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[Compbio-allhands] a group leader position at A*STAR Institute in Singapore
by Andrej Sali 04 Feb '13

04 Feb '13

get in touch with Dr. Chandra Verma, chandra(a)bii.a-star.edu.sg, http://www.bii.a-star.edu.sg/research/biography/chandra.php : i understand they would especially like to encourage female group leader candidates to apply. "a position is available for the position of a group leader in the Bioinformatics Instt (A*STAR) in Singapore. we are looking for someone with 4-5 years postdoctoral experience in the field of computational modelling of biomolecules who will develop a program involving the computational interrogation of large biomolecules and their assemblies and their significance in health and disease. the institute is a part of a large network of institutes and 2 major universities and hospitals with immense opportunities to collaborate with enthusiastic scientists from all disciplines and with clinicians. In addition, there are opportunities for the person to develop a small experimental effort to complement their computational work if necessary." -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: Bioinformatics groupleader position in Dresden, Germany
by Andrej Sali 04 Feb '13

04 Feb '13

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant, Ms. Hilary Mahon, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Sabine Jochens <jochens(a)mpi-cbg.de> > Date: February 4, 2013, 3:09:30 AM PST > To: "APArkin(a)lbl.gov" <APArkin(a)lbl.gov>, "Charles_Lawrence(a)brown.edu" <Charles_Lawrence(a)brown.edu>, "mbeisen(a)berkeley.edu" <mbeisen(a)berkeley.edu>, "tp(a)ai.mit.edu" <tp(a)ai.mit.edu>, "Alexander.Bockmayr(a)fu-berlin.de" <Alexander.Bockmayr(a)fu-berlin.de>, "Alexander.Verkhovsky(a)epfl.ch" <Alexander.Verkhovsky(a)epfl.ch>, "Amos.Bairoch(a)isb-sib.ch" <Amos.Bairoch(a)isb-sib.ch>, "Andrew.Millar(a)ed.ac.uk" <Andrew.Millar(a)ed.ac.uk>, 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"manoli(a)mit.edu" <manoli(a)mit.edu>, "marcotte(a)icmb.utexas.edu" <marcotte(a)icmb.utexas.edu>, "margit.leitner(a)uni-jena.de" <margit.leitner(a)uni-jena.de>, "mario.albrecht(a)mpi-inf.mpg.de" <mario.albrecht(a)mpi-inf.mpg.de>, "mark(a)ncmir.ucsd.edu" <mark(a)ncmir.ucsd.edu>, "martin.fussenegger(a)bsse.ethz.ch" <martin.fussenegger(a)bsse.ethz.ch>, "martin.hofmann-apitus(a)scai.fraunhofer.de" <martin.hofmann-apitus(a)scai.fraunhofer.de>, "martin.vingron(a)molgen.mpg.de" <martin.vingron(a)molgen.mpg.de>, "martin.zacharias(a)ph.tum.de" <martin.zacharias(a)ph.tum.de>, "martinetz(a)inb.uni-luebeck.de" <martinetz(a)inb.uni-luebeck.de>, "maryann(a)ncmir.ucsd.edu" <maryann(a)ncmir.ucsd.edu>, "masch(a)informatik.uni-kiel.de" <masch(a)informatik.uni-kiel.de>, "matthias.wolf(a)biozentrum.uni-wuerzburg.de" <matthias.wolf(a)biozentrum.uni-wuerzburg.de>, "mauer(a)lbl.gov" <mauer(a)lbl.gov>, "maywang(a)bme.gatech.edu" <maywang(a)bme.gatech.edu>, "mbaudis(a)imls.uzh.ch" <mbaudis(a)imls.uzh.ch>, "meijering(a)imagescience.org" <meijering(a)imagescience.org>, "mering(a)imls.uzh.ch" <mering(a)imls.uzh.ch>, "mering(a)molbio.unizh.ch" <mering(a)molbio.unizh.ch>, "mferrari(a)cebitec.uni-bielefeld.de" <mferrari(a)cebitec.uni-bielefeld.de>, "michael.krauthammer(a)yale.edu" <michael.krauthammer(a)yale.edu>, "michael.stadler(a)fmi.ch" <michael.stadler(a)fmi.ch>, "michael.unser(a)epfl.ch" <michael.unser(a)epfl.ch>, "mihaela.zavolan(a)unibas.ch" <mihaela.zavolan(a)unibas.ch>, "mikeh(a)alleninstitute.org" <mikeh(a)alleninstitute.org>, "mittag(a)eva.mpg.de" <mittag(a)eva.mpg.de>, "mitya(a)janelia.hhmi.org" <mitya(a)janelia.hhmi.org>, "mjs(a)di.fc.ul.pt" <mjs(a)di.fc.ul.pt>, "moeller(a)inb.uni-luebeck.de" <moeller(a)inb.uni-luebeck.de>, "mplatzer(a)fli-leibniz.de" <mplatzer(a)fli-leibniz.de>, "murphy(a)cmu.edu" <murphy(a)cmu.edu>, "mustafa.khammash(a)bsse.ethz.ch" <mustafa.khammash(a)bsse.ethz.ch>, "nick.monk(a)nottingham.ac.uk" <nick.monk(a)nottingham.ac.uk>, "nieselt(a)informatik.uni-tuebingen.de" <nieselt(a)informatik.uni-tuebingen.de>, "niko.beerenwinkel(a)bsse.ethz.ch" <niko.beerenwinkel(a)bsse.ethz.ch>, "nils(a)sys-bio.net" <nils(a)sys-bio.net>, "olaf.wolkenhauer(a)uni-rostock.de" <olaf.wolkenhauer(a)uni-rostock.de>, "oliver.kohlbacher(a)uni-tuebingen.de" <oliver.kohlbacher(a)uni-tuebingen.de>, "olivier.bodenreider(a)nih.gov" <olivier.bodenreider(a)nih.gov>, "p.d.moerland(a)amc.nl" <p.d.moerland(a)amc.nl>, "p.m.a.sloot(a)uva.nl" <p.m.a.sloot(a)uva.nl>, "paloy(a)irbbarcelona.org" <paloy(a)irbbarcelona.org>, "parsch(a)bio.lmu.de" <parsch(a)bio.lmu.de>, "pascal.fua(a)epfl.ch" <pascal.fua(a)epfl.ch>, "patla(a)ida.liu.se" <patla(a)ida.liu.se>, "paul.wrede(a)charite.de" <paul.wrede(a)charite.de>, "pb(a)di.fct.unl.pt" <pb(a)di.fct.unl.pt>, "pdthomas(a)usc.edu" <pdthomas(a)usc.edu>, "pedro.mendes(a)manchester.ac.uk" <pedro.mendes(a)manchester.ac.uk>, "pelkmans(a)imsb.biol.ethz.ch" <pelkmans(a)imsb.biol.ethz.ch>, "perona(a)caltech.edu" <perona(a)caltech.edu>, "peter.horvath(a)lmc.biol.ethz.ch" <peter.horvath(a)lmc.biol.ethz.ch>, "peter.kunszt(a)systemsx.ch" <peter.kunszt(a)systemsx.ch>, "peter.robinson(a)charite.de" <peter.robinson(a)charite.de>, "petros(a)ethz.ch" <petros(a)ethz.ch>, "pfbaldi(a)ics.uci.edu" <pfbaldi(a)ics.uci.edu>, "philipp.bucher(a)epfl.ch" <philipp.bucher(a)epfl.ch>, "pm286(a)cam.ac.uk" <pm286(a)cam.ac.uk>, "pohl(a)uphs.upenn.edu" <pohl(a)uphs.upenn.edu>, "ppevzner(a)ucsd.edu" <ppevzner(a)ucsd.edu>, "r.eils(a)dkfz.de" <r.eils(a)dkfz.de>, "r.vandriel(a)uva.nl" <r.vandriel(a)uva.nl>, "rainer.merkl(a)biologie.uni-regensburg.de" <rainer.merkl(a)biologie.uni-regensburg.de>, "rajewsky(a)mdc-berlin.de" <rajewsky(a)mdc-berlin.de>, "ralf.baumeister(a)biologie.uni-freiburg.de" <ralf.baumeister(a)biologie.uni-freiburg.de>, "ralf.sommer(a)tuebingen.mpg.de" <ralf.sommer(a)tuebingen.mpg.de>, "ralph.schlapbach(a)fgcz.ethz.ch" <ralph.schlapbach(a)fgcz.ethz.ch>, "rarey(a)zbh.uni-hamburg.de" <rarey(a)zbh.uni-hamburg.de>, "rd(a)sanger.ac.uk" <rd(a)sanger.ac.uk>, "reinert(a)inf.fu-berlin.de" <reinert(a)inf.fu-berlin.de>, "reinhard.guthke(a)hki-jena.de" <reinhard.guthke(a)hki-jena.de>, "reinhard.sterner(a)biologie.uni-regensburg.de" <reinhard.sterner(a)biologie.uni-regensburg.de>, "renato.paro(a)bsse.ethz.ch" <renato.paro(a)bsse.ethz.ch>, "rguigo(a)imim.es" <rguigo(a)imim.es>, "rich(a)ini.phys.ethz.ch" <rich(a)ini.phys.ethz.ch>, "rickl(a)uci.edu" <rickl(a)uci.edu>, "robert.preissner(a)charite.de" <robert.preissner(a)charite.de>, "robert.russell(a)bioquant.uni-heidelberg.de" <robert.russell(a)bioquant.uni-heidelberg.de>, "robert(a)techfak.uni-bielefeld.de" <robert(a)techfak.uni-bielefeld.de>, "roeland.merks(a)sysbio.nl" <roeland.merks(a)sysbio.nl>, "rost(a)rostlab.org" <rost(a)rostlab.org>, "sali(a)salilab.org" <sali(a)salilab.org>, "sandeep(a)ncbs.res.in" <sandeep(a)ncbs.res.in>, "sanderc(a)mskcc.org" <sanderc(a)mskcc.org>, "sandrine(a)stat.berkeley.edu" <sandrine(a)stat.berkeley.edu>, "sankoff(a)uottawa.ca" <sankoff(a)uottawa.ca>, "sat(a)mrc-lmb.cam.ac.uk" <sat(a)mrc-lmb.cam.ac.uk>, "savas.tay(a)bsse.ethz.ch" <savas.tay(a)bsse.ethz.ch>, "sbalzarini(a)inf.ethz.ch" <sbalzarini(a)inf.ethz.ch>, "sebastian.boecker(a)uni-jena.de" <sebastian.boecker(a)uni-jena.de>, "sefraser(a)caltech.edu" <sefraser(a)caltech.edu>, "serafim(a)cs.stanford.edu" <serafim(a)cs.stanford.edu>, "shimizu(a)botinst.uzh.ch" <shimizu(a)botinst.uzh.ch>, "shm(a)doc.ic.ac.uk" <shm(a)doc.ic.ac.uk>, "simon.berneche(a)unibas.ch" <simon.berneche(a)unibas.ch>, "sjb(a)cs.ucsd.edu" <sjb(a)cs.ucsd.edu>, "soeding(a)genzentrum.lmu.de" <soeding(a)genzentrum.lmu.de>, "sorin(a)cs.brown.edu" <sorin(a)cs.brown.edu>, "sridhar(a)umiacs.umd.edu" <sridhar(a)umiacs.umd.edu>, "sroth(a)cs.tu-darmstadt.de" <sroth(a)cs.tu-darmstadt.de>, "sta(a)molgen.mpg.de" <sta(a)molgen.mpg.de>, "stefan.haas(a)molgen.mpg.de" <stefan.haas(a)molgen.mpg.de>, "stefan.posch(a)informatik.uni-halle.de" <stefan.posch(a)informatik.uni-halle.de>, "stefan.rensing(a)biologie.uni-freiburg.de" <stefan.rensing(a)biologie.uni-freiburg.de>, "stefan.schu(a)uni-jena.de" <stefan.schu(a)uni-jena.de>, "stefano.fusi(a)columbia.edu" <stefano.fusi(a)columbia.edu>, "stephan(a)bio.lmu.de" <stephan(a)bio.lmu.de>, "steveh(a)fhcrc.org." <steveh(a)fhcrc.org>, "stormo(a)wustl.edu" <stormo(a)wustl.edu>, "strimmer(a)uni-leipzig.de" <strimmer(a)uni-leipzig.de>, "stuart(a)aiai.ed.ac.uk" <stuart(a)aiai.ed.ac.uk>, "student.wbbib(a)uj.edu.pl" <student.wbbib(a)uj.edu.pl>, "studla(a)bioinf.uni-leipzig.de" <studla(a)bioinf.uni-leipzig.de>, "stwong(a)tmhs.org" <stwong(a)tmhs.org>, "suzi(a)fruitfly.org" <suzi(a)fruitfly.org>, "sven.panke(a)bsse.ethz.ch" <sven.panke(a)bsse.ethz.ch>, "sysbio(a)cyanolab.de" <sysbio(a)cyanolab.de>, "szekely(a)vision.ee.ethz.ch" <szekely(a)vision.ee.ethz.ch>, "t.hoefer(a)dkfz-heidelberg.de" <t.hoefer(a)dkfz-heidelberg.de>, "taddei(a)necker.fr" <taddei(a)necker.fr>, "tandy(a)cs.utexas.edu" <tandy(a)cs.utexas.edu>, "tautz(a)evolbio.mpg.de" <tautz(a)evolbio.mpg.de>, "tdeserno(a)mi.rwth-aachen.de" <tdeserno(a)mi.rwth-aachen.de>, "terry(a)stat.berkeley.edu" <terry(a)stat.berkeley.edu>, "thattai(a)ncbs.res.in" <thattai(a)ncbs.res.in>, "thomas.rattei(a)univie.ac.at" <thomas.rattei(a)univie.ac.at>, "thornton(a)ebi.ac.uk" <thornton(a)ebi.ac.uk>, "tian(a)ieee.org" <tian(a)ieee.org>, "tideker(a)ucsd.edu" <tideker(a)ucsd.edu>, "tiedeman(a)uni-potsdam.de" <tiedeman(a)uni-potsdam.de>, "toga(a)loni.ucla.edu" <toga(a)loni.ucla.edu>, "tompa(a)cs.washington.edu" <tompa(a)cs.washington.edu>, "torda(a)zbh.uni-hamburg.de" <torda(a)zbh.uni-hamburg.de>, "Torsten.Schwede(a)unibas.ch" <torsten.schwede(a)unibas.ch>, "torsten(a)cs.uni-potsdam.de" <torsten(a)cs.uni-potsdam.de>, "tresch(a)lmb.uni-muenchen.de" <tresch(a)LMB.uni-muenchen.de>, "u.klingmueller(a)dkfz.de" <u.klingmueller(a)dkfz.de>, "udo.hahn(a)uni-jena.de" <udo.hahn(a)uni-jena.de>, "urialon(a)weizmann.ac.il" <urialon(a)weizmann.ac.il>, "v.ntziachristos(a)tum.de" <v.ntziachristos(a)tum.de>, "vassily.hatzimanikatis(a)epfl.ch" <vassily.hatzimanikatis(a)epfl.ch>, "vbafna(a)cs.ucsd.edu" <vbafna(a)cs.ucsd.edu>, "vdanos(a)inf.ed.ac.uk" <vdanos(a)inf.ed.ac.uk>, "volker.heun(a)bio.ifi.lmu.de" <volker.heun(a)bio.ifi.lmu.de>, "volkhard.helms(a)bioinformatik.uni-saarland.de" <volkhard.helms(a)bioinformatik.uni-saarland.de>, "volkmar.liebscher(a)uni-greifswald.de" <volkmar.liebscher(a)uni-greifswald.de>, "w.martin(a)hhu.de" <w.martin(a)hhu.de>, "w.mewes(a)wzw.tum.de" <w.mewes(a)wzw.tum.de>, "w_smith(a)lifesci.ucsb.edu" <w_smith(a)lifesci.ucsb.edu>, "walther(a)mpimp-golm.mpg.de" <walther(a)mpimp-golm.mpg.de>, "wcm2(a)psu.edu" <wcm2(a)psu.edu>, "weickert(a)mia.uni-saarland.de" <weickert(a)mia.uni-saarland.de>, "weigel(a)weigelworld.org" <weigel(a)weigelworld.org>, "weilp(a)mail.cbi.pku.edu.cn" <weilp(a)mail.cbi.pku.edu.cn>, "whitaker(a)cs.utah.edu" <whitaker(a)cs.utah.edu>, "whuber(a)embl.de" <whuber(a)embl.de>, "wkimwkim(a)googlemail.com" <wkimwkim(a)googlemail.com>, "wojmak(a)uni-muenster.de" <wojmak(a)uni-muenster.de>, "wolfgang.heiden(a)h-brs.de" <wolfgang.heiden(a)h-brs.de>, "wolfram.gronwald(a)klinik.uni-regensburg.de" <wolfram.gronwald(a)klinik.uni-regensburg.de>, "wolfram.weckwerth(a)univie.ac.at" <wolfram.weckwerth(a)univie.ac.at>, "wolfson(a)post.tau.ac.il" <wolfson(a)post.tau.ac.il>, "wwwadmin(a)statistik.tu-dortmund.de" <wwwadmin(a)statistik.tu-dortmund.de>, "yann(a)cs.nyu.edu" <yann(a)cs.nyu.edu>, "yliharja(a)cs.tut.fi" <yliharja(a)cs.tut.fi>, "zamboni(a)imsb.biol.ethz.ch" <zamboni(a)imsb.biol.ethz.ch>, "zdobnov(a)medecine.unige.ch" <zdobnov(a)medecine.unige.ch>, "zolli(a)aim.uzh.ch" <zolli(a)aim.uzh.ch> > Subject: Bioinformatics groupleader position in Dresden, Germany > > Dear Sir or Madam, > > On behalf of Prof. Michael Schröder I am sending out this advertisement for an open groupleader position within bioinformatics in Dresden. Please see below. > > > Dear colleague, > > we have an opening for a bioinformatics groupleader in Dresden. I'd be very grateful if you could pass this email on to anybody possibly interested. > > Bioinformatics groupleader in Dresden > Details: http://tinyurl.com/aswtk6e > Deadline: 7 March 2013 > Biotec: www.biotec.tu-dresden.de Bioinfo: www.compbio-dresden.de > > --- > Michael Schroeder, Professor in Bioinformatics > Director BiOTEC, TU Dresden > > Tatzberg 47-51, 01307 Dresden, Germany > > w: www.biotec.tu-dresden.de > t: +49 351 463 400 60 > f: +49 351 463 400 61 > e: ms(a)biotec.tu-dresden.de > > > > > Best regards, > > Sabine Jochens (Mrs) > _____________________________ > Assistant to Dr. Gene Myers, Director > Tschira Chair of Systems Biology > > Max Planck Institute of > Molecular Cell Biology and Genetics > Pfotenhauerstrasse 108 > 01307 Dresden, Germany > > Tel +49 351 210-2440 > Fax +49 351 210-1209 > E-mail: jochens(a)mpi-cbg.de > http://www.mpi-cbg.de >

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[Compbio-allhands] Fwd: 2013 Center for the Physics of Living Cells Summer School
by Jacobson, Matt 31 Jan '13

31 Jan '13

Begin forwarded message: From: "Yodh, Jaya G" <jyodh(a)illinois.edu<mailto:jyodh@illinois.edu>> Subject: 2013 Center for the Physics of Living Cells Summer School Date: January 31, 2013 5:35:59 PM PST To: "Yodh, Jaya G" <jyodh(a)illinois.edu<mailto:jyodh@illinois.edu>> Dear Colleagues, On behalf of the Center for the Physics of Living Cells (CPLC), an NSF Physics Frontier Center at the University of Illinois, Urbana-Champaign, we are writing to announce the 2013 Physics of Living Cells Summer School being offered from July 15 – 20, 2013 at theUniversity of Illinois at Urbana-Champaign. This one-week program is designed for graduate students, postdoctoral fellows and researchers in the chemical and life sciences, biophysics, physics, and engineering who would like to expand their training into the areas of single-molecule and live-cell experimental and computational biophysics. Could you please post and circulate the attached announcement to those who might be interested? For more information and to apply by March 15, please visit: http://www.cplc.illinois.edu/summerschool2013/ . Thank you, Jaya Yodh Jaya Yodh, Ph.D. Research Assistant Professor, Dept. of Physics CPLC Director of Education and Outreach University of Illinois at Urbana-Champaign Center for the Physics of Living Cells (CPLC) 1110 W. Green St., Urbana, IL 61801 Phone: 217-244-1155; Fax: 217-333-4778 E-mail: jyodh(a)illinois.edu<mailto:jyodh@illinois.edu> http://physics.illinois.edu/people/profile.asp?jyodh http://www.cplc.illinois.edu Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] 2/7/13 Seminar with Jonathan Javitch
by Nicole Takesono Flowers 31 Jan '13

31 Jan '13

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 Jonathan Javitch Columbia A tale of two substrates: a novel mechanism for neurotransmiters:sodium symport February 7, 2013 R. Edwards, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: RE: employment offering in biotech
by Tom Ferrin 29 Jan '13

29 Jan '13

-------- Original Message -------- Subject: RE: employment offering in biotech Date: Mon, 28 Jan 2013 19:34:13 +0000 From: Petropoulos, Christos <Petropc(a)labcorp.com> To: Tom Ferrin <tef(a)cgl.ucsf.edu> CC: babbitt(a)cgl.ucsf.edu <babbitt(a)cgl.ucsf.edu> Thanks for your assistance Tom! I am attaching a job description if that helps? CJP -----Original Message----- From: Tom Ferrin [mailto:tef@cgl.ucsf.edu] Sent: Monday, January 28, 2013 10:04 AM To: Petropoulos, Christos Cc: babbitt(a)cgl.ucsf.edu Subject: Re: employment offering in biotech Christos, We have an email distribution list that I would be happy to forward your message to. --tom On 1/27/13 6:23 PM, Petropoulos, Christos wrote: > Dear Dr. Ferrin and Dr. Babbitt, > > > > I am the Chief Scientific Officer of Monogram Biosciences, a > biotechnology company located in South San Francisco. We have an > opening for a scientist in our bioinformatics group and are looking > for qualified candidates. I would like to know if there is a > mechanism for posting this position on your website or an appropriate UCSF website. > > > > Sincerely, > > > > Christos J Petropoulos, PhD > > Chief Scientific Officer, Monogram Biosciences > > Vice President, Laboratory Corporation of America > > > > -This e-mail and any attachments may contain CONFIDENTIAL information, > including PROTECTED HEALTH INFORMATION. If you are not the intended > recipient, any use or disclosure of this information is STRICTLY > PROHIBITED; you are requested to delete this e-mail and any > attachments, notify the sender immediately, and notify the LabCorp > Privacy Officer at privacyofficer(a)labcorp.com or call (877) 23-HIPAA / (877) 234-4722. > -This e-mail and any attachments may contain CONFIDENTIAL information, including PROTECTED HEALTH INFORMATION. If you are not the intended recipient, any use or disclosure of this information is STRICTLY PROHIBITED; you are requested to delete this e-mail and any attachments, notify the sender immediately, and notify the LabCorp Privacy Officer at privacyofficer(a)labcorp.com or call (877) 23-HIPAA / (877) 234-4722.

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[Compbio-allhands] Fwd: [ISBRA-L] Full Professor - Bioinformatics
by Andrej Sali 27 Jan '13

27 Jan '13

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: ISBRA Mailing List <isbra-l(a)dna.engr.uconn.edu> > Subject: [ISBRA-L] Full Professor - Bioinformatics > Date: January 26, 2013 6:08:44 PM PST > To: <sali(a)salilab.org> > Reply-To: <isbrainfo(a)gmail.com> > > > The Department of Computer Science at Georgia State University invites > applications for an anticipated position of Full Professor in the > bioinformatics area beginning Fall Semester 2013, pending budgetary > approval. Earned Ph.D. in Computer Science or a related discipline is > required. An offer of employment will be conditional on background > verification. > > This position is part of a university-wide initiative that is seeking > to hire excellent faculty in several interdisciplinary areas. > Prospective candidates should demonstrate ability to bring national > and international recognition to the department as a center of > excellence for bioinformatics research and education. The hired > applicant is expected to to bring in major extramural funding, mentor > junior faculty, recruit top-quality Ph.D. students, and foster > interdisciplinary research collaborations among faculty in various > departments in GSU. > > Georgia State University, founded in 1913, is a Carnegie RU/VH > (Research University/Very High Research Activity) institution. Located > in the heart of downtown Atlanta, this major research university has > an enrollment of more than 30,000 undergraduate and graduate students > in eight colleges. Georgia State is the second-largest university in > the state, with students coming from every county in Georgia, every > state in the nation, and from over 145 countries. Georgia State > University is currently embarking on a record $1 billion campus > expansion. The Computer Science Department offers programs leading to > the B.S., M.S., and Ph.D. degrees in computer science. Currently, 20 > out of more than 60 Ph.D. students are involved in bioinformatics > research. They are supervised by 10 faculty members fully or > substantially involved in bioinformatics research through > collaboration with Computer Science and Biology faculty. Departmental > computing facilities for research and instruction include a > departmental network of PCs, Unix/Linux workstations, two > interconnected Beowulf clusters, and a 32-processor supercomputer. > The department?s faculty attracts substantial funding from many > federal agencies, including five NSF CAREER Awards. > > Women and minorities are particularly encouraged to apply. Applicants > should send letter of interest, C.V., and three letters of > recommendation to: > > Dr. Yi Pan, Chair > 2CI Bioinformatics > Department of Computer Science > Georgia State University > 34 Peachtree Street, Suite 1450 > Atlanta, Georgia 30303 > > Applications can also be sent via email to search4bio(a)cs.gsu.edu and > will be accepted until position is filled. > > > _______________________________________________ > To modify subscription preferences or unsubscribe from the ISBRA-L mailing list visit http://dna.engr.uconn.edu/cgi-bin/mailman/options/isbra-l/sali%40salilab.org

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[Compbio-allhands] Fwd: Bioinformatics Requisition at ILMN San Diego
by Jacobson, Matt 18 Jan '13

18 Jan '13

Begin forwarded message: From: "Chorny, Ilya" <ichorny(a)illumina.com<mailto:ichorny@illumina.com>> Subject: Bioinformatics Requisition at ILMN San Diego Date: January 18, 2013 8:30:23 AM PST To: "babbitt(a)cgl.ucsf.edu<mailto:babbitt@cgl.ucsf.edu>" <babbitt(a)cgl.ucsf.edu<mailto:babbitt@cgl.ucsf.edu>>, "Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, "sali(a)salilab.org<mailto:sali@salilab.org>" <sali(a)salilab.org<mailto:sali@salilab.org>> Hi All, The group that I am in is opening up a requisition in the next week or so. If you know anyone that is interested in a genomic bioinformatics position at Illumina in San Diego please have them contact me. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist II Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com/> Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] Fwd: looking for an associate
by Jacobson, Matt 18 Jan '13

18 Jan '13

Begin forwarded message: From: Tack <idkz(a)comcast.net<mailto:idkz@comcast.net>> Subject: Fwd: looking for an associate Date: January 18, 2013 9:53:08 AM PST To: Matt Jacobson <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, Brian Shoichet <bshoichet(a)gmail.com<mailto:bshoichet@gmail.com>>, Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>> Jose is a former UCSF/Kuntz Group graduate student who is a research analyst based in SF. tack Begin forwarded message: From: "Jose Haresco" <JHaresco(a)jmpsecurities.com<mailto:JHaresco@jmpsecurities.com>> Date: January 17, 2013 1:43:44 PM PST To: "'idkz(a)comcast.net<mailto:'idkz(a)comcast.net>'" <idkz(a)comcast.net<mailto:idkz@comcast.net>> Subject: looking for an associate Hi Tack, I hope this reaches you well. I was wondering if you could pass this on to any late-stage grad students. I'm looking for an associate. Our firm is on a growth trajectory and we are expanding the group. The job description is below. Interested applicants can contact me directly. Sincerely, Jose Title: Associate Equity Research Analyst, Medical-Devices and Molecular Diagnostics Location: San Francisco Keywords: equity analyst, medical devices, sell-side, buy-side, equity research The incumbent will support senior Equity Research Analysts by compiling data and formulating analysis and opinions to be used in buy/sell/hold recommendations. Specific responsibilities include financial model building, competitive analysis, market research, and company research. Candidate must be knowledgeable and proficient in working with clinical trials, researching and summarizing academic journal articles, analyzing scientific data, as well as creating comprehensive financial statements and have the ability to construct bottom-up income statements, balance sheets, and statements of cash flow. Ideally, the candidate will have experience in relevant to the medical device industry. Essential Function/Duties: 1. Develop financial models to forecast growth and profitability opportunities for publicly traded equity investments. This includes financial statement analysis, historical and projected, profitability metrics, margin analysis, and various ratio analyses. Perform valuation analysis such as discounted cash flow analysis, discount models, and other valuation calculations including, but not limited to, earnings, sales, cash flow and tangible book. 2. Assist Analysts with compilation and evaluation of all relevant research and information pertaining to equity investment ideas, their respective markets and their competitors, customers, suppliers and any other entities which might have a meaningful impact on a company’s financial outcomes. Relevant research and information comes from a variety of sources including scientific literature, industry conferences, company filings and meetings with company management, independent research firms, financial news sources and government and industry organizations. 3. Maintain and ensure accuracy of financial models, analyses and archives. Compile clinical research data across specific indications. Synthesize and summarize scientific publications. Provide summary of earnings conference calls to Analysts to assist in evaluating recent company performance. Disseminate information to internal departments as applicable. Minimum Qualifications: • Master's Degree in Bioengineering, Genetics, Nursing, Biostatistics, or a related life science field. Bachelor's degree may be considered if candidate has exceptional work experience in the field of healthcare equity research, clinical research, management consulting, or business development/marketing in healthcare fields • Position requires demonstration of excellent quantitative and analytical skill. While formal training in accounting or finance is not required, the applicant must have substantial experience using Microsoft Excel. • Advanced computer skills using Microsoft Office, with particular expertise in Excel, Word, & Powerpoint Programming experience with C++, Visual Basic, or Python helpful, but not required. • Strong verbal and writing skills. A writing sample will be required Visit us at http://www.jmpsecurities.com<http://www.jmpsecurities.com/> IMPORTANT NOTICES: This message is intended only for the addressee. If you are not the intended recipient, please notify the sender by e-mail reply. Additionally, you may not copy, disclose, distribute or otherwise make use of this message or its contents for yourself or for any other person as that action may be unlawful. ORDERS AND INSTRUCTIONS: JMP Securities ("JMP") does not accept action oriented, time sensitive instructions or transactions orders via e-mail. Such orders and/or instructions will not be accepted by JMP, and JMP will not be responsible for carrying out such orders or instructions, including orders to purchase and sell securities. CONFIDENTIALITY AND PRIVACY: JMP reserves the right to monitor and review the content of all e-mail communications sent and/or received by its employees. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] 1/24/13 Seminar with Wenying Shou
by Nicole Takesono Flowers 18 Jan '13

18 Jan '13

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 Wenying Shou Fred Hutchinson Cancer Center War and Peace: a biological basis for population segregation and mixing January 24, 2013 W. Marshall, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Bioinformatics Requisition at ILMN San Diego
by Andrej Sali 18 Jan '13

18 Jan '13

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Chorny, Ilya" <ichorny(a)illumina.com> > Subject: Bioinformatics Requisition at ILMN San Diego > Date: January 18, 2013 8:30:23 AM PST > To: "babbitt(a)cgl.ucsf.edu" <babbitt(a)cgl.ucsf.edu>, "Matt.Jacobson(a)ucsf.edu" <Matt.Jacobson(a)ucsf.edu>, "sali(a)salilab.org" <sali(a)salilab.org> > > Hi All, > > The group that I am in is opening up a requisition in the next week or so. If you know anyone that is interested in a genomic bioinformatics position at Illumina in San Diego please have them contact me. > > Thanks, > > Ilya > > > Ilya Chorny Ph.D. > Bioinformatics Scientist II > Illumina, Inc. > 9885 Towne Centre Drive > San Diego, CA 92121 > Work: 858.202.4582 > Email: ichorny(a)illumina.com > Website: www.illumina.com > >

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[Compbio-allhands] Fwd: CCL: CSA Trust Grant 2013 - Call for Applications
by Elaine Meng 16 Jan '13

16 Jan '13

Begin forwarded message: > From: "Rajarshi Guha rajarshi.guha . gmail.com" <owner-chemistry(a)ccl.net> > Date: January 16, 2013 1:13:03 PM PST > To: "Meng, Elaine -id#3ma-" <meng(a)cgl.ucsf.edu> > Subject: CCL: CSA Trust CSA Trust Grant 2013 - Call for Applications > Reply-To: "CCL Subscribers" <chemistry(a)ccl.net> > > On behalf of the CSA Trust. (Also see http://www.csa-trust.org/?page_id=9) > > > > Applications Invited for CSA Trust Jacques-Émile Dubois Grants for 2013. > > The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research. In support of its charter, the Trust has created a unique Grant Program, renamed in honor of Professor Jacques-Émile Dubois who made significant contributions to the field of cheminformatics. The Trust is currently inviting the submission of grant applications for 2013. > > Purpose of the Grants: > The Grant Program has been created to provide funding for the career development of young researchers who have demonstrated excellence in their education, research or development activities that are related to the systems and methods used to store, process and retrieve information about chemical structures, reactions and compounds. A Grant will be awarded annually up to a maximum of ten thousand U.S. dollars ($10,000). Grants are awarded for specific purposes, and within one year each grantee is required to submit a brief written report detailing how the grant funds were allocated. Grantees are also requested to recognize the support of the Trust in any paper or presentation that is given as a result of that support. > > Who is Eligible? > > Applicant(s), age 35 or younger, who have demonstrated excellence in their chemical information related research and who are developing careers that have the potential to have a positive impact on the utility of chemical information relevant to chemical structures, reactions and compounds, are invited to submit applications. While the primary focus of the Grant Program is the career development of young researchers, additional bursaries may be made available at the discretion of the Trust. All requests must follow the application procedures noted below and will be weighed against the same criteria. > > Which Activities are Eligible? > Grants may be awarded to acquire the experience and education necessary to support research activities; e.g. for travel to collaborate with research groups, to attend a conference relevant to one’s area of research, to gain access to special computational facilities, or to acquire unique research techniques in support of one’s research. > > Application Requirements: > Applications must include the following documentation: > > > A letter that details the work upon which the Grant application is to be evaluated as well as details on research recently completed by the applicant; > The amount of Grant funds being requested and the details regarding the purpose for which the Grant will be used (e.g. cost of equipment, travel expenses if the request is for financial support of meeting attendance, etc.). The relevance of the above-stated purpose to the Trust’s objectives and the clarity of this statement are essential in the evaluation of the application); > A brief biographical sketch, including a statement of academic qualifications; > Two reference letters in support of the application. Additional materials may be supplied at the discretion of the applicant only if relevant to the application and if such materials provide information not already included in items 1-4. Three copies of the complete application document must be supplied for distribution to the Grants Committee. > Deadline for Applications: > Applications must be received no later than March 14, 2013. Successful applicants will be notified no later than May 2, 2013. > > Address for Submission of Applications: > Three copies of the application documentation should be forwarded to: Bonnie Lawlor, CSA Trust Grant Committee Chair, 276 Upper Gulph Road, Radnor, PA 19087, USA. If you wish to enter your application by e-mail, please contact Bonnie Lawlor at blawlor(~)nfais.org prior to submission so that she can contact you if the e-mail does not arrive. > > > > -- > Rajarshi Guha | http://blog.rguha.net > NIH Center for Advancing Translational Science

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[Compbio-allhands] 1/17/13 Comp Together seminar with Prof. Brian Shoichet
by Siegfried Leung 16 Jan '13

16 Jan '13

Talk title: Polypharmacology: A Feature, Not A Bug? Speaker: Prof. Brian Shoichet, UCSF Date: 2013-01-17 Time: 18:00:00 Location: UCSF Mission Bay 600 16th St. Byers Hall, Room 212 San Francisco, CA 94158 Schedule: 6 -- 7 pm: check-in & networking (pizza and wine provided) 7 -- 8 pm: presentation 8 -- 8:30 pm: informal discussions & networking Talk Abstract: Protein classification typically uses structural, sequence, or functional similarity. Here we explore an organization by ligand similarity, focusing on class A GPCRs. Comparing a ligand-based and sequence-based dendograms, we identified GPCRs that were distantly linked by sequence but neighbors by ligand similarity. Experimental testing of the ligands predicted to link three of these new pairs confirmed the predicted association, with potencies ranging from the low-nanomolar to low-micromolar. We also predicted hundreds of non-GPCRs closely related to GPCRs by ligand similarity, including the CXCR2 chemokine receptor to casein kinase I, the cannabinoid receptors to epoxide hydrolase 2, and the ?2 adrenergic receptor to phospholipase D, which we confirmed experimentally. Ligand similarities among these targets may reflect the conservation of identical ligands among unrelated receptors, which signal in different time domains. The method integrates these apparently unrelated receptors into chemically coherent circuits, and suggests which of these receptors may be targeted by individual ligands.

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[Compbio-allhands] BBC Journal Club, January 22nd
by Bass, Karche 16 Jan '13

16 Jan '13

BBC Journal Club BP-BMI-CCB Tuesday, January 22nd, 10:45am-GH Auditorum Patrick Harrigan Lauschke VM., et. al. Scaling of embryonic patterning based on phase-gradient encoding. Nature, 493(7430); 101-5 (2013) Weihan Li Locke JC., et. al. Stochastic Pulse Regulation in Bacterial Stress Response Science. Science, 334(6054):366-9. (2011) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles S. Craik, Susan Miller, and Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0523 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Fwd: Open Genentech internship position in the Bioinformatics & Computational Biology Department
by Andrej Sali 15 Jan '13

15 Jan '13

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Christina Chaivorapol <chaivorapol.christina(a)gene.com> > Subject: Open Genentech internship position in the Bioinformatics & Computational Biology Department > Date: January 16, 2013 6:31:33 AM GMT+01:00 > To: sali(a)salilab.org > > Hi Andrej, > > Happy New Year. I hope you are doing well. I am looking for a computational biology intern. Could you please circulate the following internship position at UCSF to graduate students who may be interested in a computational biology internship at Genentech? > > Thanks, > Christina > > Opening for a Genentech internship position in the Bioinformatics & Computational Biology department > ---------------------------------- > An internship at Genentech is a great way to get exposure to scientific research in an industry setting and meet industry folks from various departments at Genentech. > > The intern will focus on analyzing a large-scale sequencing data set in patients with lupus (an autoimmune disease that affects millions of people worldwide). The primary goals are to: > 1) compile a database of public non-coding RNAs from various sources > 2) explore existing R statistical methods and/or develop statistical methods to query differential expression of non-coding RNAs > 3) apply the database and the appropriate statistical methods to analyze differences in expression of non-coding RNAs across various subsets to further understand disease pathogenesis > 4) use (if time permits) public and in-house computational methods to understand function and pathways > > Requirements: > 1) Proficiency in high-level programming languages is essential (preferably in R), and a working knowledge of the UNIX operating system and version control systems (e.g. SVN) is desirable > 2) Strong knowledge of biology required, immunology a plus > 3) Experience with next generation sequencing data is preferred > 4) Ph.D. candidate in Computational Biology, Bioinformatics, or related field > > All interested candidates should send their CV to chrichai(a)gene.com. > -- > Christina Chaivorapol, Ph.D. > Genentech, Inc. > Bioinformatics & Computational Biology > phone: 650-225-6903 > chrichai(a)gene.com

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[Compbio-allhands] Junior faculty tenure-track position at U Michigan
by Katrina Lexa 14 Jan '13

14 Jan '13

The University of Michigan Department of Medicinal Chemistry is currently looking to fill two junior positions, and they are particularly interested in someone with a computational chemistry background. For those interested, they would need a CV and proposal by the end of this week. The general advertisement is here: http://umjobs.org/job_detail/75392/asst_professor Katrina Lexa Postdoctoral Fellow, UCSF 408.859.6993 katrina.lexa(a)ucsf.edu

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[Compbio-allhands] 1/17/13 Seminar with David Odde
by Nicole Takesono Flowers 14 Jan '13

14 Jan '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 David Odde University of Minnesota Microtubule self-assembly kinetics January 17, 2013 W. Marshall & D. Mullins, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: AMMA: positions and funding for young researchers
by Andrej Sali 13 Jan '13

13 Jan '13

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Elizabeth Yuriev <Elizabeth.Yuriev(a)monash.edu> > Subject: AMMA: positions and funding for young researchers > Date: January 14, 2013 5:02:26 AM GMT+01:00 > Cc: "RecruitmentTeam-VIC(a)csiro.au" <RecruitmentTeam-VIC(a)csiro.au> > > Dear AMMA members, > > Happy New Year to you all. > > Please see below for: > > 1. CSIRO Graduate Fellow Program 2013 – positions in Sydney, Melbourne and Perth (Applications Close: 23 January 2013) > http://csiro.nga.net.au/?jati=d251656b-4a4d-5dac-42f7-6e3e5f1aa6c3 > > 2. CSA Trust Grant > See attachment > > Cheers, > Elizabeth > > ************ > Dr Elizabeth Yuriev > Senior Lecturer > Faculty of Pharmacy and Pharmaceutical Sciences > Medicinal Chemistry and Drug Action > Monash Institute of Pharmaceutical Sciences > Monash University (Parkville Campus) > 381 Royal Parade, Parkville VIC 3052, Australia > Tel: Int +61 3 9903 9611, Fax: +61 3 9903 9143 > E-mail: elizabeth.yuriev(a)monash.edu > www.pharm.monash.edu.au >

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[Compbio-allhands] Michael Grabe
by Jacobson, Matt 11 Jan '13

11 Jan '13

All, Michael Grabe from Pitt is doing a sabbatical here at UCSF, hosted by Bill DeGrado ... just want to make sure everyone knows this, so relevant people can interact with him. Research interests in computational membrane biophysics (roughly speaking) http://mgrabe1.bio.pitt.edu/publications.html I've cc'ed him here in case you want to contact him -- Matt Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] BBC Journal Club, January 15th
by Bass, Karche 09 Jan '13

09 Jan '13

BBC Journal Club, January 15th, 10:45 am Genentech Hall Auditorium Juan Perez Bermejo Hayashi, K., et. al. "For a fistful of frost." Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells. Cell, 146, pp. 519-532. (2011) Diego Garrido Ruiz Gorbunova , V. et. al. Cancer resistance in the blind mole rat is mediated by concerted necrotic cell death mechanism. PNAS, vol. 109 no. 47 19392-19396. (2012) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles Craik, Susan Miller, Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0943 | 7: 415-502-4690 | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] 1/10/13 Seminar with Susan Marqusee
by Nicole Takesono Flowers 04 Jan '13

04 Jan '13

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 Susan Marqusee UC Berkeley Sequence Determinants of a Protein's Energy Landscape January 10, 2013 H. Lim, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] BBC Journal Club, January 8th
by Bass, Karche 02 Jan '13

02 Jan '13

BBC Journal Club BP-BMI-CCB Tuesday, January 8th, 10:45am-GH Auditorium Alex Pankov Weeden, VJ, et. al. The Geometric Structure of the Brain Fiber Pathways. Science, Volume 335, No. 6076, pp. 1628-1634 (2012) Kate Southard Bacchus, W., et. al. Synthetic two-way communication between mammalian cells. Nature Biology, vol. 30 ,pp. 991-996 (2012) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles S. Craik, Susan Miller, and Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0523 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Fwd: open rank faculty position
by Andrej Sali 22 Dec '12

22 Dec '12

Sent from my iPhone Begin forwarded message: > From: Sergei Sheiko <sergei(a)email.unc.edu> > Date: December 22, 2012, 7:16:56 AM PST > To: Sergei Sheiko <sergei(a)email.unc.edu>, s.sacanna(a)nyu.edu, s.t.meikle(a)bton.ac.uk, s72k(a)hotmail.com, sa.ravishankar(a)cytec.com, sa454(a)georgetown.edu, saadink(a)umd.edu, saarloos(a)lorentz.leidenuniv.nl, saavedra(a)u.arizona.edu, sabatini(a)ou.edu, Sabine.Klapp(a)fluids.tu-berlin.de, sabrinaleslie(a)gmail.com, saburo(a)ph.tokushima-u.ac.jp, sac12(a)meadwestvaco.com, sacarter(a)ucsc.edu, sachdev(a)physics.harvard.edu, sachiko(a)phys.chs.nihon-u.ac.jp, sachinkinge(a)yahoo.com, sadhal(a)usc.edu, sae6z(a)virginia.edu, saeed.mohseni(a)wacker.com, saeedt(a)ucr.edu, safinya(a)mrl.ucsb.edu, safinyaweb(a)mrl.ucsb.edu, sagisaka(a)cc.hirosaki-u.ac.jp, saika(a)mun.ca, sakurada(a)apchem.gifu-u.ac.jp, sal2(a)emory.edu, saleh(a)engineering.ucsb.edu, sali(a)salilab.org, salis(a)psu.edu, salsbufr(a)wfu.edu > Subject: open rank faculty position > > Dear Colleagues, > > The Department of Chemistry at the University of North Carolina-Chapel Hill invite applications for an open rank faculty position. Areas of interest include bio-inspired materials, polymers, colloids, gels, rheology, and scattering. We would appreciate you very much if you forward this email to your colleagues, students, and postdocs who might be interested in this position. Review of applications will begin in January 2013. > > Applicants should submit a SINGLE PDF containing a cover letter, curriculum vita, research plan, and teaching statement to: http://jobs.unc.edu/2501212. Applicants should also arrange to have four pdf letters of recommendation sent electronically to chemsearch(a)unc.edu with a subject line Applied Sciences Search. > > Sincerely Yours, > > Sergei > > ______________________________________ > > Sergei S. Sheiko, PhD. > George A. Bush Jr. Distinguished Professor > Department of Chemistry CB# 3290, Caudill Laboratories, Rm. 157 > University of North Carolina at Chapel Hill Chapel Hill, NC 27599-3290 > OFFICE: (919) 843-5270 > FAX: (919) 962-2388 > E-MAIL:sergei@email.unc.edu > http://www.chem.unc.edu/people/faculty/sheikoss/sssindex.html

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[Compbio-allhands] Fwd: Oxford Summer Project 2013
by Andrej Sali 18 Dec '12

18 Dec '12

Sent from my iPhone Begin forwarded message: > From: Madeline Mitchell <madeline.mitchell(a)stats.ox.ac.uk> > Date: December 18, 2012, 7:33:15 AM PST > To: "maddy mitchell (mitchell(a)stats.ox.ac.uk)" <mitchell(a)stats.ox.ac.uk> > Subject: Oxford Summer Project 2013 > > Dear Colleague > I should be grateful if you could please pass the attached information on to anyone you think might be interested. > Many thanks > Maddy > (on behalf of Professor Jotun Hein) > > P.S. I apologise for any cross-posting > > > > We are looking for summer students to join us in a project-based summer school in Computational Biology, taking place from 8th July – 16th August 2013. > > Applications are invited from students with a strong background in mathematics, statistics, computer science, physics or chemistry, who have completed at least two years of undergraduate study. > > For more information see the attached flyer, and visit www.stats.ox.ac.uk/research/genome/summer_school > > Kind regards > > > Maddy > > Madeline Mitchell > PA to Professor Jotun Hein, Professor Chris Holmes & > Group Secretary, (Professor Peter Donnelly FRS FMedSci (WTCHG): PA +44 1865 287725) > Department of Statistics > University of Oxford > 1 South Parks Road > Oxford OX1 3TG > tel. (0)1865 285386: fax. (0)1865 285384 > email: mitchell(a)stats.ox.ac.uk > www.stats.ox.ac.uk > > >

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[Compbio-allhands] Fwd: [3dem] two positions available in computational electron cryo-microscopy
by Andrej Sali 18 Dec '12

18 Dec '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: <martyn.winn(a)stfc.ac.uk> > Subject: [3dem] two positions available in computational electron cryo-microscopy > Date: December 18, 2012 2:15:52 AM PST > To: <3dem(a)ncmir.ucsd.edu> > > The Research Complex at Harwell, Oxfordshire, UK hosts a growing number of computational scientists supporting a wide range of structural biology research. We have two vacancies for enthusiastic scientists with experience of computational methods to join the group. You will join one of two projects, both concerned with exploiting the recent growth in the application of electron cryo-microscopy (cryo-EM) to structural and cellular biology. > > Post 1: The European infrastructure project BioMedBridges (http://www.biomedbridges.eu) is constructing an e-infrastructure to allow interoperability between data and services in the biological, medical, translational and clinical domains. This post will contribute to Work Package 9 of Biomedbridges, which is a Use Case illustrating sharing of cryoEM data between structural biologists and biological database providers. You will create software for analysing, comparing and annotating cryoEM maps, in collaboration with developers at the EBI. > > Post 2: We seek an experienced scientist with an interest in software development, to work alongside the current project developer, on the Collaborative Computational Project for cryoEM (http://www.ccpem.ac.uk) You will be responsible for developing the CCP-EM software suite, in collaboration with application developers in the consortium, as well as developing and promoting community standards. > > Both posts will be located at the Research Complex at Harwell, within the Computational Biology group of Martyn Winn in the Scientific Computing Department of STFC. Further information is available online (see http://www.ccpem.ac.uk/positions.php and links to TopCareer site), and informal enquiries may be made to Martyn Winn martyn.winn(a)stfc.ac.uk > > * > * Dr. Martyn Winn > * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. > * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH) > * E-mail: martyn.winn(a)stfc.ac.uk Skype: martyn.winn > * > > > > -- > Scanned by iCritical. > _______________________________________________ > 3dem mailing list > 3dem(a)ncmir.ucsd.edu > https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem

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[Compbio-allhands] SAVE THE DATE- PETER A. KOLLMAN LECTURESHIP - February 14, 2013
by Nicole Takesono Flowers 17 Dec '12

17 Dec '12

SAVE THE DATE- THURSDAY, FEBRUARY 14, 2013 AT 12:00PM PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS. ROOM S161 Reception in Byers Hall 5th Floor Lounge at 3:30 Please see attached flyer. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Open Positions: ELBE Postdoc Program in Dresden
by Andrej Sali 30 Nov '12

30 Nov '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Gene Myers <myers(a)mpi-cbg.de> > Subject: Open Positions: ELBE Postdoc Program in Dresden > Date: November 30, 2012 6:38:35 AM PST > To: undisclosed-recipients:; > > Dear colleague, > > The Max-Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG) and the MPI for the Physics of Complex Systems (MPI-PKS) in Dresden have formed a new Systems Biology Center that is particularly focused on combining genomics, image-based, and bio-physical approaches. > We are beginning the first cycle of a fully-funded postdoctoral program and are seeking applicants. > > We kindly ask you to bring the attached one-page announcement to the attention of your students. > > Best regards, > Gene Myers > Founding Director, The Systems Biology Center at Dresden > > > Dr. Gene Myers, Director > Tschira Chair of Systems Biology > Max-Planck Institute of > Molecular Cell Biology & Genetics > Pfotenhauerstr. 108 > 01307 Dresden > > Tel: +49 351 210-1220 > Fax: +49 351 210-1209 > > > > >

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[Compbio-allhands] BBC Journal Club, December 4th
by Bass, Karche 29 Nov '12

29 Nov '12

BBC Journal Club BP-BMI-CCB Tuesday, December 4th at 10:45am-GH Auditorium Tara Friedrich Schmidt D, et. al. Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages. Cell, Volume 148, Issue 1, 335-348 (2012) Kay Aull Zhang Y, et. al. Structural Basis of Transcription Initiation. Science, vol. 338 no. 6110 pp. 1076-1080 (2012) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles S. Craik, Susan Miller, and Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0523 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Nodality is hiring...
by Schnoes, Alexandra 26 Nov '12

26 Nov '12

FYI, Nodality, who just hired Alan Barber from the Babbitt lab (and has at least two other UCSF alums that I know of) is looking for a computational biologist/bioinformatics scientist. http://www.nodality.com/company/careers/openings/scientist-bioinformatics.p… -- Alexandra Schnoes, PhD Program Coordinator Graduate Student Internships for Career Exploration (GSICE) University of California San Francisco 513 Parnassus Ave, S-224 Campus Box 0410 San Francisco, CA 94143 Tel: 415-476-0572 Fax: 415-476-0689 Email: alexandra.schnoes(a)ucsf.edu<mailto:alexandra.schnoes@ucsf.edu> Web: http://gsice.ucsf.edu<http://gsice.ucsf.edu/>

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[Compbio-allhands] 11/29/12 Seminar with Sunny Xie
by Nicole Takesono Flowers 26 Nov '12

26 Nov '12

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 Sunny Xie Harvard University Life at the Single Molecule Level November 29, 2012 D. Burkhardt, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] BBC Journal Club, November 27th
by Bass, Karche 21 Nov '12

21 Nov '12

BBC Journal Club BP-BMI-CCB November 27th at 10:45am in GH Auditorium Nicole Olson Choi, I., et. al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature, 488, pp. 621-626 (30 August 2012) Jack Yue Bencherif SA, et. al. Injectable preformed scaffolds with shape-memory properties. Proc Natl, (2012) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles S. Craik, Susan Miller, and Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0523 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] 11/28/12 Seminar with Greg Verdine **OFF DATE & TIME**
by Nicole Takesono Flowers 21 Nov '12

21 Nov '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems 4 pm Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Greg Verdine Harvard University Cancer Chemical Biology Wednesday, November 28, 2012 J. Wells, Host **Please note this is an off date and time seminar** BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: PhD position in bioinformatics
by Andrej Sali 20 Nov '12

20 Nov '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: damien.devos(a)cos.uni-heidelberg.de > Subject: PhD position in bioinformatics > Date: November 20, 2012 7:33:42 AM PST > To: Michael.Rout(a)rockefeller.edu, sali(a)salilab.org, mfiedl(a)mac.com > Cc: avalencia(a)cnio.es > > Dear colleagues, thanks to publicize the available position in my lab, purely in bioinformatics: > > https://hbigs.system08.de/intern/projectspub_project_for.php?a=030000294000… > > Please let me know if you know anyone that could be interested. > Best wishes > > Damien > > **************** > Damien Devos > Center of Organismal Studies > Ruprecht-Karls-Universitat > Im Neuenheimer Feld 230 > 69120 Heidelberg, Germany > Tel: +49 (0) 6221 546254 > > > >

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[Compbio-allhands] Fwd: Research Cluster Grant Announced by Silicon Mechanics
by Tom Ferrin 14 Nov '12

14 Nov '12

From: Art Mann <research-grant(a)siliconmechanics.net<mailto:research-grant@siliconmechanics.net>> Reply-To: Art Mann <research-grant(a)siliconmechanics.net<mailto:research-grant@siliconmechanics.net>> Date: Monday, November 12, 2012 11:09 AM To: Jeff Bluestone <jeff.bluestone(a)ucsf.edu<mailto:jeff.bluestone@ucsf.edu>> Subject: Research Cluster Grant Announced by Silicon Mechanics Silicon Mechanics Announces Our Second Annual Research Cluster Grant We are pleased to again announce our sponsorship of a unique grant opportunity: A complete High Performance Compute Cluster using the latest AMD Opteron processors and NVIDIA GPUs Silicon Mechanics, a leading manufacturer of rackmount servers, storage systems, and high-performance computing solutions, is dedicated to building relationships and collaborating with professors and researchers at universities and other research institutions Last year’s Research Cluster Grant recipient, Saint Louis University, is already making productive use of their cluster, www.siliconmechanics.com/i43744/research-cluster-grant-winners-circle.php<http://www.siliconmechanics.com/i43744/research-cluster-grant-winners-circl…> This grant program is open to all US and Canadian qualified post-secondary institutions, university-affiliated research institutions, non-profit research institutions, and researchers at federal labs with university affiliations. Submissions will be reviewed for merit and related impacts. Further details on the grant rules and the technical specifications of the cluster itself are available at: http://www.siliconmechanics.com/i43822/Research+Cluster+Grant+Information.p… We hope you will consider this opportunity to support your research by submitting a proposal, or by forwarding this to others in your department who could benefit through this grant. If you have any questions, please do not hesitate to contact us at research-grant(a)siliconmechanics.com<mailto:research-grant@siliconmechanics.com>. Best regards, Art Mann Education/Research/Gov't Vertical Group Manager Silicon Mechanics 425-420-1285 artm(a)siliconmechanics.com<mailto:artm@siliconmechanics.com> Silicon Mechanics wishes to thank our partners who have helped make this grant possible: AMD · NVDIA · Mellanox · Supermicro · Seagate · Kingston Technology · Bright Computing <http://www.siliconmechanics.com/i42364/Lunch+and+Learn+Registration.php> This message was sent to you by Silicon Mechanics. We are located at 22029 23rd Dr SE, Bothell WA 98021. If you would prefer not to get any further mailings, please click here<https://www.siliconmechanics.com/mailtool/unsub.php?magic=ykrFfdI1iN1SWsyel…>.

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[Compbio-allhands] BBC Journal Club, November 20th
by Bass, Karche 14 Nov '12

14 Nov '12

BBC Journal Club BP-BMI-CCB Tuesday, November 20th, 10:45am; Genentech Hall Auditorium Ben Spangler Mi Hyeon Cho, et. al., A magnetic switch for the control of cell death signaling in in vitro and in vivo systems. Nature Materials DOI: 10.1038/NMAT3430; (2012) Peter Fellowes Cambell, KL, et. al., Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nature Genetics: 42(6):536-40; (2010) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles S. Craik, Susan Miller, and Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0523 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] 11/15/12 Seminar with Robert Lamb
by Nicole Takesono Flowers 09 Nov '12

09 Nov '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Robert Lamb Northwestern University Activating protein re-folding to cause paramyxovirus-mediated membrane fusion November 15, 2012 W. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] BBC Journal Club, November 13th
by Bass, Karche 07 Nov '12

07 Nov '12

BBC Journal Club (BP-BMI-CCB) Tuesday, November 13th at 10:45am in GH Auditorium Amy Chang Douglas, S.m., et. al., A logic-gated nanorobot for targeted transport of molecular payloads. Science. 335(6070):831-4; (2012) Daniel Hemmelstein Reid, C.R., et. al, Slime mold uses an externalized spatial "memory" to navigate in complex environments. Proc Natl Acad Sci U S A. 109(43):17490-4 (2012) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles Craik, Susan Miller, Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0943 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] 11/8/12 Seminar with Doug Lauffenberger
by Nicole Takesono Flowers 02 Nov '12

02 Nov '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Doug Lauffenberger MIT In Vivo Systems Analysis of Cell-Cell Communication and Signaling in Inflammation November 8, 2012 K. Giacomini, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Insight Data Science Fellows Program - applications open for 2013
by Schnoes, Alexandra 01 Nov '12

01 Nov '12

The Insight Data Science Fellows Program is accepting applications for its second season. ===================== Insight Data Science Fellows Program Applications now open for 2013 http://insightdatascience.com<http://insightdatascience.com/> Silicon Valley technology companies are hiring data scientists to help them glean insights from the terabytes of data that they collect everyday. The Insight Data Science Fellows Program<http://insightdatascience.com/> is a postdoctoral training fellowship designed to bridge the gap between academia and a career in data science. Insight highlights: * 6 week fellowship in Palo Alto, CA includes tuition scholarship and a $5,000 living expense reimbursement. * 100% placement rate for Insight Fellows who completed job search in 2012. * Insight Fellows are now data scientists at LinkedIn, Facebook, Google, Twitter, Square, Microsoft and other top tech companies. For more information and to apply for the January, June and August 2013 sessions, please visit: http://insightdatascience.com<http://insightdatascience.com/> ===================== Please feel free to forward this to any appropriate mailing lists or to anyone who might be a good candidate for the Fellows Program. Also, if anyone has any questions please have them email me directly at jake(a)insightdatascience.com<mailto:jake@insightdatascience.com>. Many thanks, Jake --- Jake Klamka Founder, Insight

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Re: [Compbio-allhands] Visit from Jerry Tsai
by Jacobson, Matt 01 Nov '12

01 Nov '12

Forwarding this to the compbio listserv -- Matt Sent from my iPad On Nov 1, 2012, at 4:35 PM, "Brett T. Hannigan" <brett.hannigan(a)gmail.com<mailto:brett.hannigan@gmail.com>> wrote: Hi Dr. Jacobson, Dr. Sali, and Dr. Kortemme, I'm a PhD student in the DeGrado lab, and just wanted to let you guys know of a seminar that we have planned for next Tuesday, November 6th and 10:00 am. We will be hosting Dr. Jerry Tsai from the University of the Pacific, and he will be delivering a talk titled "An Amino Acid Code for Protein Structure." You can find his lab's website here: http://tsailab.chem.pacific.edu/ The seminar is currently scheduled to be held on the first floor of CVRI, in room SC159. We'd love to see anyone from your lab that is interested in coming. -Brett -- ****************************************** Brett T. Hannigan Belmont, CA brett.hannigan(a)gmail.com<mailto:brett.hannigan@gmail.com> ******************************************

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[Compbio-allhands] BBC Journal Club, November 6th
by Bass, Karche 31 Oct '12

31 Oct '12

BBC Journal Club (Tuesday, November 6- 10:45 am - GH Auditorium) Greg Fedewa Borodovka A., et. al., Evidence that viral RNAs have evolved for efficient, two-stage packaging. PNAS; vol 109 no. 39; (2012) Louise Goupil Frei AP., et. al,. Direct identification of ligand-receptor interactions on living cells and tissues. Frei et al. Nature Biotechnol; doi: 10.1038/nbt.2354; (2012) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles Craik, Susan Miller, Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0943 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Fwd: Postdoc position "Data Analysis" open at EMBL
by Andrej Sali 25 Oct '12

25 Oct '12

Sent from my iPhone Begin forwarded message: > From: Nina Papritz <assocdir(a)embl.org> > Date: October 25, 2012, 4:43:29 AM PDT > Cc: Matthias Hentze <hentze(a)embl.de>, Wolfgang Huber <whuber(a)embl.de> > Subject: Postdoc position "Data Analysis" open at EMBL > > Dear colleague, > > In my group at EMBL, we have a very interesting opening for a post-doc in the area of data analysis (see attached). The successful candidate will be included into the "wet-lab" projects of the Hentze group and be co-mentored by Wolfgang Huber. > > I would be very grateful if you could forward the ad to people that might be interested in such a position. > > Please feel free to contact me in case you have questions. > > Thank you very much! > > With kind regards, > Matthias > > > -- > Prof. Matthias W. Hentze, M.D. > Associate Director > European Molecular Biology Laboratory (EMBL) > Meyerhofstrasse 1 > 69117 Heidelberg > Germany > Tel: +49-(0)6221-387 8501 > Fax: +49-(0)6221-387 8144 > E-mail: hentze(a)embl.de

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[Compbio-allhands] BBC Journal Club, October 30th
by Bass, Karche 24 Oct '12

24 Oct '12

[BBC Journal Club] [BP * BMI * CCB] [Tuesday, October 30- 10:45 am - GH Auditorium] [Ben Heineike Thurman RE, et al. The accessible chromatin landscape of the human genome. Nature. 489(7414):75-82. doi: 10.1038/nature11232. 2012. Kyle Kundert Shiou Tzeng, et. al. Protein activity regulation by conformational entropy. Nature 488:236-240. 2012.] Karché K. Bass Karché K. Bass | Administrative Analyst Asst. to John D. Gross, Charles S. Craik, Susan Miller, and Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0523 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] 10/24/12 Braisted Lecture with Stuart Schreiber
by Nicole Takesono Flowers 19 Oct '12

19 Oct '12

UCSF-UCB Andrew Braisted Award Lectureship Stuart Schreiber, Ph.D. Howard Hughes Medical Institute Broad Institute of Harvard & MIT Harvard University, Department of Chemistry & Chemical Biology Cancer genetic dependencies targeted by small molecules Wednesday, October 24, 2010 4 pm Genentech Hall Byers Auditorium UCSF Mission Bay Campus Simulcast to Parnassus, Room 161 Reception in 1st Floor Atrium following talk Contact: Jim Wells, Charles Craik Sponsor: The Andrew Braisted Lecture Fund Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] BBC Journal Club, October 23
by Bass, Karche 17 Oct '12

17 Oct '12

[BBC Journal Club] [BP * BMI * CCB] [Tuesday, October 23- 10:45 am - GH Auditorium] John Haliburton Thomas E Kuhlman, et. al. Gene location and DNA density determine transcription factor distributions in Escherichia coli. Molecular Systems Biology 8; 610; doi:10.1038/msb2012.42. 2012. Jordan Carelli Winter, GE., et. al. Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML. Nat Chem Biol. doi: 10.1038/nchembio.1085. 2012. Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles Craik, Susan Miller, Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0943 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Greg Bowman seminar, Monday Oct. 22, 10-11am: "Decrypting cryptic allosteric sites"
by David Sivak 16 Oct '12

16 Oct '12

Greg Bowman "Decrypting cryptic allosteric sites" Monday, Oct 22, 10-11am Genentech S204 Abstract: Cryptic allosteric sites--pockets in a folded protein that are invisible to conventional experiments but can alter enzymatic activity via allosteric communication with the active site--are a promising opportunity for facilitating drug design by greatly expanding the repertoire of available drug targets. Unfortunately, identifying these sites is difficult, typically requiring resource intensive screening of large libraries of small molecules. I will present recent advances in using Markov state models built from extensive computer simulations (totaling hundreds of microseconds of dynamics) to identify prospective cryptic sites from the equilibrium fluctuations of proteins like β-lactamase in the absence of any ligands. This approach reveals extensive conformational heterogeneity in folded proteins that could give rise to cryptic sites. Based on this observation, I hypothesized that cryptic sites should appear as high-energy (or low population) pockets adjacent to residues displaying correlated motions with the active site. I will show that these ingredients are sufficient to retrodict a known cryptic site in β-lactamase and, more importantly, predict the existence of a multitude of new sites. Finally, I will present the results of experimental tests supporting the existence of my new sites. Personal Web site: https://sites.google.com/site/gregoryrbowman/ -- David Sivak Systems Biology Fellow University of California, San Francisco david.sivak(a)gmail.com davidsivak.com 510-541-9006

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[Compbio-allhands] Fwd: On Behalf of Taekjip Ha and Klaus Schulten - PLEASE POST AND CIRCULATE
by Andrej Sali 15 Oct '12

15 Oct '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Flanegin, Susan A" <flanegin(a)illinois.edu> > Subject: On Behalf of Taekjip Ha and Klaus Schulten - PLEASE POST AND CIRCULATE > Date: October 15, 2012 10:04:08 AM PDT > To: "Flanegin, Susan A" <flanegin(a)illinois.edu> > Cc: "Yodh, Jaya G" <jyodh(a)illinois.edu>, "ralf.blossey(a)iri.univ-lille1.fr" <ralf.blossey(a)iri.univ-lille1.fr>, "ralf.seidel(a)biotec.tu-dresden.de" <ralf.seidel(a)biotec.tu-dresden.de>, "rama.ranganathan(a)utsouthwestern.edu" <rama.ranganathan(a)utsouthwestern.edu>, "Rao, Christopher V" <cvrao(a)illinois.edu>, "rao(a)cua.edu" <rao(a)cua.edu>, "rappel(a)physics.ucsd.edu" <rappel(a)physics.ucsd.edu>, "irasnik(a)physics.emory.edu" <irasnik(a)physics.emory.edu>, "ratner(a)northwestern.edu" <ratner(a)northwestern.edu>, "reevesme(a)gwu.edu" <reevesme(a)gwu.edu>, "lynne.regan(a)yale.edu" <lynne.regan(a)yale.edu>, "ribbeck(a)mit.edu" <ribbeck(a)mit.edu>, "ebright(a)waksman.rutgers.edu" <ebright(a)waksman.rutgers.edu>, "R.Bowater(a)uea.ac.uk" <R.Bowater(a)uea.ac.uk>, "anne.ridley(a)kcl.ac.uk" <anne.ridley(a)kcl.ac.uk>, "drissin(a)quanterix.com" <drissin(a)quanterix.com>, "kpritchie(a)purdue.edu" <kpritchie(a)purdue.edu>, "erittwe(a)gwdg.de" <erittwe(a)gwdg.de>, "mr(a)jhu.edu" <mr(a)jhu.edu>, "rw144(a)le.ac.uk" <rw144(a)le.ac.uk>, "susana.rocha(a)chem.kuleuven.be" <susana.rocha(a)chem.kuleuven.be>, "rodionov(a)nso.uchc.edu" <rodionov(a)nso.uchc.edu>, "srogers(a)bio.unc.edu" <srogers(a)bio.unc.edu>, "Antonina(a)mail.nih.gov" <Antonina(a)mail.nih.gov>, "r.tuma(a)leeds.ac.uk" <r.tuma(a)leeds.ac.uk>, "chalmers(a)nottingham.ac.uk" <chalmers(a)nottingham.ac.uk>, "michael.rosen(a)utsouthwestern.edu" <michael.rosen(a)utsouthwestern.edu>, "joel.rosenbaum(a)yale.edu" <joel.rosenbaum(a)yale.edu>, "jody.rosenblatt(a)hci.utah.edu" <jody.rosenblatt(a)hci.utah.edu>, "sr2327(a)columbia.edu" <sr2327(a)columbia.edu>, "rross(a)ucsd.edu" <rross(a)ucsd.edu>, "Eli.Rothenberg(a)nyumc.org" <Eli.Rothenberg(a)nyumc.org>, "rottapel(a)uhnres.utoronto.ca" <rottapel(a)uhnres.utoronto.ca>, "a.round(a)uea.ac.uk" <a.round(a)uea.ac.uk>, "roux(a)uchicago.edu" <roux(a)uchicago.edu>, "rouzi002(a)umn.edu" <rouzi002(a)umn.edu>, "ruderman(a)hms.harvard.edu" <ruderman(a)hms.harvard.edu>, "rudner(a)hms.harvard.edu" <rudner(a)hms.harvard.edu>, "rudy(a)wustl.edu" <rudy(a)wustl.edu>, "rueda(a)chem.wayne.edu" <rueda(a)chem.wayne.edu>, "valya(a)ou.edu" <valya(a)ou.edu>, "saffarian(a)physics.utah.edu" <saffarian(a)physics.utah.edu>, "safinya(a)mrl.ucsb.edu" <safinya(a)mrl.ucsb.edu>, "Sam.Safran(a)weizmann.ac.il" <Sam.Safran(a)weizmann.ac.il>, "saikrishnan(a)iiserpune.ac.in" <saikrishnan(a)iiserpune.ac.in>, "isaito(a)ims.u-tokyo.ac.jp" <isaito(a)ims.u-tokyo.ac.jp>, "ksogawa(a)riken.jp" <ksogawa(a)riken.jp>, "saleh(a)engineering.ucsb.edu" <saleh(a)engineering.ucsb.edu>, "sali(a)salilab.org" <sali(a)salilab.org>, "hsalman(a)pitt.edu" <hsalman(a)pitt.edu>, "tsalmon(a)email.unc.edu" <tsalmon(a)email.unc.edu>, "azadeh(a)brandeis.edu" <azadeh(a)brandeis.edu>, "samuel(a)physics.harvard.edu" <samuel(a)physics.harvard.edu>, "h.sanchezgonzalez(a)erasmusmc.nl" <h.sanchezgonzalez(a)erasmusmc.nl>, "tsanden(a)kth.se" <tsanden(a)kth.se>, "sandler(a)microbio.umass.edu" <sandler(a)microbio.umass.edu>, "vahid.sandoghdar(a)phys.chem.ethz.ch" <vahid.sandoghdar(a)phys.chem.ethz.ch>, "sangerjo(a)upstate.edu" <sangerjo(a)upstate.edu>, "mark.sansom(a)bioch.ox.ac.uk" <mark.sansom(a)bioch.ox.ac.uk>, "s.a.stratmann(a)rug.nl" <s.a.stratmann(a)rug.nl>, "s.miles(a)bristol.ac.uk" <s.miles(a)bristol.ac.uk>, "sarkarsk(a)mail.nih.gov" <sarkarsk(a)mail.nih.gov>, "ycsasaki(a)spring8.or.jp" <ycsasaki(a)spring8.or.jp>, "shs(a)chem.psu.edu" <shs(a)chem.psu.edu>, "dschlaepfer(a)ucsd.edu" <dschlaepfer(a)ucsd.edu>, "schlick(a)nyu.edu" <schlick(a)nyu.edu>, "schlierf(a)bcube-dresden.de" <schlierf(a)bcube-dresden.de>, "slschmid(a)scripps.edu" <slschmid(a)scripps.edu>, "jmscholey(a)ucdavis.edu" <jmscholey(a)ucdavis.edu>, "tschroe1(a)jhem.jhu.edu" <tschroe1(a)jhem.jhu.edu>, "daniel.schwartz(a)colorado.edu" <daniel.schwartz(a)colorado.edu>, "Ulrich.Schwarz(a)kit.edu" <Ulrich.Schwarz(a)kit.edu>, "jschwarz(a)princeton.edu" <jschwarz(a)princeton.edu>, "schwille(a)biotec.tu-dresden.de" <schwille(a)biotec.tu-dresden.de>, "dschwinn(a)uw.edu" <dschwinn(a)uw.edu>, "giorgio.scita(a)ifom-ieo-campus.it" <giorgio.scita(a)ifom-ieo-campus.it>, "ned.seeman(a)nyu.edu" <ned.seeman(a)nyu.edu>, "segall(a)aecom.yu.edu" <segall(a)aecom.yu.edu>, "cseidel(a)hhu.de" <cseidel(a)hhu.de>, "Selvin, Paul R" <selvin(a)illinois.edu>, "anirvan(a)physics.rutgers.edu" <anirvan(a)physics.rutgers.edu>, "dsept(a)biomed.wustl.edu" <dsept(a)biomed.wustl.edu>, "simas(a)indiana.edu" <simas(a)indiana.edu>, "sethna(a)lassp.cornell.edu" <sethna(a)lassp.cornell.edu>, "gseydoux(a)jhmi.edu" <gseydoux(a)jhmi.edu>, "shaevitz(a)princeton.edu" <shaevitz(a)princeton.edu>, "profss(a)yahoo.com" <profss(a)yahoo.com>, "lawrenceshapiro3(a)gmail.com" <lawrenceshapiro3(a)gmail.com>, "shapiro(a)convex.hhmi.columbia.edu" <shapiro(a)convex.hhmi.columbia.edu>, "sishaw(a)indiana.edu" <sishaw(a)indiana.edu>, "shea(a)chem.ucsb.edu" <shea(a)chem.ucsb.edu>, "ms2001(a)columbia.edu" <ms2001(a)columbia.edu>, "jpshen(a)phys.sinica.edu.tw" <jpshen(a)phys.sinica.edu.tw>, "david.sherratt(a)bioch.ox.ac.uk" <david.sherratt(a)bioch.ox.ac.uk>, "William_Shih(a)dfci.harvard.edu" <William_Shih(a)dfci.harvard.edu>, "shnerbn(a)mail.biu.ac.il" <shnerbn(a)mail.biu.ac.il>, "shubeita(a)chaos.utexas.edu" <shubeita(a)chaos.utexas.edu>, "kshukla(a)nsf.gov" <kshukla(a)nsf.gov>, "stas(a)princeton.edu" <stas(a)princeton.edu> > > > Dear Colleagues, > We are writing to inform you of several postdoctoral fellowship opportunities for the coming academic year, starting September 2013, in experimental and theoretical biophysics in the "Center for the Physics of Living Cells" (CPLC), a National Science Foundation Physics Frontier Center at the University of Illinois, Urbana-Champaign. > > Research in the Center falls in one of four themes: > (1) Maximizing information content of single molecule experiments; > (2) Using synthetic nanostructures to mimic cellular environments; > (3) Observing individual events within single cells; > (4) Extending computation to biologically relevant timescales, and theory to greater biological realism. > > Fellows will be using state-of-the-art experimental and theoretical biophysical tools to accomplish these goals: optical tweezers, single-molecule and super-resolution fluorescence microscopy, fabrication of synthetic nanostructure, live cell imaging, chemical biology and genomic biology tools, microscopic and coarse-grained molecular simulations, stochastic modeling, whole cell simulations, as well as the standard methods of molecular and cellular biology and genetics. Research will involve both the development and improvement of experimental and computational techniques and the application of these techniques to particular biological processes such as replication, transcription, translation, cell transport, signaling, and motility. As projects are collaborative endeavors between several labs, the Fellows will have the opportunity to be jointly advised by two or more faculty members of the Center. > Interested applicants should apply via https://my.physics.illinois.edu/join/ no later than December 1, 2012. Applications should include: cover letter, curriculum vita, research statement, publications list, and contact information for three references. Applications received after the December 1st deadline may not be considered. A full job description can be found at: http://www.cplc.illinois.edu/opps/postdocs.asp. > > Please post and circulate the attached announcement or if interested, apply accordingly. > > For more information about CPLC, please visit http://cplc.illinois.edu . > > Thank you. > > Taekjip Ha and Klaus Schulten > Co-directors, Center for the Physics of Living Cells > director(a)cplc.illinois.edu > http://cplc.illinois.edu > University of Illinois at Urbana-Champaign > 1110 West Green Street, MC 704 > Urbana, IL 61801-3080, USA >

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[Compbio-allhands] Fwd: bioengineering, biostats/epidemiology, and biochemistry faculty positions at UC Merced
by Andrej Sali 15 Oct '12

15 Oct '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: David Ojcius <david.ojcius(a)gmail.com> > Subject: bioengineering, biostats/epidemiology, and biochemistry faculty positions at UC Merced > Date: October 14, 2012 5:45:19 PM PDT > To: sali(a)salilab.org > Reply-To: David Ojcius <dojcius(a)ucmerced.edu> > > Dear Dr. Sali: > > I'm writing to draw your attention to a search for two faculty positions in biostatistics/epidemiology and biochemistry/molecular biology at the assistant professor rank that may be of interest to your post-docs or former graduate students. The positions are in the Molecular Cell Biology group at the newest campus of the University of California (UC) in Merced. Preference will be given to candidates doing research related to cancer, diabetes, neurobiology, inflammation, infectious disease, or mechanisms of cell fate decisions. Applicants must have a Ph.D. and a record of research, publication, and teaching commensurate with a faculty appointment at the University of California. > > The university also seeks applications for an open-rank position in bioengineering. A preference will be given to candidates working on physiological modeling, but strong candidates in other areas will also be considered. > > Interested individuals can refer to the full postings at: > http://jobs.ucmerced.edu/n/academic/position.jsf?positionId=4259 > http://jobs.ucmerced.edu/n/academic/position.jsf?positionId=4252 > http://jobs.ucmerced.edu/n/academic/position.jsf?positionId=4264 > > For additional information on UC Merced or the current biomedical sciences research programs, they can refer to the following website: > http://hsri.ucmerced.edu/ > > UC Merced is an affirmative action/equal opportunity employer with a strong commitment to the achievement of diversity among its faculty, staff, and students, and we strongly encourage applications from women and underrepresented groups. > > Sincerely yours, > > David Ojcius

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[Compbio-allhands] Fwd: Expertise in computational modelling systems
by Tom Ferrin 15 Oct '12

15 Oct '12

-------- Original Message -------- Subject: Expertise in computational modelling systems Date: Mon, 15 Oct 2012 10:09:31 +0100 From: Veronique Scordia <VS(a)oakland.co.uk> To: <tef(a)cgl.ucsf.edu> Good morning, My name is Véronique Scordia and I am working for a company called Oakland Innovation, a technology research company, based in Cambridge, UK. I am working with a client, a multinational food company, that is looking to *fund a PhD or a Post-Doc position to build a computational modelling system to predict UV-Visible spectral properties of certain molecules. * Indeed, our client asked us to find academic groups with capabilities to build a computational modelling system to predict UV-Visible spectral properties of certain molecules. These molecules have certain degree of conjugation and number of aromatic groups. Additionally they would like to model the effect of solvent, changes in pH and presence of multiple molecule interaction have on the UV-Visible spectral properties of these molecules. I will call you in the next few days, please let me know if there is a particular time/day that would suit you best. I am looking forward to our conversation. Kindest regards, Véronique ** ** *Véronique Scordia PhD Senior Analyst* * Oakland Innovation Ltd 328/329 Cambridge Science Park* *Milton Road* *Cambridge CB4 0WG* *UK* *T: +44 (0) 1223 507500 F: +44 (0) 1223 507501 E: vs(a)oakland.co.uk <mailto:vs@oakland.co.uk>* *www.oakland.co.uk <file:///\\www.oakland.co.uk> * *------------------------------------------------------- * *OAKLAND: INTELLIGENT THINKING ON BUSINESS INTELLIGENCE * * *CONFIDENTIAL: The information in this document is confidential and may be legally privileged. It is intended solely for the addressee. Access to this document by anyone else is unauthorised. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is prohibited and may be unlawful. It is possible for e-mails to be intercepted or affected by viruses. Whilst we maintain virus checks on inbound e-mails, we accept no liability for viruses or other material introduced with this message. This email message has been scanned for viruses by MessageLabs.

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[Compbio-allhands] 10/18/12 Seminar with Dianne Newman
by Nicole Takesono Flowers 12 Oct '12

12 Oct '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Dianne Newman CalTech New interpretations of ancient biomarkers: exploring the functions of (2-methyl) hopanoids, steroid analogs in bacteria October 18, 2012 J. Kliegman, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Advice much appreciated - Faculty position UW High resolution electron microscopy
by Andrej Sali 11 Oct '12

11 Oct '12

Sent from my iPhone Begin forwarded message: > From: "Wim G. J. Hol" <wghol(a)uw.edu> > Date: October 11, 2012, 11:26:08 AM PDT > To: sali(a)salilab.org > Subject: Advice much appreciated - Faculty position UW High resolution electron microscopy >

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[Compbio-allhands] Fwd: The Rockefeller University - Fellow Position
by Jacobson, Matt 11 Oct '12

11 Oct '12

-- Matt Sent from my iPhone Begin forwarded message: From: Melanie Lee <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Date: October 11, 2012, 10:10:20 AM PDT To: Melanie Lee <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Subject: The Rockefeller University - Fellow Position Dear Colleague: The Center for Studies in Physics and Biology, at The Rockefeller University, expects to have a small number of postdoctoral fellowships available for appointments in September 2013. We are seeking theoretical physicists, mathematicians and computer scientists with a demonstrable interest in the interface between their discipline and biology. The Fellows are to be at that stage of career as to function as independent members of the Center, free to work alone or in collaboration with any members of The Rockefeller University faculty. Would you be so kind as to post the attached notice, and share this within your department and with your peers and colleagues. Many thanks! Melanie J. Lee Administrative Assistant Center for Studies in Physics and Biology Rockefeller University 1230 York Avenue New York, NY 10065-6399 Tel: 212-327-8636 Fax: 212-327-8544

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[Compbio-allhands] Fwd: AMMA: POSTDOCTORAL POSITIONS (3 at CSIRO and 1 at the University of Orléans, France)
by Andrej Sali 10 Oct '12

10 Oct '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Elizabeth Yuriev <Elizabeth.Yuriev(a)monash.edu> > Subject: AMMA: POSTDOCTORAL POSITIONS (3 at CSIRO and 1 at the University of Orléans, France) > Date: October 9, 2012 7:56:11 PM PDT > To: Undisclosed recipients: ; > > OCE POSTDOCTORAL POSITIONS in the VNLab at CSIRO > > 1. OCE Postdoctoral Fellow - Modelling of Graphene Oxide Nanostructures > Closing Date: Open until Filled > Reference: VIC12/03679, > Salary: AU$78K - $85K per annum plus up to 15.4% Superannuation > Duration: 36 months > > CSIRO Materials Science and Engineering is seeking to appoint a highly motivated graduate who will take a substantive role in developing a theoretical and computational framework for modelling the formation, structure, porosity, and properties of graphene oxide nanosheets and membranes. The Fellow will play an important role in the graphene capabilities in the Virtual Nanoscience Laboratory (VNLab), under the direction of Dr. Amanda Barnard, and in the collaboration with Dr Dan Li at Monash University. > > Specifically you will: > • Use an electronic structure simulation to determine the structure of graphene oxide nanosheets, and different types of sheet/sheet interactions; > • Use CSIRO’s in-house package for dynamical modelling of aggregation behaviour, to explore the self-assembly of ensembles of exemplary nanosheets as a function of time, temperature, solvation conditions and concentration; > • Develop a rigorous classification system or different types of graphene oxide nanostructure, based on their conditions of formation, and ultimate properties; > • Produce high quality scientific and technical outputs including journal articles, conference papers and presentations, patents and technical reports. > You will be mentored by senior scientists as part of CSIRO’s Postdoctoral Fellows Program which aims to train early career scientists for a research role. > > LINK: http://csiro.nga.net.au/?jati=215fcf62-0176-9bfe-d1a4-6e0cc642b3de > > > 2. OCE Postdoctoral Fellow - Zinc Oxide Nanostructures > Closing Date: 31 October 2012 > Reference: VIC12/03140, > Salary: AU$78K - $85K per annum plus up to 15.4% Superannuation > Duration: 36 months > > CSIRO Materials Science and Engineering is seeking to appoint a highly motivated PhD graduate who will take a substantive role in developing a theoretical and computational framework for modelling the nanomorphology, environmental stability, and surface properties of zinc oxide (ZnO) nanoparticles. The Fellow will play an important role in the oxide nanomaterials capabilities in the Virtual Nanoscience Laboratory (VNLab), under the direction of Dr. Amanda Barnard, and become an important advisor and partner to the experimental effort under the direction of Dr. Phil Casey (CSIRO). This project is part of a collaboration with Dr Michelle Spencer at La Trobe University, and the Fellow will be encouraged to engage in the University research activities and interact with graduate students. > > Specifically you will: > •Using electronic structure simulations to determine the equilibrium structure and chemical terminations of ZnO surfaces, based on crystallographic orientations and chemical configurations; > •Predict the relative stability of each configuration as a function of temperature and partial pressure (or chemical species) using ab initio thermodynamics to generated a sets of surface phase diagrams under environmentally and industrially relevant; > •Establish the equilibrium morphology of ZnO as a function size and thermochemical conditions, and the relative stability of non-equilibrium morphologies (based on observations of the research team); > •Develop a range of different structure/property maps predicting efficiency of different ZnO nanostructures, under different conditions > •Work collaboratively with scientists in different domains, including computational members of the Virtual Nanoscience laboratory, computational and experimental scientists within CSIRO, and computational colleagues at La Trobe University. > > LINK: http://csiro.nga.net.au/publicfiles/csiro/jobs/B852DE11-66E2-B439-7321-6DE4… > > > 3. OCE Postdoctoral Fellow - Modelling of Inhibitor/Surface Interactions > Closing Date: 31 October 2012 > Reference: VIC12/03140, > Salary: AU$78K - $85K per annum plus up to 15.4% Superannuation > Duration: 36 months > > CSIRO Materials Science and Engineering is seeking to appoint a highly motivated graduate who will take a substantive role in developing a fundamental understanding of the interaction of inhibitors ( both organic and inorganic) with metal surfaces. > > You will combine both modelling of inhibitor/surface interactions with a targeted experimental program to investigate specific elements of binding of inhibitors to the surface and their role in controlling the electrochemistry of the metal/oxide/liquid interface. You will benefit from the established molecular modelling techniques in Dr Barnard’s Virtual Nano-Science laboratory and from both the experimental techniques and extensive data base on inhibiting performance within Dr Cole’s Environmental Surface Design team. > > Specifically you will: > •Predict the interaction of inhibitor molecules with metal and metal oxide surfaces using density functional methodologies; > •Determine the effect of interfaces and features within the metal/metal oxide surface on the interaction with inhibitors ; > •Determine the effect of surface charge and potential variation and the associated double layer effects on surface/inhibitor effects; > •Carry out experimental studies (incl. Electrochemical and analytical approaches) to verify the nature of surface/inhibitor interactions; > •Produce high quality scientific and technical outputs including journal articles, conference papers and presentations; > •Work collaboratively with scientists in different domains, including both computational members of the, computational and experimental scientists within Environmental surface design and Virtual Nanoscience. > > LINK: http://csiro.nga.net.au/?jati=639BF3DD-1BC5-9B3D-7185-6DFB1675D727 > > -Amanda > > > Post-Doctoral position at the University of Orléans in Structural Bioinformatics & Chemoinformatics group – please see attached > > > > Cheers, > Elizabeth > > > ************ > Dr Elizabeth Yuriev > Secretary, > Association of Molecular Modellers of Australasia (AMMA) > > Senior Lecturer > Faculty of Pharmacy and Pharmaceutical Sciences > Medicinal Chemistry and Drug Action > Monash Institute of Pharmaceutical Sciences > Monash University (Parkville Campus) > 381 Royal Parade, Parkville VIC 3052, Australia > Tel: Int +61 3 9903 9611, Fax: +61 3 9903 9143 > E-mail: elizabeth.yuriev(a)monash.edu > www.pharm.monash.edu.au

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[Compbio-allhands] BBC Journal Club, October 16th, GH Auditorium
by Bass, Karche 10 Oct '12

10 Oct '12

[BBC Journal Club] [BP * BMI * CCB] [Tuesday, October 9- 10:45 am - GH Auditorium] Amy Jacobson Khare, S.D., et al. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat. Chem. Biol. 8, 294-300 (2012). Andrew VanBenschoten Wang L et.al. Allosteric control of the ribosome by small-molecule antibiotics. Nature Structural & Molecular Biology. 19:9 957-963. (2012) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles Craik, Susan Miller, Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0943 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Fwd: PI position
by Andrej Sali 05 Oct '12

05 Oct '12

Sent from my iPhone Begin forwarded message: > From: "Chandra, Verma" <chandra(a)bii.a-star.edu.sg> > Date: October 5, 2012, 4:27:22 PM PDT > To: sali(a)salilab.org > Subject: PI position > > dear prof sali > > we have an opening at a PI level for someone who has had at least 4-5 years postdoctoral experience in the field of biomolecular modelling and computational chemistry. if you do know of someone who may be interested I would be grateful if you could please ask them to contact me > > many thanks > > chandra verma > a*star, singapore >

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[Compbio-allhands] 10/11/12 Seminar with Caleb Bashor
by Nicole Takesono Flowers 05 Oct '12

05 Oct '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Caleb Bashor Clements Lecture Modular strategies for reprograming signal transduction pathways: rewiring the yeast mating pathway October 11, 2012 Wendell Lim, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] reminder
by Jacobson, Matt 04 Oct '12

04 Oct '12

Talk by David Shaw, in Genentech Hall, noon Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] Fwd: multiple qBio positions at UCSD
by Andrej Sali 04 Oct '12

04 Oct '12

Begin forwarded message: > From: Terry Hwa <hwa(a)ucsd.edu> > Subject: multiple qBio positions at UCSD > Date: October 4, 2012 11:14:12 AM PDT > To: Terry Hwa <thwa(a)ucsd.edu> > > > Dear Colleagues, > > I am writing to tell you about some exciting opportunities at the interface of the physical and biological sciences at U.C. San Diego. This is the second year of a major campus-wide initiative in quantitative biology (qBio). Following five successful qBio hires last year, there will be another cluster of hirings conducted across biology, physics, chemistry, and bioengineering, as well as on-going searches for senior biophysics theory positions. We expect additional positions in complementary fields next year. > > It is our goal to use these positions to assemble a dream team in quantitative biology, building on the vast base of biological research in the La Jolla basin, and a well established tradition of collaboration between the physical and biological sciences at UCSD. We encourage you to pass this information to interested junior and senior colleagues to pursue these dreams together. > > thank you and best wishes, > > Terry Hwa > >

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[Compbio-allhands] BBC Journal Club, Tuesday, October 9th
by Bass, Karche 03 Oct '12

03 Oct '12

BMI ~ BP ~ CCB Tuesday, October 9th, 2012 10:45 am, GH Auditorium Thomas Stevens Santos, Silvia D M et al. Spatial Positive Feedback at the Onset of Mitosis. Cell 149.7 (2012): 1500-13. Marian Deuker A CXCL1 Paracrine Network Links Cancer Chemoresistance and Metastasis bioinformatics ~ biophysics ~ chemistry and chemical biology Karché K. Bass Karché K. Bass | Administrative Analyst Asst. to John D. Gross, Charles S. Craik, Susan Miller, and Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0523 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Fwd: FACULTY POSITIONS OPEN--Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
by Jacobson, Matt 01 Oct '12

01 Oct '12

-- Matt Sent from my iPad Begin forwarded message: From: imbwww <imbwww(a)imb.sinica.edu.tw<mailto:imbwww@imb.sinica.edu.tw>> Date: September 30, 2012 7:27:36 PM PDT Cc: vivi chiang <vivi(a)imb.sinica.edu.tw<mailto:vivi@imb.sinica.edu.tw>> Subject: FACULTY POSITIONS OPEN--Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan Dear colleagues, The Institute of Molecular Biology (Academia Sinica, Taiwan) is recruiting young and talented faculty to join the research groups. We would like to seek your help in distributing this advertisement to potentialcandidates in your laboratory or to those who you think might be interested in. Your kind assistance is highly appreciated. Best regards, ************************ The recruitment committee Institute of Molecular Biology Academia Sinica, Taipei, Taiwan

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[Compbio-allhands] Seminar October 4, noon
by Jacobson, Matt 28 Sep '12

28 Sep '12

David Shaw will give a seminar at noon on Thursday, October 4, in Genentech Hall auditorium, entitled "Millisecond-long molecular dynamics simulations of proteins" http://www.deshawresearch.com/ Hope to see you there (No BBC seminar was scheduled for this date, so we are using that time slot for this somewhat impromptu seminar. I've included all the listservs that I have access to on this email, but feel free to forward.) -- Matt Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] BBC Journal Club, Tuesday, October 2- 10:45AM, GH Aud
by Bass, Karche 26 Sep '12

26 Sep '12

BMI ~ BP ~ CCB Tuesday, October 2nd 10:45 am, GH Auditorium Kyle Barlow, BMI Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748-1759 (2012). Noah Younger, CCB Illing PT et al. Immune self-reactivity triggered by drug-modified HLA-peptide repertoire. Nature. 2012; 486:554-558. bioinformatics ~ biophysics ~ chemistry and chemical biology Karché K. Bass Karché K. Bass | Administrative Analyst Asst. to John D. Gross, Charles Craik, Susan Miller, Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA •: 415-502-0943 | 7: | •: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Fwd: CADD position at BMS
by Jacobson, Matt 25 Sep '12

25 Sep '12

Begin forwarded message: From: "Johnson, Stephen" <stephen.johnson(a)bms.com<mailto:stephen.johnson@bms.com>> Subject: CADD position at BMS Date: September 25, 2012 2:30:27 PM PDT To: "Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Dear Professor Jacobson, Debbie Loughney and I were discussing our visit to UCSF earlier this year as we just recently opened a new position within the CADD group at BMS. In short, the scientist that fills the position will be expected to help us expand and extend our toolset for addressing off-target liabilities including both ADMET and selectivity issues. The scientist will be active in the development of new methodology and its application in discovery projects. As such, we’re hoping to find someone with reasonable programming skills, in addition to being a top-tier CADD scientist. I wonder if you might have any current or former students/postdocs that you think may be a good fit for the position? Anyone that is interested can view the position profile and apply here: https://bms.taleo.net/careersection/jobdetail.ftl?job=45378&lang=en&sns_id=… They are also welcome to email directly in addition to applying through the website. Regards, Steve ================= Stephen Johnson Sr. Principal Scientist, CADD Head, Molecular Analytics Bristol-Myers Squibb, Co. stephen.johnson(a)bms.com<mailto:stephen.johnson@bms.com> ________________________________ This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] 9/27/12 Seminar with Sheng Zhong
by Nicole Takesono Flowers 21 Sep '12

21 Sep '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Sheng Zhong University of Illinois Comparative Epigenomics: a case study of human, mouse and pig pluripotent stem cells. September 27, 2012 Bo Huang, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Postdoctoral opening
by Jacobson, Matt 20 Sep '12

20 Sep '12

As some of you know, I think very highly of Gilson's work Begin forwarded message: From: "Michael K. Gilson" <mgilson(a)ucsd.edu<mailto:mgilson@ucsd.edu>> Subject: Postdoctoral opening Date: September 20, 2012 1:56:32 PM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Dear Matt, I thought I would mention that there is a current opening for a postdoctoral position in my lab. It is posted here on the computational chemistry list: http://www.ccl.net/cca/jobs/joblist/mess0025099.shtml I would be grateful if you could pass this along to trainees who might be interested. Feel free to contact me if you would like any more information. All the best, Mike -- Michael K. Gilson, M.D., Ph.D. Professor, Skaggs School of Pharmacy and Pharmaceutical Sciences Director, UCSD Drug Discovery Institute U. C. San Diego 9500 Gilman Drive Pharmaceutical Sciences Building, Room 3224 La Jolla, CA 92093-0736 Voice: 858-822-0622 Fax: 858-822-7726 http://gilson.ucsd.edu http://www.bindingdb.org http://drugdiscovery.ucsd.edu Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] Fwd: Faculty position in medicinal/pharmaceutical chemistry preferrably with computational research emphasis
by Brian Shoichet 19 Sep '12

19 Sep '12

FYI ---------- Forwarded message ---------- From: Peter Oelschlaeger <poelschlaeger(a)westernu.edu> Date: Wed, Sep 19, 2012 at 11:53 AM Subject: Faculty position in medicinal/pharmaceutical chemistry preferrably with computational research emphasis To: Peter Oelschlaeger <poelschlaeger(a)westernu.edu> Dear Professors,**** ** ** I would like to let you know about a faculty position in medicinal/pharmaceutical chemistry (preferably with a computational research emphasis) that the Department of Pharmaceutical Sciences in the College of Pharmacy at Western University of Health Sciences is offering.*** * ** ** Could you please inform any postdocs or colleagues that might be interested in applying?**** A posting with job description and instructions on how to apply has been posted on Science Careers:**** http://scjobs.sciencemag.org/jobs/153661-91602/**** ** ** Thank you very much for your help,**** ** ** Peter**** ** ** ************************************************************* *Peter Oelschlaeger, PhD* *Assistant Professor* *Department of Pharmaceutical Sciences* *College of Pharmacy* *Western University of Health Sciences* *309 E. Second St., Pomona, CA 91766* *Phone: 909-469-8232 (office), 909-469-8234 (lab)* *Fax: 909-469-5600* *Email: poelschlaeger(a)westernu.edu* *http://www.westernu.edu/stp/bios.php?bio=poelschlaeger* ** ** ** ** -- Brian Shoichet Professor University of California, San Francisco Dept. of Pharmaceutical Chemistry phone: 415-514-4126; fax: 415-514-4260 http://shoichetlab.compbio.ucsf.edu

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[Compbio-allhands] Informal Seminar: David Minh, "Molecular Docking: Foundations in Statistical Mechanics"; Friday, 10:30am, GH S204
by David Sivak 19 Sep '12

19 Sep '12

Informal Seminar: Friday, September 21, 10:30am, Genentech S204 Molecular Docking: Foundations in Statistical Mechanics David Minh (mccammon.ucsd.edu/~dminh/) I will describe implicit ligand theory, a new formalism for noncovalent binding free energies that separates the calculation into two simulation stages: (i) sampling receptor configurations and (ii) calculating the binding PMF - the affinity of a ligand to a rigid receptor - for each receptor snapshot. Molecular docking may be interpreted as applying a dominant state approximation to each stage. Implicit ligand theory provides a pathway for the improvement of scoring functions. Recommended reading: http://arxiv.org/abs/1208.4885 -- David Sivak Systems Biology Fellow University of California, San Francisco david.sivak(a)gmail.com davidsivak.com 510-541-9006

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[Compbio-allhands] Fwd: A postdoc to work with Peter Minary in Computer Science at Oxford University
by Andrej Sali 17 Sep '12

17 Sep '12

Begin forwarded message: > From: "Michael Levitt" <michael.levitt(a)stanford.edu> > Subject: A postdoc to work with Peter Minary in Computer Science at Oxford University > Date: September 17, 2012 1:20:07 PM PDT > To: "'Michael Levitt'" <michael.levitt(a)stanford.edu> > > Dear Colleague and Friend, > > I am writing to ask for your help in identifying suitable candidates for a postdoctoral fellow to collaborate with Dr. Peter Minary. Peter has moved from Stanford to an independent position in Computer Science at Oxford and I can recommend him to any person who would like to become an expert at the most amazing methods for sampling macromolecular conformations. > > Searching Pubmed (http://www.ncbi.nlm.nih.gov/pubmed?term=minary%20p) shows Peter recent publications. His program remarkable program MOSAICS is athttp://csb.stanford.edu/minary/MOSAICS.html/ . > > This position has been advertised in Nature and Science. I append the Science add here (http://www.2020science.net/news/fellowship-computational-biology ). > > So many thanks and with all best regards, > Michael > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: Subject: Postdoc opportunities at Princeton
by Andrej Sali 17 Sep '12

17 Sep '12

Sent from my iPhone Begin forwarded message: > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Date: September 17, 2012 1:07:08 PM PDT > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Cc: William Bialek <wbialek(a)Princeton.EDU>, "Curtis G. Callan Jr." <ccallan(a)Princeton.EDU>, "Wingreen, Ned S." <wingreen(a)Princeton.EDU>, "Chase P. Broedersz" <cbroeder(a)Princeton.EDU>, "Ben Machta (ben.machta(a)gmail.com)" <ben.machta(a)gmail.com>, "Rava A. da Silveira (rava(a)ens.fr)" <rava(a)ens.fr> > Subject: Subject: Postdoc opportunities at Princeton > > Dear colleagues, > > We are searching for young theorists with interests at the interface of physics and biology, and hope that you will bring this opportunity to the attention of likely candidates. As described in the attached advertisement (also available at http://www.princeton.edu/physics/about/employment/biophysics/index.xml) problems of current interest in our group cover a wide range of topics, and we always welcome people who will bring new questions of their own devising. Our community is very interactive, with multiple opportunities for collaboration, both among theorists and with many friendly local experimentalists. > > Many thanks for your help, > > Bill, Chase, Curt, Ben, Rava, and Ned > > William Bialek > John Archibald Wheeler/Battelle Professor in Physics > > Chase P. Broedersz > Lewis-Sigler Theory Fellow > > Curtis G. Callan, Jr. > James S. McDonnell Distinguished University Professor of Physics > > Benjamin Machta > Lewis-Sigler Theory Fellow > > Rava A. da Silveira > Princeton Global Scholar > > Ned S. Wingreen > Howard A. Prior Professor in the Life Sciences > > >

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[Compbio-allhands] Fwd: AMMA: job and postdoc opportunities
by Andrej Sali 16 Sep '12

16 Sep '12

Begin forwarded message: > From: Elizabeth Yuriev <Elizabeth.Yuriev(a)monash.edu> > Subject: AMMA: job and postdoc opportunities > Date: September 16, 2012 6:01:13 PM PDT > To: Undisclosed recipients: ; > > 1. Postdoctoral Research Associate, University of Liverpool > > £31,020 - £31,948 pa > Faculty of Science and Engineering, School of Physical Sciences, Department of Chemistry > Location: Liverpool City Centre > Ref: R-580533/WWW > Closing date for receipt of applications: 5 October 2012 > Joining a team of five postdoctoral researchers to develop a lead candidate compound, you will form part of a joint collaborative programme between the Departments of Chemistry and Pharmacology in a programme funded by the Medical Research Council (MRC). You should have a MChem degree and a PhD (or about to be obtained) in molecular modelling or closely related area. > The project involves the rational design, via molecular modelling, of novel analgesic compounds and will focus on exploring the structure activity relationships of molecules, their isosteres and optimising pharmacokinetic properties. Crucial to the vision is the use of molecular modelling to lead laboratory synthesis and testing to achieve compounds that are fit for purpose. The post is available for 12 months in the first instance. > > http://www.liv.ac.uk/working/job_vacancies/research/R-580533.htm > > Dr Neil Berry > Department of Chemistry > University of Liverpool > Liverpool > L69 7ZD > Tel: +44(0)151 794 3877 > Fax: +44(0)151 794 3588 > http://www.liv.ac.uk/~ngberry > > > 2. Senior Software Developer, Lhasa Limited > > There is more than one post on offer. There is no set closing date at the moment – but applications to be made as soon as possible. > Anyone interested in the job should contact my colleague Menaz Tabassum, who is responsible for recruitment here at Lhasa. Menaz’s email address is:- > Menaz.tabassum(a)lhasalimited.org > > (please see attachment for details) > > > 3. Postdoc position on Computational Protein Design at LAAS-CNRS, Toulouse, France > > The Robotics and Interactions group at LAAS-CNRS (Toulouse, France) is seeking for a postdoctoral researcher to work in an interdisciplinary project on Computational Protein Design. The project, ProtiCAD, is funded by the French National Research Agency (ANR). It involves three research groups with expertise in computer science / robotics, computational biology and enzyme engineering, and a start-up company. The work will mainly involve the development of algorithms to efficiently explore very large state-spaces, which correspond to different sequences and conformations of a protein. > > Candidates should have strong background in search algorithms and combinatorial optimization methods, as well as excellent programming skills. > Research will be carried in close collaboration with people in the other laboratories; therefore, applicants should enjoy teamwork and have very good communication skills. > Good English level is mandatory and notions of French would be a plus. > Toulouse is a beautiful, dynamic and safe city situated in the South West of France, within only 1.5 hour drive from the Pyrenees and the Mediterranean Sea. Toulouse offers outstanding opportunities for culture, entertainment and outdoor activities. > The position is available from December 2012, for a duration of up to two years. > Applications, including a CV, a cover letter and contact information of at least two references, should be sent by email to Juan Cortés (juan.cortes(a)laas.fr) with subject: "ProtiCAD postdoc application". > > > > > > > > > > ************ > Dr Elizabeth Yuriev > Senior Lecturer > Faculty of Pharmacy and Pharmaceutical Sciences > Medicinal Chemistry and Drug Action > Monash Institute of Pharmaceutical Sciences > Monash University (Parkville Campus) > 381 Royal Parade, Parkville VIC 3052, Australia > Tel: Int +61 3 9903 9611, Fax: +61 3 9903 9143 > E-mail: elizabeth.yuriev(a)monash.edu > www.pharm.monash.edu.au > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: New positions at Janssen
by Andrej Sali 13 Sep '12

13 Sep '12

Begin forwarded message: > From: "Szalma, Sandor [JRDUS]" <sszalma(a)its.jnj.com> > Subject: FW: New positions at Janssen > Date: September 13, 2012 12:15:23 PM PDT > To: <trey.ideker(a)gmail.com>, <pbourne(a)ucsd.edu>, <ajayr(a)us.ibm.com>, <sali(a)salilab.org>, <jmccammo(a)mccammon.ucsd.edu>, "Athey, Brian" <bleu(a)umich.edu>, <brookscl(a)umich.edu>, <case(a)rutgers.edu>, <eperakslis(a)gmail.com>, <eneumann(a)mindspring.com>, <gergely.toth(a)gmail.com>, <gyanbhanot(a)gmail.com>, "Jill P. Mesirov" <mesirov(a)broad.mit.edu>, <alb(a)neu.edu>, "Martin Leach" <mleach(a)broadinstitute.org>, <piotr_cieplak(a)yahoo.com>, "Meroueh, Samy" <smeroueh(a)iupui.edu>, <vajda(a)bu.edu>, <taisung(a)yahoo.com>, <taisung(a)gmail.com>, <zszallasi(a)chip.org>, <nanjie_deng(a)yahoo.com>, "John Vu" <johnvu(a)andrew.cmu.edu> > > Hi, > > Please find below a couple of new jobs posting from Janssen – feel free to forward. > > > Head, High Performance Computing: > http://jobview.monster.com/Head-of-High-Performance-Computing-HPC-Job-New-Y… > > Senior Scientist, High Performance Computing: > http://jobview.monster.com/Senior-Scientist-High-Performance-Computing-HPC-… > > Head, Computational & Systems Biology: > http://jobview.monster.com/Head-Computational-Systems-Biology-Job-New-York-… > > Senior Scientist, Computational & Systems Biology: > http://jobview.monster.com/Senior-Scientist-Computational-Systems-Biology-J… > > Thank you! > > Sándor > > > Dr. Sándor Szalma > > Senior Research Fellow & Head, External Innovation, R&D IT > > Janssen Research & Development, LLC > Adjunct Professor, Rutgers, The State University of New Jersey > > 3210 Merryfield Row #1624 > San Diego, CA 92121, USA > T: +1 858 320 3445 > C: +1 858 603 3441 > F: +1 858 458 3746 > E: sszalma(a)its.jnj.com > > This e-mail message is confidential and for the sole use of the intended recipient(s) and may contain privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not an intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Thank you. > >

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[Compbio-allhands] Fwd: computational scientist for GBT
by Andrej Sali 13 Sep '12

13 Sep '12

Begin forwarded message: > From: Steve Gwaltney <sgwaltney(a)globalbloodtx.com> > Subject: computational scientist for GBT > Date: September 10, 2012 6:14:45 PM PDT > To: Matt Jacobson <matt.jacobson(a)ucsf.edu>, Andrej Sali <sali(a)salilab.org> > Cc: Brian Metcalf <bmetcalf(a)globalbloodtx.com>, Kathy Stafford <kstafford(a)globalbloodtx.com> > > Hi Matt and Andrej, > > I am looking to hire a computational scientist to help us with compound design, structural biology issues, predictive tools, etc. Please find attached a job description for this position. If you know of good scientists who are qualified, please forward this to them. > > Thank you, > Steve > > Stephen L. Gwaltney, II, PhD > Vice President, Chemistry > Global Blood Therapeutics > 455 Mission Bay Blvd South > Suite 575 > San Francisco, CA 94158 > 415-766-3626 >

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[Compbio-allhands] Fwd: seminar announcement
by Jacobson, Matt 11 Sep '12

11 Sep '12

From: Matthew Jacobson <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: seminar announcement Date: September 10, 2012 3:46:12 PM PDT To: <allhands(a)compbio.ucsf.edu<mailto:allhands@compbio.ucsf.edu>>, <BPSTUDENTS(a)LISTSRV.UCSF.EDU<mailto:BPSTUDENTS@LISTSRV.UCSF.EDU>> David Shaw will be giving a talk on October 4; there is no BBC seminar scheduled that day, so we will use the noon timeslot. I'll send out a title and a reminder later. Seminar: Thursday, October 4, 2012 from 12-1PM, Location: GH Auditorium For those who don't know him: http://www.deshawresearch.com/ -- Matt Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org/>

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[Compbio-allhands] Fwd: Post-doctoral advert
by Andrej Sali 30 Aug '12

30 Aug '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Prof. C.E. Rudd" <cer51(a)cam.ac.uk> > Subject: Post-doctoral advert > Date: August 31, 2012 9:38:55 AM GMT+12:00 > To: lavy(a)stevens.edu > Cc: caterina.strambio(a)unige.ch, sali(a)salilab.org > > > Dear Colleague > > Would it be possible to ask you to post this advert for a post-doctoral fellow position in Cambridge University? We recently uncovered a novel immune cell specific adaptor that binds to the cytoplasmic face of the NPC in T-cells and which regulates RanGAP activity. > > Thank you for your help with this. > > Chris > > > -- > Christopher E. Rudd, Ph.D, D.Sc. > Professor of Molecular Immunology > Head, Cell Signalling Section > Department of Pathology > University of Cambridge > Tennis Court Road > Cambridge, UK > CB2 1QP > Tel: 44 1223 765 661 > Fax: 44 1223 764 733 > and > Cambridge Institute of Medical Research > Hills Road, Cambs CB2 0XY > 01223-769087 (lab: 01223-769086) > > http://www.cimr.cam.ac.uk/investigators/rudd/index.html > http://www.path.cam.ac.uk/pages/rudd/ > > http://www.immunology.cam.ac.uk/directory/profile.php?cerudd > http://www.infectiousdisease.cam.ac.uk/directory/cer51@cam.ac.uk > > >

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[Compbio-allhands] Fwd: open positions
by Jacobson, Matt 30 Aug '12

30 Aug '12

position open just across the street from UCSF Begin forwarded message: From: Michael Gonzales <mgonzales(a)celgene.com<mailto:mgonzales@celgene.com>> Subject: open positions Date: August 30, 2012 12:18:23 PM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Matt, Hope all is going well with you. I'm wondering if you know anyone that might be a fit for a couple open positions that I have in my group. The positions are "contract" but I intend to make these full time after successful completion of the project. I'm looking for someone to essentially lead NGS analysis for my group. Specifically I need someone who is experienced in: - rigorous analysis of RNA-seq data (ideally from clinical samples) - GEP, mutations, splice form quantification, gene fusions, etc - putting together the infrastructure to analyze NGS data (db, algorithms, etc) Here's my wish list of qualifications: ============================= REQUIRED QUALIFICATIONS · Graduate-level degree (Ph.D. preferred) in a life science discipline (bioinformatics, biology, biochemistry, medicinal chemistry, bioengineering, etc.). Candidates with a degree in another natural science, computer science, information technology or a related discipline will also be considered but must have a track record of research experience in computational life science · Two years post-graduate work experience conducting computational biology research (academic, government, or industry) · Proven record of working with Next-Gen Sequence (NGS) analysis including RNA-seq, ChIP-seq, whole genome assembly. · Extensive experience with large genomic data sets, as exemplified by the following areas: microarray analysis, high-throughput sequence analysis, automated annotation, gene prediction, population genomics, quantitative genetics, comparative genomics · Experience working in a command line environment including compiling and configuring bioinformatics software · Experience with extracting, manipulating, and integrating data from public biological data repositories (e.g. NCBI, Ensembl, UCSC). · Proficient programming skills with at least one scripting language (Perl, R, Python, Ruby, etc) · Strong interest in science and technology and ability to rapidly adopt and adapt to leading edge technologies · Excellent oral presentation and communications skills · Advanced ability to work independently under established deadlines and as part of a team PREFERRED QUALIFICATIONS · Demonstrated success in publishing computational science results and in presenting data to senior management · Experience managing projects involving advanced computing and information technologies used in life science research in academia, government laboratories, and/or industry · Proven ability to promote and support the use of computing, visualization, networking, and massive data storage systems to scientists to expand their research impact ============================= ------------------------------------------------------- Michael B. Gonzales, Ph.D. Director, Computational Biology Celgene Corporation 1500 Owens Street, Suite 600 San Francisco, CA 94158 T: 415.839.7113 │ F: 415.839.7011 ********************************************************* THIS ELECTRONIC MAIL MESSAGE AND ANY ATTACHMENT IS CONFIDENTIAL AND MAY CONTAIN LEGALLY PRIVILEGED INFORMATION INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR INDIVIDUALS NAMED ABOVE. If the reader is not the intended recipient, or the employee or agent responsible to deliver it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please reply to the sender to notify us of the error and delete the original message. Thank You. ********************************************************* Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] Fwd: Research Fellow in Computational Structural Biology
by Andrej Sali 30 Aug '12

30 Aug '12

Begin forwarded message: > From: Jennifer Wilkinson <jennifer.wilkinson(a)cs.ox.ac.uk> > Subject: Research Fellow in Computational Structural Biology > Date: August 30, 2012 9:40:21 PM GMT+12:00 > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Dr. Sali, > > We currently are advertising a research fellowship vacancy in Oxford, and would be grateful if you could distribute details to anyone who may be interested within your group. I have pasted details of the position below. > > Many thanks, > > Jennifer > > Research Fellow in Computational Structural Biology > > Grade 7: Salary £29,249-£35,938 (with a discretionary range to £39,257) > Fixed term contract for up to 2 years duration > > We are looking for a highly motivated researcher with a documented track record of successful research projects and a desire to do interdisciplinary research. This 24 month post-doctoral position will focus on the development and application of new methods in structure-based modelling and bioinformatics. The research will be carried out under the supervision of Prof. Charlotte Deane and Dr. Peter Minary in collaboration with the Structural Genomics Consortium and the EPSRC funded2020 Science programme. > > Candidates who have a doctorate in a relevant discipline and experience in scientific computing, software development and structural biology are particularly sought; however, exceptional candidates in all areas will be considered. Excellent programming and statistical skills are essential, as is experience of working with large-scale data sets. You will be expected to produce leading scientific research, publish results in top scientific journals, and interact closely with other members of the group and group collaborators. > > The post is available for up to 2 years, has a salary on the University grade 07S scale (currently £29,249 to £35,938), includes membership of the University pension scheme and has an annual leave entitlement of 38 days per year (inclusive of all public holidays and university closed periods). Requests to work on a part time or flexible basis will be considered. > > In addition candidates should arrange for the two letters of reference to be sent directly to the Administration Department (Vacancies), 1 South Parks Road, Oxford, OX1 3TG, email: jobs(a)stats.ox.ac.uk, before the closing date (a letter by email is sufficient). > > Please direct informal enquiries to the Administrator (email: jobs(a)stats.ox.ac.uk) Please quote reference: 104157 on all correspondence. > > To apply for this role and for further details, including the job description and selection criteria, please click here. All applications for this vacancy are to be made online > > Only applications received before the closing date 12 noon (UK time) Monday 1 October, 2012, can be considered. > > > > Jennifer Wilkinson > Project Manager > ___________ > University of Oxford > Department of Computer Science > Wolfson Building > Parks Road > Oxford OX1 3QD > > +44(0)1865 610782 > > *Please note, I am only in the office on Thursdays and Fridays. > > http://www.2020science.net >

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[Compbio-allhands] Fwd: Of Interest?
by Andrej Sali 28 Aug '12

28 Aug '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Gregory A. Voth" <gavoth(a)uchicago.edu> > Subject: Of Interest? > Date: August 29, 2012 9:20:18 AM GMT+12:00 > To: "cgtheory(a)vothgroup.uchicago.edu" <cgtheory(a)vothgroup.uchicago.edu> > > > Dear Colleagues, > > The attached add is for a postdoc position at Genentech. Someone in your group may be interested in it so please pass it on. The email address to apply is on the add. The work is in part to be done in collaboration with my group (see attached). > > Best wishes, > Greg Voth > > __________________________________________________________________ > > Gregory A. Voth, Ph.D. > Haig P. Papazian Distinguished Service Professor > Department of Chemistry, The James Franck Institute, and > The Institute for Biophysical Dynamics > Senior Fellow, Computation Institute > Senior Scientist, Argonne National Laboratory > > Department of Chemistry > The University of Chicago > 5735 S. Ellis Avenue > Chicago, Illinois 60637 > Phone: 773-702-9092 > Fax: 773-795-9106 > Administrative Assistant: 773-702-9096 > Email: gavoth(a)uchicago.edu > Office: 231 Searle > Admin Office: 233 Searle > ___________________________________________________________________ > > > _______________________________________________ > Cgtheory mailing list > Cgtheory(a)vothgroup.uchicago.edu > http://vothgroup.uchicago.edu/cgi-bin/mailman/listinfo/cgtheory

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[Compbio-allhands] Fwd: Of Interest?
by Jacobson, Matt 28 Aug '12

28 Aug '12

Begin forwarded message: From: "Gregory A. Voth" <gavoth(a)uchicago.edu<mailto:gavoth@uchicago.edu>> Subject: Of Interest? Date: August 28, 2012 2:24:12 PM PDT To: "proteins(a)vothgroup.uchicago.edu<mailto:proteins@vothgroup.uchicago.edu>" <proteins(a)vothgroup.uchicago.edu<mailto:proteins@vothgroup.uchicago.edu>> Dear Colleagues, The attached add is for a postdoc position at Genentech. Someone in your group may be interested in it so please pass it on. The email address to apply is on the add. The work is in part to be done in collaboration with my group (see attached). My apologies for any duplicate email you may receive on this. Best wishes, Greg Voth __________________________________________________________________ Gregory A. Voth, Ph.D. Haig P. Papazian Distinguished Service Professor Department of Chemistry, The James Franck Institute, and The Institute for Biophysical Dynamics Senior Fellow, Computation Institute Senior Scientist, Argonne National Laboratory Department of Chemistry The University of Chicago 5735 S. Ellis Avenue Chicago, Illinois 60637 Phone: 773-702-9092 Fax: 773-795-9106 Administrative Assistant: 773-702-9096 Email: gavoth(a)uchicago.edu<mailto:gavoth@uchicago.edu> Office: 231 Searle Admin Office: 233 Searle ___________________________________________________________________ _______________________________________________ Proteins mailing list Proteins(a)vothgroup.uchicago.edu<mailto:Proteins@vothgroup.uchicago.edu> http://vothgroup.uchicago.edu/cgi-bin/mailman/listinfo/proteins Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] FW: Sr. Bioinformatics Scientist - SF - Position Details
by Schnoes, Alexandra 22 Aug '12

22 Aug '12

They are aggressively trying to staff 2 positions, looking for people who know RNA-seq and R. This is for a biotech based inside SF. Feel free to pass around. REQUIRED QUALIFICATIONS * Graduate-level degree (Ph.D. preferred) in a life science discipline (bioinformatics, biology, biochemistry, medicinal chemistry, bioengineering, etc.). Candidates with a degree in another natural science, computer science, information technology or a related discipline will also be considered but must have a track record of research experience in computational life science * Two years post-graduate work experience conducting computational biology research (academic, government, or industry)* Proven record of working with Next-Gen Sequence (NGS) analysis including RNA-seq, ChIP-seq, whole genome assembly. * Extensive experience with large genomic data sets, as exemplified by the following areas: microarray analysis, high-throughput sequence analysis, automated annotation, gene prediction, population genomics, quantitative genetics, comparative genomics * Experience working in a command line environment including compiling and configuring bioinformatics software * Experience with extracting, manipulating, and integrating data from public biological data repositories (e.g. NCBI, Ensembl, UCSC). * Proficient programming skills with at least one scripting language (Perl, R, Python, Ruby, etc) * Strong interest in science and technology and ability to rapidly adopt and adapt to leading edge technologies * Excellent oral presentation and communications skills * Advanced ability to work independently under established deadlines and as part of a team PREFERRED QUALIFICATIONS * Demonstrated success in publishing computational science results and in presenting data to senior management * Experience managing projects involving advanced computing and information technologies used in life science research in academia, government laboratories, and/or industry * Proven Appreciate you reaching out to you network!! Cheers, Amanda Amanda McDermott Consultant, Bioinformatics and Genomics Real Staffing Group One Sansome Street, San Francisco, CA 94101 ------------------------------------------------ T: 415-796-8050 E. a.mcdermott(a)realstaffing.com<mailto:a.mcdermott@realstaffing.com> Global Village: 232 7038 ------------------------------------------------ www.realstaffing.com<http://www.realstaffing.com> [Picture (Metafile)] Join my LinkedIn network<http://www.linkedin.com/in/amandamcdermottbioinformatics> [Picture (Metafile)]We want to provide you with the best service possible - click here<http://www.keysurvey.co.uk/f/444734/26ec/> to submit your feedback You can view our privacy statement at http://www.realstaffing.com/page/privacy_policy. If you do not wish to receive future electronic e-mails from us about our service please email: data-protection(a)realstaffing.com<mailto:data-protection@realstaffing.com> This electronic transmission is confidential and intended solely for the addressee(s). If you are not an intended addressee, you must not disclose, copy, distribute or take any action in reliance upon this transmission. If you have received this transmission in error, please notify Real Staffing Group, http://www.realstaffing.com/page/registration_details

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[Compbio-allhands] Juergen Haas Seminar -- ROOM CHANGE TODAY -- new room GH S204 -- 11AM TODAY, AUG. 10
by Hilary Mahon 10 Aug '12

10 Aug '12

--- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] Fwd: Two postdoctoral positions available
by Andrej Sali 02 Aug '12

02 Aug '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Patrick Aloy <paloy(a)irbbarcelona.org> > Subject: Two postdoctoral positions available > Date: August 2, 2012 7:19:18 AM PDT > To: undisclosed-recipients:; > > Dear friends and colleagues, > > we have two open postdoctoral positions in the group, one computational and one experimental, and I should be grateful if you could advertise them in your institutes and forward the message to people that might be interested (job adverts attached). Despite everything you might read on the newspapers, Barcelona is still an attractive place for research ;-) > > Best, > > PTCK. > > -- > Patrick Aloy, ICREA Research Professor > Structural Bioinformatics & Network Biology > Institute for Research in Biomedicine - Barcelona Science Park > c/ Baldiri i Reixac 10-12, 08028 Barcelona, Spain > > Email: patrick.aloy(a)irbbarcelona.org http://sbnb.irbbarcelona.org > Tel : +34 93 4039690 Fax : +34 93 4039954 >

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[Compbio-allhands] Seminar - Dr. Juergen Haas, University of Basel - Friday, Aug. 10, 2012 - 11:00am - 12:00pm - Byers Hall 212
by Hilary Mahon 31 Jul '12

31 Jul '12

Please see attached for information about Dr. Haas's seminar, "New developments in the Continuous Automated Model EvaluatiOn (CAMEO) system". Thank you. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] Giovanni Bussi Seminar - July 27
by Hilary Mahon 23 Jul '12

23 Jul '12

Please see information about Dr. Bussi's seminar. Thank you, Hilary --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] Fwd: Rapid Molecular Dynamics Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande
by Andrej Sali 09 Jul '12

09 Jul '12

Begin forwarded message: > From: "Joy P. Ku" <joyku(a)stanford.edu> > Subject: Rapid Molecular Dynamics Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande > Date: July 9, 2012 9:43:06 PM PDT > To: <sali(a)salilab.org> > > Hi Dr. Sali, > > I’m the Director of Simbios, an NIH National Center for Biomedical Computing focused on physics-based simulations of biological structures based at Stanford University. Based on your research activities, I thought you would be interested in our upcoming workshop on rapid prototyping and simulations of molecular dynamics on GPUs that we are hosting with Dr. Vijay Pande. Please see the announcement below for the details. > > We invite you to attend and would appreciate you forwarding the announcement to colleagues and those in your lab that may be interested. > > Thank you. > > Regards, > Joy Ku > On behalf of Vijay Pande and the OpenMM team > --------------------------------------------------------------------------------------------------------- > Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. > OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs) [see benchmarks]. > And with the new application layer in its recent release, OpenMM will allow non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs. > > ***WORKSHOP: RAPID MOLECULAR DYNAMICS PROTOTYPING AND SIMULATIONS ON GPUS *** > > Where: Stanford University > When: September 6-7, 2012 > Description: > > During the workshop, you will gain hands-on experience using OpenMM’s new application layer and application programming interface (API). Learn to: > > * Set up and run an MD simulation on your GPU using both PDB and AMBER files > > * Create a custom force to apply to your simulations > > * Customize the simulation through Python scripting > > You will also have time to work with the OpenMM development team on your own research project. > > This workshop is designed for those interested in accelerating MD simulations on GPUs and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. No programming background is required, thoughprogramming topics will also be covered for those who are interested in them. > Registration: > > Registration is free but required and spaces are limited. To register or for more information, visithttp://simbios.stanford.edu/MDWorkshop.htm. > > OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. > > [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. > [2]Eastman, P. and Pande, V.S., “Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit,” J. Comp. Chem., 2010, 31(6):1268-1272. > > > > > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise
by Tom Ferrin 02 Jul '12

02 Jul '12

-------- Original Message -------- Subject: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise Date: Mon, 2 Jul 2012 13:14:05 -0700 (PDT) From: Joy P. Ku <joyku(a)stanford.edu> To: <dissemination-simbiosnews(a)simtk.org>, <openmm-news(a)simtk.org>, <simbios_postdocs(a)mailman.stanford.edu>, <simbios_all(a)mailman.stanford.edu> Dear Simbios friends: We have an opening for a software engineer with expertise in molecular dynamics simulations and high performance scientific computing. Details about the position are given below. To learn more or to apply, please visit http://bit.ly/ypYq8w. Please forward this to others who may be interested. Thank you, Joy *Software Engineer, Exempt, 4P3, 2 Year Fixed Term * Simbios, the Center for Physics-based Simulation of Biological Structures, is one of eight national centers funded by the National Institutes of Health to build a biomedical-computing infrastructure to speed progress in biomedical research. We are looking for a software engineer with expertise in molecular dynamics simulations and high performance scientific computing to support and extend the functionality of our OpenMM and Folding@Home software projects. OpenMM (http://simtk.org/home/openmm) is an open-source molecular dynamics prototyping and simulation software package that runs accelerated calculations on GPUs. Folding@home (http://folding.stanford.edu) is a distributed computing project that uses the power of hundreds of thousands of CPUs and GPUs around the world to study protein folding. This position is a fixed term position that will be conterminous with our grant funding from NIH. Our NIH grant is scheduled to end on August 31, 2014. Should our funding continue beyond this date, this position would likely be extended. *JOB DETAILS* You will be responsible for the entire software pipeline, including but not limited to: * Develop new algorithms and improve the performance of OpenMM, * Test and validate OpenMM * Migrate OpenMM code into the Folding@home framework * Coordinate the release of new Folding@home GPU cores * Act as liaison to GPU manufacturers NVIDIA and AMD * Actively participate in both the OpenMM and Folding@home support forums * Contribute to user documentation *QUALIFICATIONS* */Minimum Requirements /* * Experience in scientific algorithm development, high performance computing applications, and molecular dynamics simulations * Requires a minimum of five years programming experience * Four year college degree or equivalent years of applicable experience. * Experience and comfort with professional software development practices * Excellent communication skills, both written and oral * Possess an understanding of the underlying biology */Desired Requirements /* * MS or PhD in physics, biochemistry, bioinformatics, computer science, engineering, or life sciences or an equivalent combination of education and experience * Experience programming in C++, Python, and OpenCL * Experience programming graphics processing units (GPUs) * Experience with Windows, Unix, Linux, Mac platform cross-development * Has experience working in an interdisciplinary environment Resume & Cover Letter are mandatory for consideration. *The final candidate will need to successfully pass a background check to be considered for this position.* /Stanford University values diversity and is committed to equal opportunity in employment./ To learn more or to apply, please visit http://bit.ly/ypYq8w / / / / / / /_______________________________________________/ / / /Joy P. Ku, PhD/ /Director, Simbios/ /http://simbios.stanford.edu/ / / /Director of Communications & Training,/ /National Center for Simulation in Rehabilitation Research/ /http://opensim.stanford.edu/ / / /(W) 650.736.8434, (F) 650.723.7461/ /Email: joyku(a)stanford.edu <mailto:joyku@stanford.edu>/

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[Compbio-allhands] Fwd: Post Doctorant positions_BiMoDyM_France
by Andrej Sali 25 Jun '12

25 Jun '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Luba Tchertanov <luba.tchertanov(a)lbpa.ens-cachan.fr> > Subject: Post Doctorant positions_BiMoDyM_France > Date: June 25, 2012 3:16:39 AM PDT > To: kuriyan(a)berkeley.edu, Mark Sansom <mark.sansom(a)bioch.ox.ac.uk>, jmccammon(a)ucsd.edu, ruthnu(a)helix.nih.gov, roux(a)uchicago.edu, rebecca.wade(a)eml-r.villa-bosch.de, Frank Noe <frank.noe(a)fu-berlin.de>, shoshana.wodak(a)sickkids.ca, "Bahar, Ivet" <bahar(a)pitt.edu>, sali(a)salilab.org, "Ronald M. Levy" <ronlevy(a)lutece.rutgers.edu>, jonuchic(a)ucsd.edu, modesto.orozco(a)irbbarcelona.org, klebe(a)mailer.uni-marburg.de, igor.pivkin(a)usi.ch, mzoppe(a)ifc.cnr.it, Woody.Sherman(a)schrodinger.com, Ruben Abagyan <ruben(a)ucsd.edu>, maculan(a)cos.ufrj.br, okeskin(a)ku.edu.tr, marc_vidal(a)dfci.harvard.edu, "Prof. Haim J. Wolfson" <wolfson(a)tau.ac.il>, pascal.hersen(a)univ-paris-diderot.fr, Fabian Theis <fabian.theis(a)helmholtz-muenchen.de>, jaxelrod(a)stanford.edu, stas(a)princeton.edu, kandt(a)bit.uni-bonn.de, Jaroslaw Polanski <jaroslaw.polanski(a)us.edu.pl>, okamoto(a)phys.nagoya-u.ac.jp, denispt(a)pasteur.fr, yamato(a)phys.nagoya-u.ac.jp, akimura(a)tb.phys.nagoya-u.ac.jp, caflisch(a)bioc.uzh.ch, philippe.derreumaux(a)ibpc.fr, Chantal Prevost <chantal(a)ibpc.fr>, cragnolini(a)ibpc.fr, phuong.nguyen(a)ibpc.fr, francesco.oteri(a)ibpc.fr, charles.robert(a)ibpc.fr, Sophie.Sacquin-Mora(a)ibpc.fr, heidi.koldsoe(a)bioch.ox.ac.uk, michal.linial(a)huji.ac.il, taly(a)ibpc.fr, Viet Duc <frauman05(a)yahoo.de>, Elena.Papaleo(a)bio.ku.dk, Fabian Theis <fabian.theis(a)helmholtz-muenchen.de>, Sara Nichols <sara.nichols(a)gmail.com>, gregor.lichetner(a)fu-berlin.de, "Coulon, Antoine (NIH/NIDDK) [F]" <antoine.coulon(a)nih.gov>, johannes.schoeneberg(a)fu.berlin.de, alexander.ullrich(a)fu-berlin.de, mickael.lelimousin(a)bioch.ox.ac.uk, matthieu.chavent(a)bioch.ox.ac.uk > > Dears Colleagues, > > Two post doctoral research positions are available at the Bioinformatics, Molecular Dynamics and Modeling (BiMoDyM) team (http://tinyurl.com/tchertanov) Molecular Oncology and Pharmacology, LBPA, ENS de Cachan (http://www.ens-cachan.fr/) France. > The required profiles of candidats are descibed in the attached documents. > Thank you very much for larger distribution of this information. > > Sincerely your, > Luba Tchertanov > > ********************* > Dr. Luba Tchertanov > Directeur de Recherche, CNRS > > Membre du Comité de Pilotage du LabEx LERMIT > Coordinateur ENSC-UFRJ > Collége Universitaire Franco-Brésilien Santos Dumont > > Resp. BiMoDyM > LBPA-CNRS, ENS de Cachan, > 61 avenue du Président Wilson > 94235 CACHAN CEDEX, FRANCE > > Tel: +33 (0)1 4740 7662 > Cell: +33 (0)6 6115 9611 > Fax: +33(0)1 4740 7671 > e-mail: Luba.Tchertanov(a)lbpa.ens-cachan.fr > > >

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[Compbio-allhands] Fwd: postdoctoral and PhD positions
by Andrej Sali 25 Jun '12

25 Jun '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Michael Nilges <michael.nilges(a)pasteur.fr> > Subject: postdoctoral and PhD positions > Date: June 25, 2012 5:03:38 AM PDT > To: Alexandre Bonvin <a.m.j.j.bonvin(a)uu.nl>, Andrej Sali <sali(a)salilab.org>, annick.dejaegere(a)igbmc.fr, Axel Brunger <brunger(a)stanford.edu>, carol.robinson(a)chem.ox.ac.uk, Catherine Etchebest <catherine.etchebest(a)univ-paris-diderot.fr>, Cheryl Arrowsmith <carrow(a)uhnres.utoronto.ca>, Christian Griesinger <cigr(a)nmr.mpibpc.mpg.de>, Christoph Mueller <christoph.mueller(a)embl.de>, "David A. Agard" <agard(a)msg.ucsf.edu>, DavidBaker <dabaker(a)u.washington.edu>, David Perahia <david.perahia(a)ens-cachan.fr>, Dmitri Svergun <svergun(a)embl-hamburg.de>, Edward Egelman <egelman(a)virginia.edu>, Ernest Laue <e.d.laue(a)bioc.cam.ac.uk>, "G. Klebe" <Klebe(a)staff.uni-marburg.de>, Gerald Kneller <gerald.kneller(a)cnrs-orleans.fr>, Gerhard Wagner <gerhard_wagner(a)hms.harvard.edu>, Gilles Labesse <Gilles.Labesse(a)cbs.cnrs.fr>, Helmut Grubmueller <hgrubmu(a)gwdg.de>, Hoch Jeffrey <hoch(a)uchc.edu>, Ivano Bertini <bertini(a)cerm.unifi.it>, Jody Puglisi <puglisi(a)stanford.edu>, Julie Forman-Kay <forman(a)sickkids.ca>, Juri Rappsilber <juri.rappsilber(a)ed.ac.uk>, Konrad Hinsen <research(a)khinsen.fastmail.net>, liliane.mouawad(a)curie.u-psud.fr, Lewis Kay <kay(a)pound.med.utoronto.ca>, Luba Tchertanov <luba.tchertanov(a)lbpa.ens-cachan.fr>, Marc Baaden <baaden(a)smplinux.de>, Marc Baldus <maba(a)mpibpc.mpg.de>, Marius Clore <mariusc(a)intra.niddk.nih.gov>, Martin Beck <martin.beck(a)embl.de>, Michael Levitt <michael.levitt(a)stanford.edu>, Michael Sattler <sattler(a)helmholtz-muenchen.de>, michel kochoyan <michel(a)cbs.cnrs.fr>, Michele Vendruscolo <mv245(a)cam.ac.uk>, Oliver Lange <oliver.lange(a)tum.de>, Roland STOTE <rstote(a)igbmc.fr>, Aebersold Rudolf <aebersold(a)imsb.biol.ethz.ch>, Rebecca Wade <rebecca.wade(a)h-its.org>, ZINN Sophie 140275 <Sophie.ZINN(a)cea.fr>, Tom Simonson <Thomas.Simonson(a)polytechnique.fr>, William.Degrado(a)ucsf.edu, Wolfgang Baumeister <baumeist(a)biochem.mpg.de> > > Dear collegues, > > I would be very grateful indeed if you could transmit the information on the available positions to interested candidates. > > Best regards > > Michael > > Applications are invited for Postdoctoral and PhD positions funded by the ERC project BayCellS, to work on the development of innovative molecular modeling concepts for cellular structural biology. The successful candidates will join the Structural Bioinformatics Unit in the Department of Structural Biology and Chemistry at the Pasteur Institute in Paris, France. > > To characterize 3D structures of the large and often flexible macromolecular complexes that govern cellular processes, high resolution structure determination is the exception, and multiple sources of structural data at multiple resolutions are employed. Integrating these data into one consistent picture poses particular difficulties: data are much more sparse than in high resolution methods; data sets from heterogeneous sources are of highly different and unknown quality and may be mutually inconsistent; data are in general averaged over large ensembles and long measurement times. The project is to develop a consistent framework for this highly complex data integration problem, principally based on Bayesian probability theory. Appropriate models for the major data types used in hybrid approaches (electron microscopy, cross-linking/ mass spectrometry, various spectroscopy techniques, SAXS, ...) will be developed, as well as representations to include structural knowledge for individual components of the complexes. The new methods will be applied to a series of problems with increasing complexity. The ideal candidate has a strong background in mathematics/ statistics, theoretical biophysics or molecular modeling applied to macromolecular structure determination; experience in programming (Python, C); and an interest in Bayesian probability theory. > > Contact: Michael Nilges, Department of Structural Biology and Chemistry, Structural Bioinformatis Unit; michael.nilges(a)pasteur.fr > > > > > > > > ================ > Prof. Michael Nilges > Structural Bioinformatics Unit, Head > Department of Structural Biology and Chemistry, Head > Institut Pasteur, CNRS URA 2185 > 25-28 rue du docteur Roux, F-75015 Paris, France. > Tel: +33 1 45 68 82 30; Fax: +33 1 45 68 87 19 > secrétariat: +33 1 44 38 91 09 > > >

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[Compbio-allhands] FW: Hiring a Computational Biologist
by Jacobson, Matt 22 Jun '12

22 Jun '12

Brian was a BMI graduate student … very good scientist From: brian tuch <brian.tuch(a)gmail.com<mailto:brian.tuch@gmail.com>> Date: Friday, June 22, 2012 1:30 PM To: "btuch(a)onyx.com<mailto:btuch@onyx.com>" <btuch(a)onyx.com<mailto:btuch@onyx.com>> Subject: Hiring a Computational Biologist Hi all, I am looking for the best industry-bound graduate students and postdocs you know to join my new genomics group at Onyx. Onyx is small, but rapidly growing oncology therapeutics company in South San Francisco. My group's goals are to understand why certain patients respond to our existing drugs and to identify new drug targets in patients that do not. A lot of interesting basic and clinical research is involved in these efforts and I expect we will be publishing many of our findings. We will be starting with copious clinical samples and a generous budget, but not much else; our genomics infrastructure must be built from the ground up. This is my group's first hire, so I'm hoping to find an adaptable, star computational scientist, someone you might have thought to hire when you first started your labs. The hire will rapidly gain knowledge of cancer biology and the pharmaceutical process here, so those are not requirements. The most important characteristics are analytical chops and enthusiasm. The job description and specific requirements are attached. Please feel free to circulate this message. Thank you for your assistance. Cheers, Brian

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[Compbio-allhands] Fwd: Open Position for Computer System Administrator
by Andrej Sali 14 Jun '12

14 Jun '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Montelione, Gaetano" <guy(a)cabm.rutgers.edu> > Subject: Open Position for Computer System Administrator > Date: June 14, 2012 7:49:06 AM PDT > To: "Tejero, Roberto" <Roberto.Tejero(a)uv.es>, Honig Barry <bh6(a)columbia.edu>, Burkhard Rost <rost(a)columbia.edu>, "Y. Janet Huang" <yphuang(a)cabm.rutgers.edu>, "Ronald M. Levy" <ronlevy(a)lutece.rutgers.edu>, "Gerstein, Mark(a)yale.edu" <Mark.Gerstein(a)yale.edu>, Andrej Sali <sali(a)salilab.org>, "David A. Case" <case(a)biomaps.rutgers.edu> > Cc: John Everett <everett.jk(a)gmail.com> > > Phil Kostenbader, our computer system administrator, has taken a new job and will > be leaving CABM shortly. > > So we are looking for a new full time computer system administrator. Person > should be familiar with Linux system administration, including: > > - experience with Linux cpu clusters > - web server administration / Apache experience > - LDAP authentication > - network and system security /firewall DMZ > > > We will prepare a formal ad soon -- but I will appreciate if you can > circulate this to anyone you know who might be interested. They > can contact me directly > > Guy Montelione

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[Compbio-allhands] Fwd: Postdoc position available -- interactive molecular graphics -- Uppsala, Sweden
by Tom Ferrin 12 Jun '12

12 Jun '12

-------- Original Message -------- Subject: Postdoc position available -- interactive molecular graphics -- Uppsala, Sweden Date: Fri, 8 Jun 2012 12:47:08 -0500 From: Samuel Flores <samuelfloresc(a)gmail.com> To: tef(a)cgl.ucsf.edu Hi Tom, I hope all is well with you. As a longtime user of Chimera, I am familiar with your work. I think you may be able to help me identify a brilliant almost- or recently-graduated PhD for an opening in my lab. I am looking for a rare skill set -- someone who can make a next-generation interactive 3D modeling tool based on my internal coordinate MMB code and a graphics library (Blender, Rasmol, etc). The tool will go far beyond existing viewers, allowing users to assemble macromolecules, flexibilize them where desired, and rearrange domains interactively, as well as performing a number of dynamics tasks supported by MMB. I am attaching the job announcement and hope you can distribute it widely by email and (if possible) on bulletin boards at UCSF. I will be in Palo Alto July 2nd and perhaps 3rd and would love to drop by and chat, so as to receive your advice on this project, if you have the time. Sam

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[Compbio-allhands] Fwd: Referred by Christine Humblet
by Andrej Sali 04 Jun '12

04 Jun '12

Hi Andrej, If you decide to post these positions to your email list please have the students and postdocs contact me at the information below. Jared Jared Kaleck Account Executive Klein Hersh International 215-830-9211 Ext. 116 jkaleck(a)kleinhersh.com www.kleinhersh.com Begin forwarded message: > From: Jared Kaleck <JKaleck(a)kleinhersh.com> > Subject: RE: Referred by Christine Humblet > Date: June 4, 2012 11:26:00 AM PDT > To: Andrej Sali <sali(a)salilab.org> > > > > Eli Lilly – Indianapolis, IN > Principal Research Scientist/Senior Research Scientist > Computational Chemistry > The Discovery Chemistry Research and Technology Division at Eli Lilly Company is looking to further enhance the scientific talent base of the organization by identifying individuals with high potential and emerging track record of delivering drug discovery innovation. > > Ideal Individuals to Compliment Lilly’s Scientific Team > · Talented Ph.D. Computational Chemistry with broad expertise in Computer-Aided Design approaches. > · Creative thinking and problem solving skills – ability to bring new ways of applying or pioneering computational approaches and/or new initiatives to facilitate and enhance drug discovery projects. > · Proven/emerging scientific leadership abilities – must include leadership work with outside partners and/or scientists from academia. > · Ability to influence scientific direction across research sites, discovery functions and teams. A proven desire to make an impact on projects through cross-functional teamwork. > · Strong background in medicinal chemistry and lead generation/lead optimization approaches. > · Organizational development and mentoring skills. > · Excellence in communication and networking skills. > · Demonstrated abilities to multi-task. > · Entrepreneurial and innovative approach to science; good judgment, risk taking and intuition. > · Programming skills (Perl, Python, Pipelining) preferred. > > > > NOVARTIS – Cambridge, MA > Computational Chemical-Biology Research Investigator (Ph.D) > > Job Description: > > A position is available for a highly motivated scientist in the in silico Lead Discovery group of the Center for Proteomic Chemistry platform. This is an exciting opportunity to perform cutting-edge computational research at our Cambridge USA site. The position will be responsible for the development of robust computational hypothesis with a variety of drug discovery project teams for the purposes of lead discovery. You will apply state of the art computational approaches to elucidate the biological profile of small molecules regarding their targets, off-targets and phenotypic outcome via an in-depth understanding of biological networks, systems biology, bioinformatics and cheminformatics > > Minimum requirements: > > The ideal candidates will possess the following qualifications: > > · Ph.D. degree in computational biology, systems biology, bioinformatics, cheminformatics or a related field. > · Experience with 'omics analysis (transcriptomics, proteomics, metabolomics, chemogenomics). > · Ability to computationally navigate molecular pathways and networks and form hypotheses about compounds, targets, phenotype, and disease associations > · Familiarity with compound databases, such as ChEMBL or PubChem, and public bioinformatics databases. > · Understanding of up-to-date biological screening paradigms like reporter assays, mRNA signatures, assays for transcription, translation, stability, and post-translational modifications and high content screens. > · A solid understanding of quantitative data analysis, data mining and pattern recognition methods. > · Ability to work independently and collaborate in multidisciplinary teams locally and globally. > · Strong analytical and problem-solving skills and scientific creativity are essential. > · Excellent oral and written communication skills and organizational skills are required. > · Familiarity with life sciences software (R, Spotfire, Pipeline Pilot, Knime, Cytoscape, GeneGo) is desirable, as is a working knowledge of Relational Databases and SQL. > > > > NOVARTIS – Cambridge, MA > Computational Chemistry or Biology Research Investigator (Ph.D) > > Job Description: A position is available for a highly-motivated scientist to join a dynamic group in the Center for Proteomic Chemistry/Lead Finding Platform. This is an exciting opportunity to perform cutting-edge research at our Cambridge site. > First, you will be responsible for the analysis and development of HTS screening hits to leads. You will apply state of the art chemometric or bioinformatics approaches for the elucidation of the biological profile of small molecules regarding their targets, off-targets and phenotypic outcome. Second, you will provide support, maintenance and further development of key infrastructure related to virtual screening databases and methods, and an internally developed computational services framework. > > Minimum requirements: The ideal candidate will possess the following qualifications: > • Ph.D. degree in computational biology, bioinformatics, cheminformatics or a related field. > • Databases: MySQL, SQL Server and Oracle > • Languages: C, C#, Perl, Python, Web Applications and Tools: HTML, ASP.net, > • Experience with 'omics data and molecular pathway/network analysis to enhance target knowledge. > • Familiarity with compound information databases such as ChEMBL or PubChem. > • Understanding of up-to-date biological screening paradigms like reporter assays, mRNA signatures, assays for transcription, translation, stability, and post-translational modifications and high content screens. > • A solid understanding of basic statistics and quantitative data analysis, data mining and pattern recognition methods. > • Familiarly with PipelipePilot and Knime – a big plus > • Ability to both work independently and collaborate in multidisciplinary teams. > • Strong analytical and problem-solving skills and scientific creativity are essential. > • Excellent oral and written communication skills and organizational skills > > > > > > > > Jared Kaleck > Account Executive > Klein Hersh International > 215-830-9211 Ext. 116 > jkaleck(a)kleinhersh.com > www.kleinhersh.com >

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[Compbio-allhands] Fwd: reminder, seminar by Chia-en Chang
by Jacobson, Matt 01 Jun '12

01 Jun '12

Just a reminder about this seminar, 1pm, BH212 Begin forwarded message: I'm hosting Chia-en Chang on Friday June 1. She will give a seminar at 1 pm in BH212; title and abstract below. Chia-en did her graduate work with Mike Gilson and postdoc with Andy McCammon, and has been at UC Riverside for about 4 years now. The mining minima work she will be discussing is some of the most impressive free energy calculations I've seen. http://chem.ucr.edu/chang If you'd like to meet with her, Lili is helping to coordinate her schedule. Title: Insights from Free Energy Calculations: Protein Conformational Equilibrium, Driving Forces and Ligand Binding Processes Abstract: To accurately calculate ligand-protein binding affinity is still challenging in computational chemistry. In this presentation, we used a free energy calculation method, the mining minima algorithm (M2), to compute the binding affinities of various types of inhibitors to p38α MAP kinase. This end-point approach uses an empirical force field and implicit solvent models to find stable conformations in the free and bound states of a system and then compute the binding free energy of each species. Here we selected 30 different p38α inhibitors that can bind to either DFG-in or DFG-out conformations. Notably, some analogs do not have ligand-p38 co-crystal structures. Our computed absolutely binding free energies yield excellent agreement with experimental data and reveal the driving forces of binding. Our results also show the dynamic equilibrium in the DFG-in and DFG-out states and explain why the conformations can co-exist. In addition, I will introduce a novel method to study ligand binding processes in chemical host-guest system. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] seminar on Friday
by Jacobson, Matt 30 May '12

30 May '12

I'm hosting Chia-en Chang on Friday June 1. She will give a seminar at 1 pm in BH212; title and abstract below. Chia-en did her graduate work with Mike Gilson and postdoc with Andy McCammon, and has been at UC Riverside for about 4 years now. The mining minima work she will be discussing is some of the most impressive free energy calculations I've seen. http://chem.ucr.edu/chang If you'd like to meet with her, Lili is helping to coordinate her schedule. Title: Insights from Free Energy Calculations: Protein Conformational Equilibrium, Driving Forces and Ligand Binding Processes Abstract: To accurately calculate ligand-protein binding affinity is still challenging in computational chemistry. In this presentation, we used a free energy calculation method, the mining minima algorithm (M2), to compute the binding affinities of various types of inhibitors to p38α MAP kinase. This end-point approach uses an empirical force field and implicit solvent models to find stable conformations in the free and bound states of a system and then compute the binding free energy of each species. Here we selected 30 different p38α inhibitors that can bind to either DFG-in or DFG-out conformations. Notably, some analogs do not have ligand-p38 co-crystal structures. Our computed absolutely binding free energies yield excellent agreement with experimental data and reveal the driving forces of binding. Our results also show the dynamic equilibrium in the DFG-in and DFG-out states and explain why the conformations can co-exist. In addition, I will introduce a novel method to study ligand binding processes in chemical host-guest system. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] QBC Journal Club, Tuesday, June 5- 10:45AM, GH Aud
by Nicole Takesono Flowers 30 May '12

30 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, June 5 10:45 am, GH Auditorium Jessica Thomaston, CCB Experimental adaptation of an influenza H5 HA confers respiratoryrndroplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Imai, Masaki et al. Nature. Available online May 2012. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Faculty positions
by Andrej Sali 25 May '12

25 May '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: pettitt <mpettitt(a)utmb.edu> > Subject: Faculty positions > Date: May 25, 2012 12:58:39 PM PDT > To: sali(a)salilab.org > > Dear Andrej, > > To expand our programs in structural biology at the University of Texas Medical Branch in Galveston, we are beginning searches to fill three senior-level faculty positions in the Sealy Center for Structural Biology and Molecular Biophysics. We currently seek individuals whose connection to structural biology is through cryo EM, x-ray or NMR (nominally one position each) and who wish to take advantage of a rich collaborative environment. This is part of a large investment by the university in structural biology and ten related hires are expected over the next 5 years. The first individual(s) hired will have a significant role in selecting the remaining senior and junior individuals hired into the program. > > We have facilities with excellent instrumentation and fully staffed with high quality individuals. Ours is a research resource supported by the University so there are no core charges for Center faculty to use our facilities. That and our location on the outskirts of Houston with proximity to the Texas Medical Center are attractive features. > > If you know of anyone that may have interest, we would be delighted to hear about it. Further information about the position(s) can be found attached. As well, additional information about the Sealy Center for Structural Biology may found on the web at http://www.scsb.utmb.edu/ > Thank you in advance for any help that you can provide in identifying suitable senior-level candidates for these positions. > > Sincerely, > Monte > > B. Montgomery Pettitt > Robert A. Welch Professor of Chemistry > in Pharmacology and Toxicology > Professor of Biochemistry and Molecular Biology > Director, Sealy Center for Structural Biology > and Molecular Biophysics > University of Texas Medical Branch > mpettitt(a)utmb.edu

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[Compbio-allhands] 5/31/12 Seminar with Ira Mellman
by Nicole Takesono Flowers 25 May '12

25 May '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Jim Ferrell Stanford University Dissecting the Mitotic Trigger May 31, 2012 W. Lim, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Request for assistance - Associate Scientist opportunity with Genentech - Absorption process & PK/PD Formulation
by Jacobson, Matt 23 May '12

23 May '12

-- Matt Sent from my iPhone Begin forwarded message: From: Keith Terry <terry.keith(a)gene.com<mailto:terry.keith@gene.com>> Date: May 23, 2012 11:00:23 AM PDT To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Request for assistance - Associate Scientist opportunity with Genentech - Absorption process & PK/PD Formulation Hi Matthew, My name is Keith Terry and I am an internal recruiter with Genentech in South San Francisco. I am reaching out to you today to ask for your assistance. I am supporting Genentech’s Early Research and Development (gRED) department in the area of formulation development small molecules. We have an outstanding opportunity for a passionate and innovative Ph.D. to join our group. I thought that you might know of a dynamic scientist (either a recent graduate or currently in post doc) that would be interested in the attached job. Potential candidates DO NOT need previous pharmaceutical industry experience. A well published Ph.D. who has recently graduated from a highly regarded program would be perfect. To summarize what we are looking for: • Ph.D. level candidates with strong scientific knowledge in Pharmaceutical Sciences and a proven record of publications. • In-depth knowledge absorption process, PK/PD and application of such knowledge in science-based formulation approaches and drug delivery design. • Good communication and problem-solving skills and be a team player. • Must have a Ph.D in Pharmaceutics, Chemistry, or related fields with minimum of 0-5 years-experience in the Pharmaceutical Industry. Please feel free to pass the attached flier along to individuals that you feel would be qualified and potentially interested. You are welcome to post the flier on your department’s job board. If you have any questions at all regarding this opportunity or would like to learn more about Genentech, please feel to call me directly. Thanks so much for your assistance. Cheers, Keith Keith Terry Talent Acquisition Specialist Genentech, A Member of the Roche Group 650-467-1557<tel:650-467-1557> terry.keith(a)gene.com<mailto:terry.keith@gene.com> Why is Genentech such a great place to work? Check out this video! Our People<http://www.youtube.com/watch?v=DMalKJ0_8-A> (click to view)

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[Compbio-allhands] QBC Journal Club, Tuesday, May 29- 10:45AM, GH Aud
by Nicole Takesono Flowers 23 May '12

23 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 29 10:45 am, GH Auditorium Yu Jack Yue, iPQB Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication. Megan Y. Dennis, et al. Cell 149, 4, 912-922. 2012 Diego Garrido Ruiz, iPQB Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing. Hopf, Thomas A., Colwell, Lucy J.,Sheridan, Robert, Rost, Burkhard, Sander, Chris, Marks, Debora S. Cell, Available online May 2012. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Genentech postdoc position: request for candidates
by Andrej Sali 22 May '12

22 May '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Isidro (Dan) Zarraga" <zarraga.isidro(a)gene.com> > Subject: Genentech postdoc position: request for candidates > Date: May 22, 2012 2:31:30 PM PDT > To: sali(a)salilab.org > Cc: hilary(a)salilab.org > > Dear Prof. Sali, > > Please find attached a description of a Genentech postdoc opportunity. Kindly circulate to those who might be interested. We would like to fill the position soon so those interested are encouraged to send their resumes as soon as possible. Thank you very much. > > Sincerely, > > Dan E. Zarraga, PhD > Late Stage Pharmaceutical Development > Genentech Bldg 56 Rm 2119 > South San Francisco CA 94030 > Tell: 650 2257617

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[Compbio-allhands] 5/24/12 Seminar with Ira Mellman
by Nicole Takesono Flowers 18 May '12

18 May '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Ira Mellman Genentech Next Generation Approaches to Basic Cell Biology & Drug Discovery May 24, 2012 Justin Rettenmeier, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, May 22- 10:45AM, GH Aud
by Nicole Takesono Flowers 16 May '12

16 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 22 10:45 am, GH Auditorium Andrew Van Benschoten, iPQB Sexual Deprivation Increases Ethanol Intake in Drosophila. Shohat-Ophir et al. Science, 2012 Mar 16; 335 (6074): 1351-5. Naomi Yonis, CCB Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress. Lee, I.H. et al. Science ,336, 225 (2012). bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 5/17/12 Seminar with Jennifer Lippincott-Schwartz
by Nicole Takesono Flowers 11 May '12

11 May '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Jennifer Lippincott-Schwartz NIH Mitochondria, metabolism and cell cycle control: an imaging perspective May 17, 2012 Amanda Silber & Si-Han Chen, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, May 15- 10:45AM, GH Aud
by Nicole Takesono Flowers 10 May '12

10 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 15 10:45 am, GH Auditorium Russell Goodman, iPQB Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. Soranno A. et al., Proc Natl Acad Sci. 2012 Apr 6. James Webber, iPQB DNA breaks and chromosome pulverization from errors in mitosis. Crasta K et al, Nature. 2012 Feb 2; 482(7383):53-8. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, May 8- 10:45AM, GH Aud
by Nicole Takesono Flowers 02 May '12

02 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 8 10:45 am, GH Auditorium Xiaoming Liang, PSPG A PGC1-α-dependent myokine that drives brown-fat-like development of white fat and thermogenesis. Bostrom P. et al. Nature. Jan 11;481(7382):463-8. 2012 Stephen Nayfach-Battilana, iPQB Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota. Iverson, V et al. Science Vol. 335 no. 6068 pp. 587-590. 2012. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 5/3/12 Seminar with Russ Altman
by Nicole Takesono Flowers 27 Apr '12

27 Apr '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Russ Altman Stanford The emerging network of data for linking genes and drugs May 3, 2012 Chris Wen, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Position in structural biology available at Lilly Biotechnology Center in San Diego
by Andrej Sali 26 Apr '12

26 Apr '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "J. Michael Sauder" <sauder_j_michael(a)lilly.com> > Subject: Position in structural biology available at Lilly Biotechnology Center in San Diego > Date: April 26, 2012 11:06:01 AM PDT > To: "J. Michael Sauder" <sauder_j_michael(a)lilly.com> > > A position is opening for a person with significant experience in structural biology and broad knowledge of several therapeutic areas. It is an opportunity to work in an industrial, drug-discovery setting and make significant contributions to a world class structural biology team. > > Details are available on the lilly.com website (Careers, job id 50448492), or by following this link: > https://careers.peopleclick.com/careerscp/client_lilly/external/jobDetails.… > > Please feel free to forward this message to anyone you think might be interested. > > Mike > > J. Michael Sauder, Ph.D. > Research Advisor, Structural Biology > Lilly Biotechnology Center > 10300 Campus Point Dr, San Diego, CA 92121 > michael.sauder(a)lilly.com > office: 858-638-8802 main: 858-597-4990 >

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[Compbio-allhands] Fwd: Intern Positions at Janssen Pharmaceutical R&D
by Andrej Sali 25 Apr '12

25 Apr '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Stephens, Susan [JRDUS]" <sstephens1(a)ITS.JNJ.COM> > Subject: Intern Positions at Janssen Pharmaceutical R&D > Date: April 25, 2012 5:14:59 PM PDT > To: "Stephens, Susan [JRDUS]" <sstephens1(a)ITS.JNJ.COM> > > The In Silico Immunology team in Janssen Pharmaceutical Research & Development L.L.C., a member of Johnson and Johnson's family of companies, is recruiting for two Research Scientists for 2012 Pharmaceutical R&D internships, located in Radnor, PA. > > Please share information about the positions with any candidates that may be interested. Formal applications should be made on the J&J Career Web site (http://careers.jnj.com) > > Kind regards, > > Susie > > > 2012 PHARMACEUTICAL R&D INTERNSHIPS in In Silico Immunology - 000004FN > > 1. Network Pharmacology > > Janssen Pharmaceutical Research & Development is seeking a graduate student with strong computational skills interested in an internship position in the Network Pharmacology group. The candidate’s current research area should be Systems Biology, Bioinformatics, Computer Science or Engineering, have a solid understanding of network analysis methods and biology as well as programming experience and ability to write R, Matlab and/or Perl script. Experience with large-scale genomics data and a solid understanding of bioinformatics tools and databases is a plus. The successful candidate will focus on the development of bioinformatics approaches to integrate and analyze data from various cutting-edge projects in the Immunology Therapeutic Area. > > The candidate will develop and investigate methods to understand dysregulated mechanisms in disease using Network Pharmacology approaches. They will conduct network analysis and inference on large-scale data that provides a global view of the disease that would help determining its representation in the relevant in-vivo and in-vitro models. > > · Construct biological networks from molecular profiling data and from molecular interaction data stored in databases > > · Conduct research on topological analysis to find key regulatory genes/proteins via biological network and genomic data > > · Identify robust sub-networks using different data modalities (mRNA, proteins, DNA, etc.) > > · Reconstruct network modules from the identified key regulators to discover affected biological processes and disease-related genes > > > 2. Lifecycle Management > > Janssen Pharmaceutical Research & Development is seeking a graduate student with strong computational skills interested in an internship position in focused on Lifecycle Management. The candidate’s current research area should be Systems Biology, Bioinformatics, Computer Science or Engineering. The intern will be responsible for developing algorithms and workflows that will facilitate the analysis of preclinical and clinical data. Through the implementation of these workflows, the intern will explore potential new disease indications for marketed and late stage development clinical compounds across the large and small molecule Immunology Therapeutic Area portfolio. The successful intern will work with the In Silico Immunology team to develop computational methodologies that will enable the combination of data outputs from different software platforms to build in silico networks of autoimmune and pulmonary diseases. > > Experience in computational algorithms and mathematical modeling, preferably of biological or disease networks, is required for this position. Analysis of large datasets, especially microarray data, is preferred. Expertise in computer software such as R, Matlab, Ingenuity Pathways, and Cytoscape is also desirable. > > > > >

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[Compbio-allhands] QBC Journal Club, Tuesday, May 1- 10:45AM, GH Aud
by Nicole Takesono Flowers 24 Apr '12

24 Apr '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 1 10:45 am, GH Auditorium Katherine Southard, CCB Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. R. Rodriguez et al. Nature chemical biology 8 (3) p. 301-10. 2012. Graham Heimberg, iPQB The most expensive cold diagnosis ever Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes Rui Chen et al. Cell 148, 1293-1307. March 16, 2012. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 4/26/12 Seminar with Howard Hang
by Nicole Takesono Flowers 20 Apr '12

20 Apr '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Howard Hang Harvard Chemical Reporters for Protein S-Palmitoylation in Cell Biology and Innate Immunity April 26, 2012 Danica Galonic Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, April 24- 10:45AM, GH Aud
by Nicole Takesono Flowers 18 Apr '12

18 Apr '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, April 24 10:45 am, GH Auditorium Alex Pankov, iPQB Detecting novel associations in large datasets. D. N. Reshef, Y. A. Reshef, H. K. Finucane, S. R. Grossman, G. McVean, P. J. Turnbaugh,E. S. Lander, M. Mitzenmacher, P. C. Sabeti. Science, 334: 1518-1524, (2011). Christina Fitzsimmons, CCB To Knot or Not? Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. A.L. Mallam & S.E. Jackson. Nature Chemical Biology, 2012, 8, 147-153. doi: 10.1038/nchembio.742. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Automated Function Prediction: and ISMB Special Interest Group Meeting
by Alexandra Schnoes 17 Apr '12

17 Apr '12

---------- Forwarded message ---------- From: Iddo Friedberg <idoerg(a)gmail.com> Date: Tue, Apr 17, 2012 at 8:27 AM Subject: Automated Function Prediction: and ISMB Special Interest Group Meeting To: ISB(a)listserv.it.northwestern.edu Locale: Long Beach, California USA Date: July 14, 2012 (Just before ISMB 2012) URL: http://biofunctionprediction.org Important dates: April 25, 2012: Deadline for submitting abstracts. (extended!) May 9, 2011: Notifications for accepted abstracts e-mailed to corresponding authors May 16, 2011: Deadline for presenters to confirm acceptance of invitation to speak. July 14, 2011: AFP SIG preceding ISMB 2012 An ISMB Special Interest Group Meeting Automated Protein Function Prediction Sequence and structure genomics have generated a wealth of data, but extracting meaningful information from genomic information is becoming an increasingly difficult challenge. Both the number and the diversity of discovered sequences are increasing, while the fraction of genes whose function is known is decreasing.In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software which is out there. For these reasons and many more, automated protein function prediction is rapidly gaining interest among computational biologists in academia and industry. The AFP SIG has been part of ISMB since 2005. We call upon all researchers involved in gene and protein function prediction to submit an abstract to the AFP meeting. Authors of select abstracts will be invited to give a talk and/or present a poster. This year, AFP is delighted to have Jonathan Eisen from the University of California, Davis as its keynote speaker. Prof. Eisen is a pioneer in the field of function prediction. >From his lab page: http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/Main_Page "Dr. Eisen has published more than 200 scientific papers and is a co-author of a relatively recently published Evolution Textbook. Dr. Eisen is also a strong proponent of the Open Access movement in scientific publishing and is Academic Editor in Chief of PLoS Biology. For recent news see http://twitter.com/phylogenomics" For further instructions on how to submit abstracts to AFP 2012, please go here: http://biofunctionprediction.org/node/415 We are looking forward to seeing you in Long Beach, California! Iddo Friedberg on behalf of the AFP organizing committee -- Iddo Friedberg http://iddo-friedberg.net/contact.html -- Alexandra Schnoes, Ph.D. Scientist, Babbitt Laboratory Program Coordinator, Graduate Student Internships for Career Exploration University of California San Francisco Tel: 415-502-1248 Fax: 415-514-9656 Email: schnoes(a)gmail.com

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[Compbio-allhands] 4/19/12 Seminar with Alan Engelman
by Nicole Takesono Flowers 13 Apr '12

13 Apr '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Alan Engelman Harvard Retroviral integrase function and drug resistance mechanisms April 19, 2012 Bob Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 5/31/12 Seminar with Greg Verdine- CANCELLED
by Nicole Takesono Flowers 12 Apr '12

12 Apr '12

Due to unforeseen circumstances, the seminar scheduled on 5/31/12 has been cancelled. Please stay tuned for a new speaker announcement. Thank you, Nicole Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, April 17- 10:45AM, GH Aud
by Nicole Takesono Flowers 11 Apr '12

11 Apr '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, April 17 10:45 am, GH Auditorium Marian Deuker, CCB The molecular basis of acid insensitivity in the African naked mole-rat. Smith ES, Omerbasic 263; D, Lechner SG, Anirudhan G, Lapatsina L, Lewin GR. Science. 2011 Dec 16;334(6062):1557-60. Liz Howe, BMI Host Cell Invasion by Apicomplexan Parasites: Insights from the Co-Structure of AMA1 with a RON2 peptide ML Tonkin, M Roques, MH Lamarque, M Pugniere, D Douguet, J Crawford, M Lebrun, MJ Boulanger. Science 22 July 2011: Vol. 333 no. 6041 pp. 463-467. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 4/12/12 Seminar with Michelle Chang
by Nicole Takesono Flowers 05 Apr '12

05 Apr '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Michelle Chang UC Berkeley Building new chemical function in living organisms April 12, 2012 Kevan Shokat & Jack Taunton, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, April 10- 10:45AM, GH Aud
by Nicole Takesono Flowers 04 Apr '12

04 Apr '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, April 10 10:45 am, GH Auditorium Sarah Woldemariam, CCB Critical Role of Amyloid-like Oligomers of Drosophila Orb2 in the Persistence of Memory Cell, Volume 148, Pages 515-529, Published February 3, 2011 Kyle Barlow, iPQB Of mice and men: an Alzheimer's cure for our murine brethren ApoE-Directed Therapeutics Rapidly Clear Β-Amyloid and Reverse Deficits in AD Mouse Models Cramer, Paige E, John R Cirrito, Daniel W Wesson, C. Y. Daniel Lee, J. Colleen Karlo, Adriana E Zinn, Brad T Casali, et al. Science 335, no. 6075 (March 23, 2012): 1503-1506. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 4/5/12 Seminar with Ian Wilson
by Nicole Takesono Flowers 02 Apr '12

02 Apr '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Ian Wilson Scripps Broad neutralization of HIV and influenza viruses April 5, 2012 Bob Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Hiring at the Friedberg lab
by Alexandra Schnoes 30 Mar '12

30 Mar '12

---------- Forwarded message ---------- From: Iddo Friedberg <idoerg(a)gmail.com> Date: Wed, Mar 28, 2012 at 8:26 AM Subject: Hiring at the Friedberg lab To: Dear Friends, Apologies for the mass email. Please pass this on to interested parties. PDF version attached. Location: Miami University, Oxford OH, USA Department: Microbiology Start date: as soon as possible Salary: competitive and commensurate with experience and qualifications The Friedberg Lab is looking to hire a Scientific Programmer/ Bioinfromatics Specialist to implement and maintain a genomic database web site; implement data management tools including relational database management applications for efficient storage and retrieval of genomic data; perform other duties as related to the position such as data and project management to ensure data are being processed in an efficient and timely manner; contribute to writing scientific manuscripts. Three year position renewed annually depending on funding and performance. *Required qualifications*: BS or BA in Computer Science, bioinformatics, or a related discipline; demonstrated programming experience, particularly in Python and SQL databases; demonstrated web programming experience; knowledge of Linux/Unix; excellent spoken and written communication and documentation skills. *Preferred qualifications*: Advanced degree (M.Sc. or Ph.D) or equivalent in Computer Science, Bioinformatics, Molecular Biology or a related discipline; experience in development of bioinformatic algorithms; knowledge of R programming; experience in development of or contribution to open source projects; experience in collaborative software development such as the use of version control software, writing and following software specifications, participation in code review; knowledge of basic molecular biology; experience with genomic browser programming, such as GMOD or equivalent. Candidates should send a CV or resume and have three letters of reference sent separately to Dr. Iddo Friedberg at friedberg.lab.jobs(a)gmail.comScreening of applications begins April 14, 2012 and will continue until the position is filled. Miami University is an affirmative action/equal opportunity employer with smoke-free campuses. Consumer Information http://www.miami.muohio.edu/about-miami/publications-and-policies/student-c…. Hard copy upon request. -- Iddo Friedberg http://iddo-friedberg.net/contact.html ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----. .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>> >>----.<--.>++++++.<<<<------------------------------------.

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[Compbio-allhands] QBC Journal Club, Tuesday, April 3- 10:45AM, GH Aud
by Nicole Takesono Flowers 27 Mar '12

27 Mar '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, April 3 10:45 am, GH Auditorium Aishjay Jayagopal, PSPG First-in-Human Testing of a Wirelessly Controlled Drug Delivery Microchip. R. Farra et al, Science Translational Medicine, Feb 2012. Tara Friedrich, iPQB Multiple Epigenetic Modifiers Induce Aggressive Viral Extinction in Extraembryonic Endoderm Stem Cells. M.C. Golding, L. Zhang, M.R.W. Mann. Cell Stem Cell, Volume 6, Issue 5, 457-467, 7 May 2010. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] David Sivak Seminar - Monday, April 2 - 11am - 12pm, Byers Hall 212
by Hilary Mahon 26 Mar '12

26 Mar '12

Please see attached for Dr. Sivak of the Lawrence Berkeley Lab. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] QBC Journal Club, Tuesday, March 27- 10:45AM, GH Aud
by Nicole Takesono Flowers 21 Mar '12

21 Mar '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, March 27 10:45 am, GH Auditorium Amy Jacobson, CCB Antiparallel EmrE exports drugs by exchanging between asymmetric structures. Moarrison E.A., et al. Nature 481, 45-50 (2012). Kale Kundert, iPQB Identification of oxadiazoles as new drug leads for the control of schistosomiasis. A. Sayed, A. Simeonov, C. Thomas, J. Inglese, C. Austin and D. Williams. Nature Medicine 14, 407-412 (2008). bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] NO BBC Journal Club 3/20/12
by Nicole Takesono Flowers 19 Mar '12

19 Mar '12

Hi all, Just a reminder that there the BBC Journal Club will NOT be held tomorrow, Tuesday, March 20. Thank you, Nicole Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Time/Room Change - March 13, Adrian Elcock Seminar
by Hilary Mahon 12 Mar '12

12 Mar '12

Please see attached for updated time and room. Thank you, Hilary --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] Fwd: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise
by Tom Ferrin 09 Mar '12

09 Mar '12

-------- Original Message -------- Subject: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise Date: Fri, 9 Mar 2012 13:00:36 -0800 (PST) From: Joy P. Ku <joyku(a)stanford.edu> To: <dissemination-simbiosnews(a)simtk.org>, <simbios_postdocs(a)mailman.stanford.edu>, <simbios_all(a)mailman.stanford.edu> Dear Simbios friends: We have an opening for a software engineer with expertise in molecular dynamics simulations and high performance scientific computing. Details about the position are given below. To learn more or to apply, please visit http://bit.ly/ypYq8w. Please forward this to others who may be interested. Thank you, Joy *Software Engineer, Exempt, 4P3, 2 Year Fixed Term * Simbios, the Center for Physics-based Simulation of Biological Structures, is one of eight national centers funded by the National Institutes of Health to build a biomedical-computing infrastructure to speed progress in biomedical research. We are looking for a software engineer with expertise in molecular dynamics simulations and high performance scientific computing to support and extend the functionality of our OpenMM and Folding@Home software projects. OpenMM (http://simtk.org/home/openmm) is an open-source molecular dynamics prototyping and simulation software package that runs accelerated calculations on GPUs. Folding@home (http://folding.stanford.edu) is a distributed computing project that uses the power of hundreds of thousands of CPUs and GPUs around the world to study protein folding. This position is a fixed term position that will be conterminous with our grant funding from NIH. Our NIH grant is scheduled to end on August 31, 2014. Should our funding continue beyond this date, this position would likely be extended. *JOB DETAILS* You will be responsible for the entire software pipeline, including but not limited to: * Develop new algorithms and improve the performance of OpenMM, * Test and validate OpenMM * Migrate OpenMM code into the Folding@home framework * Coordinate the release of new Folding@home GPU cores * Act as liaison to GPU manufacturers NVIDIA and AMD * Actively participate in both the OpenMM and Folding@home support forums * Contribute to user documentation *QUALIFICATIONS* */Minimum Requirements /* * Experience in scientific algorithm development, high performance computing applications, and molecular dynamics simulations * Requires a minimum of five years programming experience * Four year college degree or equivalent years of applicable experience. * Experience and comfort with professional software development practices * Excellent communication skills, both written and oral * Possess an understanding of the underlying biology */Desired Requirements /* * MS or PhD in physics, biochemistry, bioinformatics, computer science, engineering, or life sciences or an equivalent combination of education and experience * Experience programming in C++, Python, and OpenCL * Experience programming graphics processing units (GPUs) * Experience with Windows, Unix, Linux, Mac platform cross-development * Has experience working in an interdisciplinary environment Resume & Cover Letter are mandatory for consideration. *The final candidate will need to successfully pass a background check to be considered for this position.* /Stanford University values diversity and is committed to equal opportunity in employment./ /_______________________________________________/ / / /Joy P. Ku, PhD/ /Director, Simbios/ /http://simbios.stanford.edu/ / / /Director of Communications & Training,/ /National Center for Simulation in Rehabilitation Research/ /http://opensim.stanford.edu/ / / /(W) 650.736.8434, (F) 650.723.7461/ /Email: joyku(a)stanford.edu <mailto:joyku@stanford.edu>/

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[Compbio-allhands] Fwd: Opening for Professor in Spatiotemporal Modeling of Biological Processes
by Andrej Sali 08 Mar '12

08 Mar '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Torsten Schwede <torsten.schwede(a)unibas.ch> > Subject: Opening for Professor in Spatiotemporal Modeling of Biological Processes > Date: March 8, 2012 1:46:20 PM PST > To: Torsten Schwede <Torsten.Schwede(a)unibas.ch> > > Dear colleagues, > > there is an opening for a professorship in computational biology at the Biozentrum in Basel. If you know somebody working in the field of Spatiotemporal Modeling of Biological Processes who might be interested, could you please forward the announcement? > > Thanks a lot for your help, > > Torsten > > > ========================== > Professor in Spatiotemporal Modeling of Biological Processes > > Job Specification > The Biozentrum of the University of Basel in Switzerland invites applications for a professorship in modeling of spatiotemporal processes in biology. The position can be filled at the Assistant (Tenure-track), Associate or Full Professor level depending on the qualifications of the applicant. > > We are searching for applicants that are at the forefront of research and methods development in the field of spatiotemporal modeling in biology including multiscale modeling. The ideal candidate should combine her/his activity in the development of novel computational modeling and analysis methods with a deep understanding of biology and focus on concrete biological questions from a well-defined area of molecular or cell biology in which spatiotemporal processes play an important role. Areas of interest include, but are not limited to, spatiotemporal patterns of gene expression, morphogenesis, and the dynamics of the cell cycle, of membranes, and of chromatin organization. Applications from candidates that combine cutting-edge computational modeling with wet lab approaches are encouraged. The successful candidate will have a strong research record and communication skills, should complement the research portfolio of the Biozentrum, have a desire to engage in local collaborations, and will actively participate in teaching at the undergraduate and postgraduate level. > > The Biozentrum offers an outstanding scientific environment and an attractive research endowment. Basel is the home of a vibrant international life science community and provides a high standard of living and a superb cultural atmosphere. > > Applications, including CV, list of publications and a short research summary, should be sent by e-mail (pdf or zip) to Prof. Dr. Martin Spiess, Dean, Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland, to dekanat-philnat-at-unibas.ch. For informal inquiries please contact Prof. Dr. Erich A. Nigg (erich.nigg-at-unibas.ch, phone: +41-61-267 16 56). > > The deadline for receipt of applications is March 19, 2012. The University of Basel is an equal opportunity employer and encourages applications from female candidates. > > Contact > > Universität Basel > Philosophisch-Naturwissenschaftliche Fakultät Dekanat > Klingelbergstrase 50 > 4056 Basel > Switzerland > > http://www.biozentrum.unibas.ch/open-positions/ > >

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[Compbio-allhands] 3/15/12 Seminar with Harmit Malik
by Nicole Takesono Flowers 07 Mar '12

07 Mar '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Harmit Malik FHCRC Genetic conflicts: the usual suspects and beyond March 15, 2012 John Gross, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Announcing the 'Frontiers in Systems Biology' Symposium on Monday, March 19th, 2012
by Lee, Connie 07 Mar '12

07 Mar '12

FRONTIERS IN SYSTEMS BIOLOGY SYMPOSIUM featuring young scientists in an emerging field MONDAY, MARCH 19th, 2012 Genentech Hall (Byers) Auditorium 9:30 - 10:00 am Light Breakfast in atrium 10:00 - 10:40 am Joshua Weinstein | Stanford University 'From zebrafish to humans: what snapshots of antibody repertoires can tell us about immune dynamics' 10:40 - 11:20 am Sean Summers | ETH 'Systems, biology, and control: from cell function discovery to cyborg cells' 11:20 - 12:00 pm Moran Yassour | Hebrew University / Broad Institute 'Characterizing transcriptomes from high throughput sequencing data: from yeast to mammals and back' 12:00 - 12:45 pm Lunch on your own 12:45 - 1:25 pm Marisa Eisenberg | Ohio State University 'Identifiability and parameter estimation for modeling human disease' 1:25 - 2:05 pm Mohammed AlQuraishi | Stanford University 'Predicting protein-DNA interactions from first principles' 2:05 - 2:45 pm Sean Stromberg | Emory University 'Dynamics of chronic infections and passive demethylation' 3:00 - 5:00 pm Poster session & reception in atrium All are welcome to attend | no registration required Sponsored by the UCSF Center for Systems & Synthetic Biology ------------------------------------------ Connie M. Lee, Ph.D. Associate Director Center for Systems & Synthetic Biology University of California, San Francisco 1700 4th Street, Byers Hall 408A, Box 2540 San Francisco, CA 94158 +1 (415) 514-1290 connie.lee2(a)ucsf.edu<mailto:connie.lee2@ucsf.edu> http://systemsbiology.ucsf.edu/ http://www.facebook.com/pages/UCSF-Center-for-Systems-Synthetic-Biology/231… ------------------------------------------

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[Compbio-allhands] QBC Journal Club, Tuesday, March 13- 10:45AM, GH Aud
by Nicole Takesono Flowers 07 Mar '12

07 Mar '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, March 13 10:45 am, GH Auditorium Nicole Olson, CCB Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride. JL Baker, N Sudarsan, Z Weinberg, A Roth, RB Stockbridge, RR Breaker. Science, 13 January 2012, 335 (6065): 233-235. Greg Fedewa, iPQB Flavor network and the principles of food pairing. YY Ahn, SE Ahnert, JP Bagro, AL Barabasi. Scientific Reports Vol 1. 2011 bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Postdoctoral Research Fellowship Opportunities-- Stanford Molecular Imaging Scholars Program
by Tom Ferrin 06 Mar '12

06 Mar '12

-------- Original Message -------- Subject: Postdoctoral Research Fellowship Opportunities-- Stanford Molecular Imaging Scholars Program Date: Fri, 02 Mar 2012 09:53:12 -0800 From: Sofia Gonzales <sofias(a)stanford.edu> To: tef(a)cgl.ucsf.edu CC: jmolla(a)cgl.ucsf.edu, nicole(a)picasso.ucsf.edu Dear Dr. Ferrin, The Stanford Molecular Imaging Scholars (SMIS) Program is currently recruiting 3 postdoctoral fellows (flyer attached). We would appreciate it if you could forward this information on to your graduate students or postdocs. More information can be found at: http://mips.stanford.edu/grants/smis/ Thank you, Sofia ~~~~~ Sofia Gonzales Program Coordinator Stanford Molecular Imaging Scholars (SMIS) Program Stanford University Tel: (650) 724-9139; Fax: (650) 721-6619 Email: sofias(a)stanford.edu SMIS web site: http://mips.stanford.edu/grants/smis/

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[Compbio-allhands] Fwd:
by Brian Shoichet 06 Mar '12

06 Mar '12

FYI. ---------- Forwarded message ---------- From: Shahriar Mobashery <mobashery(a)nd.edu> Date: Tue, Mar 6, 2012 at 11:27 AM Subject: To: shoichet <shoichet(a)cgl.ucsf.edu> Dear Brian: I have a computational postdoctoral position open in my lab (description enclosed), which I hope that you would bring to the attention of suitable candidates. Best regards, S. -- Shahriar Mobashery Navari Family Professor of Life Sciences Department of Chemistry and Biochemistry 423 Nieuwland Science Center University of Notre Dame Notre Dame, IN 46556 USA phone: (574) 631-2933 fax: (574) 631-6652 email: mobashery(a)nd.edu Web site: http://chemistry.nd.edu/**faculty/detail/smobashe/<http://chemistry.nd.edu/faculty/detail/smobashe/> THIS MESSAGE IS INTENDED FOR THE USE OF THE PERSON TO WHOM IT IS ADDRESSED. IT MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE UNDER APPLICABLE LAW. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. -- Brian Shoichet Professor University of California, San Francisco Dept. of Pharmaceutical Chemistry phone: 415-514-4126; fax: 415-514-4260 http://shoichetlab.compbio.ucsf.edu

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[Compbio-allhands] QBC Journal Club, Tuesday, March 6- 10:45AM, ROCK HALL Aud
by Nicole Takesono Flowers 29 Feb '12

29 Feb '12

Please note the location change. Please also be advised that this date must start on time, and end promptly at 11:45 as there is another group coming in directly after. BMI ~ BP ~ CCB ~ PSPG Tuesday, March 6 10:45 am, ROCK HALL Auditorium Adrian Stecula, PSPG Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development. Stephens, Philip J, Chris D Greenman, Beiyuan Fu, Fengtang Yang, Graham R Bignell, Laura J Mudie, Erin D Pleasance, et al. Cell 144 (1) pp. 27-40. January 7, 2011. Javona White Bear, iPQB TBA bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: 2012 Center for the Physics of Living Cells Summer School
by Andrej Sali 24 Feb '12

24 Feb '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Yodh, Jaya G" <jyodh(a)illinois.edu> > Subject: RE: 2012 Center for the Physics of Living Cells Summer School > Date: February 24, 2012 2:12:17 PM PST > To: "Yodh, Jaya G" <jyodh(a)illinois.edu> > > Dear Colleagues, > On behalf of the Center for the Physics of Living Cells (CPLC), an NSF Physics Frontier Center at the University of Illinois, Urbana-Champaign, we are writing to announce the 2012 Physics of Living Cells Summer School being offered from July 30 – August 4, 2012 at the University of Illinois at Urbana-Champaign. This one-week program is designed for graduate students, postdoctoral fellows and researchers in the chemical and life sciences, biophysics, physics, and engineering who would like to expand their training into the areas of single-molecule and live-cell experimental and computational biophysics. > Could you please post and circulate the attached announcement to those who might be interested? For more information and to apply by April 1, please visit: http://cplc.illinois.edu/summerschool2012/. > Thank you, > Jaya Yodh > Jaya Yodh, Ph.D. > Research Assistant Professor, Dept. of Physics > CPLC Director of Education and Outreach > University of Illinois at Urbana-Champaign > Center for the Physics of Living Cells (CPLC) > 1110 W. Green St., Urbana, IL 61801 > Phone: 217-244-1155; Fax: 217-333-4778 > E-mail: jyodh(a)illinois.edu > http://physics.illinois.edu/people/profile.asp?jyodh > http://www.cplc.illinois.edu >

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[Compbio-allhands] Seminar - Dr. Adrian Elcock - Tuesday, Mar. 13, 1pm, Byers Hall 211
by Hilary Mahon 24 Feb '12

24 Feb '12

Please see attached for more information. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] Seminar - Dr. Juri Rappsilber - Monday, Mar. 12, 10am - Byers Hall 211
by Hilary Mahon 24 Feb '12

24 Feb '12

Please see attached for more information. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] 3/1/12 Seminar with Rami Hannoush
by Nicole Takesono Flowers 24 Feb '12

24 Feb '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Rami Hannoush Genentech Chemical tools to perturnb and image Wnt signaling March 1, 2012 D. Galonic Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, February 28- 10:45AM, GH Aud
by Nicole Takesono Flowers 22 Feb '12

22 Feb '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, February 28 10:45 am, GH Auditorium Louise Goupil, CCB Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity. Paulsen, C.E. et al.. Nature Chemical Biology 8, 57-64 (2011). Robert Schiemann, iPQB RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses. Garrett, Sandra, Rosenthal, Joshua. Science DOI: 10.1126/science.1212795.. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Oxford Summer School in Computational Biology 2012
by Andrej Sali 22 Feb '12

22 Feb '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Madeline Mitchell <madeline.mitchell(a)stats.ox.ac.uk> > Subject: Oxford Summer School in Computational Biology 2012 > Date: February 22, 2012 3:56:40 AM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > > Dear Colleague > > This is the second and final announcement of the "Oxford Summer School in Computational Biology 2012", where the final deadline now is 12 days away. If you know top undergraduate students in mathematics, statistics, computer science, physics or a related field, please pass this flier to them. It is already clear that less than 10% of the applicants will be accepted, so applicants should have very good qualifications to apply. > > With thanks and best wishes > > > Maddy > > > Madeline Mitchell > PA to Professor Jotun Hein, Professor Chris Holmes & > Group Secretary, (Professor Peter Donnelly FRS FMedSci (WTCHG): PA +44 1865 287725) > Department of Statistics > University of Oxford > 1 South Parks Road > Oxford OX1 3TG > tel. (0)1865 285386: fax. (0)1865 285384 > email: mitchell(a)stats.ox.ac.uk > www.stats.ox.ac.uk > > >

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[Compbio-allhands] 2/23/12 Seminar with Amy Palmer
by Nicole Takesono Flowers 17 Feb '12

17 Feb '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Amy Palmer University of Colorado Developing fluorescent tools for live cell imaging February 23, 2012 X. Shu, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, February 21- 10:45AM, GH Aud
by Nicole Takesono Flowers 15 Feb '12

15 Feb '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, February 21 10:45 am, GH Auditorium Jordan Carelli, CCB A photoactivatable small-molecule inhibitor for light-controlled spatiotemporal regulation of Rho kinase in live embryos. Morckel, a. R., Lusic, H., Farzana, L., Yoder, J. a., Deiters, a., and Nascone-Yoder, N. M. Development 139, 437-442. 2011. Peter Fellowes, iPQB Non-genetic heterogeneity from stochastic partitioning at cell division. Huh and Paulsson. Nature Genetics 43, 95–100. 2011. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Summer internships at Amgen
by Ryan G. Coleman 14 Feb '12

14 Feb '12

Hi All, One of my past mentors, Alan Cheng, has some openings for a molecular modeling summer internship at Amgen in South San Francisco. Alan is also a UCSF alum (Biophysics 2001). Amgen also has other summer internships, see the attached flyer for more or the description below for Alan's positions. You have to apply online but you can email Alan at chenga(a)amgen.com if you'd like more information. Thanks, -Ryan Therapeutic Discovery Grad (#13069BR) and Undergrad (#13068)Intern: Specific projects designed by our scientists will provide the intern with hands-on drug discovery experience, such as designing and synthesizing novel compounds for potential drug candidates, molecular biology, protein engineering, cell biology, immunology, protein chemistry, chemical database information management, small molecule analytics, developing and applying automation and miniaturization technology and biochemical pharmacological screening of drug targets and candidates. The intern will gain valuable experience using the latest laboratory equipment and tools and a unique insight into the drug discovery environment.

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[Compbio-allhands] Fwd: CIBM postdoctoral fellowship
by Jacobson, Matt 11 Feb '12

11 Feb '12

-- Matt Sent from my iPad Begin forwarded message: From: Qiang Cui <cui(a)chem.wisc.edu<mailto:cui@chem.wisc.edu>> Date: February 11, 2012 3:05:00 PM PST To: Tanja Kortemme <kortemme(a)cgl.ucsf.edu<mailto:kortemme@cgl.ucsf.edu>> Cc: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Fwd: CIBM postdoctoral fellowship Hi, Tanja and Matt - We have a project on developing mathematical/continuum mechanics models for coiled coils - the ultimate aim is to construct molecular models for myosin rods, which are fascinating assembly of coiled coils. The work is in collaboration with my colleague in the biochemistry department, Prof. Ivan Rayment, a renowned crystallographer, especially in the area of myosin related proteins. If you have a student interested in pursing this line of research for postdoc, please ask him/her to contact me. The support for CIBM postdocs is quite generous... Thanks! Best regards QC --------------- To: CIBM (Computation and Informatics in Biology and Medicine) Faculty Re: Nominations for a CIBM Postdoctoral Traineeship We are calling for nominations for several postdoctoral traineeships in the Computation and Informatics in Biology and Medicine (CIBM) Training Program, funded by the NLM Grant 5T15LM007359, to begin July, 2012 or later. We are attaching a form you can use to nominate outstanding candidates for the CIBM Training Program. The postdoctoral traineeship is for a one- to two-year period, and the traineeship award is contingent on the awarding of the renewal of the NLM Grant supporting the CIBM Training Program. These traineeships are designed for cross-disciplinary training - thus we are asking that the candidate have a secondary mentor in addition to the primary mentor (one from computational / informatics areas, and the other from biological areas). A list of the CIBM trainers is available on the CIBM website (<http://www.cibm.wisc.edu/>www.cibm.wisc.edu<http://www.cibm.wisc.edu> <<http://www.cibm.wisc.edu/>http://www.cibm.wisc.edu> ). The National Library of Medicine has changed its focus for its informatics training programs in the next five-year period to emphasize translational bioinformatics in addition to its current focuses on clinical research informatics and health/clinical informatics. Translational bioinformatics is defined to be bioinformatics research that has a clear linkage to health. The CIBM Training Program is interested in research in all three areas. All nominations should reflect one (or more) of these focuses. The due date for the nominations is Monday, March 19th, 2012 (by 3 p.m. in the CIBM Office, Rm. 3420 Biotechnology Center Addition). If you have questions, please contact myself (<mailto:lpape@wisc.edu>lpape(a)wisc.edu<mailto:lpape@wisc.edu>), Karen Nafzger (<mailto:nafzger@biotech.wisc.edu>nafzger(a)biotech.wisc.edu<mailto:nafzger@biotech.wisc.edu>), or a member of the CIBM Management Committee. They include: -Amit Acharya (<mailto:acharya.amit@mcrf.mfldclin.edu>acharya.amit(a)mcrf.mfldclin.edu<mailto:acharya.amit@mcrf.mfldclin.edu>) -Patricia Brennan (<mailto:pbrennan@engr.wisc.edu>pbrennan(a)engr.wisc.edu<mailto:pbrennan@engr.wisc.edu>) -Mark Craven (<mailto:craven@biostat.wisc.edu>craven(a)biostat.wisc.edu<mailto:craven@biostat.wisc.edu> -Eneida Mendonca (<mailto:emendonca@biostat.wisc.edu>emendonca(a)biostat.wisc.edu<mailto:emendonca@biostat.wisc.edu>) -C. David Page (<mailto:page@biostat.wisc.edu>page(a)biostat.wisc.edu<mailto:page@biostat.wisc.edu>) -George Phillips (<mailto:phillips@biochem.wisc.edu>phillips(a)biochem.wisc.edu<mailto:phillips@biochem.wisc.edu>) -Jude Shavlik (<mailto:shavlik@cs.wisc.edu>shavlik(a)cs.wisc.edu<mailto:shavlik@cs.wisc.edu>) Regards, Louise Louise Pape, PhD Coordinator Computation and Informatics in Biology and Medicine (CIBM) Training Program University of Wisconsin-Madison 3445 Biotechnology Center 425 Henry Mall Madison WI 53706 608-265-7935 Best Regards QC Qiang Cui ------------------------------------------------------------ Professor of Chemistry Department of Chemistry and Theoretical Chemistry Institute, Rm8305I University of Wisconsin, Madison 1101 University Avenue Madison, WI 53706 ------------------------------------------------------------ Phone: (+1)-608-262-9801 Fax: (+1)-608-262-9918 Email: <mailto:cui@chem.wisc.edu> cui(a)chem.wisc.edu<mailto:cui@chem.wisc.edu> Web: <http://www.chem.wisc.edu/users/cui> http://www.chem.wisc.edu/users/cui Group: <http://www.chem.wisc.edu/~cui> http://www.chem.wisc.edu/~cui

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[Compbio-allhands] 2/16/12 Seminar with Minna Bissell
by Nicole Takesono Flowers 10 Feb '12

10 Feb '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Minna Bissell LBNL Why don't we get more cancer? The proposed role of the microenvironment in tissue specificity and breast cancer. February 16, 2012 C. Nyitray, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: [ISBRA-L] Full Professor in Bioinformatics
by Andrej Sali 10 Feb '12

10 Feb '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: ISBRA Mailing List <isbra-l(a)dna.engr.uconn.edu> > Subject: [ISBRA-L] Full Professor in Bioinformatics > Date: February 10, 2012 9:12:30 AM PST > To: <sali(a)salilab.org> > Reply-To: <isbrainfo(a)gmail.com> > > > The Department of Computer Science at Georgia State University invites applications for an anticipated position of Full Professor in the bioinformatics area beginning Fall Semester 2012, pending budgetary approval. Earned Ph.D. in Computer Science or a related discipline is required. An offer of employment will be conditional on background verification. > > Prospective candidates should demonstrate ability to bring national and international recognition to the department as a center of excellence for bioinformatics research and education. The hired scholar is expected to bring in major extramural funding, mentor junior faculty, recruit top-quality Ph.D. students, and foster interdisciplinary collaborations among faculty in various departments in GSU. > > This position is part of a university-wide initiative <http://www.gsu.edu/secondcentury> that is seeking to hire excellent faculty in several interdisciplinary areas. Prospective candidates should demonstrate ability to bring national and international recognition to the department. The hired applicant is expected to foster interdisciplinary research collaborations among faculty in various departments in GSU. > > Georgia State University, founded in 1913, is a Carnegie Doctoral/Research Extensive university. Located in the heart of downtown Atlanta, this major research university has an enrollment of more than 30,000 undergraduate and graduate students in six colleges. Georgia State is the second-largest university in the state, with students coming from every county in Georgia, every state in the nation, and from over 145 countries. Georgia State University is currently embarking on a record $1 billion campus expansion. The Computer Science Department offers programs leading to the B.S., M.S., and Ph.D. degrees in computer science. Currently, 20 out of more than 60 Ph.D. students are involved in bioinformatics research. They are supervised by 10 faculty members fully or substantially involved in bioinformatics research through collaboration with Computer Science and Biology faculty. Departmental computing facilities for research and instruction include a departmental network of PCs, Unix/Linux workstations, two interconnected Beowulf clusters, and a 24-processor supercomputer. The department's faculty attracts substantial funding from many federal agencies, including five NSF CAREER Awards. > > Applicants should send letter of interest, C.V., and three letters of recommendation to: > > Dr. Yi Pan, Chair > Department of Computer Science > Georgia State University > 34 Peachtree Street, Suite 1450 > Atlanta, Georgia 30303 > > > _______________________________________________ > To modify subscription preferences or unsubscribe from the ISBRA-L mailing list visit http://dna.engr.uconn.edu/cgi-bin/mailman/options/isbra-l/sali%40salilab.org

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[Compbio-allhands] QBC Journal Club, Tuesday, February 14- 10:45AM, GH Aud
by Nicole Takesono Flowers 08 Feb '12

08 Feb '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, February 14 10:45 am, GH Auditorium Juan Perez Bermejo, iPQB Love in the Time of Chagas Costales JA, Daily JP, Burleigh BA. Cytokine-dependent and –independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling. BMC Genomics 10:252, 2009. Rose Citron, iPQB The Ribosome Modulates Nascent Protein Folding. Christian M. Kaiser, et al. Science 334, 1723, 2011. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Open positions in Computational Structural Biology in Barcelona (Spain)
by Andrej Sali 08 Feb '12

08 Feb '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Subject: Open positions in Computational Structural Biology in Barcelona (Spain) > Date: February 8, 2012 8:38:41 AM PST > To: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > > Dear Friends and Colleagues, > > We have an opening in our group for a Postdoc on chromatin biophysics. The successful candidate will team with other members of our group in our efforts towards elucidating the 3D structure of genomic domains and genomes. Recent publication from the group in this field include: > > - Umbarger, M. A., Toro, E., Wright, M. A., Porreca, G. J., Baù, D., Hong, S.-H., Fero, M. J., et al. (2011). Molecular Cell, 44(2), 252–264 > - Marti-Renom, M. A., & Mirny, L. A. (2011). PLoS Computational Biology, 7(7), e1002125 > - Sanyal, A., Baù, D., Martí-Renom, M. A., & Dekker, J. (2011). Current Opinion in Cell Biology. doi:10.1016/j.ceb.2011.03.009 > - Baù, D., Sanyal, A., Lajoie, B. R., Capriotti, E., Byron, M., Lawrence, J. B., Dekker, J., et al. (2011). Nature Structural & Molecular Biology, 18(1), 107–114. > > More details are included in the attached PDF file. > > I would appreciate if you could forward this announcement to whom may be interested. > > Many thanks in advance! > Marc > ------- > Marc A. Marti-Renom, Group Leader > Structural Genomics Group, National Center for Genomic Analysis (CNAG) > Parc Cientific de Barcelona - Torre I - Baldiri Reixac, 4 - 2a.p - 08028 - Barcelona > Tel +34 934 033 743 Fax +34 934 037 279 > email mmarti(a)pcb.ub.cat web http://marciuslab.org & http://cnag.cat > > *** Consider the environment. Print responsibly. *** >

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[Compbio-allhands] Fwd: Merck Summer Internships for Computational Chemists
by Andrej Sali 03 Feb '12

03 Feb '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Voigt, Johannes" <johannes.voigt(a)merck.com> > Subject: Merck Summer Internships for Computational Chemists > Date: February 3, 2012 3:08:38 PM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Professor Sali, > > I am writing to inform you that Merck Research Labs will be offering 2012 summer internships in the Chemistry Modeling and Informatics groups at the Rahway, NJ, Boston, MA, or West Point, PA research facilities. Internships will begin in early June 2012, and will run for 10-12 weeks. > Qualified graduate students in computational chemistry or a related life sciences field who are selected for these positions will have the opportunity to conduct research on a project relevant to drug discovery. > They will gain firsthand experience in modern drug discovery, and will also make valuable contacts within industry. > > Interested candidates can apply online at > https://merck.taleo.net/careersection/merck_university_recruiting_career_se… > > To complete the application, candidates must upload a cover letter, CV, and transcript. Please note that the application deadline is February 13, 2012. > > Sincerely, > > Johannes H. Voigt Ph. D. on behalf of Global Structural Chemistry, Merck Research Laboratories > Head – Chemistry Modeling & Informatics Rahway > Merck & Co., Inc. > 126 East Lincoln Ave > RY50SW-100 > Rahway, NJ 07065 > phone: (732) 594-3938 > fax: (732) 594-0670 > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), 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: Rapid MD Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande
by Andrej Sali 03 Feb '12

03 Feb '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Joy P. Ku" <joyku(a)stanford.edu> > Subject: Rapid MD Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande > Date: February 3, 2012 1:19:41 PM PST > To: <sali(a)salilab.org> > > Hi Dr. Sali, > > I’m the Director of Simbios, an NIH National Center for Biomedical Computing focused on physics-based simulations of biological structures based at Stanford University. Based on your research activities, I thought you would be interested in our upcoming workshop on rapid prototyping and simulations of molecular dynamics on GPUs that we are hosting with Dr. Vijay Pande. Please see the announcement below for the details. > > We invite you to attend and would appreciate you forwarding the announcement to colleagues and those in your lab that may be interested. > > Thank you. > > Regards, > Joy Ku > On behalf of Vijay Pande and the OpenMM team > --------------------------------------------------------------------------------------------------------- > Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. > OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs) [seebenchmarks]. > And with the new application layer in its recent release, OpenMM will allow non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs. > > ***WORKSHOP: RAPID MOLECULAR DYNAMICS PROTOTYPING AND SIMULATIONS ON GPUS *** > > Where: Stanford University > When: Mar. 12-13, 2012 > Description: > > During the workshop, you will gain hands-on experience using OpenMM’s new application layer and application programming interface (API). Learn to: > > * Set up and run an MD simulation on your GPU using both PDB and AMBER files > > * Create a custom force to apply to your simulations > > * Customize the simulation through Python scripting > > You will also have time to work with the OpenMM development team on your own research project. > > This workshop is designed for those interested in accelerating MD simulations on GPUs and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. No programming background is required, though programming topics will also be covered for those who are interested in them. > Registration: > > Registration is free but required and spaces are limited. To register or for more information, visithttp://simbios.stanford.edu/MDWorkshops.htm. > > OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visithttp://simbios.stanford.edu. > > [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. > [2]Eastman, P. and Pande, V.S., “Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit,” J. Comp. Chem., 2010, 31(6):1268-1272. > > > > > >

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[Compbio-allhands] QBC Journal Club, Tuesday, February 7- 10:45AM, GH Aud
by Nicole Takesono Flowers 02 Feb '12

02 Feb '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, February 7 10:45 am, GH Auditorium Rahel Woldeyes, CCB HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Goldstone, D. C., Ennis-Adeniran, V., Hedden, J. J., Groom, H. C. T., Rice, G. I., Christodoulou, E., et al. (2011). Nature, 480, 379-382. Sara Calhoun, iPQB Hot Spots for Allosteric Regulation on Protein Surfaces. Reynolds, K.A., McLaughlin, R.N., and Ranganathan, R. (2011) Cell, 147:1564-1575 bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] BMS talk Wednesday
by Jacobson, Matt 30 Jan '12

30 Jan '12

Wednesday Feb 1, 11:30 pm, in BH212 Deborah Loughney, Stan Krystek, and Steve Johnson from BMS stopped by UCSF for a visit and I suggested that they give a talk on Wednesday. I will send out a title when I receive it, but it sounds like they will split the time and give two short talks, one on small molecule work and the other on macromolecular drugs. Stan has an interesting position in that he's focused 100% on computer-aided design for biologics. Following the talk, I will ask postdocs from my group to take them to lunch for informal conversations. If you would like to join, let me know and I'll see what I can do. -- Matt Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] QBC Journal Club, Tuesday, January 31- 10:45AM, GH Aud
by Nicole Takesono Flowers 25 Jan '12

25 Jan '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, January 31 10:45 am, GH Auditorium Ben Heineike, iPQB A sensing array of radically coupled genetic 'biopixels'. Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J. Nature Volume: 481, Pages: 39–44. 2011 Ryan Conrad, PSPG SIRT6 Promotes DNA Repair Under Stress by Activating PARP1 Mao et al. Science Vol. 332 no. 6036 pp. 1443-1446. 2011 bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 1/26/12 Seminar with Robert Austin
by Nicole Takesono Flowers 20 Jan '12

20 Jan '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Robert Austin Princeton Darwinian Evolution: Not As Slow As You Might Think January 26, 2012 W. Marshall, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] eMolecules presentation: Fri Jan 20th, 11 to 12 noon (tomorrow)
by John Irwin 19 Jan '12

19 Jan '12

Dear Allhands eMolecules, a small molecule procurement company, will make a short presentation and take Q&A tomorrow for one hour starting at 11am (11:10am) in BH513. RSVP to me only jji(a)cgl.ucsf.edu so I can get an approximate head count. Please forward to anyone you think might be interested. John

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[Compbio-allhands] 1/16/12 Seminar with Kristala Jones Prather
by Nicole Takesono Flowers 18 Jan '12

18 Jan '12

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Kristala Jones Prather MIT Parts, Devices, and Chassis in Support of Metabolic Engineering January 19, 2012 D. Booth, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, January 24- 10:45AM, GH Aud
by Nicole Takesono Flowers 18 Jan '12

18 Jan '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, January 24 10:45 am, GH Auditorium Megan Li, PSPG Therapeutic siRNA silencing in inflammatory monocytes in mice. Leuschner F et al. Nat Biotechnol. 2011; 29 (11): 1005-10 Patrick Harrigan, iPQB Predicting mutation outcome from early stochastic variation in genetic interactions partners. Burga, A. et al. Nature 2011; 480: 250-253. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, January 17- 10:45AM, GH Aud
by Nicole Takesono Flowers 11 Jan '12

11 Jan '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, January 17 10:45 am, GH Auditorium Benjamin Spangler, CCB Chemically Crosslinking the Active Site of O-GlcNAc transferase. A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase Jiang, et al. Nature Chem. Bio. Amy Chang, iPQB Electrical Spiking in Escherichia coli Probed with a Fluorescent Voltage-Indicating Protein Kralj et al. Science. July 15, 2011. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Institute for Advanced Study Offers Summer Program
by Andrej Sali 09 Jan '12

09 Jan '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Susan Higgins <shiggins(a)ias.edu> > Subject: Institute for Advanced Study Offers Summer Program > Date: January 9, 2012 10:38:49 AM PST > To: sali(a)SALILAB.ORG > > INSTITUTE FOR ADVANCED STUDY > SCHOOL OF NATURAL SCIENCES > PRINCETON, NEW JERSEY, USA > > Dear Colleague, > > From July 9-20, 2012, the Institute for Advanced Study will offer its annual Prospects in Theoretical Physics (PiTP) summer program on the Institute campus in Princeton, New Jersey, USA. > > The 2012 PiTP Program, "Computation and Biology," will explore, for the first time, a range of topics at the interface of theoretical computer science, statistical physics and quantitative biology. > > This program is intended for graduate students and postdoctoral scholars in all three fields of computer science, theoretical physics and quantitative biology. A list of topics to be covered, and the lecturers expected to speak on each topic, are noted below: > > - "Errors and codes": Måns Ehrenberg (Uppsala University) and Tsvi Tlusty (Institute for Advanced Study) > > - "Viruses and immunity": Guillaume Bonfante (Université de Nancy), Arup Chakraborty (Massachusetts Institute of Technology), and Arnold Levine (Institute for Advanced Study) > > - "Growth and form": Przemyslaw Prusinkiewicz (University of Calgary) and Enrico Coen (John Innes Centre, Norwich) > > - "Natural algorithms": Bernard Chazelle (Princeton University), Jean-Louis Deneubourg (Université Libre de Bruxelles), and Guy Theraulaz (Université Paul Sabatier, Toulouse) > > - "Learning & robotics": Hod Lipson (Cornell University), Dario Floreano (École Polytechnique Fédérale de Lausanne), and Michale Fee (Massachusetts Institute of Technology) > > Attached is a poster for the PiTP 2012 program, which we kindly ask you to please print and display as appropriate. Information about application procedures and a program schedule can be found on the PiTP website: www.ias.edu/pitp. > > We would be grateful if you would bring this program to the attention of students and postdocs in your department, as well as to the attention of colleagues in your department and elsewhere. In particular, we encourage the participation of women, minorities, and students from institutions with smaller programs in the areas of computer science, theoretical physics and quantitative biology. > > We hope that you will encourage any young researcher who would benefit from this kind of program to apply. > > Sincerely, > > Bernard Chazelle, Princeton University > David Huse, Princeton University > Stanislas Leibler, Institute for Advanced Study > > > > > >

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[Compbio-allhands] Fwd: Bioinformatics positions at Illumina in San Diego
by Jacobson, Matt 04 Jan '12

04 Jan '12

Begin forwarded message: From: Ilya Chorny <ichorny(a)gmail.com<mailto:ichorny@gmail.com>> Date: January 4, 2012 5:00:14 PM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, <babbitt(a)cgl.ucsf.edu<mailto:babbitt@cgl.ucsf.edu>>, Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>>, Ken Dill <dill(a)laufercenter.org<mailto:dill@laufercenter.org>>, "Crawford, Douglas" <douglas.crawford(a)qb3.org<mailto:douglas.crawford@qb3.org>>, Robert Stroud <stroud(a)msg.ucsf.edu<mailto:stroud@msg.ucsf.edu>> Subject: Bioinformatics positions at Illumina in San Diego Hi All, Happy New Year!! We have a bioinformatics position open in our group in San Diego. Please pass this along to any interested parties. They can contact me if they would like to know more about the position or working at Illumina. https://www.illumina.apply2jobs.com/ProfExt/index.cfm?fuseaction=mExternal.… Thanks, Ilya -- Ilya Chorny Ph.D. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] QBC Journal Club, Tuesday, January 3- 10:45AM, GH Aud
by Nicole Takesono Flowers 28 Dec '11

28 Dec '11

BMI ~ BP ~ CCB ~ PSPG Tuesday, January 3 10:45 am, GH Auditorium Katherine Aull, iPQB Dynamic Exchange at Regulatory Elements During Chromatin Remodeling Underlies Assisted Loading Mechanism Voss et al, Cell 146:4 544-554. 2011 Weihan Li, iPQB Growth Rate-Dependent Global Effects on Gene Expression in Bacteria Stefan Klumpp, Zhongge Zhang, and Terence Hwa, Cell 139, 1366-1375. 2009 bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Four tenure track faculty positions in high end RNA research available at University at Albany!---Rama
by Andrej Sali 20 Dec '11

20 Dec '11

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Ramaswamy Sarma <rsarma(a)ALBANY.EDU> > Subject: Four tenure track faculty positions in high end RNA research available at University at Albany!---Rama > Date: December 19, 2011 10:12:58 PM PST > To: DNA-DYNAMICS(a)listserv.albany.edu > Reply-To: Ramaswamy Sarma <rsarma(a)ALBANY.EDU> > > My Dear Colleague: > > I could not be any more excited; we are indeed announcing the opening of FOUR tenure track faculty lines -three in the Chemistry Dept, and one in the Dept of Biological Sciences -- all with concentration in RNA chemistry and biology affiliated with the University at Albany's fast growing RNA Institute. > > http://www.albany.edu/rna/ > > The attached contains detailed descriptions of the positions open and how to apply. > > If you are a young RNA researcher looking for a starting faculty position in an urban University with great future, these openings are for you. > > You may know of some highly talented young professionals in RNA field, and if so, I will appreciate a great deal, if you will encourage them to apply. > > Within 2-3 weeks, we will commence planning for the 18th Albany Conversation, June 2013, and so I will be contacting you again soon. > > I thank you for your interest and help. > > Cheers > > > Rama > ****** > Prof. Ramaswamy H. Sarma > Department of Chemistry > State University of New York at Albany > Albany NY 12222 USA > > phone: 518-456-9362 > fax: 518-452-4955 > email: rhs07(a)albany.edu > > > > > >

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[Compbio-allhands] Scientific Web Applications Developer Wanted
by Custer, Ashley 15 Dec '11

15 Dec '11

Hi all, The Babbitt lab has an urgent and immediate need for a web applications developer. If you know anyone looking for a permanent, temporary, or part-time position in this area, please pass it on. Thanks. Patsy Babbitt -- Patricia Babbitt Professor and Vice Chair, Department of Bioengineering & Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94158-2330, USA (CA 94158 for direct delivery by courier) Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu<mailto:babbitt@cgl.ucsf.edu> <mailto:babbitt@cgl.ucsf.edu> Web: http://babbittlab.ucsf.edu/ Assistant: Ms. Ashley Custer, +1 415-514-1214, 415-514-4861 Ashley.Custer(a)ucsf.edu<mailto:Ashley.Custer@ucsf.edu>

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[Compbio-allhands] Fwd: please advertise this postdoc position
by Andrej Sali 13 Dec '11

13 Dec '11

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Chandra Verma <chandra(a)bii.a-star.edu.sg> > Subject: please advertise this postdoc position > Date: December 13, 2011 6:37:25 PM PST > To: undisclosed-recipients:; > > dear colleagues > > i would be very grateful if you could, when you have some time spare, please help by advertising this amongst those who you think may be interested. > > thanks very much > > chandra > > > a postdoctoral position is available in singapore for 3 years. the applicant should be good at computational chemistry/modelling/simulations in the field of biomolecular mechanisms. the successful applicant will work with teams of experimentalists. Projects will be focused with a view to developing mechanistic models and also designing small molecules/peptides. a major project here examines several aspect of the p53 pathway including peptide/small molecule design as well as mechanisms underlying basic biology, such as effects of post-translational mechanisms. most of our work is tested in the laboratories of collaborators.the job is expected to start early 2012. if interested, please email your cv and have 2-3 letters of reference sent to chandra(a)bii.a-star.edu.sg. > also open to experimentalists with biochemical/biophysical/structural training interested in switching to simulations. >

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[Compbio-allhands] Fwd: CTBP 2012 Postdoctoral Fellowships
by Andrej Sali 07 Dec '11

07 Dec '11

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Christopher M. Smith" <csmith(a)ctbp.ucsd.edu> > Subject: CTBP 2012 Postdoctoral Fellowships > Date: December 7, 2011 3:04:09 PM PST > To: sali(a)salilab.org > > On behalf of Profs Herbert Levine, Jose Onuchic and Peter Wolynes, I am happy to announce that the Center for Theoretical Biological Physics at Rice University (Houston, Texas) and the University of California San Diego will be offering several Postdoctoral Fellowships in Biological Physics in 2012 for positions at Rice and UCSD. > > I would greatly appreciate your assistance in conveying this opportunity to graduate students in your lab and/or department who will be looking for postdoctoral positions next year. I have also taken the liberty of attaching CTBP Postdoctoral Fellowship recruitment flyers for both the positions at Rice and UCSD. > > ----------------------------------------------------------- > > CTBP is a consortium of researchers from UCSD, the Salk Institute for Biological Studies and Rice University, involved in research on fundamental problems at the interface between physics and biology. Current synergy research areas include, Cellular Tectonics, the dynamic mesoscale structure of the intracellular milieu; Computational Approaches to Intracellular and Intercellular Communication, chemical-based reaction-diffusion governed communication across complex spaces; and Gene Regulatory Networks, genetic/signaling networks exhibit specificity and robustness in the face of intrinsic stochasticity, and yet retain evolvability. Our research ranges from fundamental issues in molecular biophysics, cell and multicellular biology, and genetic networks to pressing biomedical questions raised by the study of diseases such as cancer. > > We are actively recruiting recent quantitative science (physics, mathematics, chemistry, etc.) Ph.D. graduates for postdoctoral positions beginning in 2012. We are looking to fill several positions with postdoctoral candidates that are well-versed in quantitative science, but who are very interested in learning and tackling > research problems in the realm of biology and biomedicine. Previous experience in working on living systems may be beneficial, but is not necessary. CTBP postdoctoral scholars will participate in leading-edge research with world-renowned faculty and at the same time will be provided opportunities to expand career-enhancing skill sets (grant writing, teaching, mentoring undergraduate research students/projects, etc.). CTBP postdoctoral scholars will also share in unique opportunities to gain hands-on experience in biological techniques while working closely with experimental scientists. An initial review of applications will begin in early February 2012. > > Applicants are asked to visit http://ctbp.rice.edu for additional information on CTBP Postdoctoral opportunities, or they may contact Christopher M. Smith, PhD, CTBP/UCSD, 9500 Gilman Drive, MC0374, San Diego, CA 92093-0374, 858-534-8370, csmith@ctbp@ucsd.edu. > > ----------------------------------------------------------- > > Christopher M. Smith, PhD. > Center for Theoretical Biological Physics > University of California / Rice University > csmith(a)ctbp.ucsd.edu (858) 534-8370 >

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[Compbio-allhands] Fwd: JOB: Fellowship/Junior academic posts at Edinburgh Informatics
by Tom Ferrin 07 Dec '11

07 Dec '11

-------- Original Message -------- Subject: JOB: Fellowship/Junior academic posts at Edinburgh Informatics Date: Wed, 07 Dec 2011 12:40:21 +0000 From: Bob Fisher <rbf(a)inf.ed.ac.uk> Organization: School of Informatics, The University of Edinburgh To: tef(a)cgl.ucsf.edu Fellowship/Junior academic posts in Informatics The University of Edinburgh has announced a large number of 5 year fellowships which gradually transform into permanent academic posts over the 5 years. The academic posts will be entry level (Lecturer/Assistant Professor). The School of Informatics is one of the world's top research leaders in computer science/informatics. The University of Edinburgh is one of the world's top research universities, in one of the world's most pleasant cities. One of the priority areas is 'Data Intensive Research', which can include computer vision/image analysis researchers. (The other 5 non-imaging areas are listed below.) Your main focus MUST be on the 'Data Intensive' aspects, but the source of the data could be imagery/video and its linkage to other large data sources, eg web, large image databases, broadcast TV streams, etc. These posts are for top candidates only. You MUST have a minimum of 2 excellent publications, such as in PAMI or ICCV/ECCV/ACCV/CVPR oral papers. Anything less will not be considered in this recruitment round. The general advert is at : http://www.jobs.ed.ac.uk/vacancies/index.cfm?fuseaction=vacancies.detail&va… and there are a small number of Informatics-specific details at: http://www.jobs.ed.ac.uk/vacancies/index.cfm?fuseaction=vacancies.furtherde… There are three closing dates: 16th January, 29th February and 16th April 2012. You can apply at any of them. There are 5 other priority areas in case you have colleagues who might be interested: - Software Engineering: model-driven development, testing, verification and security - Computational Cognitive Science - Systems: particularly operating systems and multicore - Networks - Data Intensive Research - Modelling & Simulation For queries about the Data Intensive area, contact me: rbf(a)inf.ed.ac.uk For queries about the other themes, contact the Head of School: Prof. David Robertson, dr(a)inf.ed.ac.uk ================ Prof. Robert B. Fisher, School of Informatics, Univ. of Edinburgh Dean of Research, College of Science and Engineering 1.26 Informatics Forum, 10 Crichton St, Edinburgh EH8 9AB, UK +44-(131)-651-3441 (direct line), +44-(131)-651-3443 (secretary) Fax: +44-(131)-650-6899 E-MAIL: r.b.fisher A@T ed.ac.uk http://www.inf.ed.ac.uk/people/staff/Robert_Fisher.html The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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[Compbio-allhands] 12/7/11 Seminar with Tom Tuschl
by Nicole Takesono Flowers 02 Dec '11

02 Dec '11

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems **Wednesday, 2 PM** Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Tom Tuschl Rockefeller University Characterization of regulatory small RNAs and RNA-binding proteins December 7, 2011 M. McManus, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 12/1/11 Seminar with Doug Lauffenberger
by Nicole Takesono Flowers 30 Nov '11

30 Nov '11

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Doug Lauffenberger MIT Quantitative Cell Bioengineering Analysis of EGF Receptor Inhibitor Effectiveness in Cancer Therapeutics December 1, 2011 K. Giacomini, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Nodality Job Opening
by Tom Ferrin 30 Nov '11

30 Nov '11

-------- Original Message -------- Subject: Nodality Job Opening Date: Wed, 30 Nov 2011 14:48:40 +0000 From: David Spellmeyer <david.spellmeyer(a)nodality.com> To: Jacobson, Matt <Matt.Jacobson(a)ucsf.edu>, tef(a)cgl.ucsf.edu <tef(a)cgl.ucsf.edu>, Shoichet, Brian <shoichet(a)cgl.ucsf.edu> Hi Matt, Tom and Brian, We have an opening <http://www.nodality.com/careers/openings/scientist-bioinformatics.phtml> for a bioinformatics scientist in our computational sciences group here at Nodality. We are looking for an individual who wants to join a dynamic, growing organization working to make a difference in the lives of patients in cancer and autoimmunity. The technology we use detects and quantifies protein function at the single cell level and correlates those changes to drug response. Our group works very closely with our research biologists, clinical development, instrumentation and automation experts. We have a track record of publishing <http://www.nodality.com/publications/> our results in high-impact journals and presenting our work at major conferences. Would you have any recommendations for individuals you think might be a good fit for the group? Please feel free to forward this to anyone you think might be interested. Thank you, David ===== David Spellmeyer | CTO & CIO | Nodality | 201 Gateway Blvd | South San Francisco, CA 94080 | david.spellmeyer(a)nodality.com <mailto:david.spellmeyer@nodality.com> | 650-827-8016 (P) | 650-827-8001 (F) | 510-915-4153 (M) The material in this transmission may contain confidential information intended only for the addressee. If you are not the addressee, any disclosure or use of this information by you is strictly prohibited. If you have received this transmission in error, please delete it, destroy all copies, and notify the sender immediately by reply or by calling 1-650-827-8016.

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[Compbio-allhands] Fwd: REMINDER: On Behalf of Taekjip Ha and Klaus Schulten - Postdoctoral Fellowship Opportunities with NSF's Center for the Physics of Living Cells (CPLC) - PLEASE CIRCULATE
by Andrej Sali 28 Nov '11

28 Nov '11

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Flanegin, Susan A" <flanegin(a)illinois.edu> > Subject: REMINDER: On Behalf of Taekjip Ha and Klaus Schulten - Postdoctoral Fellowship Opportunities with NSF's Center for the Physics of Living Cells (CPLC) - PLEASE CIRCULATE > Date: November 28, 2011 11:01:26 AM PST > To: "Flanegin, Susan A" <flanegin(a)illinois.edu> > > > Dear Colleagues, > We are writing to remind you of several postdoctoral fellowship opportunities for the coming academic year, starting September 2012, in experimental and theoretical biophysics in the "Center for the Physics of Living Cells" (CPLC), a National Science Foundation Physics Frontier Center at the University of Illinois, Urbana-Champaign. > > Research in the Center for the Physics of Living Cells falls into one of four themes: > > 1. Maximizing information content of single molecule experiments; > > 2. Using synthetic nanostructures for high speed single molecule spectroscopy; > > 3. Observing individual events within single cells; and > > 4. Extending computation to biologically relevant timescales, and theory to greater biological realism. > > Fellows will use state-of-the-art experimental and theoretical biophysical tools to accomplish these goals: optical tweezers, single-molecule fluorescence microscopy, fabrication of synthetic nanostructure, high-speed, low-noise electrical measurements, live cell imaging, microscopic and coarse-grained molecular simulations, stochastic modeling, as well as the standard methods of molecular and cellular biology and genetics. Research will involve both the development and improvement of experimental and computational techniques and the application of these techniques to particular biological processes such as replication, transcription, translation, cell transport and motility. As projects are collaborative endeavors between several labs, the fellows will have the opportunity to be jointly advised by two or more faculty members of the CPLC. > > Apply via https://my.physics.illinois.edu/join/ no later than December 2, 2011. Applications should include: cover letter; curriculum vita; research statement; publications list; and contact information for three references. Applications received after the December 2nd deadline may not be considered. A full job description can be found at: http://www.cplc.illinois.edu/opps/postdocs.asp > > Please post and circulate the attached announcement or if interested, apply accordingly. > > For more information about CPLC, please visit http://cplc.illinois.edu/opps/postdocs.asp > > Thank you. > > Taekjip Ha and Klaus Schulten > Co-directors, Center for the Physics of Living Cells > http://www.cplc.illinois.edu > University of Illinois at Urbana-Champaign > 1110 West Green Street, MC 704 > Urbana, IL 61801-3080, USA >

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[Compbio-allhands] QBC Journal Club, Tuesday, November 15- 10:45AM, GH Aud
by Nicole Takesono Flowers 23 Nov '11

23 Nov '11

BMI ~ BP ~ CCB ~ PSPG Tuesday, November 29 10:45 am, GH Auditorium Daniel Himmelstein, iPQB Ontology engineering Alterovitz et al. Nature Biotechnology 28, 128-130 (2010) Noah Younger, CCB Selective killing of cancer cells by small molecule targeting the stress response to ROS. Lakshmi Raj, et. al. Nature. Vol. 475, pp 231-234 (2011) bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] QBC Journal Club, Tuesday, November 22- 10:45AM, GH Aud
by Nicole Takesono Flowers 16 Nov '11

16 Nov '11

BMI ~ BP ~ CCB ~ PSPG Tuesday, November 22 10:45 am, GH Auditorium Justin Meyerowitz, CCB Organization of intracellular reactions with rationally designed RNA assemblies. Delebecque CJ, Lindner PA, Aldaye FA. Science 333:470-474; July 2011. John Haliburton, iPQB Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling Seung Chul Shin, et al. Science 334, 670 (2011) bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Junior Professorship in computational biology at Saarland University
by Florian Lauck 15 Nov '11

15 Nov '11

Hello, The Center for Bioinformatics at Saarland University has an opening. Basically, candidates can apply right after their PhD, but a few years as a postdoc are typical. See details and contact below. Best, Florian Begin forwarded message: > From: Volkhard Helms <volkhard.helms(a)bioinformatik.uni-saarland.de> > Date: November 15, 2011 12:12:00 AM PST > To: <Florian.Lauck(a)ucsf.edu> > Subject: Juniorprofessur am ZBI [...] > > UNIVERSITÄT DES SAARLANDES - W1 Computational Biology - Frist: 01.12.2011 > Saarland University is a Campus university with international alignment and pronounced research profile. A number of research institutes in the vicinity of the university and dedicated support for the foundation of start up companies bring about an ideal field for innovation and technology transfer. The Center for Bioinformatics (CBI) at Saarland University is one of the five centers for excellence for Computational Biology that received startup funding by the German Research Foundation (Deutsche Forschungsgemeinschaft). In the CBI 10 institutes of Saarland University from the areas of life sciences, mathematics and informatics collaborate with the research divisions of the Max-Planck Institute for Informatics, the German Research Center for Artificial Intelligence GmbH (DFKI) and the Fraunhofer Institute for Biomedical Engineering. Saarland University is seeking an outstanding scientist for the full-time position of a Junior Professor for Computational Biology (W1) offered for a three-year term, with a possible extension of another three years, dependable on a teaching evaluation and an external evaluation of the research activities. We are seeking to attract an individual with an excellent international reputation in Computational Biology. The applicant must have a Ph.D. degree and should exhibit internationally regarded previous research results in the field of computational biology. The position is supposed to strengthen the focus of the center on the analysis of the genetic, epigenetic, or transcriptomics basis of diseases, both concerning the human host and, in the case of infections, the pathogen. Basic research as well as research targeted towards new approaches in diagnosis, prognosis and therapy are considered. Research on evolutionary processes in disease development is of special interest. We expect the candidate to participate in collaborative interdisciplinary research projects with partners both on and off campus. The candidate is expected to participate in teaching in the curricula of the center in computational biology and related study programs. The teaching requirement amounts to 4 SWS (6 credits) per semester. Female candidates are encouraged to apply and will be treated favorably in case of equal qualification. Given equal qualifications, handicapped applicants will be considered on a preferential basis. All applications should include curriculum vitae, list of publications, short research plan, copies of degree certificates, copies of the five most important publications and a list of five references. Please send your application no later than December 1, 2011 to Prof. Dr. Dr. Thomas Lengauer, Center for Bioinformatics at Saarland University, Building E2 1, 66123 Saarbrücken, Germany. Should you have any further questions don´t hesitate to contact Mrs. P. Scherer-Geiss, CEO of Center for Bioinformatics Tel. +49-(0)681/302-64705, psg(a)bioinf.uni-sb.de > ___________________________________________________________________ Florian Lauck, MSc Assistant Specialist Babbitt Lab Department of Bioengineering and Therapeutic Sciences 1700 4th Street University of California, San Francisco San Francisco, CA 94143-2330, USA +1 (415) 502 1248 babbittlab.ucsf.edu/florian.html linkedin.com/in/flolauck

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[Compbio-allhands] QBC Journal Club, Tuesday, November 15- 10:45AM, GH Aud
by Nicole Takesono Flowers 09 Nov '11

09 Nov '11

BMI ~ BP ~ CCB ~ PSPG Tuesday, November 15 10:45 am, GH Auditorium Brittany Fotsch, CCB Complement factor H binds malondialdehyde epitopes and protects from oxidative stress. Weissmann, et. al. Nature 478, 76-81 (06 October 2011) David Mavor, iPQB DNA stretching by bacterial initiators promotes replication origin opening Duderstadt et al Nature, 478:209 bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Peptoid computation post-doc openings
by Andrej Sali 06 Nov '11

06 Nov '11

Andrej (Sent from my iPhone) Begin forwarded message: > From: Ronald Zuckermann <rnzuckermann(a)lbl.gov> > Date: November 6, 2011 5:20:36 PM PST > To: matt.jacobson(a)ucsf.edu, Brian Shoichet <shoichet(a)cgl.ucsf.edu>, kortemme(a)cgl.ucsf.edu, Andrej Sali <sali(a)salilab.org>, "Wells, Jim" <Jim.Wells(a)ucsf.edu>, Joseph DeRisi <joe(a)derisilab.ucsf.edu>, Ken Dill <dill(a)maxwell.compbio.ucsf.edu>, "CRAIK, CHARLES" <craik(a)cgl.ucsf.edu>, Zev Gartner <Zev.Gartner(a)ucsf.edu>, shokat(a)cmp.ucsf.edu > Cc: Steve Whitelam <SWhitelam(a)lbl.gov> > Subject: Peptoid computation post-doc openings > > Dear UCSF Colleagues, > > I wanted to alert you to a couple of computational post-doc openings at the Molecular Foundry to study the folding and self-assembly of peptoids: > > MD simulations of peptoid folding: http://nanotheory.lbl.gov/images/position_description_atomistic.pdf > Coarse-grain modeling of peptoid self-assembly: http://nanotheory.lbl.gov/images/position_description_coarsegrained.pdf > > These positions are with my close Theory collaborator, Steve Whitelam. We are interactively making molecules and studying them computationally, and are looking for post-docs who would enjoy this interplay between theory and experiment. > > Please pass this along and let people know we are happy to discuss more details anytime! Thanks and best regards, > > -Ron > > > -- > > Ronald Zuckermann, Ph.D. > Biological Nanostructures Facility > The Molecular Foundry > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd.; MS 67-5117 > Berkeley, CA 94720 > > (510) 486-7091 > rnzuckermann(a)lbl.gov > http://foundry.lbl.gov >

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[Compbio-allhands] Fwd: University of Illinois - Urbana-Champaign, Experimental Biological Physics Faculty position
by Andrej Sali 04 Nov '11

04 Nov '11

Begin forwarded message: > From: "taekjip ha" <taekjipha(a)physics.illinois.edu> > Subject: University of Illinois - Urbana-Champaign, Experimental Biological Physics Faculty position > Date: November 4, 2011 6:31:34 AM PDT > To: "taekjip ha" <taekjipha(a)physics.illinois.edu> > > Dear Colleagues, > > I would like to bring to your attention the attached position for a full-time tenured or tenure-track position at the University of Illinois Department of Physics. This position is in the area of experimental biological physics, with an emphasis in cellular or systems-level biophysics, complementing strengths in molecular biophysics. > > Start date is as early as August 16, 2012. A Ph.D., or equivalent, is required along with the ability to teach effectively at both undergraduate and graduate levels and to conduct a vigorous and significant program in an area of contemporary biological physics. The successful applicant will be joining a department with active programs in both experimental and theoretical biological physics. > > Applicants should go online to: https://jobs.illinois.edu to complete and submit an application form. A curriculum vitae, a publication list, a summary of research interests and accomplishments, a statement of teaching interests and experience, and the names and addresses of four references should be submitted at that time. Applicants will be evaluated upon submission of materials. > > Closing date is December 1, 2010. Applications submitted after this date will be accepted but are not guaranteed full consideration. Salary will be competitive and commensurate with qualifications. Online applications are strongly preferred but applications by mail will be accepted (send care of Margie Gamel, Dept. of Physics, University of Illinois, Urbana-Champaign, 1110 W. Green St., Urbana, Illinois 61801-3080, U.S.A.). Illinois is an Affirmative Action /Equal Opportunity Employer and welcomes individuals with diverse backgrounds, experiences, and ideas who embrace and value diversity and inclusivity. (www.inclusiveillinois.illinois.edu) > > Further information may be found at: https://jobs.illinois.edu/default.cfm?page=job&jobID=4172 > > If you have received this in error, or in duplicate, I apologize; please forward it to an interested colleague. > > For the Search Committee, > > > Taekjip Ha > Investigator, Howard Hughes Medical Institute > Professor, University of Illinois at Urbana-Champaign > 133 Loomis Laboratory of Physics, MC 704 > 1110 W. Green St.; Urbana, IL 61801-3080 > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: On Behalf of Taekjip Ha and Klaus Schulten - Postdoctoral Fellowship Opportunities with NSF's Center for the Physics of Living Cells (CPLC) - PLEASE POST and CIRCULATE
by Andrej Sali 02 Nov '11

02 Nov '11

Begin forwarded message: > From: "Flanegin, Susan A" <flanegin(a)illinois.edu> > Subject: FW: On Behalf of Taekjip Ha and Klaus Schulten - Postdoctoral Fellowship Opportunities with NSF's Center for the Physics of Living Cells (CPLC) - PLEASE POST and CIRCULATE > Date: November 2, 2011 2:13:07 PM PDT > To: "mchee(a)prognosysbio.com" <mchee(a)prognosysbio.com>, "mcolvin(a)ucmerced.edu" <mcolvin(a)ucmerced.edu>, "mdiez(a)mit.edu" <mdiez(a)mit.edu>, "meganmayerle(a)yahoo.com" <meganmayerle(a)yahoo.com>, "meglio(a)lps.ens.fr" <meglio(a)lps.ens.fr>, "merkiene(a)fermentas.lt" <merkiene(a)fermentas.lt>, "mhingorani(a)wesleyan.edu" <mhingorani(a)wesleyan.edu>, "micah(a)neu.edu" <micah(a)neu.edu>, "michael.elbaum(a)weizmann.ac.il" <michael.elbaum(a)weizmann.ac.il>, "michael.rosen(a)utsouthwestern.edu" <michael.rosen(a)utsouthwestern.edu>, "michael_paesler(a)ncsu.edu" <michael_paesler(a)ncsu.edu>, "michaelis(a)lmu.de" <michaelis(a)lmu.de>, "michalet(a)chem.ucla.edu" <michalet(a)chem.ucla.edu>, "minhash(a)rsc.org" <minhash(a)rsc.org>, "minhash(a)rsc.org" <minhash(a)rsc.org>, "Mitsuo.Ikebe(a)umassmed.edu" <Mitsuo.Ikebe(a)umassmed.edu>, "modesto.orozco(a)bsc.es" <modesto.orozco(a)bsc.es>, "modesto(a)mmb.pcb.ub.es" <modesto(a)mmb.pcb.ub.es>, "Mohamed_Sobhy(a)hms.harvard.edu" <Mohamed_Sobhy(a)hms.harvard.edu>, "mokhalil(a)mit.edu" <mokhalil(a)mit.edu>, "MORIMOTO(a)northwestern.edu" <MORIMOTO(a)northwestern.edu>, "mpoirier(a)mps.ohio-state.edu" <mpoirier(a)mps.ohio-state.edu>, "m-ratner(a)nwu.edu" <m-ratner(a)nwu.edu>, "mteruel(a)stanford.edu" <mteruel(a)stanford.edu>, "mtoku(a)lab.nig.ac.jp" <mtoku(a)lab.nig.ac.jp>, "mtraksel+(a)pitt.edu" <mtraksel+(a)pitt.edu>, "mulbrich(a)berkeley.edu" <mulbrich(a)berkeley.edu>, "mwiener(a)virginia.edu" <mwiener(a)virginia.edu>, "myoshida(a)res.titech.ac.jp" <myoshida(a)res.titech.ac.jp>, "nathan.baker(a)wustl.edu" <nathan.baker(a)wustl.edu>, "naumann(a)chem.iupui.edu" <naumann(a)chem.iupui.edu>, "ned.seeman(a)nyu.edu" <ned.seeman(a)nyu.edu>, "nfschere(a)midway.uchicago.edu" <nfschere(a)midway.uchicago.edu>, "Nir.Gov(a)weizmann.ac.il" <Nir.Gov(a)weizmann.ac.il>, "nlallbri(a)uci.edu" <nlallbri(a)uci.edu>, "noga.kozer(a)ludwig.edu.au" <noga.kozer(a)ludwig.edu.au>, "nwalter(a)umich.edu" <nwalter(a)umich.edu>, "nwells(a)lanl.gov" <nwells(a)lanl.gov>, "oby(a)cs.tu-berlin.de" <oby(a)cs.tu-berlin.de>, "olga.mayans(a)unibas.ch" <olga.mayans(a)unibas.ch>, "ortoleva(a)indiana.edu" <ortoleva(a)indiana.edu>, "oshea(a)biochem.ucsf.edu" <oshea(a)biochem.ucsf.edu>, "pantoja(a)caltech.edu" <pantoja(a)caltech.edu>, "pappu(a)wustl.edu" <pappu(a)wustl.edu>, "pastor(a)cber.FDA.gov" <pastor(a)cber.FDA.gov>, "pclark1(a)nd.edu" <pclark1(a)nd.edu>, "peter.moore(a)yale.edu" <peter.moore(a)yale.edu>, "Petra.Fromme(a)asu.edu" <Petra.Fromme(a)asu.edu>, "petros(a)ethz.ch" <petros(a)ethz.ch>, "pierce(a)caltech.edu" <pierce(a)caltech.edu>, "pks(a)tbi.univie.ac.at" <pks(a)tbi.univie.ac.at>, "porte001(a)umn.edu" <porte001(a)umn.edu>, "ptso(a)mit.edu" <ptso(a)mit.edu>, "pwkr(a)centrosome.dna.caltech.edu" <pwkr(a)centrosome.dna.caltech.edu>, "pwolynes(a)ucsd.edu" <pwolynes(a)ucsd.edu>, "quxh(a)berkeley.edu" <quxh(a)berkeley.edu>, "raldrich(a)mail.utexas.edu" <raldrich(a)mail.utexas.edu>, "rama.ranganathan(a)utsouthwestern.edu" <rama.ranganathan(a)utsouthwestern.edu>, "ramaro(a)mccammon.ucsd.edu" <ramaro(a)mccammon.ucsd.edu>, "rao(a)cua.edu" <rao(a)cua.edu>, "rfishel(a)osu.edu" <rfishel(a)osu.edu>, "richard.lavery(a)ibcp.fr" <richard.lavery(a)ibcp.fr>, "rjgarcia(a)mail.bio.tamu.edu" <rjgarcia(a)mail.bio.tamu.edu>, "rk2(a)uark.edu" <rk2(a)uark.edu>, "RL1(a)york.ac.uk" <RL1(a)york.ac.uk>, "Robert.Bittl(a)physik.FU-Berlin.de" <Robert.Bittl(a)physik.FU-Berlin.de>, "robertop(a)intra.niddk.nih.gov" <robertop(a)intra.niddk.nih.gov>, "robphillips(a)mageos.com" <robphillips(a)mageos.com>, "roderick.lim(a)unibas.ch" <roderick.lim(a)unibas.ch>, "roskies(a)cpwsca.psc.edu" <roskies(a)a.psc.edu>, "roux(a)uchicago.edu" <roux(a)uchicago.edu>, "roy.bar-ziv(a)weizmann.ac.il" <roy.bar-ziv(a)weizmann.ac.il>, "rtompkins(a)partners.org" <rtompkins(a)partners.org>, "ruthnu(a)helix.nih.gov" <ruthnu(a)helix.nih.gov>, "sabeysi1(a)jhu.edu" <sabeysi1(a)jhu.edu>, "sali(a)salilab.org" <sali(a)salilab.org>, "sandler(a)microbio.umass.edu" <sandler(a)microbio.umass.edu>, "Sandrine.Etienne-Manneville(a)curie.fr" <Sandrine.Etienne-Manneville(a)curie.fr>, "saveez(a)hms.harvard.edu" <saveez(a)hms.harvard.edu>, "sb10031(a)cam.ac.uk" <sb10031(a)cam.ac.uk>, "schlick(a)NYU.EDU" <schlick(a)nyu.edu>, "schlierf(a)bcube-dresden.de" <schlierf(a)bcube-dresden.de>, "SCHWI001(a)MC.DUKE.EDU" <SCHWI001(a)MC.DUKE.EDU>, "schwille(a)biotec.tu-dresden.de" <schwille(a)biotec.tu-dresden.de>, "scraig(a)jhmi.edu" <scraig(a)jhmi.edu>, "se.praly(a)lps.ens.fr" <se.praly(a)lps.ens.fr>, "Sean.Decatur(a)oberlin.edu" <Sean.Decatur(a)oberlin.edu>, "seg(a)u.washington.edu" <seg(a)u.washington.edu>, "shannonyan(a)berkeley.edu" <shannonyan(a)berkeley.edu>, "shawn(a)physics.ucsb.edu" <shawn(a)physics.ucsb.edu>, "shokri.l(a)neu.edu" <shokri.l(a)neu.edu>, "shs(a)chem.psu.edu" <shs(a)chem.psu.edu>, "shubeita(a)chaos.utexas.edu" <shubeita(a)chaos.utexas.edu>, "shwhite(a)uci.edu" <shwhite(a)uci.edu>, "simon.rainville(a)phy.ulaval.ca" <simon.rainville(a)phy.ulaval.ca>, "simons(a)mpi-cbg.de" <simons(a)mpi-cbg.de>, "singer(a)chemistry.ohio-state.edu" <singer(a)chemistry.ohio-state.edu>, "singlemolecule(a)gmail.com" <singlemolecule(a)gmail.com>, "sivasank(a)stanford.edu" <sivasank(a)stanford.edu>, "sjb1(a)psu.edu" <sjb1(a)psu.edu> > > > Dear Colleagues, > We are writing to inform you of several postdoctoral fellowship opportunities for the coming academic year, starting September 2012, in experimental and theoretical biophysics in the "Center for the Physics of Living Cells" (CPLC), a National Science Foundation Physics Frontier Center at the University of Illinois, Urbana-Champaign. > > Research in the Center for the Physics of Living Cells falls into one of four themes: > > 1. Maximizing information content of single molecule experiments; > > 2. Using synthetic nanostructures for high speed single molecule spectroscopy; > > 3. Observing individual events within single cells; and > > 4. Extending computation to biologically relevant timescales, and theory to greater biological realism. > > Fellows will use state-of-the-art experimental and theoretical biophysical tools to accomplish these goals: optical tweezers, single-molecule fluorescence microscopy, fabrication of synthetic nanostructure, high-speed, low-noise electrical measurements, live cell imaging, microscopic and coarse-grained molecular simulations, stochastic modeling, as well as the standard methods of molecular and cellular biology and genetics. Research will involve both the development and improvement of experimental and computational techniques and the application of these techniques to particular biological processes such as replication, transcription, translation, cell transport and motility. As projects are collaborative endeavors between several labs, the fellows will have the opportunity to be jointly advised by two or more faculty members of the CPLC. > > Apply via https://my.physics.illinois.edu/join/ no later than December 2, 2011. Applications should include: cover letter; curriculum vita; research statement; publications list; and contact information for three references. Applications received after the December 2nd deadline may not be considered. A full job description can be found at: http://www.cplc.illinois.edu/opps/postdocs.asp > > Please post and circulate the attached announcement or if interested, apply accordingly. > > For more information about CPLC, please visit http://cplc.illinois.edu/opps/postdocs.asp > > Thank you. > > Taekjip Ha and Klaus Schulten > Co-directors, Center for the Physics of Living Cells > http://www.cplc.illinois.edu > University of Illinois at Urbana-Champaign > 1110 West Green Street, MC 704 > Urbana, IL 61801-3080, USA > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] 11/3/11 Seminar with Adam Cohen
by Nicole Takesono Flowers 31 Oct '11

31 Oct '11

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Adam Cohen Harvard University Fluorescent voltage-indicating proteins: imaging spiking from E. coli to neurons November 3, 2011 B. Huang, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Faculty Position in Chemical Biology at UNC
by Brian Shoichet 31 Oct '11

31 Oct '11

Fyi Brian Shoichet Professor Dept. of Pharmaceutical Chemistry UCSF http://shoichetlab.compbio.ucsf.edu ---------- Forwarded message ---------- From: "Weeks, Kevin" <weeks(a)unc.edu> Date: Oct 31, 2011 4:01 AM Subject: Faculty Position in Chemical Biology at UNC To: Dear Colleagues, The Carolina Center for Genome Sciences is partnering with the Department of Chemistry to conduct a junior faculty search with a research focus in Chemical Biology and Chemical Genomics. This new colleague will join a group of highly inventive laboratories spanning the Departments of Biology, Chemistry and Computational Biology in the new Genome Sciences Building at UNC. The formal advertisement is attached. We ask you to encourage exceptional candidates to apply. With best regards, Kevin -- Kevin M Weeks . Kenan Distinguished Professor Department of Chemistry . Kenan Labs . 125 South Road University of North Carolina . Chapel Hill NC 27599-3290 http://www.chem.unc.edu/rna

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[Compbio-allhands] 10/27/11 Seminar with Jim Ferrell
by Nicole Takesono Flowers 26 Oct '11

26 Oct '11

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Jim Ferrell Stanford University Dissecting the Mitotic Trigger October 27, 2011 W. Lim, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Biochemistry Assistant Professor Position at Utah State University
by Brian Shoichet 24 Oct '11

24 Oct '11

Brian Shoichet Professor Dept. of Pharmaceutical Chemistry UCSF http://shoichetlab.compbio.ucsf.edu ---------- Forwarded message ---------- From: "Geraldine Child" <geri.child(a)usu.edu> Date: Oct 24, 2011 9:15 AM Subject: Biochemistry Assistant Professor Position at Utah State University To: Dear Colleagues, I would like to bring to your attention our current search for an assistant professor in the area of Biochemistry. Details of the position and application process are given below. Please pass this information on to appropriate postdoctoral associates in your laboratory. We are especially interested in receiving applications from female and minority candidates. Thank you, Alvan C. Hengge Department Head, Professor Department of Chemistry and Biochemistry Utah State University Logan UT 84322-0300 ____________________________________________________________________________________ Assistant Professor Biochemistry Utah State University The Department of Chemistry and Biochemistry at Utah State University invites applications for a R. Gaurth Hansen tenure-track assistant professor position in Biochemistry to begin Fall 2012. The successful candidate will develop a research program that complements at least one departmental focus area, such as macromolecular structure and function, or catalysis and reaction mechanism. Applicants must have a PhD in biochemistry, chemistry, or a related field, and postdoctoral experience. The position requires the development of an externally-funded research program, as well as teaching at the undergraduate and graduate levels. Candidates capable of teaching biophysical chemistry are particularly encouraged to apply. Applicants should submit a curriculum vitae, a concise description of future research projects, a description of how the research to be pursued complements existing research focus areas in the Department, a description of teaching experience and preferred teaching area(s), and the names and email addresses of three references. Apply online at http://jobs.usu.edu (REQ ID 052891). Evaluation of applicants will begin November 1, 2011 and will continue until the position is filled. Utah State University, located in Logan, Utah, is an Equal Opportunity/Affirmative Action Employer committed to assembling a diverse faculty. Women and members of minority groups are strongly encouraged to apply.

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[Compbio-allhands] Fwd: Opportunity for young investigators in Sweden
by Andrej Sali 24 Oct '11

24 Oct '11

Begin forwarded message: > From: Arne Elofsson <arne(a)bioinfo.se> > Subject: Opportunity for young investigators in Sweden > Date: October 24, 2011 5:41:31 AM PDT > To: Christine Orengo <orengo(a)biochem.ucl.ac.uk>, David Baker <dabaker(a)u.washington.edu>, Andrej Sali <sali(a)salilab.org>, d.jones(a)cs.ucl.ac.uk, e.bornberg(a)uni-muenster.de, Frishman Dmitrij <d.frishman(a)wzw.tum.de>, "David A. Liberles" <liberles(a)uwyo.edu> > > > Dear Colleagues > > At the moment there are openings for excellent young scientists in Sweden through a very well funded program named Wallenber Academy Fellows, see below for a link to a Swedish announcement. Therefore if you have any very good candidates with a PhD awarded between 2004 and 2007 and that have a serious interest to move to Sweden and work in an area related to ours, I would very much appreciate if you forwarded this mail to them. > > The application procedure is two steps. First the department can nominate candidates to the head of the university with a deadline of Dec 3 and then the university will select up to 10 candidates (of which 40% needs to be external). These will then have until Feb 29 to write the application. The grant is for 5 years and between 1 and and 1.5 MSEK (110-165 kEuro) per year and in addition the university will guarantee 50% of the salary and provide some sort of tenure track. > > > Here is the link (in Swedish) > > http://www.wallenberg.com/docs/kaw/nomineringsinbjudan-wallenberg-academy-f… > > Yours > > Arne > > --------------------------------------------------------- > Prof. Arne Elofsson Dep of Biochemistry and Biophysics > Tel:+46-8-16 4672 Stockholm University > Fax:+46-8-15 3679 10691 Stockholm, Sweden > Mobile: +46 70 695 1045 > Directions: see http://bioinfo.se/misc/directions.html > Net: arne(a)bioinfo.se http://bioinfo.se/ > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Comp Bio/Drug Discovery Internship opportunity at Novartis Emeryville
by Schnoes, Alexandra 21 Oct '11

21 Oct '11

Hello, This was circulated a bit ago but they are still looking. If you are interested please contact Eric Martin (below). I get the feeling they would love to take someone from UCSF. I know a little bit about the position, so if you have some basic questions you can shoot them to me too. Job description for Student Internship in Compuational Drug Discovery Most drug leads are discovered through experimental high-throughput screens, which cost about $1,000,000 and take 6-9 months. Efforts over many years to develop computational “in silico” screens have not resulted in sufficiently accurate models to provide a practical alternative. Recently, at Novartis, a protein family-based approach has produced models approximating experimental accuracy for the special cases of kinase and serine/cisteine protease enzyme families. These families include many pharmaceutically important drug targets. This 1-year internship involves learning to train and employ these models on new and existing drug discovery targets. The ideal candidate would understand the physical properties of organic compounds and proteins, and how they can interact, as well as familiarity with computer programming and running scientific calculations. Eric Martin ( eric.martin(a)novartis.com<mailto:eric.martin@novartis.com> ) Director, Computational Chemistry Novartis 4560 Horton St. Emeryville, CA 94608 510-923-3306 -- Alexandra Schnoes, PhD Program Coordinator, Graduate Student Internships for Career Exploration Scientist, Babbitt Laboratory University of California San Francisco 513 Parnassus Ave, S-224 Campus Box 0410 San Francisco, CA 94143 Tel: 415-476-0572 Fax: 415-476-0689 Email: alexandra.schnoes(a)ucsf.edu<mailto:alexandra.schnoes@ucsf.edu> Web: http://gsice.ucsf.edu<http://gsice.ucsf.edu/>

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[Compbio-allhands] Friday Seminar: The Role of Conformational Dynamics of G-Protein Coupled Receptors in Drug Design
by JoAnne Williams 19 Oct '11

19 Oct '11

This seminar may be of interest to you: -------------------------------------------- *Date: Friday, October 21, 2011* *Time: 11:00a-12:00p* *Location: BH215* *Speaker: **Prof. Nagarajan Vaidehi* *Department of Immunology, Beckman Research Institute, City of Hope Cancer* *Research Center* *The Role of Conformational Dynamics of G-Protein Coupled* *Receptors in Drug Design* Abstract: The superfamily of membrane proteins known as G-protein coupled receptors (GPCRs), mediate signal transduction in a wide array of different cell types. Drugs targeting GPCRs represent the core of modern medicine. Upon stimulation by a variety of signaling molecules (ranging from light to small molecules and large proteins), GPCRs trigger a diverse set of signaling pathways in the cell, by coupling to different intracellular proteins to transduce the signal. This functional diversity in signaling is achieved by the structural conformational dynamics of these receptors. In this talk, I will demonstrate that the combination of computational methods, X-ray crystallography, and fluorescence spectroscopy provides insight into the conformational ensemble sampled by GPCRs. Additionally, the effect of how the ligand binding leads to a shift in the relative population density in this ensemble will be discussed. An example of how structural insights gained from these fundamental biophysical techniques can be used to design drugs targeting a specific signaling pathway that is relevant in pancreatic cancer will be outlined. -- JoAnne Williams, Admin Analyst Shoichet & Jacobson Labs Department of Pharmaceutical Chemistry University of California, San Francisco UCSF MC 2550 Byers Hall, Rm 508 1700 4th Street San Francisco, CA 94158-2517 tel: (415) 514-4261 or (415) 502-7050 email: *joanne(a)picasso.ucsf.ed <http://joanne@picasso.ucsf.edu/>u* * * * *

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[Compbio-allhands] Fwd: International PhD Program - Announcement Spring Selection 2012
by Andrej Sali 19 Oct '11

19 Oct '11

Begin forwarded message: > From: "Wolf, Ingrid" <inwolf(a)biochem.mpg.de> > Subject: International PhD Program - Announcement Spring Selection 2012 > Date: October 19, 2011 7:32:25 AM PDT > To: "'Sali'" <sali(a)salilab.org> > > Dear Prof. Sali, > > Please find enclosed the announcement of our international PhD program in molecular and cellular life sciences. > > The International Max Planck Research School for Molecular and Cellular Life Sciences is jointly conducted by the Max Planck Institutes of Biochemistry, Neurobiology and Psychiatry, the Ludwig Maximilian University Munich and the Technical University Munich. The program, covering the disciplines of biochemistry, cell biology, molecular medicine, neurobiology and structural biology, offers a research oriented comprehensive and interdisciplinary training to doctoral students from all over the world. More than 60 distinct research projects are currently available. > > Qualified candidates are now invited to apply for the spring selection 2012. Deadline for application is January 15th, 2012. > All students accepted to the program will receive a generous PhD fellowship covering tuition and living expenses. > Further information and application details are available at: www.imprs-ls.de<http://www.imprs-ls.de/> > > We kindly ask you to communicate this announcement to potentially interested students or to display the flyer at your departmental bulletin board. > > > Yours sincerely, > > Ingrid Wolf > > __________________________________________________________________________________________ > Dr. Ingrid Wolf > Scientific Coordinator > International Max Planck Research School > for Molecular and Cellular Life Sciences > Am Klopferspitz 18 > 82152 Martinsried/Munich, Germany > phone: ++49 89 8578-2855 (Wed., Thu., Fri.) > fax: ++49 89 8578-2859 > email: inwolf(a)biochem.mpg.de > web: www.imprs-ls.de > > If you don't want to receive further mails from IMPRS-LS, please send us a reply email with the note "sign out" in the header. > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: help please in idenifying a candidate
by Brian Shoichet 18 Oct '11

18 Oct '11

FYI. ---------- Forwarded message ---------- From: Chandra Verma <chandra(a)bii.a-star.edu.sg> Date: Tue, Oct 18, 2011 at 3:11 AM Subject: help please in idenifying a candidate To: Brian Shoichet <shoichet(a)cgl.ucsf.edu> dear brian hope all is well. i need your help in identifying a suitable candidate - given that yours is one of the few places that combines computational with experimental. we have an opening for a person with 4-5 years postdoctoral experience to set up a small lab here in our institute in singapore. here is the ad i am planning on putting out. many thanks for your help and if you could suggest some other labs i could write to, will be much obliged. regards chandra A position is available for a team leader with a background in chemical biology to start a small group combining computational and experimental methods for screening small molecules against targets of therapeutic interest. The person will have at least 5-6 years of postdoctoral experience in this area. The institute has a variety of teams pursuing computational studies combining them with experimental work. The candidate will be expected to develop their own research program as well as work with other teams in setting up assays to test hypotheses generated. There are several opportunities to collaborate with academic, pharmaceutical and clinical groups in Singapore. The position will be in the Division of Modelling & Design in the Bioinformatics Institute (A*STAR) (http://www.bii.a-star.edu.sg/**research/bmad/bmad.php<http://www.bii.a-star.edu.sg/research/bmad/bmad.php> ). Please submit a resume and a research proposal and have 3 letters of reference sent to bettyk(a)bii.a-star.edu.sg and to chandra(a)bii.a-star.edu.sg. Informal enquiries may be made from chandra(a)bii.a-star.edu.sg -- Brian Shoichet Professor University of California, San Francisco Dept. of Pharmaceutical Chemistry phone: 415-514-4126; fax: 415-514-4260 http://shoichetlab.compbio.ucsf.edu

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[Compbio-allhands] Fwd: I have money for excellent semi-independent position for post-postdoc for a few years
by Andrej Sali 18 Oct '11

18 Oct '11

Begin forwarded message: > From: Burkhard Rost <rost(a)in.tum.de> > Subject: I have money for excellent semi-independent position for post-postdoc for a few years > Date: October 18, 2011 5:06:53 AM PDT > To: Schneider Reinhard <reinhard.schneider(a)uni.lu>, Kelso Janet <kelso(a)eva.mpg.de>, Bromberg Yana <YanaB(a)rci.rutgers.edu>, Michal Linial <michall(a)cc.huji.ac.il>, Ofran Yanay <yanay.ofran(a)gmail.com>, Ben-Tal Nir <NirB(a)tauex.tau.ac.il>, Schlessinger Avner <schles(a)salilab.org>, Sali Andrej <sali(a)salilab.org>, Lupas Andrei <andrei.lupas(a)tuebingen.mpg.de>, Sippl Manfred <sippl(a)came.sbg.ac.at>, Orengo Christine <orengo(a)biochemistry.ucl.ac.uk>, Valencia Alfonso <valencia(a)cnio.es>, Tramontano Anna <Anna.Tramontano(a)uniroma1.it>, Punta Marco <mp13(a)sanger.ac.uk>, Gaasterland Terry <tgaasterland(a)ucsd.edu> > > Dear Friends: > > I have funding for the position that Marco Punta just left in April this year to join Pfam. The official position is as Fellow ("for life" with funding for <3 years; official 'title' Carl von Linde Fellow: mind you is one those who helped toward inventing the fridge and one of those scientists who went out and made money) of the Institute of Advanced Studies @ the TUM. It comes with a lot of freedom, high visibility, and fair funding. Applicants would have to be in Germany most of the time and would be expected to use this as a jump board to find a tenure-track position somewhere. > > Any of you has any proposal? Ideally, I'd like to find a woman for this, because those are very much underrepresented in the list of current fellows. > > As always, this is unfortunately very urgent (application deadline: Nov 1). > > thanks for your help. > best wishes, > burkhard > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Seminar - Boris Turk, Josef Stefan Institute, Slovenia - Friday, Oct. 21 - 2pm - BH 413
by Hilary Mahon 17 Oct '11

17 Oct '11

Please see attached for additional information. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] Fwd: Postdoctoral opportunities at Princeton
by Andrej Sali 17 Oct '11

17 Oct '11

Begin forwarded message: > From: "Biophysics" <biophys(a)princeton.edu> > Subject: Postdoctoral opportunities at Princeton > Date: October 17, 2011 1:51:35 PM PDT > To: "Biophysics" <biophys(a)princeton.edu> > Cc: <wbialek(a)princeton.edu>, "'Wingreen, Ned S.'" <wingreen(a)princeton.edu>, "Curtis Callan" <ccallan(a)princeton.edu>, "Chase P. Broedersz" <cbroeder(a)princeton.edu> > > Dear colleagues, > > We are in the midst of our annual search for young theorists interested in problems at the interface of physics and biology, and ask your help in bringing these opportunities to the attention of > interested (and interesting) candidates. The full text of the > advertisement, with application instructions, is attached below. > > Postdoctoral fellows have included a mix of people who have experience in biological physics, as well as those who are changing into the field from more traditional areas of physics. Lewis-Sigler Fellows are expected to have enough experience and maturity to articulate their own research program, although for both positions we favor fresh PhDs. All applicants will be considered for both positions. > > We have been fortunate in recent years, attracting a stream wonderful young colleagues who have now moved on to excellent faculty > positions. We hope you can help us as we try to replenish our > community. > > Although the nominal deadline has just passed, we are still reading new applications. Please do encourage people to act soon, though. We would like to interview promising candidates before the end of the calendar year. > > Many thanks, > > William Bialek > Chase Broedersz > Curtis Callan > Ned Wingreen > > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] 10/20/11 Clements Lecture with Anselm Levskaya
by Nicole Takesono Flowers 14 Oct '11

14 Oct '11

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Anselm Levskaya Clements Lecture Closed Loop Optogenetics for the Study of Neural Circuitry In Vivo October 20, 2011 C. Voigt, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: quantitative biology positions at UC San Diego
by Andrej Sali 05 Oct '11

05 Oct '11

Begin forwarded message: > From: Terry Hwa <hwa(a)ucsd.edu> > Subject: quantitative biology positions at UC San Diego > Date: October 4, 2011 9:16:27 PM PDT > To: Terence Hwa <thwa(a)ucsd.edu> > > > > Dear Friends, > > I am writing to tell you about some exciting opportunities for growth in the general area of quantitative biology at U.C. San Diego. Attached is a joint ad for 5 experimental searches at an assortment of levels being conducted across biology, physics, and chemistry, as well as two senior theorist positions (one in physics, another in chemistry). These positions are a part of a multi-year initiative to establish a world-class program in quantitative biology, broadly interpreted as an iterated dialogue between quantitative experimentation and theoretical reasoning of living systems. A similar number of positions are expected in the next two years. > > It is our goal to use these positions judiciously to assemble a dream team in quantitative biology, building on the vast base of biological research in the La Jolla basin, and leading the way to a new era in the biosciences. We encourage you to pass this information to interested junior and senior colleagues to pursue these opportunities together. > > thank you and best wishes, > > Terry Hwa > > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: looking for postdoc
by Jacobson, Matt 03 Oct '11

03 Oct '11

Begin forwarded message: From: Jeremy Schmit <schmit(a)phys.ksu.edu<mailto:schmit@phys.ksu.edu>> Date: October 3, 2011 12:55:27 PM PDT To: Fyl Pincus <fyl(a)mrl.ucsb.edu<mailto:fyl@mrl.ucsb.edu>>, Alex Levine <alevine(a)chem.ucla.edu<mailto:alevine@chem.ucla.edu>>, Jané Kondev <kondev(a)brandeis.edu<mailto:kondev@brandeis.edu>>, Seth Fraden <fraden(a)brandeis.edu<mailto:fraden@brandeis.edu>>, Bulbul Chakraborty <bulbul(a)brandeis.edu<mailto:bulbul@brandeis.edu>>, <hagan(a)brandeis.edu<mailto:hagan@brandeis.edu>>, Steve Whitelam <swhitelam(a)lbl.gov<mailto:swhitelam@lbl.gov>>, Steve Presse <stevenpresse(a)gmail.com<mailto:stevenpresse@gmail.com>>, Justin MacCallum <justin.maccallum(a)me.com<mailto:justin.maccallum@me.com>>, Chris Fennell <cfennell(a)me.com<mailto:cfennell@me.com>>, Kevin Plaxco <plaxco(a)chem.ucsb.edu<mailto:plaxco@chem.ucsb.edu>>, Paul Wiggins <wiggins(a)wi.mit.edu<mailto:wiggins@wi.mit.edu>>, Rob Phillips <phillips(a)pboc.caltech.edu<mailto:phillips@pboc.caltech.edu>>, <quake(a)stanford.edu<mailto:quake@stanford.edu>>, "Muschol, Martin" <mmuschol(a)usf.edu<mailto:mmuschol@usf.edu>>, adrian elcock <adrianelcock(a)gmail.com<mailto:adrianelcock@gmail.com>>, Tuomas Knowles <tpjk2(a)cam.ac.uk<mailto:tpjk2@cam.ac.uk>>, <dave.thirumalai(a)gmail.com<mailto:dave.thirumalai@gmail.com>>, <jliang(a)uic.edu<mailto:jliang@uic.edu>>, <draleigh(a)notes.cc.sunysb.edu<mailto:draleigh@notes.cc.sunysb.edu>>, Ken DIll <dill(a)laufercenter.org<mailto:dill@laufercenter.org>>, Yan Levin <levin(a)if.ufrgs.br<mailto:levin@if.ufrgs.br>>, <cjr(a)UDel.Edu<mailto:cjr@UDel.Edu>>, <baronp(a)engineering.ucsb.edu<mailto:baronp@engineering.ucsb.edu>>, <John.Carpenter(a)ucdenver.edu<mailto:John.Carpenter@ucdenver.edu>>, <tessier(a)rpi.edu<mailto:tessier@rpi.edu>>, "Laurence, Jennifer S" <laurencj(a)ku.edu<mailto:laurencj@ku.edu>>, <middaugh(a)ku.edu<mailto:middaugh@ku.edu>>, <pesmith(a)k-state.edu<mailto:pesmith@k-state.edu>>, <lednev(a)albany.edu<mailto:lednev@albany.edu>>, <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, <sen(a)buffalo.edu<mailto:sen@buffalo.edu>>, <Elan.Eisenmesser(a)ucdenver.edu<mailto:Elan.Eisenmesser@ucdenver.edu>>, <derouchey(a)uky.edu<mailto:derouchey@uky.edu>>, <lois(a)ccmr.cornell.edu<mailto:lois@ccmr.cornell.edu>>, <gary_pielak(a)unc.edu<mailto:gary_pielak@unc.edu>>, <enrique.delacruz(a)yale.edu<mailto:enrique.delacruz@yale.edu>>, <lattman(a)hwi.buffalo.edu<mailto:lattman@hwi.buffalo.edu>>, <fandrich(a)enzyme-halle.mpg.de<mailto:fandrich@enzyme-halle.mpg.de>>, <jsschreck(a)gmail.com<mailto:jsschreck@gmail.com>>, <zgw(a)cheme.caltech.edu<mailto:zgw@cheme.caltech.edu>>, <rakiyama(a)chem.kyushu-univ.jp<mailto:rakiyama@chem.kyushu-univ.jp>>, Claudio Chamon <chamon(a)bu.edu<mailto:chamon@bu.edu>>, <redner(a)bu.edu<mailto:redner@bu.edu>>, <lenhoff(a)UDel.Edu<mailto:lenhoff@UDel.Edu>>, <prausnit(a)cchem.berkeley.edu<mailto:prausnit@cchem.berkeley.edu>>, <nickpace(a)tamu.edu<mailto:nickpace@tamu.edu>>, <sudipta.maiti(a)gmail.com<mailto:sudipta.maiti@gmail.com>>, <belfog(a)rpi.edu<mailto:belfog@rpi.edu>>, <buddhapriya.chakrabarti(a)durham.ac.uk<mailto:buddhapriya.chakrabarti@durham.ac.uk>>, <Brewster(a)caltech.edu<mailto:Brewster@caltech.edu>>, <csantang(a)physics.umass.edu<mailto:csantang@physics.umass.edu>>, <bruinsma(a)physics.ucla.edu<mailto:bruinsma@physics.ucla.edu>>, <grason(a)mail.pse.umass.edu<mailto:grason@mail.pse.umass.edu>>, <muthu(a)polysci.umass.edu<mailto:muthu@polysci.umass.edu>>, Kings Ghosh <kingshuk.ghosh(a)du.edu<mailto:kingshuk.ghosh@du.edu>>, <ashok.prasad(a)colostate.edu<mailto:ashok.prasad@colostate.edu>>, <tolya(a)rice.edu<mailto:tolya@rice.edu>>, <drr2103(a)columbia.edu<mailto:drr2103@columbia.edu>>, <aalexand(a)mit.edu<mailto:aalexand@mit.edu>>, <gbrannigan(a)temple.edu<mailto:gbrannigan@temple.edu>>, <TLHead-Gordon(a)lbl.gov<mailto:TLHead-Gordon@lbl.gov>>, "Vinothan N. Manoharan" <vnm(a)seas.harvard.edu<mailto:vnm@seas.harvard.edu>>, <yal209(a)lehigh.edu<mailto:yal209@lehigh.edu>>, <dreeves(a)mit.edu<mailto:dreeves@mit.edu>>, <sam.safran(a)weizmann.ac.il<mailto:sam.safran@weizmann.ac.il>>, <v-chandrasekhar(a)northwestern.edu<mailto:v-chandrasekhar@northwestern.edu>>, <gsgrest(a)sandia.gov<mailto:gsgrest@sandia.gov>>, <rnzuckermann(a)lbl.gov<mailto:rnzuckermann@lbl.gov>>, <ARUNAN.NADARAJAH(a)utoledo.edu<mailto:ARUNAN.NADARAJAH@utoledo.edu>>, Paul Forster <Paul.Forster(a)unlv.edu<mailto:Paul.Forster@unlv.edu>>, <p.g.bolhuis(a)uva.nl<mailto:p.g.bolhuis@uva.nl>>, <gecrooks(a)lbl.gov<mailto:gecrooks@lbl.gov>>, <theodore.randolph(a)colorado.edu<mailto:theodore.randolph@colorado.edu>>, <craigmaloney(a)cmu.edu<mailto:craigmaloney@cmu.edu>>, Mark Henle <markhenle12(a)gmail.com<mailto:markhenle12@gmail.com>>, <vvoelz(a)gmail.com<mailto:vvoelz@gmail.com>>, John Chodera <jchodera(a)gmail.com<mailto:jchodera@gmail.com>>, <Sefika.Ozkan(a)asu.edu<mailto:Sefika.Ozkan@asu.edu>>, <siege017(a)umn.edu<mailto:siege017@umn.edu>>, <ilya.chorny(a)simprota.com<mailto:ilya.chorny@simprota.com>>, <vojko.vlachy(a)fkkt.uni-lj.si<mailto:vojko.vlachy@fkkt.uni-lj.si>>, <dlmobley(a)uno.edu<mailto:dlmobley@uno.edu>>, <rbrandman(a)gmail.com<mailto:rbrandman@gmail.com>>, <vageli(a)math.unm.edu<mailto:vageli@math.unm.edu>>, <apposite(a)gmail.com<mailto:apposite@gmail.com>>, <ggf(a)stanford.edu<mailto:ggf@stanford.edu>>, <mscottshell(a)gmail.com<mailto:mscottshell@gmail.com>>, <pande(a)stanford.edu<mailto:pande@stanford.edu>>, <johnvandrie(a)mindspring.com<mailto:johnvandrie@mindspring.com>>, <dkern(a)brandeis.edu<mailto:dkern@brandeis.edu>>, <fbrown(a)chem.ucsb.edu<mailto:fbrown@chem.ucsb.edu>> Subject: looking for postdoc Dear Friends, I am looking to hire a postdoc and am writing ask if you know of any qualified and interested candidates. The work will be developing theoretical models of protein rheology and aggregation (crystalline, amyloid, particulate, etc.) My emphasis is on analytic models, but simple Monte Carlo simulations may be involved depending on the project. The job description and application instructions can be found in the link below and more details about the research can be found on my group website (see signature). http://www.phys.ksu.edu/main/jobs/2011/schmit-postdoc.html Thanks, Jeremy -- Jeremy Schmit Assistant Professor Department of Physics Kansas State University http://www.phys.ksu.edu/personal/schmit/

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[Compbio-allhands] Fwd: faculty positions in systems biology and biostatistics
by Tom Ferrin 01 Oct '11

01 Oct '11

-------- Original Message -------- Subject: faculty positions in systems biology and biostatistics Date: Sat, 01 Oct 2011 12:12:59 -0700 From: David Ojcius <david.ojcius(a)gmail.com> Reply-To: dojcius(a)ucmerced.edu To: tef(a)cgl.ucsf.edu Dear Dr. Ferrin, I'm writing to draw your attention to a search for two tenure-track faculty positions in systems biology and biostatistics that may be of interest to your post-docs or former graduate students. The positions are in the Molecular Cell Biology group at the newest campus of the University of California (UC) in Merced. Applications of special relevance to research emphases include stem cell biology, diseases such as metabolic or inflammatory disorders, and microbial systems relevant to human disease. Interested individuals can refer to the full postings at: http://jobs.ucmerced.edu/n/academic/position.jsf?positionId=3523 http://jobs.ucmerced.edu/n/academic/position.jsf?positionId=3528 Sincerely yours, David Ojcius Professor, Molecular Cell Biology University of California, Merced e-mail:dojcius@ucmerced.edu <mailto:dojcius@ucmerced.edu>

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[Compbio-allhands] Fwd: Voelz lab seeking postdoctoral candidates
by Andrej Sali 26 Sep '11

26 Sep '11

Begin forwarded message: > From: Vincent Voelz <vvoelz(a)gmail.com> > Subject: Voelz lab seeking postdoctoral candidates > Date: September 26, 2011 9:42:50 AM PDT > To: Vincent Voelz <voelz(a)temple.edu> > > Dear colleagues: > > The Voelz lab is looking for potential postdoctoral candidates to join our new group at Temple University in Philadelphia, PA. If you know of talented individuals interested in the development and application of new biomolecular simulation methods for prediction and design, please pass on our job announcement below. > > Thanks so much for your help, > > Dr. Vincent Voelz > voelz(a)temple.edu > > Assistant Professor of Chemistry > Temple University > http://voelzlab.org > > ---------------- > Postdoctoral position in biomolecular simulation at Temple University, Philadelphia, PA > > A postdoctoral position is available in the laboratory of Dr. Vincent Voelz, Department of Chemistry at Temple University, Philadelphia, PA. > > Our lab is developing new computational methods to design folding and binding properties of proteins and peptide mimetics. Projects include (1) developing Markov State Model (MSM) approaches for modeling the folding reaction and designing sequences for folding properties (2) simulation-based prediction and design of non-biological (e.g. peptoid) foldamers (3) multiscale fragment-based approaches for predicting binding affinities and specificities of protein-peptide interactions. > > Our lab benefits greatly from high-performance computing resources and collaborations available through the Institute for Computational Molecular Science (http://www.temple.edu/cst/icms) and inter-disciplinary collaborations through the new Moulder Center for Drug Discovery in the School of Pharmacy. > > More information at http://voelzlab.org > > Applicant should have a Ph.D in computational/physical chemistry, biophysics, chemical engineering, or related field, and a strong background in molecular simulation, physical chemistry, statistical mechanics of biomolecular systems, and/or computational biophysics. Relevant research experience may include: conformational sampling using molecular dynamics or Monte Carlo simulation, free energy estimation, methods for estimating protein-ligand affinities, protein structure prediction, forcefield development, multiscale modeling. > > Good programming skills are essential, as the applicant will be responsible for writing new simulation algorithms and extending existing code bases. Other relevant skills include: familiarity with simulation/modeling packages such as AMBER, GROMACS, OpenMM; Python scripting experience; familiarity with UNIX; experience with large-scale scientific computing. Experience with parallel computing and/or GPUs a plus. > > Start date: negotiable (early 2012) > Salary: Competitive and commensurate with experience. > One-year appointment, with the option to extend contingent on satisfactory progress. > > To apply: Email a cover letter and your full CV (details of all academic degrees obtained, research skills and experience, publications, conference presentations) preferrably as a single PDF, along with 2-3 letters of recommendation, to Prof. Vincent Voelz (voelz(a)temple.edu) > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Voelz lab seeking postdoctoral candidates
by Vincent Voelz 26 Sep '11

26 Sep '11

Dear colleagues: The Voelz lab is looking for potential postdoctoral candidates to join our new group at Temple University in Philadelphia, PA. If you know of talented individuals interested in the development and application of new biomolecular simulation methods for prediction and design, please pass on our job announcement below. Thanks so much for your help, Dr. Vincent Voelz voelz(a)temple.edu Assistant Professor of Chemistry Temple University http://voelzlab.org ---------------- Postdoctoral position in biomolecular simulation at Temple University, Philadelphia, PA A postdoctoral position is available in the laboratory of Dr. Vincent Voelz, Department of Chemistry at Temple University, Philadelphia, PA. Our lab is developing new computational methods to design folding and binding properties of proteins and peptide mimetics. Projects include (1) developing Markov State Model (MSM) approaches for modeling the folding reaction and designing sequences for folding properties (2) simulation-based prediction and design of non-biological (e.g. peptoid) foldamers (3) multiscale fragment-based approaches for predicting binding affinities and specificities of protein-peptide interactions. Our lab benefits greatly from high-performance computing resources and collaborations available through the Institute for Computational Molecular Science (http://www.temple.edu/cst/icms) and inter-disciplinary collaborations through the new Moulder Center for Drug Discovery in the School of Pharmacy. More information at http://voelzlab.org Applicant should have a Ph.D in computational/physical chemistry, biophysics, chemical engineering, or related field, and a strong background in molecular simulation, physical chemistry, statistical mechanics of biomolecular systems, and/or computational biophysics. Relevant research experience may include: conformational sampling using molecular dynamics or Monte Carlo simulation, free energy estimation, methods for estimating protein-ligand affinities, protein structure prediction, forcefield development, multiscale modeling. Good programming skills are essential, as the applicant will be responsible for writing new simulation algorithms and extending existing code bases. Other relevant skills include: familiarity with simulation/modeling packages such as AMBER, GROMACS, OpenMM; Python scripting experience; familiarity with UNIX; experience with large-scale scientific computing. Experience with parallel computing and/or GPUs a plus. Start date: negotiable (early 2012) Salary: Competitive and commensurate with experience. One-year appointment, with the option to extend contingent on satisfactory progress. To apply: Email a cover letter and your full CV (details of all academic degrees obtained, research skills and experience, publications, conference presentations) preferrably as a single PDF, along with 2-3 letters of recommendation, to Prof. Vincent Voelz (voelz(a)temple.edu)

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[Compbio-allhands] Fwd: IT Manager Position at J&J
by Andrej Sali 13 Sep '11

13 Sep '11

Begin forwarded message: > From: "Stephens, Susan [JRDUS]" <sstephens1(a)ITS.JNJ.COM> > Subject: IT Manager Position at J&J > Date: September 13, 2011 5:17:13 AM PDT > To: "Stephens, Susan [JRDUS]" <sstephens1(a)ITS.JNJ.COM> > > J&J is looking to hire an IT manager. > > The successful candidate will have proven experience in one or more of the following areas: > - Database technologies (RDBMS and /or document databases) > - Rich data analysis and/or visualization > - Modeling technologies > - Data Integration technologies (ETL, Semantic technologies, virtual datawarehousing) > - LIMS and/or eLN > - Search Technologies > > Please go to the following link to read the full job description and to apply: > https://jnjc.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=47197 > > Cheers, > > Susie > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: Faculty Position. Biochemistry. University of Utah
by Andrej Sali 09 Sep '11

09 Sep '11

Begin forwarded message: > From: Linda VanOrden <linda(a)biochem.utah.edu> > Subject: Faculty Position. Biochemistry. University of Utah > Date: September 9, 2011 11:13:35 AM PDT > To: Linda VanOrden <linda(a)biochem.utah.edu> > Cc: Chris Hill <chris(a)biochem.utah.edu> > > Message sent on behalf of Chris Hill > > > Dear Colleague, > > The Department of Biochemistry at the University of Utah aims to hire five new tenure-track faculty members over the next few years. Our faculty is highly ranked for scholarship and we enjoy close interactions with colleagues in other School of Medicine departments as well as elsewhere on campus. A supportive, collaborative environment fosters creative science and our combined interdepartmental graduate programs in Biological Chemistry and Molecular Biology provide a good stream of outstanding students. While our emphasis is firmly on scientific excellence, we are fortunate to be located at the interface of a vibrant yet affordable city and pristine, accessible mountain wilderness. > > Our priorities for new faculty colleagues are scientific excellence and potential synergy with areas of strength in the Department and elsewhere on campus. Your research interests are among our target areas for a new faculty recruit. We hope that you will encourage especially talented postdoctorals in your lab, and other well-qualified candidates that you know, to apply to our open search via the web site: > > Department: http://medicine.utah.edu/biochemistry/ > Current Open Position: https://utah.peopleadmin.com/postings/7839 > > Many Thanks and Best Wishes, > > > > Christopher P. Hill, D.Phil. > Department Co-Chair > Distinguished Professor > Dr. Leo T. and Barbara K. Samuels Presidential Endowed Chair > Department of Biochemistry > University of Utah School of Medicine > 15 N. Medical Drive East, Rm. 4100 EEJ > Salt Lake City > Utah 84112-5650 > Tel 801.585.5536 FAX 801.581-7959 > chris(a)biochem.utah.edu -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: Mobley lab seeking postdoctoral candidates you might know
by Andrej Sali 08 Sep '11

08 Sep '11

Begin forwarded message: > From: David Mobley <dlmobley(a)uno.edu> > Subject: Mobley lab seeking postdoctoral candidates you might know > Date: September 8, 2011 8:31:25 PM PDT > To: David Mobley <dlmobley(a)uno.edu> > > Dear Colleague, > > I need your help identifying potential candidates for a postdoctoral research position in my lab in the Department of Chemistry at the University of New Orleans. If you have suitable candidates with experience in molecular simulations and/or molecular modeling who might be interested, please pass on the below information. Thanks so much for your valuable time. > > Advertisement: I seek a postdoctoral candidate with experience in molecular simulations or molecular modeling to work on an exciting research project at the interface of chemistry, physics and biology. The research focuses on extending and applying molecular dynamics-based free energy methods for predicting binding between small molecules (such as potential pharmaceutical drugs) and protein receptors. For reference, see my published work in this area. An ideal candidate would have substantial background in molecular modeling, ideally including molecular dynamics simulations and/or Monte Carlo, including applications and methodology work. Experience with free energy techniques is also a plus. Interested applicants should send a cover letter plus a CV to dlmobley(a)uno.edu. Additionally, please have at least three letters of reference sent to the same address as well. All application materials should be received by Oct. 1, 2011. Prospective applicants are welcome to contact me for more information. The position will likely start in January, 2012. > > The University of New Orleans, and the New Orleans area, provide exciting opportunities for work in this area. In addition to the Mobley Lab at UNO, we maintain close contacts with Steve Rick's group, also in Chemistry at UNO, and Chris Summa's experiment/theory group in Computer Science. Both labs have interests in molecular simulations, free energy calculations, and statistical mechanics. We also interact with the groups of Hank Ashbaugh and Lawrence Pratt at Tulane University and a variety of experimental collaborators. > > Thank you so much. > > > > Sincerely, > > David Mobley > > Department of Chemistry > > University of New Orleans > > 504-383-3662 > > > -- > David Mobley > Assistant Professor > Department of Chemistry > University of New Orleans > dlmobley(a)uno.edu > ph. 504-383-3662 > fax 504-280-6860 > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: Carnegie Institution - Bioinformatics
by Hao Li 06 Sep '11

06 Sep '11

FYI --Hao -------- Original Message -------- Subject: Carnegie Institution - Bioinformatics Date: Tue, 6 Sep 2011 10:00:50 -0400 From: Christine Pratt <applicants(a)ciwemb.edu> To: Hao Li <haoli(a)genome.ucsf.edu> Dear Dr. Li, I write to call your attention to a research faculty level position now available at the Department of Embryology. Please encourage any qualified and interested individual you know of to apply. Your assistance is greatly appreciated. Sincerely, Allan Spradling, Director Department of Embryology

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[Compbio-allhands] Fwd: Call for nominations for Postdoctoral Fellowships at Princeton Center for Theoretical Science
by Hao Li 15 Aug '11

15 Aug '11

FYI --Hao -------- Original Message -------- Subject: Call for nominations for Postdoctoral Fellowships at Princeton Center for Theoretical Science Date: Fri, 12 Aug 2011 15:51:50 +0000 From: Charlene Borsack <cborsack(a)PRINCETON.EDU> Reply-To: Charlene Borsack <cborsack(a)PRINCETON.EDU> To: pcts_nominators(a)Princeton.EDU Dear Colleague, We are writing to encourage you to submit nominations for the Princeton Center for Theoretical Science Postdoctoral Fellowships. Center Postdoctoral Fellowships are the most prestigious postdoctoral positions offered in the theoretical sciences at Princeton. They are intended for early-career theoretical scientists, broadly construed, including the fields of astrophysics, biology, chemistry, geosciences, physics, and engineering. The nominees should be individuals with outstanding talent and accomplishment who are eager to broaden their scientific horizons. Fellows receive a three-year appointment in the Center fully supported by Center funds, an office in the Center facility, and have full freedom to develop their scientific interests with the support and mentoring of the resident senior Faculty Fellows. It is our intention that the Center experience will have a profound impact on the scientific development and future careers of the Fellows. *The deadline for receipt of the Postdoctoral nomination, reference letters, and supporting materials from the _nominee_, is _October 15, 2011,_ so it is important for you to submit your nomination /as soon as possible/ to give your candidate and their references time to complete their parts. ** * * * The nomination process is very simple: go to our website http://pcts.princeton.edu/pcts and submit the candidate's name, email address, and a nomination letter. The nominees will then be sent information necessary to complete their application and to submit letters for reference. The PCTS Faculty Fellows begin evaluation and invitation to interview on October 15, 2011. (The website will continue to accept late nominations and applications, but there can be no assurance they will be considered.) The mission of the Center is to foster interaction and collaboration between theorists across the natural sciences at Princeton to enhance research and education. We pursue this goal through our Center Postdoctoral Fellowships and our sponsorship of focused programs of study in frontier areas in theoretical science that cut across traditional disciplinary boundaries. A group of Senior Faculty Fellows, coming from a broad range of disciplines and departments, take active responsibility for guiding the intellectual life of the Center. Sincerely, Paul Steinhardt (Director) steinh(a)princeton.edu Igor Klebanov (Associate Director) klebanov(a)princeton.edu <mailto:klebanov@princeton.edu> Ravindra Bhatt (Acting Associate Director) ravin(a)princeton.edu <mailto:ravin@princeton.edu> /Note that Princeton University is an equal opportunity employer and complies with applicable EEO and affirmative action regulations./

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[Compbio-allhands] Fwd: Software Engineer and Bioinformatic Analysis opportunities at the Broad
by Andrej Sali 07 Aug '11

07 Aug '11

Begin forwarded message: > From: "Mark A. DePristo" <depristo(a)broadinstitute.org> > Subject: Software Engineer and Bioinformatic Analysis opportunities at the Broad > Date: August 6, 2011 4:38:01 PM PDT > To: "Mark A. DePristo" <depristo(a)broadinstitute.org> > > Hi all, > > We've opened two new positions in my group at the Broad Institute. If you are interested or know someone who is, please have them contact me at depristo(a)broadinstitute.org. > > Best, > > Mark A. DePristo, Ph.D. > Manager, Medical and Population Genetics Analysis > Broad Institute of MIT and Harvard > depristo(a)broadinstitute.org > mark(a)depristo.com > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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