek a full-time Research Scientist to work as part of the IDM malaria team and collaborate on the development, refinement, and utilization of sophisticated infectious disease models for epidemiological research and eradication-campaign planning. The IDM team architects advanced models of disease transmission, develops computational tools to inform global disease eradication policy, conducts innovative analysis of epidemiologically- and policy-relevant data (programmatic data, financial data, clinical trials data, and cluster surveys data), and identifies epidemiologically critical knowledge gaps. As part of our work, we routinely collaborate with groups at the World Health Organization, the Center for Disease Control, PATH, the Bill and Melinda Gates Foundation, ministries of health in the developing world, as well as universities and research institutes. As part of this group, the researcher will design and build new modules for the existing malaria disease model. The researcher will configure, calibrate, and exercise disease models to answer questions aimed at refining the malaria research agenda, improving understanding of disease dynamics, informing effective public health campaigns, and guiding rational development of new public-health interventions. The research, models, and results will be presented to key stakeholders, displayed at conferences, and published in academic journals. Joining our group provides unique opportunities to interact with global-health policymakers, to collaborate with world-class research laboratories and non-profit organizations, and to contribute to global and national disease-eradication strategies. Responsibilities: · Reviews scientific literature and determines which aspects of biology, demography, geography, and climate are relevant to the model. · Builds new modules for existing disease models; builds and develops new disease models. · Works closely with the modelers, programmers, and statisticians on the team to refine the models and use them to conduct sensitivity analyses, explore tradeoffs among possible interventions, and optimize eradication plans for time, cost, or other factors. · Finds sources for the necessary input data to the models and helps to organize the necessary data for input to the models. · Writes software code (in C/C++) to implement model features. · Collects, analyzes, and presents data on model results and performance. · Assists in the preparation of research articles and conference presentations communicating the project and its results to the scientific community. Key Qualifications and Required Skills: · Ph.D. in a quantitative field (e.g. Applied Mathematics, Statistics, Epidemiology, Quantitative Biology) · Numerical analysis, dynamical systems, stochastic processes, and biostatistics. · Read and write research articles in biology and applied mathematics. · Principles, techniques, and tools of computational epidemiology. · Work extended hours to meet a deadline; demonstrated ability to work productively as part of a small team. · At least 2 years’ experience in C/C++ software development. · Proficiency in at least one data-analysis or scripting language (e.g. MATLAB, python, R) · Multiple published articles in peer-reviewed scientific journals (to be submitted with application). · Knowledge of developing-world public health issues and the malaria disease system preferred.

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[Compbio-allhands] Fwd: Recruiting two postdocs for GROMACS improvements and development
by Jacobson, Matt 02 Aug '16

02 Aug '16

- Matt Begin forwarded message: From: Michael R Shirts <Michael.Shirts(a)Colorado.EDU<mailto:Michael.Shirts@Colorado.EDU>> Subject: Recruiting two postdocs for GROMACS improvements and development Date: August 2, 2016 at 1:22:52 AM PDT To: Michael R Shirts <Michael.Shirts(a)Colorado.EDU<mailto:Michael.Shirts@Colorado.EDU>> Cc: Peter Kasson <kasson(a)virginia.edu<mailto:kasson@virginia.edu>> Hello, all- Myself and Peter Kasson, in close cooperation with Erik Lindahl and Mark Abraham at KTH, have recently obtained funding for GROMACS development work on the US side. We now have two postdoc positions open, as detailed below, one based in Virginia and one in Colorado. We’d love it if you could pass on this email to current or former students of yours, or others you may know who may be interested. The mandate on the Virginia side involves API design and implementation and cloud- and dataflow-based parallelization, while on the Colorado side it involves statistical physics to test and diagnose simulation validity, improving the testing framework, and new Monte Carlo methods. Strong software engineering skills are a must, and we would particularly appreciate active members of the molecular simulation development community. As always, members of groups under-represented in the molecular simulation field are especially encouraged to apply. Please refer anyone you think appropriate or apply at the links below. Thanks! Michael Shirts ------------------------ The Shirts research group in the Department of Chemical and Biological Engineering is hiring a highly capable research associate to help develop the GROMACS molecular simulation package. GROMACS is an open-source project with a strong international development community as well as a 10,000+ user base. This position is part of a new NIH funded collaborative effort between the Shirts group and the Kasson group (at the University of Virginia) to improve the robustness, functionality, and usability of GROMACS, offering the candidate the opportunity to positively affect the work of thousands of researchers across the globe. Candidates will have the opportunity to learn state-of-the-art simulation methodology and work collaboratively with a global team of developers. This position requires a Ph.D. in Chemistry, Chemical Engineering, Physics, Computer Science or a related field. It requires very strong statistical mechanical, molecular simulation and theoretical skills, as well as significant software engineering experience and ability. Experience in C++ and Python is preferred, as well as experience with version control, code review systems, and team-oriented software development. Competitive candidates will have a track record of scientific success in graduate study with a strong publication record. Apply at https://cu.taleo.net/careersection/2/jobdetail.ftl?job=05979&lang=en&sns_id… ----------- The Kasson laboratory located within the Department of Molecular Physiology & Biological Physics at the University of Virginia seeks a talented postdoctoral scholar to help further the development of the GROMACS molecular simulation package. GROMACS is an open-source project with a strong international development community as well as a 10,000+ user base. The Kasson and Shirts laboratories have recently secured funding to contribute new development to GROMACS. We are seeking a postdoctoral scholar with strong software engineering skills to help build this widely-used scientific software package. This scholar will gain experience in and exposure to the broad base of GROMACS users and developers as well as skills in API design and parallel cloud-computing analytics. Skills not only in C++ and Python programming but also version control and code review systems are essential. A track record of contributions to open-source software is desired as well. Scientific background related to simulation science is desired; competitive candidates will have a track record of scientific success in graduate study with a strong publication record. For inquiry into the position, please refer to the posting number 0619061. Apply at https://jobs.virginia.edu/applicants/Central?quickFind=79490 ~~~~~~~~~~~~~~~~ Michael Shirts Associate Professor michael.shirts(a)colorado.edu<mailto:michael.shirts@colorado.edu> http://www.colorado.edu/lab/shirtsgroup/ Phone: (303) 735-7860 Office: JSCBB D317 Department of Chemical and Biological Engineering University of Colorado Boulder

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[Compbio-allhands] Fwd: Tenure-Track Assistant Professor in Biochemistry position
by Brian Shoichet 19 Jul '16

19 Jul '16

FYI. ---------- Forwarded message ---------- From: Spencer Anthony-Cahill <Spencer.Anthony-Cahill(a)wwu.edu> Date: Mon, Jul 18, 2016 at 6:15 PM Subject: Tenure-Track Assistant Professor in Biochemistry position To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu> Dear Professor Shoichet: I am reaching out to prominent structural biologists and biophysicists to bring to your attention a job posting we have for a tenure track assistant professorship in biochemistry. Western Washington University is a predominantly undergraduate institution. Our mission is to primarily serve our undergraduate population and engage them in meaningful research projects, which are commonly funded through federal grants and often result in quality peer-reviewed publications. Additionally, our Masters graduate program has grown over the past few years, which also bolsters our research infrastructure. We are keenly interested in attracting outstanding new faculty members who are motivated to work in this environment and excel in both teaching and research. We are particularly interested in candidates with interests in biochemistry and/or biophysics. If you know of any quality candidates that would be a good fit for our department, please encourage them to apply. Here is the link to our job posting: https://jobs.wwu.edu/JobPosting.aspx?JPID=7056 With best regards, Spencer. Spencer Anthony-Cahill, Ph.D. Professor of Chemistry, and Department Chair Email: Spencer.Anthony-Cahill(a)wwu.edu Tel: 360 650 3071 Morse Hall (CB) 270 516 High Street Bellingham, WA 98225-9150 -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

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[Compbio-allhands] Fwd: Job ads
by Jacobson, Matt 07 Jul '16

07 Jul '16

- Matt Begin forwarded message: From: "Lexa, Katrina W" <katrina.lexa(a)merck.com<mailto:katrina.lexa@merck.com>> Subject: Job ads Date: July 7, 2016 at 7:22:44 AM PDT To: Matt Jacobson <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt! A good friend of mine from Michigan works in the Chemistry department at Rollins College, just outside of Orlando. They’re hiring for a tenure-track assistant level professor position to start in August 2017, and they’re hoping for someone with a computational background: http://jobs.rollins.edu/cw/en-us/job/492307/assistant-professor-chemistry Also, Merck is hiring for two computational positions, one in Boston https://taleo.msd.com/careersection/merck_external_career_section/jobdetail… And one in West Point PA https://taleo.msd.com/careersection/merck_external_career_section/jobdetail… If you know anyone who might be interested, please pass the word along. Thanks! Hope everything in SF is going well, ------------------------------- Katrina Lexa Merck & Co., Inc. 126 East Lincoln Ave RY800-C364 Rahway, NJ 07065 phone: (732) 594-7058 office: RY800-D365 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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[Compbio-allhands] Fwd: Research Associate (postdoc) in Structural Bioinformatics of Genetic Variants @ Imperial London
by Andrej Sali 01 Jul '16

01 Jul '16

> Begin forwarded message: > > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: FW: Research Associate (postdoc) in Structural Bioinformatics of Genetic Variants @ Imperial London > Date: July 1, 2016 at 11:29:38 AM GMT+2 > To: Undisclosed recipients:; > > Please forward to suitable applicants > Thanks > > Mike > > > > Imperial College London – Structural Bioinformatics of Genetic Variants > > > Salary £33,860-£42,830 per annum > > South Kensington Campus > > Applications are invited for a Research Associate position to join Prof Mike Sternberg’s Structural Bioinformatics Group at the South Kensington Campus, Imperial College London. 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 will 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. You must also be able to demonstrate an understanding of the application of statistics in bioinformatics. > > You must be able to express scientific concepts (especially those in bioinformatics) precisely and clearly, both verbally and in writing, and have experience of developing high-level code to a professional standard of robustness and clarity. 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 Wellcome Trust for up to three years. > > > Deadline: 30 July 2016 (midnight BST) > > > > For initial enquiries please contact Professor Michael Sternberg by <>email: m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > > > Full details on how to apply see: > > 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…>..

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[Compbio-allhands] Fwd: Hiring computational chemist at Denali Therapeutics
by Brian Shoichet 20 Jun '16

20 Jun '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "JW Feng" <feng(a)dnli.com> Date: Jun 20, 2016 7:46 PM Subject: Hiring computational chemist at Denali Therapeutics To: <shoichet(a)cgl.ucsf.edu> Cc: Hi Brian, This is JW Feng at Denali Therapeutics, a neuroscience startup in South San Francisco. We met while I was a computational chemist at Genentech. I joined Denali a year ago to lead the data science group and we are looking for an outstanding computational chemist to join our growing team. As you may know, Denali raised a historic biotech series A funding at $217 million. We have a world class team of scientists to discover drugs to treat neurodegenerative diseases. It would be great if you can recommend students or postdocs that would be interested in the job. Online job description: http://www.denalitherapeutics.com/careers?gh_jid=235936 Best, JW ___________________ JW Feng, Ph.D. Denali Therapeutics Inc. 201 Gateway Blvd. South San Francisco, CA 94080 | (650) 270-0628

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[Compbio-allhands] Fwd: Postdoc opening at Stanford
by Jacobson, Matt 10 Jun '16

10 Jun '16

- Matt Begin forwarded message: From: Ron Dror <rondror(a)stanford.edu<mailto:rondror@stanford.edu>> Subject: Postdoc opening at Stanford Date: June 10, 2016 at 1:15:01 AM PDT Dear colleagues, I have an opening for a postdoc to lead one or more projects in my group at Stanford. If you can recommend a promising candidate, please let me know. I’d welcome applications from outstanding researchers with backgrounds in molecular simulation (either methods development or biological applications), molecular modeling, protein design, or related areas. A description of the position is below. Best, Ron Applications are invited for postdoctoral research positions in Prof. Ron Dror’s lab at Stanford University. Successful applicants will use a variety of computational techniques to address key scientific questions in biochemistry and to enable advances in drug discovery, particularly for G-protein-coupled receptors (GPCRs), which represent the largest class of drug targets. This work will be carried out in close collaboration with world-class experimentalists. Candidates must have an outstanding record of research and academic performance, strong communication skills, and an ability to work independently and collaborate effectively. Experience with molecular dynamics simulation, enhanced sampling methods, programming, protein design, or molecular modeling of membrane proteins is desirable, but candidates are not expected to have experience in all of these areas. Dr. Dror’s lab focuses on computational approaches to studying the spatial organization and dynamics of biomolecules and cells. Our work spans fields ranging from biophysics and computational chemistry to high-performance computing, image processing, and machine learning. We have access to substantial computational and experimental facilities and are based in an interdisciplinary biosciences building immediately adjacent to Stanford’s medical, science, and engineering schools. Stanford, one of the world’s top universities, is located on a beautiful campus in the San Francisco Bay Area. Stanford has long been a magnet for talent in computing and the biosciences, and is considered the birthplace and spiritual center of Silicon Valley, an unparalleled center of technological and scientific innovation. Stanford University is an equal opportunity employer. To apply, please send the following to drorlabopenings(a)gmail.com<mailto:drorlabopenings@gmail.com>: a CV, a cover letter explaining your interest in the position, contact information for three referees, and a document you wrote that has not been edited by anyone else (for example, a report, an early draft of a manuscript, or an email to a colleague about a scientific topic). -- Ron Dror Associate Professor of Computer Science and, by courtesy, Molecular and Cellular Physiology and Structural Biology Stanford University http://drorlab.stanford.edu/

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[Compbio-allhands] Fwd: Postdoc opening at Stanford
by Andrej Sali 10 Jun '16

10 Jun '16

> Begin forwarded message: > > From: Ron Dror <rondror(a)stanford.edu> > Subject: Postdoc opening at Stanford > Date: June 10, 2016 at 1:17:03 AM PDT > To: "Lennart.Nilsson(a)ki.se" <Lennart.Nilsson(a)ki.se>, "bojan.zagrovic(a)univie.ac.at" <bojan.zagrovic(a)univie.ac.at>, "hgrubmu(a)gwdg.de" <hgrubmu(a)gwdg.de>, "c.de.graaf(a)vu.nl" <c.de.graaf(a)vu.nl>, "gerhard.hummer(a)biophys.mpg.de" <gerhard.hummer(a)biophys.mpg.de>, "schlick(a)nyu.edu" <schlick(a)nyu.edu>, "p.carloni(a)grs-sim.de" <p.carloni(a)grs-sim.de>, "ursula.roethlisberger(a)epfl.ch" <ursula.roethlisberger(a)epfl.ch>, "Michael.Grabe(a)ucsf.edu" <Michael.Grabe(a)ucsf.edu>, "sali(a)salilab.org" <sali(a)salilab.org>, "peter(a)kolblab.org" <peter(a)kolblab.org>, Koby Levy <Koby.Levy(a)weizmann.ac.il> > Cc: Ron Dror <ron.dror(a)stanford.edu> > > Dear colleagues, > > I have an opening for a postdoc to lead one or more projects in my group at Stanford. If you can recommend a promising candidate, please let me know. I’d welcome applications from outstanding researchers with backgrounds in molecular simulation (either methods development or biological applications), molecular modeling, protein design, or related areas. A description of the position is below. > > Best, > Ron > > > Applications are invited for postdoctoral research positions in Prof. Ron Dror’s lab at Stanford University. Successful applicants will use a variety of computational techniques to address key scientific questions in biochemistry and to enable advances in drug discovery, particularly for G-protein-coupled receptors (GPCRs), which represent the largest class of drug targets. This work will be carried out in close collaboration with world-class experimentalists. > > Candidates must have an outstanding record of research and academic performance, strong communication skills, and an ability to work independently and collaborate effectively. Experience with molecular dynamics simulation, enhanced sampling methods, programming, protein design, or molecular modeling of membrane proteins is desirable, but candidates are not expected to have experience in all of these areas. > > Dr. Dror’s lab focuses on computational approaches to studying the spatial organization and dynamics of biomolecules and cells. Our work spans fields ranging from biophysics and computational chemistry to high-performance computing, image processing, and machine learning. We have access to substantial computational and experimental facilities and are based in an interdisciplinary biosciences building immediately adjacent to Stanford’s medical, science, and engineering schools. > > Stanford, one of the world’s top universities, is located on a beautiful campus in the San Francisco Bay Area. Stanford has long been a magnet for talent in computing and the biosciences, and is considered the birthplace and spiritual center of Silicon Valley, an unparalleled center of technological and scientific innovation. > > Stanford University is an equal opportunity employer. > > To apply, please send the following to drorlabopenings(a)gmail.com <mailto:drorlabopenings@gmail.com>: a CV, a cover letter explaining your interest in the position, contact information for three referees, and a document you wrote that has not been edited by anyone else (for example, a report, an early draft of a manuscript, or an email to a colleague about a scientific topic). > > -- > > Ron Dror > Associate Professor of Computer Science and, by courtesy, Molecular and Cellular Physiology and Structural Biology > Stanford University > http://drorlab.stanford.edu/ <http://drorlab.stanford.edu/>

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[Compbio-allhands] Fwd: An announcement from COMP Together
by Magdalena Korczynska 02 Jun '16

02 Jun '16

June COMP Together. > Begin forwarded message: > > From: comp_together(a)acscomp.org > Subject: An announcement from COMP Together > Date: June 2, 2016 at 8:43:50 AM PDT > To: Magdalena Korczynska <mkucsf(a)gmail.com> > Reply-To: BinQing Wei <wei.binqing(a)gmail.com> > > The COMP Together champions in your area would like to announce the following event: > > Speaker: Max Kuhn, Pfizer > Ignacio Aliagas, Genentech > Title: Two talks on machine learning and applications in drug discovery > Date: 2016-06-28 > Time: 6:00 PM > Event ID: 34 > Sponsor: Gilead > > Location > Gilead > 333 Lakeside Drive > > Foster City CA 94404 > > Description and Notes > 6-7 pm networking over pizza & drinks > > 7-7:45pm 1st talk, Max Kuhn, Pfizer > > Title: Under the Hood of Cubist > Abstract: Cubist model rules are a relatively unknown machine learning model that has been extensively utilized in QSAR. The model is related to work published by Ross Quinlan in the early 90’s but had remained closed source until 2010. This talk will describe the model and its mechanics and an illustrative example will be shown to demonstrate the result. > > 7:45-8:15pm 2nd talk, Ignacio Aliagas, Genentech > > Title: The Importance of Being Earnest: Assessing Risk in Model Predictions > Abstract: QSAR models for the prediction of properties and DMPK end points can play a very important role to guide synthesis and advance compounds in the drug discovery paradigm. For prediction models to be used efficiently and with ease, integration with other modeling tools and software can facilitate their use. At the same time, it is critical to provide validation tools to quickly inform on the models’ domain of applicability within a given therapeutic project or chemical series. We describe a probabilistic approach to model prediction and how various QSAR models and validation tools are being delivered to drug discovery scientists at Genentech. > > 8:30pm End > > > If you would like to attend this COMP Together event, please visit the COMP website and register using the > http://app.acscomp.org/COMP_Together/meeting_signup.php?event_id=34. > > If you have any questions about this event, please contact BinQing Wei atwei.binqing(a)gmail.com. > > If you would like to update your COMP Together registration or unsubscribe, please visit http://app.acscomp.org/COMP_Together/reg_update/update_login.php

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[Compbio-allhands] Fwd: Job openings at Schrodinger
by Brian Shoichet 02 Jun '16

02 Jun '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF ---------- Forwarded message ---------- From: "Devleena Shivakumar" <devleena.shivakumar(a)schrodinger.com> Date: Jun 2, 2016 1:03 AM Subject: Job openings at Schrodinger To: "Brian Shoichet" <bshoichet(a)gmail.com> Cc: Hi Brian, We are looking to hire Applications Scientists in San Diego, Boston and Europe Job Description: Schrödinger, a technology leader specializing in software solutions for life science research and development, is searching for an Applications Scientist to be based in Boston. Applications Scientists work on applying Schrodinger's computational chemistry software to address challenging problems in drug discovery. The position also involves the development of new computational methods for drug discovery, scientific publications, and helping customers with using Schrodinger software. Responsibilities include drug discovery project support, engaging in scientific discussions with customers, giving presentations at conferences, demonstrating optimal use of the software, and providing customer training. Applications Scientists gain familiarity with our entire suite of structure-based and ligand-based software, including packages for docking, molecular simulations, homology modeling, pharmacophore modeling, cheminformatics, and quantum mechanics. A strong background in molecular modeling and computational chemistry with application to biological problems is highly desired. Exceptional communication skills, an outgoing personality, and a willingness to travel are required. Experience working on drug discovery projects is highly desirable. *Requirements:* - Ph.D. in computational chemistry or biophysics plus experience with pharmaceutical applications of molecular modeling software tools - Excellent interpersonal, communication, and organizational skills - Strong problem-solving ability - A broad knowledge of molecular modeling theory and applications - Ability to conduct independent research *Preferred:* - Post-doctoral research and/or relevant experience in the commercial sector - Biologics modeling and *in silico *protein engineering - Python programming experience If you know anyone looking to join my super amazing team, please have them contact me directly. Anyone from your group would be great! Best, Devleena -- Devleena Shivakumar, Ph.D. Senior Applications Scientist Schrödinger, Inc. http://www.schrodinger.com (201) 455-4980 (Phone) (212) 295-5801 (FAX) http://www.linkedin.com/in/devleena

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[Compbio-allhands] Christos Ouzounis seminar Friday, June 3, 2 pm, BH212
by Patricia Babbitt 31 May '16

31 May '16

Hi all, Christos Ouzounis is giving an informal seminar this Friday, detailed in the subject line of this email. He has been a major contributor to many aspects of the field and was a founding officer of the International Society for Computational Biology. One of his early efforts was the development of clustering algorithms for biological networks, including creation of TRIBE-MCL, an approach used for rapid and accurate clustering of protein sequences into families. The method relies on the Markov cluster (MCL) algorithm for the assignment of proteins into families based on precomputed sequence similarity information (PMID: 11917018). The title of Friday's talk is "Comparative Genomics 2.0: From reading to writing" -- 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. Sydney Russell Leed, +1 415-514-1214, 415-514-9816 Sydney.RussellLeed(a)ucsf.edu <mailto:Sydney.RussellLeed@ucsf.edu>

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[Compbio-allhands] Christos Ouzounis seminar Friday, June 3, 2 pm, BH212
by Patricia Babbitt 31 May '16

31 May '16

Hi all, Christos Ouzounis is giving an informal seminar this Friday, detailed in the attached flyer. He has been a major contributor to many aspects of the field and was a founding officer of the International Society for Computational Biology. One of his early efforts was the development of clustering algorithms for biological networks, including creation of TRIBE-MCL, an approach used for rapid and accurate clustering of protein sequences into families. The method relies on the Markov cluster (MCL) algorithm for the assignment of proteins into families based on precomputed sequence similarity information (PMID: 11917018). The title of Friday's talk is "Comparative Genomics 2.0: From reading to writing" -- 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. Sydney Russell Leed, +1 415-514-1214, 415-514-9816 Sydney.RussellLeed(a)ucsf.edu <mailto:Sydney.RussellLeed@ucsf.edu>

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[Compbio-allhands] a computational / structural biology job at Biodesy, South San Francisco
by Andrej Sali 24 May '16

24 May '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

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[Compbio-allhands] Fwd: A New Job Posting for 'Computational Protein Engineering' at Amgen Thousand Oaks
by Jacobson, Matt 19 May '16

19 May '16

- Matt From: <Alba>, Ben <balbaphd(a)amgen.com<mailto:balbaphd@amgen.com>> Date: Thursday, May 19, 2016 at 10:01 AM To: Charles Craik <charles.craik(a)ucsf.edu<mailto:charles.craik@ucsf.edu>> Subject: A New Job Posting for 'Computational Protein Engineering' at Amgen Thousand Oaks Hi Charly, I hope you are well!! Thousand Oaks is looking for a talented ‘Computational Protein Engineer’ (e.g. PhD. in computational biophysics or related fields). Do you have any candidates who might fit this bill? Best, Ben http://careers.amgen.com/job-en/6072153/scientist-computational-protein-eng… Scientist – Computational Protein Engineering and Design Category: Scientific Job ID: R-14827 Location: Thousand Oaks, CA Posted Date:May 13, 2016 Amgen is seeking a scientist with expertise in computational protein engineering and design to join the Therapeutic Discovery Department at our campus in Thousand Oaks, CA. The candidate will be part of multidisciplinary teams that seek to advance our biologics drug discovery programs, spanning multiple modalities including therapeutic proteins, antibodies, and bispecific molecules. The work involves protein structure analysis and modeling, biophysical property prediction, protein-protein interaction analysis, as well as novel molecular design. Basic Qualifications: Doctorate degree OR Master’s degree & 4 years of scientific experience OR Bachelor’s degree & 6 years of scientific experience Preferred Qualifications: PhD. in computational biophysics or related fields Strong track record of research accomplishment with three or more scientific publications or conference presentations in the area of computational protein modeling and design Strong communication and interpersonal skills and the ability to work flexibly in a cross-functional team environment Experience in antibody modeling and engineering Experience with one or more protein modeling software packages (MOE, Discovery Studio, Schrodinger, etc.). Experience working on a biologics project in a biopharmaceutical setting. Amgen is an Equal Opportunity employer and will consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability status. Benjamin Alba, Ph.D. Senior Scientist Biologics Amgen, Inc. 1120 Veterans Blvd Drop Zone ASF5/234 South San Francisco, CA 94080 650-228-4943 (cell); 650-244-3119 (desk) "This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message."

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[Compbio-allhands] Fwd: Recommendations for job positions @ GSK
by Brian Shoichet 19 May '16

19 May '16

FYI. ---------- Forwarded message ---------- From: Brian Shoichet <shoichet(a)cgl.ucsf.edu> Date: Thu, May 19, 2016 at 9:38 AM Subject: Re: Recommendations for job positions @ GSK To: Eric Manas <eric.s.manas(a)gsk.com> Cc: Constantine Kreatsoulas <constantine.x.kreatsoulas(a)gsk.com>, Kris Brown <Kristin.K.Brown(a)gsk.com> Hi Guys, I'll keep my eyes open, and pass this around. No one in my lab is quite ready yet, but there are certainly other talented folks in the comp. chem. groups here at UCSF. brian On Thu, May 19, 2016 at 9:14 AM, Eric Manas <eric.s.manas(a)gsk.com> wrote: > Hi Brian, > > Just to chime in...some of the skill sets we are looking for are around > protein modeling, physics of equilibrium binding and kinetics, structure > based design...etc. As Kris suggested we'd be happy to chat more at any > time. > > Eric > > Sent from my iPhone > > On May 19, 2016, at 5:02 PM, Kris Brown <Kristin.K.Brown(a)gsk.com> wrote: > > Dear Brian: > > > > I wanted to reach out to let you know that we are currently recruiting for > several open positions in the computational molecular design group at GSK. > The job descriptions are given as links below. If you know of anyone who > might be interested please feel free to pass along the job descriptions and > my contact information. I’d be happy to schedule a phone call if you’d like > to hear more detail about what these positions entail. > > > > Best Regards, > > Kris Brown > > > > > > Grade 7 Cheminformatics: WD64811 - http://tinyURL.gsk.com/91fd3f > <http://tinyurl.gsk.com/91fd3f> > > Grade 6/7 Data Science: WD59234 - http://tinyURL.gsk.com/2e27fa > <http://tinyurl.gsk.com/2e27fa> > > Grade 7 Investigator: WD58496 - http://tinyURL.gsk.com/55ac18 > <http://tinyurl.gsk.com/55ac18> > > > > > > *Kristin Brown* > > *Director**, Molecular Design US* > > Computational & Modeling Sciences > > RD Platform Technology & Science > > > > *GlaxoSmithKline* > > 709 Swedeland Road UW2412, King of Prussia, PA 19406 > > *Email *Kristin.K.Brown(a)gsk.com > > *Tel *610-270-4638 > > > > -- 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 -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

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[Compbio-allhands] 5/19/16 Seminar with Xiaowei Zhuang
by Flowers, Nicole 13 May '16

13 May '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.) Xiaowei Zhuang Harvard Illuminating Biology at the Nanoscale with Single-molecule and Super-resolution Imaging May 19, 2016 B. Huang, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers 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] computational postdoc @ ucsf
by Michael Keiser 10 May '16

10 May '16

FYI. Recommendations & help getting the word out much appreciated! -- We're looking for highly motivated postdoctoral candidates with a background in machine learning, systems pharmacology, computational chemistry, bioinformatics, or a related field. The candidate would work to integrate deep learning with pharmacology. The project involves the design of deep neural networks for the prediction of small molecule binding activities and their role in phenotypic screens. Desired, albeit not strictly required, skills include experience with theano, lasagne/keras, TensorFlow, pandas, and sklearn. Expertise with CUDA and/or massive dataset analysis (e.g., NoSQL, AWS, Google Cloud) is a plus. A productive track record with at least one first-author publication is required. We seek a driven individual who will lead his/her research independently and communicate frequently and clearly to the field. Just north of Silicon Valley, the Keiser lab’s location at UCSF Mission Bay directly adjoins SoMa district and the heart of SF’s tech and artificial intelligence startup scene. Interested candidates should submit a CV and arrange that three letters of reference be sent directly to apply(a)keiserlab.org. Please reference “postdoc-dnn”. -- Michael J Keiser, PhD Assistant Professor, UCSF Dept Pharmaceutical Chemistry Dept Bioengineering & Therapeutic Sciences Institute for Neurodegenerative Diseases p/1-415-886-7651 keiserlab.org <http://www.keiserlab.org> calendly.com/mjke

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[Compbio-allhands] Fwd: Comp Chem position at MD Anderson Cancer Center
by Jacobson, Matt 10 May '16

10 May '16

-- Matt Sent from my iPhone Begin forwarded message: From: "Cross,Jason B" <JBCross(a)mdanderson.org<mailto:JBCross@mdanderson.org>> Date: May 10, 2016 at 9:32:58 AM PDT To: "'matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>'" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Comp Chem position at MD Anderson Cancer Center Dear Dr. Jacobson, I’m contacting you to let you know that I currently have a junior position available, appropriate for a newly minted PhD or someone completing their post-doctoral training. The position is in the Institute for Applied Cancer Science (IACS) at the University of Texas MD Anderson Cancer Center in Houston, providing computational chemistry support for ongoing drug discovery projects. IACS is part of the cancer moonshots program and has essentially been built as a “biotech” within the cancer center, populated mostly by ex-pharma drug discovery scientists, and is a great environment for junior scientists to learn and contribute to exciting projects. If you have current or former students, or know of others within your network, that would be interested, I would appreciate if you could forward this information. Links to the position description and the MD Anderson IACS website are listed below. Interested applicants will need to apply through the career website, but can also forward their CVs directly to me. Job posting<https://mdanderson.referrals.selectminds.com/jobs/institute-rsch-investigat…> Institute for Applied Cancer Science<http://www.cancermoonshots.org/platforms/institute-for-applied-cancer-scien…> Thank you for your time and consideration. Best regards, Jason Jason Cross, Ph.D. Institute Senior Research Scientist Institute for Applied Cancer Science University of Texas – MD Anderson Cancer Center South Campus Research Bldg 3 (3SCR3.3438) Houston, TX 77054 Office: 713-745-7499 Email: jbcross(a)mdanderson.org<mailto:jbcross@mdanderson.org> The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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[Compbio-allhands] Fwd: job opportunity in disease modeling
by Jacobson, Matt 09 May '16

09 May '16

- Matt Begin forwarded message: From: Jaline Gerardin <jgerardin(a)idmod.org<mailto:jgerardin@idmod.org>> Subject: job opportunity in disease modeling Date: May 9, 2016 at 11:37:29 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, My team at the Institute for Disease Modeling<http://www.idmod.org/> is looking to hire a few research scientists. Could you circulate our job posting below to the compbio listserv? This is a great opportunity for anyone with a quantitative background who wants to continue doing research but not necessarily in an academic environment. Previous knowledge of malaria or epidemiology is not required. Thanks, Jaline TITLE: Research Scientist – Malaria LOCATION: Bellevue, WA, USA The Institute for Disease Modeling (IDM) team is composed of research scientists and software professionals who focus on creating powerful and innovative disease modeling and data analysis tools to help researchers and policy makers understand diseases, their causes, the way they spread, and the best types of interventions to use for the particular situation faced. IDM partners with selected universities, NGOs, government ministries, and other research and public health institutions focused on researching new ways to understand and combat diseases both locally and globally. We seek a full-time Research Scientist to work as part of the IDM malaria team and collaborate on the development, refinement, and utilization of sophisticated infectious disease models for epidemiological research and eradication-campaign planning. The IDM team architects advanced models of disease transmission, develops computational tools to inform global disease eradication policy, conducts innovative analysis of epidemiologically- and policy-relevant data (programmatic data, financial data, clinical trials data, and cluster surveys data), and identifies epidemiologically critical knowledge gaps. As part of our work, we routinely collaborate with groups at the World Health Organization, the Center for Disease Control, PATH, the Bill and Melinda Gates Foundation, ministries of health in the developing world, as well as universities and research institutes. As part of this group, the researcher will design and build new modules for the existing malaria disease model. The researcher will configure, calibrate, and exercise disease models to answer questions aimed at refining the malaria research agenda, improving understanding of disease dynamics, informing effective public health campaigns, and guiding rational development of new public-health interventions. The research, models, and results will be presented to key stakeholders, displayed at conferences, and published in academic journals. Joining our group provides unique opportunities to interact with global-health policymakers, to collaborate with world-class research laboratories and non-profit organizations, and to contribute to global and national disease-eradication strategies. Responsibilities: · Reviews scientific literature and determines which aspects of biology, demography, geography, and climate are relevant to the model. · Builds new modules for existing disease models; builds and develops new disease models. · Works closely with the modelers, programmers, and statisticians on the team to refine the models and use them to conduct sensitivity analyses, explore tradeoffs among possible interventions, and optimize eradication plans for time, cost, or other factors. · Finds sources for the necessary input data to the models and helps to organize the necessary data for input to the models. · Writes software code (in C/C++) to implement model features. · Collects, analyzes, and presents data on model results and performance. · Assists in the preparation of research articles and conference presentations communicating the project and its results to the scientific community. Key Qualifications and Required Skills: · Ph.D. in a quantitative field (e.g. Applied Mathematics, Statistics, Epidemiology, Quantitative Biology) · Numerical analysis, dynamical systems, stochastic processes, and biostatistics. · Read and write research articles in biology and applied mathematics. · Principles, techniques, and tools of computational epidemiology. · Work extended hours to meet a deadline; demonstrated ability to work productively as part of a small team. · At least 2 years’ experience in C/C++ software development. · Proficiency in at least one data-analysis or scripting language (e.g. MATLAB, python, R) · Multiple published articles in peer-reviewed scientific journals (to be submitted with application). · Knowledge of developing-world public health issues and the malaria disease system preferred. Jaline Gerardin Senior Research Scientist jgerardin(a)idmod.org<mailto:jgerardin@idmod.org> T - 425.691.3343 [cid:image001.png@01D1A9E7.29107920] This message may contain confidential information which may also be legally privileged information. If you are not an intended recipient of the message, please delete it and notify the sender via reply email. Any unauthorized dissemination, distribution or copying of the material in this message, and any attachments to the message, is strictly forbidden.

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[Compbio-allhands] 5/12/16 Seminar with Chris Voigt
by Flowers, Nicole 06 May '16

06 May '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.) Chris Voigt MIT Cello: A programming language for living cells May 12, 2016 W. Lim, 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] 5/5/16 Seminar with David Savage
by Flowers, Nicole 29 Apr '16

29 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.) David Savage UC Berkeley Fixed: Synthetic biological approaches for probing cellular physiology May 5, 2016 J. Fraser, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & 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] helpers needed for Software Carpentry Workshops April 29 and 30 at Mission Bay
by Patricia C. Babbitt 26 Apr '16

26 Apr '16

The UCSF Library is hosting a Software Carpentry Python workshop this Friday and Saturday, April 29th and 30th at Mission Bay and we need your help to make it successful! We will have 80 UCSF researchers at this event – 46 beginners and 34 advanced beginners. Here is what we need: 1 person with technical competence in Python who is willing to be helpers to the Software Carpentry Instructors during both days of the bootcamp. Workshops will run from 9 - 5 on Friday and Saturday (workshop info can be found here:http://bsmith89.github.io/2016-04-29-ucsf/). As a helper you will have the interpersonal skills to spot people who are confused and help them get unstuck during the practical sessions. Helpers are vital to keeping workshops flowing smoothly. More details on the role of the helper is here:https://software-carpentry.org/workshops/checklists/helpers.html Here is what you will get if you are the right person for this role: * $100 Visa Gift Card * Breakfast and coffee/snacks each day * An opportunity to learn the material well enough to teach it yourself in the future * Credit on the workshop materials and you can put this effort on your CV as service to the UCSF community, showing you have teaching experience in these areas If you are interested in this opportunity please emailariel.deardorff(a)ucsf.edu<mailto:ariel.deardorff@ucsf.edu> to get more details and see if you are a good fit for this role. -- 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. Sydney Russell Leed, +1 415-514-1214, 415-514-9816 Sydney.RussellLeed(a)ucsf.edu <mailto:Sydney.RussellLeed@ucsf.edu>

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[Compbio-allhands] Fwd: IGBMC call for Group Leader positions
by Andrej Sali 26 Apr '16

26 Apr '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 <mailto:assistant@salilab.org>, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org <mailto:sali@salilab.org>; Web http://salilab.org <http://salilab.org/> > Begin forwarded message: > > From: Directeur IGBMC <directeur.igbmc(a)igbmc.fr> > Subject: IGBMC call for Group Leader positions > Date: April 26, 2016 at 7:53:10 AM PDT > To: Undisclosed recipients:; > > > Dear Colleagues, > > The IGBMC is currently seeking outstanding scientists to take-up group leader positions within its Departements of Functional Genomics, Development and Stem Cells, and Integrated Structural Biology. Our attractive new call has just been launched and will be opened until July 30th 2016 (see attached advertisement). > > We would be grateful if you could post the attached poster to your notice board and disseminate the information to your organization/network and to people who might be interested. > > Many thanks in advance. > > With best regards, > > > Dr. Bertrand SERAPHIN > IGBMC Director > > > //\//\//\//\//\//\//\//\//\//\//\//\/ > > Bertrand Séraphin > > IGBMC > CNRS UMR 7104/INSERM U964/UDS > 1 Rue Laurent Fries > BP 10142 > 67404 Illkirch CEDEX > France > > Tel +33 (0)3 88 65 32 16 > Fax +33 (0)3 88 65 32 03 > > //\//\//\//\//\//\//\//\//\//\//\//\/ >

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[Compbio-allhands] Fwd: Antibody & Protein Engineering positions at Bayer - San Francisco
by Andrej Sali 25 Apr '16

25 Apr '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 <mailto:assistant@salilab.org>, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org <mailto:sali@salilab.org>; Web http://salilab.org <http://salilab.org/> > Begin forwarded message: > > From: Shaun Lippow <slippow(a)gmail.com> > Subject: Antibody & Protein Engineering positions at Bayer - San Francisco > Date: April 25, 2016 at 1:09:10 PM PDT > To: Shaun Lippow <shaun.lippow(a)bayer.com> > > Hi all, > > Apologies for the mass email, but I'd like to get your help to distribute two great positions now open in my group. Please forward (or apply!). Applications should go through Bayer's website but recommendations direct to me are welcome and I'll try to expedite. Thanks! > > Position #1: Technical Staff Research Scientist - Antibody and Protein Engineering > Group/Department: Protein Platform Technologies group, in the Lead Discovery department > Company/Location: Bayer, US Innovation Center, Mission Bay, San Francisco > Primary Responsibilities: (1) Support antibody lead discovery, set strategies, manage projects; (2) Develop novel antibody technologies. See attached Job Description for more info > Minimum Experience: PhD with 4+ years relevant experience or equivalent -- but stellar new PhDs welcome to apply and position level will be adjusted accordingly > Start Date: ASAP > To Apply: www.career.bayer.us <http://www.career.bayer.us/> reference code 0000162405 (link here <https://career.bayer.us/job/Technical-Staff-Research-Scientist-Antibody-and…>) > > Position #2: Industrial Post Doc - Antibody and Protein Engineering > Group/Department: Protein Platform Technologies group, in the Lead Discovery department > Company/Location: Bayer, US Innovation Center, Mission Bay, San Francisco > Primary Responsibility: Develop novel protein and antibody technologies. See attached Job Description for more info > Minimum Experience: PhD or equivalent > Start Date: ASAP > To Apply: www.career.bayer.us <http://www.career.bayer.us/> reference code 0000162426 (link here <https://career.bayer.us/job/Industrial-Post-Doc-Ab-Protein-Engineer--000016…>) > > Best regards, > Shaun >

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[Compbio-allhands] 4/28/16 Seminar with Debbie Nickerson
by Flowers, Nicole 22 Apr '16

22 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.) Debbie Nickerson University of Washington Lessons learned from scaling the analysis of Mendelian conditions April 28, 2016 T. Friedrich, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: opening in Computational Proteing Engineering at Illumina
by Jacobson, Matthew 21 Apr '16

21 Apr '16

-- Matt Sent from my iPhone Begin forwarded message: From: "Peisajovich, Sergio" <speisajovich(a)illumina.com<mailto:speisajovich@illumina.com>> Date: April 21, 2016 at 11:26:08 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: opening in Computational Proteing Engineering at Illumina Dear Matt, I am a former postdoc from Wendell’s lab who is now working in Protein Engineering at Illumina. I am contacting you regarding an opening for a computational protein scientist in our Protein Engineering group, based in San Diego. I am attaching the job description here, I was hoping you could circulate this among postdocs or grad students in your lab that you believe are close to move on with their careers. If anyone is interested, please forward them my contact info, they can reach out to me directly. Please let me know if you have any questions or need more information. Thanks so much for your help on this. Cheers sergio Sergio Peisajovich, Ph.D. Associate Director, Scientific Research Illumina, Inc Tel:(858) 255-5451 speisajovich(a)illumina.com<mailto:speisajovich@illumina.com> www.illumina.com<http://www.illumina.com/>

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[Compbio-allhands] Fwd: opening in Computational Proten Engineering at Illumina
by Andrej Sali 21 Apr '16

21 Apr '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: "Peisajovich, Sergio" <speisajovich(a)illumina.com> > Subject: opening in Computational Proten Engineering at Illumina > Date: April 21, 2016 at 11:16:42 AM PDT > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Andrej, > > I am a former postdoc from Wendell’s lab who is now working in protein engineering at Illumina. > > I am contacting you regarding an opening for a computational protein scientist in our Protein Engineering group at Illumina, based in San Diego. > > I am attaching the job description here, I was hoping you could circulate this among postdocs or grad students in your lab that you believe are close to move on with their careers. If anyone is interested, please forward them my contact info, they can reach out to me directly. > > Please let me know if you have any questions or need more information. > > Thanks so much for your help on this, > > Best > > sergio > Sergio Peisajovich, Ph.D. > Associate Director, Scientific Research > Illumina, Inc > Tel:(858) 255-5451 > speisajovich(a)illumina.com <mailto:speisajovich@illumina.com> > www.illumina.com <http://www.illumina.com/> >

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[Compbio-allhands] Fwd: Employment opportunities in computational protein modeling for students and postdocs
by Andrej Sali 14 Apr '16

14 Apr '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 <mailto:assistant@salilab.org>, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org <mailto:sali@salilab.org>; Web http://salilab.org <http://salilab.org/> > Begin forwarded message: > > From: Greg Lakatos <glakatos(a)zymeworks.com> > Subject: Fwd: Employment opportunities in computational protein modeling for students and postdocs > Date: April 14, 2016 at 11:00:48 AM PDT > To: sali(a)salilab.org > > Dear Professor Sali, > > I apologize for contacting you again, however the job postings didn't make it through with my previous email. > > Thank you again, > > Greg > > > From: Greg Lakatos <glakatos(a)zymeworks.com> > To: <sali(a)salilab.org> > Sent: 4/14/2016 10:54 AM > Subject: Employment opportunities in computational protein modeling for students and postdocs > > Dear Professor Sali, > > I am writing on behalf of Zymeworks Inc., a computational biotechnology company located in Vancouver, Canada. Zymeworks has developed a set of computational protein modeling tools that have been successfully used to design a novel antibody-based drug platform. As part of our on-going efforts to improve our protein modeling capabilities, we are currently recruiting scientists to join our simulation and modeling team. I have attached copies of our current job postings, and I would be grateful if you could forward these postings to members of your group, or any other students or postdocs who may be interested. More information about Zymeworks is available at our website (www.zymeworks.com <http://www.zymeworks.com/>). I am also happy to answer questions about our openings, and I can be reached at glakatos(a)zymeworks.com <mailto:glakatos@zymeworks.com> > > Thank you for your time and assistance. > > Sincerely, > > Greg Lakatos > Principal Scientist and Simulations Team Lead > Zymeworks Inc. > > > > Notice of Confidentiality: The information transmitted is intended only for the > person or entity to which it is addressed and may contain confidential and/or > privileged material. Any review, re-transmission, dissemination or other use of > or taking of any action in reliance upon this information by persons or entities > other than the intended recipient is prohibited. If you received this in error > please contact the sender immediately by return electronic transmission and then > immediately delete this transmission including all attachments without copying, > distributing or disclosing the same.

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[Compbio-allhands] Fwd: Employment opportunities in computational protein modeling for students and postdocs
by Jacobson, Matthew 14 Apr '16

14 Apr '16

- Matt Begin forwarded message: From: Greg Lakatos <glakatos(a)zymeworks.com<mailto:glakatos@zymeworks.com>> Subject: Employment opportunities in computational protein modeling for students and postdocs Date: April 14, 2016 at 10:49:03 AM PDT To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Professor Jacobson, I am writing on behalf of Zymeworks Inc., a computational biotechnology company located in Vancouver, Canada. Zymeworks has developed a set of computational protein modeling tools that have been successfully used to design a novel antibody-based drug platform. As part of our on-going efforts to improve our modeling tools, we are currently recruiting scientists to join our simulation and modeling team. I have attached copies of our current job postings and I would be grateful if you could forward these postings to members of your group, or any other students or postdocs who may be interested. More information about Zymeworks is available at our website (www.zymeworks.com<http://www.zymeworks.com>). I am also happy to answer questions about our openings, and I can be reached at glakatos(a)zymeworks.com<mailto:glakatos@zymeworks.com> Thank you for your time and assistance. Sincerely, Greg Lakatos Principal Scientist and Simulations Team Lead Zymeworks Inc. Notice of Confidentiality: The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, re-transmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error please contact the sender immediately by return electronic transmission and then immediately delete this transmission including all attachments without copying, distributing or disclosing the same.

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