October 2012 - compbio-allhands@cgl.ucsf.edu

[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 October 2012