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

[Compbio-allhands] Register for Introduction to Pathway Analysis
by Zainab Yusufsada 20 Sep '22

20 Sep '22

<https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> View in Your Browser <https://mailchi.mp/gladstone/data-analysis-with-r-for-absolute-beginners-63…> DATA SCIENCE TRAINING PROGRAM *Introduction toPathway Analysisand Visualization* September 23, 2022 1–4pm • Online Join to learn about functional enrichment pathway analysis and how to visualize your data in pathways. Learn how to go from a list of genes to effective data visualizations. LEARN MORE AND REGISTER <https://gladstone.org/events/introduction-pathway-analysis-and-visualizatio…> *Zainab Yusuf Sada* | Executive Administrator Gladstone Institute of Data Science & Biotechnology 1650 Owens Street, San Francisco, CA 94518 T 415.734.4827|zainab.yusufsada(a)gladstone.ucsf.edu

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[Compbio-allhands] Canceled: 9/22/22 BBC Seminar with Greg Bowman, PhD
by Flowers, Nicole 19 Sep '22

19 Sep '22

This seminar has been cancelled due to unforeseen circumstances. Please be on the lookout for a rescheduled date.

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[Compbio-allhands] 9/22/22 BBC Seminar with Greg Bowman, PhD
by Flowers, Nicole 16 Sep '22

16 Sep '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Genentech Hall Byers Auditorium Livestream: http://tiny.ucsf.edu/AbdeVL Greg Bowman, PhD University of Pennsylvania Protein dynamics and energy landscape design September 22, 2022 M. Jacobson, host Calendar also available at https://ccb.ucsf.edu/seminars-events/bbc-seminar-series, https://biophysics.ucsf.edu/seminars-events/bbc-seminar-series, https://bioinformatics.ucsf.edu/seminars-events/bbc-seminar-series BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Fwd: NIGMS Recruiting Program Officer in Bioinformatics and Computational Biology
by Tom Ferrin 14 Sep '22

14 Sep '22

Job opportunity at NIH... -------- Forwarded Message -------- Subject: NIGMS Recruiting Program Officer in Bioinformatics and Computational Biology Date: Fri, 2 Sep 2022 11:55:46 +0000 From: Nguyen, Han (NIH/NIGMS) [E] <han.nguyen(a)nih.gov> To: Nguyen, Han (NIH/NIGMS) [E] <han.nguyen(a)nih.gov> CC: Yuan, Jean (NIH/NIGMS) [E] <jean.yuan(a)nih.gov> Dear NIH applicants/grantees, Our Branch in Bioinformatics and Computational Biology at NIGMS/NIH has an opening for a Program Officer position. I’d like to ask you for a favor of forwarding the message below to any relevant PIs and societies so we can reach a broad audience for this opening. Thanks a lot for spreading the words! Best regards, Han Han Nguyen, PhD, Program Director Division of Biophysics, Biomedical Technology, and Computational Biosciences National Institute of General Medical Sciences, NIH Subject: NIGMS Recruiting Program Officer in Bioinformatics and Computational Biology Greetings, We are looking to hire a Program Officer <https://www.nigms.nih.gov/about/job_vacancies/Pages/bbcb-program-director-s…> with experience in bioinformatics, computational biology, and/or biostatistics to join our Bioinformatics and Computational Biology <https://www.nigms.nih.gov/about/overview/BBCB/Biophysics/Pages/biophysics.a…>(BCB)**Branch of the Division of Biophysics, Biomedical Technology, and Computational Biosciences (BBCB) <https://www.nigms.nih.gov/about/overview/Pages/BBCB.aspx> at NIGMS. The successful candidate will be responsible for scientific and administrative management of grants portfolio in development and integration of computing, data modeling, statistics, and mathematics approaches into biomedical sciences. Applicants should have broad expertise in one or more of the following areas: computational biology, bioinformatics, applied mathematics or data science in biomedical sciences, biostatistics, and biophysics. Candidates must be *U.S. citizens* and should have a Ph.D., M.D., or equivalent degree in one of the sciences underlying these research areas. Familiarity with NIH extramural funding as an applicant, reviewer, or NIH scientific administrator is a plus, and outstanding written and oral communication skills are essential. Interested candidates are encouraged to read this Program Officer <https://www.nigms.nih.gov/about/job_vacancies/Pages/bbcb-program-director-s…>**post,send an email of interest that describes your specific interests in BCB-managed programs to Jean Yuan <mailto:xin.yuan@nih.gov> (jean.yuan(a)nih.gov)and Dorothy Beckett <mailto:dorothy.beckett@nih.gov> (dorothy.beckett(a)nih.gov) Prepare to apply to the upcoming NIH Global Recruitment <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhr.nih.go…> announcement for Health Scientist Administrators (HSA) position through *USAjobs.gov* <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.usajo…>, which will only be open between *September 21 *through*September 30, 2022*. There will be two GS-12/13/14 HSA (Program Officer) vacancy announcements: One for current federal employees and one for the public. *Please help us to spread the news.* ** *The NIH encourages the application and nomination of qualified women, minorities, and individuals with disabilities. HHS and NIH are Equal Opportunity Employers.* *_More Information?_* Submit your application starting *September 21* through*September 30, 2022 */-->/ *Global Recruitment: Recruiting for all of NIH:* https://hr.nih.gov/jobs/global-recruitment <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhr.nih.go…>/./ *NIGMS /“Tip Sheet”/* https://www.nigms.nih.gov/about/job_vacancies/Documents/Global-Recruitment-… <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nigms…> *Applying for Scientific Administration Jobs at NIGMS* https://loop.nigms.nih.gov/2013/04/applying-for-scientific-administration-j… <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Floop.nigm…> Best Regards, Jean Yuan, PhD Chief, Bioinformatics and Computational Biology Branch Division of Biophysics, Biomedical Technology, and Computational Biosciences National Institute of General Medical Sciences (NIGMS), National Institutes of Health Email: Jean.Yuan(a)nih.gov

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[Compbio-allhands] faculty position at Univ of Michinga, Ann Arbor
by Andrej Sali 08 Sep '22

08 Sep '22

Med Chem department at Univ of Michigan, Ann Arbor, an open search this year for someone focused on computational chemistry: https://apply.interfolio.com/107765 <https://urldefense.com/v3/__https://apply.interfolio.com/107765__;!!LQC6Cpw…>. -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: Open positions in the Lab, please distribute. Thanks!
by Andrej Sali 31 Aug '22

31 Aug '22

> Begin forwarded message: > > From: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > Subject: Open positions in the Lab, please distribute. Thanks! > Date: August 31, 2022 at 2:35:55 AM PDT > To: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > > This Message Is From an External Sender > This message came from outside your organization. > Dear friends and colleagues, > > Apologies for the mass posting. I hope you could please advertise these positions we have open in the lab. > > Keywords —> 3DGenomics; 4DNucleomics; Imaging; 3D'Omics > > Postdoc1 👉🏻 https://tinyurl.com/marciuspd1 <https://urldefense.com/v3/__https://tinyurl.com/marciuspd1__;!!LQC6Cpwp!o9a…> > Postdoc2 👉🏻 https://tinyurl.com/marciuspd2 <https://urldefense.com/v3/__https://tinyurl.com/marciuspd2__;!!LQC6Cpwp!o9a…> > SpeTech 👉🏻 https://tinyurl.com/marciusst <https://urldefense.com/v3/__https://tinyurl.com/marciusst__;!!LQC6Cpwp!o9a2…> > > Thanks in advance! > Marc > ... > Marc A. Marti-Renom, ICREA Research Professor > Structural Genomics Group Leader > Centre Nacional d’Anàlisi Genòmica - Centre de Regulació Genòmica (CNAG-CRG) > The Barcelona Institute of Science and Technology (BIST) > Parc Científic de Barcelona – Torre I (10th floor) > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email: martirenom(a)cnag.crg.eu <mailto:martirenom@cnag.crg.eu> · martirenom(a)gmail.com <mailto:martirenom@gmail.com> > Web: http://marciuslab.org <https://urldefense.com/v3/__http://marciuslab.org__;!!LQC6Cpwp!o9a2QydrEda0…> · http://cnag.crg.eu <https://urldefense.com/v3/__http://cnag.crg.eu__;!!LQC6Cpwp!o9a2QydrEda0TG6…> · http://crg.cat <https://urldefense.com/v3/__http://crg.cat__;!!LQC6Cpwp!o9a2QydrEda0TG6rd4f…> > > *** Consider the environment. Print responsibly. ***

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[Compbio-allhands] Fwd: UMass Chan Tenured / Tenure-Track Faculty Search Biochemistry and Molecular Biotechnology
by Andrej Sali 23 Aug '22

23 Aug '22

Sent from my iPhone Begin forwarded message: > From: "Schiffer, Celia" <Celia.Schiffer(a)umassmed.edu> > Date: August 23, 2022 at 5:38:52 AM PDT > To: kornberg(a)stanford.edu, koshland(a)berkeley.edu, t.kouzarides(a)gurdon.cam.ac.uk, mkre(a)uchicago.edu, rek(a)stowers.org, pkkuhl(a)uw.edu, monika.hobrack(a)biophys.mpg.de, kunkel(a)enders.tch.harvard.edu, kuriyan(a)berkeley.edu, mkuroda(a)genetics.med.harvard.edu, a.i.lamond(a)dundee.ac.uk, lander(a)broadinstitute.org, eas2125(a)columbia.edu, lanzavecchia(a)irb.usi.ch, laub(a)mit.ed, ledoux(a)cns.nyu.edu, ruth.lehmann(a)med.nyu.edu, msl2(a)princeton.edu, ol235(a)cam.ac.uk, slinn(a)berkeley.edu, lipman(a)ncbi.nlm.nih.gov, dan.littman(a)med.nyu.edu, lodish(a)wi.mit.edu, srl(a)stanford.edu, loogerl(a)janelia.hhmi.org, losick(a)mcb.harvard.edu, andrew.lumsden(a)kcl.ac.uk, lluo(a)stanford.edu, hitenmadhani(a)gmail.com, hsmalik(a)fhcrc.org, tm2472(a)columbia.edu, jlm2(a)columbia.edu, dan(a)bigbird.uchicago.edu, bmargoli(a)umich.edu, arm42(a)columbia.edu, marletta(a)berkeley.edu, marrackp(a)njhealth.org, gail.r.martin(a)ucsf.edu, john.mascola(a)nih.gov, j-massague(a)ski.mskcc.org, dm(a)hms.harvard.edu, dbsmpt(a)nus.edu.sg, dg-office(a)embl.org, maunsell(a)uchicago.edu, jmccammon(a)ucsd.edu, suemcc(a)stanford.edu, Steven.McKnight(a)utsouthwestern.edu, amcmahon(a)med.usc.edu, andrew.mcmichael(a)ndm.ox.ac.uk, caroline.mcmillen(a)newcastle.edu.au, bruce.mcnaughton(a)uleth.ca, ruslan.medzhitov(a)yale.edu, melloc(a)ohsu.edu, jane.mellor(a)bioch.ox.ac.uk, dmelton(a)harvard.edu, bjmeyer(a)berkeley.edu, meyerow(a)caltech.edu, milinski(a)evolbio.mpg.de, timothy_mitchison(a)hms.harvard.edu, kmizu(a)helix.nih.gov, sm(a)bio.dtu.dk, guy(a)cabm.rutgers.edu, hmooney(a)stanford.edu, vamsi(a)hms.harvard.edu, david.morgan(a)ucsf.edu, r.g.m.morris(a)ed.ac.uk, morrison@utsouthwestern, milan.mrksich(a)northwestern.edu, "Tom W. Muir - PRINCETON" <muir(a)princeton.edu>, mueller(a)embl-grenoble.fr, murdoch(a)lifesci.ucsb.edu, kmurphy(a)wustl.edu, awm(a)mcb.harvard.edu, mnachman(a)berkeley.edu, lee_nadler(a)dfci.harvard.edu, kim.nasmyth(a)trinity.ox.ac.uk, egneilson(a)northwestern.edu, wjnelson(a)stanford.edu, eric.nestler(a)mssm.edu, bill(a)www-v6.stanford.edu, rasmus_nielsen(a)berkeley.edu, twn(a)cwru.edu, christer.nilsson(a)umu.se, denis.noble(a)dpag.ox.ac.uk, enogales(a)lbl.gov, harry(a)nuvolari.ucsc.edu, rnusse(a)stanford.edu, so104(a)medschl.cam.ac.uk, maileric.olson(a)utsouthwestern.edu, stuart_orkin(a)dfci.harvard.edu, mosley(a)salud.unm.edu, pacala(a)princeton.edu, Miles.Padgett(a)glasgow.ac.uk, page_admin(a)wi.mit.edu, peter.palese(a)mssm.edu, mpalmer(a)umd.edu, spalumbi(a)stanford.edu, liam(a)stat.colubia.edu, Paradal(a)mskcc.org, renato.paro(a)bsse.ethz.ch, Ardem Patapoutian <ardem(a)scripps.edu>, nipam(a)berkeley.edu, perrimon(a)genetics.med.harvard.edu, wap3g(a)virginia.edu, phillips(a)pboc.caltech.edu, william.phillips(a)nist.gov, georgep(a)rice.edu, pietro.decamilli(a)yale.edu, martin.plenio(a)uni-ulm.de, ploegh(a)wi.mit.edu, mpoo(a)berkeley.edu, jpriess(a)fredhutch.org, mp3284(a)columbia.edu, S.E.Radford(a)leeds.ac.uk, hraff(a)mcw.edu, m.raff(a)ucl.ac.uk, klaus.rajewsky(a)mdc-berlin.de, "V. Ramakrishnan" <ramak(a)mrc-lmb.cam.ac.uk>, yrao(a)pku.edu.cn, tom_rapoport(a)hms.harvard.edu, raulet(a)berkeley.edu, aregev(a)broad.mit.edu, Danny.Reinberg(a)nyumc.org, richmond(a)mol.biol.ethz.ch, mrief(a)ph.tum.de, christopher.robinson(a)imp.ac.at, generobi(a)life.illinois.edu, rolston(a)umd.edu, rosbash(a)brandeis.edu, michael.rosen(a)utsouthwestern.edu, mrosenfeld(a)ucsd.edu, janet.rossant(a)sickkids.ca, mr(a)purdue.edu, Davide.Ruggero(a)ucsf.edu, sabatini(a)wi.mit.edu, sali(a)salilab.org, asaltiel(a)ucsd.edu, vahid.sandoghdar(a)mpl.mpg.de, eff.sands(a)emory.edu, sanesj(a)mcb.harvard.edu, philippe.sansonetti(a)pasteur.fr, jhwinsto(a)utmb.edu, bobsauer(a)mit.edu, david_scadden(a)harvard.edu, cshatz(a)stanford.edu, schekman(a)berkeley.edu, philipp.scherer(a)utsouthwestern.edu, schier(a)fas.harvard.edu, schmiedmayer(a)atomchip.org, Agnes.Schonbrunn(a)uth.tmc.edu, erin.schuman(a)brain.mpg.de, sedat(a)msg.ucsf.edu, ned.seeman(a)nyu.edu, cseidman(a)genetics.med.harvard.edu, seyfarth(a)psych.upenn.edu, shair(a)chemistry.harvard.edu, shapiro(a)stanford.edu, sharppa(a)mit.edu, cshatz(a)stanford.edu, mls7(a)columbia.edu, tshenk(a)princeton.edu, ASHER(a)niaid.nih.gov, charles.sherr(a)stjude.org, tobert.sherwin(a)yale.edu, yshi(a)hms.harvard.edu, kevan.shokat(a)ucsf.edu, gerald.shulman(a)yale.edu, sas8(a)cumc.columbia.edu, curt-sigmund(a)uiowa.edu, yaron.silberberg(a)weizmann.ac.il, tsilhavy(a)princeton.edu, rsilverstein(a)mcw.edu, James_Simmons(a)brown.edu, simpson(a)kdna.ucla.edu, david_sinclair(a)hms.harvard.edu, susan.smyth(a)uky.edu, ssnyder(a)jhmi.edu, ralf.sommer(a)tuebingen.mpg.de, peter_sorger(a)hms.harvard.edu, bruce_spiegelman(a)dfci.harvard.edu, jspudich(a)stanford.edu, d.st.johnston(a)gen.cam.ac.uk, dastahl(a)uw.edu, stask(a)berkeley.edu, ljoan.steitz(a)yale.edu, thomas.steitz(a)yale.edu, pws(a)caltech.edu, stillman(a)cshl.edu, mstitt(a)mpimp-golm.mpg.de, stock(a)cabm.rutgers.edu, stroud(a)msg.ucsf.edu, gs20(a)cumc.columbia.edu, stubbe(a)mit.edu, wes(a)biochem.utah.edu, sved(a)pitt.edu, szostak(a)molbio.mgh.harvard.edu, tabin(a)genetics.med.harvard.edu, takahashi(a)utsouthwestern.edu, tallal(a)andromeda.rutgers.edu, dwtank(a)princeton.edu, staylor(a)ucsd.edu, smt(a)princeton.edu, tilman(a)umn.edu, gasper.tkacik(a)ist.ac.at, tonegawa(a)mit.edu, Peter_Tonellato(a)hms.harvard.edu, etopol(a)scripps.edu, jt233(a)cam.ac.uk, tsaiasst(a)mit.edu, richard.tsien(a)nyulangone.org, rtsien(a)ucsd.edu, unanue(a)wustl.edu, ungerlel(a)mail.nih.gov, ron.vale(a)ucsf.edu, jsv(a)chem.ucla.edu, rvance(a)berkeley.edu, edward.vates(a)urmc.rochester.edu, vaux(a)wehi.edu.au, slv8(a)cornell.edu, iverma(a)ucsd.edu, virgin(a)wustl.edu, vogelbe(a)welch.jhu.edu, ewagner(a)cnio.es, slwagner(a)ucsd.edu, gunter.wagner(a)yale.edu, edward.wakeland(a)utsouthwestern.edu, gwalker(a)mit.edu, christopher.walsh(a)childrens.harvard, peter(a)walterlab.ucsf.edu, jywang(a)ucsd.edu, mwang(a)master-7rqtwti-mm3lcf5ygjhvq.us-4.platformsh.site, graham.warren(a)mfpl.ac.at, Robert Weinberg <weinberg(a)wi.mit.edu>, bill.weis(a)stanford.edu, aweiss(a)medicine.ucsf.edu, jonathan.weissman(a)ucsf.edu, irv(a)stanford.edu, welch(a)berkeley.edu, jim.wells(a)ucsf.edu, wherry(a)pennmedicine.upenn.edu, wickens(a)biochem.wisc.edu, linda.wicker(a)cimr.cam.ac.uk, daylite(a)pitt.edu, m.wild(a)auckland.ac.nz, jcwingfield(a)ucdavis.edu, owenwitte(a)mednet.ucla.edu, cwolberg(a)jhmi.edu, pwolynes(a)rice.edu, jlw(a)stowers.org, wuc(a)janelia.hhmi.org, g.j.l.wuite(a)vu.nl, sunneyxie(a)pku.edu.cn, weiy(a)mail.nih.gov, young(a)wi.mit.edu, zhangf(a)mit.edu, yzhang(a)genetics.med.harvard.edu, zhuang(a)chemistry.harvard.edu, lzipursky(a)mednet.ucla.edu, hzoghbi(a)bcm.edu, zon(a)enders.tch.harvard.edu, cz2195(a)columbia.edu > Cc: "Rhind, Nick" <Nick.Rhind(a)umassmed.edu> > Subject: UMass Chan Tenured / Tenure-Track Faculty Search Biochemistry and Molecular Biotechnology > > > This Message Is From an External Sender > This message came from outside your organization. > Dear Colleagues, > > The Department of Biochemistry & Molecular Biotechnology at the University of Massachusetts Chan Medical School seeks applicants for a tenured or tenure track faculty position. Our faculty is committed to tackling significant biological questions at a molecular level, with research programs spanning a broad range of topics. In this new period of growth, we are recruiting faculty members working to elucidate important biological mechanisms, placing special emphasis on integrative methods and research using the physical sciences (physics, chemistry, math and engineering) to solve fundamental molecular problems in biology. We are an interactive group who encourages research at the interface of multiple disciplines, the development of enabling technologies, and team science. More information about the department can be found on our website <www.umassmed.edu/bmb>. > > We are searching for a highly motivated and enthusiastic individual, committed to diversity, creativity, and collaboration, to join our team of actively engaged faculty. The successful candidate will develop and lead an internationally-recognized extramurally-funded research program, contribute to our missions of education, inclusion and service, and play an active role in the Department as we expand in a new phase of growth. Qualified applicants will have earned a Ph.D. in a life or physical science discipline and have a demonstrated track record of outstanding accomplishment. Applicants of all academic ranks with a strong commitment to enhancing diversity and inclusivity are encouraged to apply. > > We are especially eager to consider applicants who will support and elevate the UMass Chan commitment to diversity, equity and inclusion, and foster an environment of inclusive collaborative excellence where all faculty can thrive. As an equal opportunity and affirmative action employer, UMass recognizes the power of a diverse community and encourages applications from individuals with varied experiences, perspectives, and backgrounds. > > The Department is housed on two floors of a modern, well-equipped, 340,000 sq ft research building on a rapidly expanding Medical School campus. Core facilities within our department include world class cryo-electron microscopy, X-ray crystallography, NMR spectroscopy, small molecule screening, structure-based drug design and mass spectrometry. Additional core facilities, including proteomics, genotyping, fluorescence-activated cell sorting, microscopy/imaging, deep sequencing, genomics/bioinformatics, transgenic/knockout mice, and metabolic phenotyping, are available. More information about core facilities on campus may be found online <www.umassmed.edu/research/cores>. > > More information can be found at https://jobs.sciencecareers.org/job/612069. > And applications are accepted at https://academicjobsonline.org/ajo/jobs/22273. Applications will be accepted until November 1, 2022. Evaluation of applications will begin as soon as they are received. > > Thanks very much > > Nick Rhind > Chair of the Faculty Search Committee, > Nick Rhind, Ph.D. > Professor Biochemistry and Molecular Biotechnology > nick.rhind(a)umassmed.edu > > and > > > Celia Schiffer, Ph.D. > Professor and Chair > Department of Biochemistry and Molecular Biotechnology > Director Institute of Drug Resistance > University of Massachusetts Chan Medical School > Celia.Schiffer(a)umassmed.edu > > Karen.Welch(a)umassmed.edu > Executive Assistant >

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[Compbio-allhands] 2022 Fall BBC Seminar Series Calendar
by Flowers, Nicole 22 Aug '22

22 Aug '22

Dear all, Attached, please find the calendar of scheduled speakers for this fall’s BBC Seminar Series. You can also view the full calendar here: https://biophysics.ucsf.edu/seminars-events/bbc-seminar-series Weekly outlook invites will be sent, but you can also subscribe to the calendar using these links: Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> Thank you, Nicole Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94158-2517 Phone: (415) 502-6518

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[Compbio-allhands] Fwd: SCB GL in Structural or Molecular Systems Biology
by Andrej Sali 09 Aug '22

09 Aug '22

> Begin forwarded message: > > From: Christoph Mueller <christoph.mueller(a)embl.de> > Subject: SCB GL in Structural or Molecular Systems Biology > Date: August 9, 2022 at 7:04:22 AM PDT > To: sali(a)salilab.org > > This Message Is From an External Sender > This message came from outside your organization. > Dear Andrej, > > The Structural and Computational Biology Unit at EMBL in Heidelberg is looking to recruit a highly motivated group leader in the area of structural or molecular systems biology to address fundamental questions in life sciences. We are looking to attract candidates that pursue experimental or computational approaches, which can contribute to or interface with integrated structural biology. Research areas are diverse, including chemical biology, (high-throughput) biochemistry, biophysics, proteomics, metabolomics, synthetic biology, modelling and simulation of biological systems. The research should extend or enrich structural systems biology, a broad concept that the unit is pursuing, in conjunction with a strong computational biology programme. > > More information in the enclosed advert. Don’t hesitate to get in touch if you have any questions and please do forward to promising young researchers in your group/institute. > > Thanks for your help! > > Best regards, > Christoph > ______________________________________________________________________ > Dr. Christoph W. Müller > Head of Structural and Computational Biology Unit > > EMBL > Meyerhofstrasse 1 > 69117 Heidelberg, Germany > > email: cmueller(a)embl.de <mailto:cmueller@embl.de>, christoph.mueller(a)embl.org <mailto:christoph.mueller@embl.org> > phone: 0049-6221-387-8320 > https://www.embl.org <https://urldefense.com/v3/__https://www.embl.org__;!!LQC6Cpwp!v1ufINgv94aza…> > https://www.embl.org/groups/mueller/ <https://urldefense.com/v3/__https://www.embl.org/groups/mueller/__;!!LQC6Cp…> > _______________________________________________________________________ >

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[Compbio-allhands] Immediately available: Two postdoctoral positions in stochastic thermodynamics
by David Sivak 29 Jun '22

29 Jun '22

We seek to hire two postdoctoral fellows to work on projects probing the fundamentals of nonequilibrium statistical physics, thermodynamics, information theory, and control theory. Both positions are at Simon Fraser University, home to a leading research effort on these questions and related areas of biophysics. We are just outside Vancouver, British Columbia, Canada, universally agreed to be one of the most livable cities in the world. One position is for a theorist, supervised by David Sivak, dsivak(a)sfu.ca. For details, see http://davidsivak.com/. One position is for an experimentalist, supervised by John Bechhoefer, johnb(a)sfu.ca. For details, see http://www.sfu.ca/chaos/. Interested candidates should send a cover letter and CV (including publication list and contact information for 2-3 references) to the appropriate address above. We are committed to ensuring that no individual is denied access to employment opportunities for reasons unrelated to ability or qualifications. Candidates who belong to underrepresented groups in Physics are particularly welcome to apply. Please forward this announcement to any interested parties. Thank you in advance! David Sivak John Bechhoefer -- David Sivak Assoc. Prof., Dept. of Physics, Simon Fraser U Tier-II Canada Research Chair, Nonequilibrium Statistical Biophysics dsivak(a)sfu.ca | davidsivak.com | 778-928-7995

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[Compbio-allhands] Summer 2022 Gladstone Data Science Training Program
by Zainab Yusufsada 27 Jun '22

27 Jun '22

<https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> View in Your Browser <https://mailchi.mp/gladstone/summer-2022-gladstone-data-science-training-pr…> GLADSTONE DATA SCIENCE PROGRAM*Bioinformatics Series Summer 2022* The Gladstone Data Science Training Program <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> provides learning opportunities and hands-on workshops to improve your skills in bioinformatics and computational analysis. Gain new skills and get support with your questions and data. The Data Science Training Program is virtual. Register for one or more of the workshops offered and you’ll learn helpful skills and get hands-on experience to master the bioinformatic tools you need to analyze your data. Summer 2022 Series <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> Introduction to R for Data Analysis <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> *Ayushi Agrawal, Michela Traglia* July 12 & 14, 2022 • 9am–12pm PDT Register <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> Introductory RNA-Seq <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> *Ayushi Agrawal, Michela Traglia* July 21–22, 2022 • 9am–12pm PDT Register <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> Hypothesis Testing <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> *Reuben Thomas* August 15-16, 2022 • 1–3pm PDT Register <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> Intermediate RNA Seq Analysis Using R <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> *Michela Traglia, Min-Gyoung Shin* September 13, 2022 • 9am–12pm PDT Register <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> VIEW THE SERIES <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> The Gladstone Data Science Training Program <https://gladstoneinstitutes.us10.list-manage.com/track/click?u=1a62a392ffda…> was started in 2018 to provide trainees with learning opportunities and hands-on workshops to improve their skills in bioinformatics and computational analysis. This program offers a series of workshops throughout the year to enable trainees to gain new skills and get support with their questions and data. View in Your Browser <https://mailchi.mp/gladstone/summer-2022-gladstone-data-science-training-pr…> © 2022 Gladstone Institutes. All rights reserved. Want to change how you receive these emails? Update your preferences <https://gladstoneinstitutes.us10.list-manage.com/profile?u=1a62a392ffda799e…> or unsubscribe from this list. <https://gladstoneinstitutes.us10.list-manage.com/unsubscribe?u=1a62a392ffda…> Gladstone Institutes 1650 Owens Street San Francisco, CA 94158 Add us to your address book <https://gladstoneinstitutes.us10.list-manage.com/vcard?u=1a62a392ffda799ebd…> Cordially, *Zainab Yusuf Sada* | Administrative Specialist Gladstone Institute of Data Science & Biotechnology 1650 Owens Street, San Francisco, CA 94518 T 415.734.4827|zainab.yusufsada(a)gladstone.ucsf.edu

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[Compbio-allhands] Fwd: Looking for a compchemist
by Brian Shoichet 24 Jun '22

24 Jun '22

FYI ---------- Forwarded message --------- From: Daniel Ortwine <dortwine(a)nestedtx.com> Date: Fri, Jun 24, 2022 at 11:27 AM Subject: Looking for a compchemist To: shoichet(a)cgl.ucsf.edu <shoichet(a)cgl.ucsf.edu> Cc: Aysegul Ozen <aozen(a)nestedtx.com> Hi Brian, As you are aware I am consulting for Nested Pharmaceuticals (as well as Genentech). They are looking for a computational chemist, preferably with MD and some scripting experience. I attached the job description here. The hiring manager is Aysegul Ozen (copied here), who you know... Would you by chance have or know of any students or postdocs finishing up (or others, for that matter) that might be interested in working for Nested? I would very much appreciate you sending any candidates my way. Hopefully I'll see you at a future conference - I'll be at ACS Chicago this August and hopefully at the Gordon CADD conference next summer. Thanks in advance! Cheers, Dan Ortwine Ortwine Consulting LLC -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] Summer 2022 Gladstone Data Science Training Program
by Zainab Yusufsada 21 Jun '22

21 Jun '22

The Gladstone Data Science Training Program provides learning opportunities and hands-on workshops to improve your skills in bioinformatics and computational analysis. Gain new skills and get support with your questions and data. The Data Science Training Program is virtual. Register for one or more of the workshops offered and you’ll learn helpful skills and get hands-on experience to master the bioinformatic tools you need to analyze your data. Summer 2022 Series <https://gladstone.org/events?series=data-science-training-program> Introduction to R for Data Analysis Session 1-2 July 12 & 14, 2022 Register <https://gladstone.zoom.us/meeting/register/tJcsfuGupzwiGtce9atpUdrFzu_oJRKM…> Introductory RNA-Seq, Session 1-2 July 21-22,2022 Register <https://gladstone.zoom.us/meeting/register/tJEoceiqqzgvGtyOAA2Gs6Xw8SspY4G3…> Hypothesis tTesting Session 1-2 August 15-16, 2022 Register <https://gladstone.zoom.us/meeting/register/tJ0of-uqrzwvGd3BhiiYSxb7P2iMNS7U…> Intermediate RNA Seq Analysis Using R September 13, 2022 Register <https://gladstone.zoom.us/meeting/register/tJUpf-CsrTwsHNQwLJg8w_3QH0Jtfl83…>

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[Compbio-allhands] UPDATED: 6/30/22 Seminar with Hao Wu, Noon, GH Auditorium
by Flowers, Nicole 21 Jun '22

21 Jun '22

________________________________ From: Kwong, Michelle <Michelle.Kwong(a)ucsf.edu> Sent: Tuesday, June 21, 2022 11:48 AM To: Flowers, Nicole <Nicole.Flowers(a)ucsf.edu> Subject: Re: Vallee **UPDATED** Sorry!! Hi All, Hope you’re doing well! We have a special guest, Hao Wu, Ph.D., coming from Harvard Medical School. She will be holding a seminar about the inner workings of the inflammasome engine on Thursday, June 30th, 2022 from 12pm-1pm in Byers Auditorium in Genentech Hall, Mission Bay. Please see the flyer for more details. Anyone is welcome to come. We’re looking forward to seeing you there! Thank you!! Best, Michelle

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[Compbio-allhands] 6/30/22 Seminar with Hao Wu, Noon, GH Auditorium
by Flowers, Nicole 21 Jun '22

21 Jun '22

Hi All, Hope you’re doing well! We have a special guest, Hao Wu, Ph.D., coming from Harvard Medical School. She will be holding a seminar about the inner workings of the inflammasome engine on Friday, June 30th, 2022 from 12pm-1pm in Byers Auditorium in Genentech Hall, Mission Bay. Please see the flyer for more details. Anyone is welcome to come. We’re looking forward to seeing you there! Thank you!! Best, Michelle

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[Compbio-allhands] Fwd: AI/ML research opportunities at Genentech Research
by Lyu, Jiankun 15 Jun '22

15 Jun '22

FYI Begin forwarded message: From: "Kangway Chuang (CHUANGK4)" <chuang.kangway(a)gene.com<mailto:chuang.kangway@gene.com>> Subject: AI/ML research opportunities at Genentech Research Date: June 15, 2022 at 2:48:04 PM PDT To: jiankun.lyu(a)ucsf.edu<mailto:jiankun.lyu@ucsf.edu> This Message Is From an External Sender This message came from outside your organization. Dear JK, I wanted to pass along opportunities that may interest any graduating students or postdocs you might know. We have a few positions in my lab in the new Department of AI and ML within Genentech Research and Early Development. It's a unique balance of academic-style research with a focus on publishing with the opportunity to impact our real drug discovery efforts while collaborating with scientists across the entire organization. 1. We have one opening for a Postdoctoral Fellow with sponsorship for up to 4 years. Postdocs at Genentech are well-compensated, have a tremendous amount of intellectual freedom, and have a strong emphasis on publishing. Postdoctoral Fellow, Artificial Intelligence and Machine Learning in Drug Discovery<https://urldefense.com/v3/__https://careers.gene.com/us/en/job/GENEUS202206…> 2. There are additionally two open positions for full-time employees in our AI/ML department with a focus on machine learning for drug discovery. Again, there's flexibility in their exact focus depending on research interests, with opportunities to work on both applied and foundational machine learning problems, e.g. in geometric deep learning, virtual screening, molecular optimization, chemical reactions, and much more: AI Scientist / Sr. AI Scientist - Artificial Intelligence and Machine Learning<https://urldefense.com/v3/__https://careers.gene.com/us/en/job/GENEUS202205…> AI Scientist / Sr. AI Scientist - Artificial Intelligence and Machine Learning in Drug Discovery<https://urldefense.com/v3/__https://careers.gene.com/us/en/job/GENEUS202203…> Please don't hesitate to reach out if you have any questions and thanks in advance. All my best, Kangway Chuang, Ph. D. (he/him/his) Senior AI Scientist and Group Lead AI | ML Department in Research Biology Genentech Research and Early Development +1 (805) 754-0058 chuang.kangway(a)gene.com<mailto:chuang.kangway@gene.com>

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[Compbio-allhands] 6/2/22 BBC Seminar with Jiaoyang Jiang, PhD, Noon
by Flowers, Nicole 25 May '22

25 May '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF Jiaoyang Jiang, PhD University of Wisconsin-Madison Decoding sweet regulation at substrate-level implications for signaling disease. June 2, 2022 J. Weaver, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…>

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[Compbio-allhands] Fwd:
by Brian Shoichet 19 May '22

19 May '22

FYI. ---------- Forwarded message --------- From: Peter Schultz <schultz(a)scripps.edu> Date: Thu, May 19, 2022 at 7:24 AM Subject: To: shoichet(a)cgl.ucsf.edu <shoichet(a)cgl.ucsf.edu> Brian, we are looking for computational chemists to do structure-based design at Calibr as a PI. If you know of anyone that might be interested, I would love to chat with them. Thanks, Pete -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] 5/19/22 BBC Seminar with Liz Kellogg, PhD
by Flowers, Nicole 13 May '22

13 May '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Genentech Hall Byers Auditorium Livestream: http://tiny.ucsf.edu/Y5D1RO Liz Kellogg, PhD Cornell University Mechanisms driving molecular innovation: Cryo-EM studies of CRISPR-associated transposons May 19, 2022 D. Chen, host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Fwd: Hiring two people - share in your group? Connect soon?
by Andrej Sali 12 May '22

12 May '22

> Begin forwarded message: > > From: "James Arnold (ARNOLJ12)" <arnold.james(a)gene.com> > Subject: Hiring two people - share in your group? Connect soon? > Date: May 12, 2022 at 12:26:18 PM PDT > To: sali(a)salilab.org > > This Message Is From an External Sender > This message came from outside your organization. > Hi Andrej, > > I hope you are doing well, and I'd love to connect and catch up as your time allows. > > I am hiring for two roles, and looking for two great people. Here are the links to the postings. If you have a chance, could you please share with your groups, and others within our larger UCSF community? These two people can really make a difference, I think they will benefit from being on the team, and I'd appreciate your help finding them. > > Principal Data Scientist, Genentech > https://careers.gene.com/us/en/job/202203-109575/Senior-Principal-Data-Scie… <https://urldefense.com/v3/__https://careers.gene.com/us/en/job/202203-10957…> > > Lead/Senior Data Engineer, Genentech > https://careers.gene.com/us/en/job/GENEUS202204117622EXTERNALENUS/Lead-Seni… <https://urldefense.com/v3/__https://careers.gene.com/us/en/job/GENEUS202204…> > > Are there good times to connect in the coming weeks? > > Jim > > > James Arnold, PhD > Director, Data Science and Artificial Intelligence > Genentech > m: 415-216-5655, e: arnolj12(a)gene.com <mailto:faretta@gene.com>

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[Compbio-allhands] TODAY! 4 PM in GH Auditorium! Peter Kollman Lectureship with Ken Dill, PhD
by Flowers, Nicole 05 May '22

05 May '22

PETER A. KOLLMAN LECTURESHIP Ken Dill Stonybrook Thursday, May 5, 2022 4:00 PM Brian Shoichet, Host Genentech Hall Byers Auditorium Livestream: http://tiny.ucsf.edu/Y5D1RO Reception to follow in Genentech Hall 1st Floor Atrium

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[Compbio-allhands] Register for Advanced Cytoscape Automation
by Zainab Yusufsada 04 May '22

04 May '22

GLADSTONE DATA SCIENCE PROGRAM*Advanced Cytoscape Automation* May 10, 2022 • 1–4pm Alex Pico Online Join this workshop if you’re already using R or Python and are curious about network analysis and visualization. You’ll learn how to integrate Cytoscape’s network capabilities into your bioinformatic workflows. LEARN MORE AND REGISTER <https://gladstone.org/events/advanced-cytoscape-automation-0>

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[Compbio-allhands] 5/5/22 Peter Kollman Lectureship with Ken Dill, PhD
by Flowers, Nicole 29 Apr '22

29 Apr '22

PETER A. KOLLMAN LECTURESHIP Ken Dill Stonybrook Thursday, May 5, 2022 4:00 PM Brian Shoichet, Host Genentech Hall Byers Auditorium Livestream: http://tiny.ucsf.edu/Y5D1RO Reception to follow in Genentech Hall 1st Floor Atrium

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[Compbio-allhands] Fwd: question - re: co-crystal structure ligand based design
by Brian Shoichet 28 Apr '22

28 Apr '22

FYI ---------- Forwarded message --------- From: Robert Batey <rob.batey(a)utoronto.ca> Date: Thu, Apr 28, 2022 at 8:08 AM Subject: Re: question - re: co-crystal structure ligand based design To: Brian Shoichet <bshoichet(a)gmail.com> Dear Brian Hope that you are well. I don’t know whether you saw this, but we have a full-time tenure stream position in the area of computational chemistry applied to medicinal chemistry and chemical biology. The appointment is at the rank of Associate Professor or Professor with an expected start date of July 1, 2023. The posting for this position can be found here: https://jobs.utoronto.ca/job/Toronto-Associate-ProfessorProfessor-Computati…. All application materials, including reference letters, must be received by *May 17, 2022.* Successful candidates may also be nominated for a *Canada Excellence Research Chair <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cerc.…>* in Medicinal Chemistry, AI/Machine Learning and Computational Chemistry, Chemical Biology valued at $1 million/year for 8 years. The Canada Excellence Research Chairs (CERC) program is intended to support world‑renowned researchers and their teams in establishing ambitious research programs at Canadian universities. Nominees to the CERC opportunity will be internationally leading researchers whose proposed research program aligns with one or more of the *Government of Canada’s Science, Technology and Innovation priority areas <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cerc.…>*. The labs would be primarily located in the Princess Margaret Cancer Centre. I wonder whether you know anyone who you think might be appropriate? Would you share this opening with your networks? Let me know if you have any questions. Cheers Rob *From: *Undisclosed Recipients <rob.batey(a)utoronto.ca> *Date: *Wednesday, March 16, 2022 at 1:50 PM *To: *Brian Shoichet <bshoichet(a)gmail.com> *Cc: *Daniel Erlanson <erlanson(a)gmail.com> *Subject: *Re: question - re: co-crystal structure ligand based design Dear Brian and Dan (nice to be virtually acquainted btw, I enjoy the blog) Thanks for this – very helpful, and two interesting examples. In the case we have the two orientations are linked by a single bond rotation, and it enabled us to design an entirely new class of compound that allowed for both of the two orientations to be mimicked in a single compound. Cheers Rob –––––––––––––– Robert A. Batey, Ph. D. Professor and Chair Department of Chemistry <https://www.chemistry.utoronto.ca/>, LM 151 University of Toronto <https://www.utoronto.ca/> 80 St. George St., Toronto, ON CANADA, M5S 3H6 Chair's office: 416-978-3566; fax: 416-978-1631 Web: http://www.chem.utoronto.ca/staff/RAB/index.html Linked-In: https://www.linkedin.com/in/robert-batey-156221a2 I wish to acknowledge this land on which the University of Toronto operates <https://indigenous.utoronto.ca/about/land-acknowledgement/>. For thousands of years it has been the traditional land of the Huron-Wendat, the Seneca, and the Mississaugas of the Credit. Today, this meeting place is still the home to many Indigenous people from across Turtle Island and we are grateful to have the opportunity to work on this land. –––––––––––––– *From: *Brian Shoichet <bshoichet(a)gmail.com> *Date: *Saturday, February 5, 2022 at 8:47 PM *To: *Undisclosed Recipients <rob.batey(a)utoronto.ca> *Cc: *Daniel Erlanson <erlanson(a)gmail.com> *Subject: *Fwd: question - re: co-crystal structure ligand based design You don't often get email from bshoichet(a)gmail.com. Learn why this is important <http://aka.ms/LearnAboutSenderIdentification> Dear Rob, I rec'd these references from Dan Erlanson, copied. They speak to your case, I think you'll find them useful in framing your cool story. Brian ---------- Forwarded message --------- From: *Daniel Erlanson* <erlanson(a)gmail.com> Date: Sat, Feb 5, 2022 at 7:59 AM Subject: Re: question - re: co-crystal structure ligand based design To: Brian Shoichet <bshoichet(a)gmail.com> Hi Brian, Nice to hear from you! A couple examples come to mind, though I feel like there are more: https://practicalfragments.blogspot.com/2020/05/merging-two-of-same-fragmen… <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpractical…> https://practicalfragments.blogspot.com/2013/10/fragment-merging-revisited-… <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpractical…> BTW I liked your recent SARS-CoV-2 aggregation paper - unfortunately too much crap got published in the past couple years. Cheers, Dan -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbkslab.or…>* -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] 4/28/22 BBC Seminar with Karlene Cimprich, PhD
by Flowers, Nicole 22 Apr '22

22 Apr '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Genentech Hall Byers Auditorium Livestream: http://tiny.ucsf.edu/Y5D1RO Co-sponsored by the [cid:93c19575-2d2a-4361-a102-7fb3b8de7827] Karlene Cimprich, PhD Stanford University RNA Meets DNA: Dangerous Liaisons in the Genome April 28, 2022 L. Weinberger, host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] 4/21/22 BBC Seminar Cancelled
by Flowers, Nicole 15 Apr '22

15 Apr '22

Next week Thursday's BBC Seminar with Dr. Elizabeth Villa has been postponed. Please stay tuned for a rescheduled date. Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94158-2517 Phone: (415) 502-6518

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[Compbio-allhands] 4/14/22 BBC Seminar with Tanja Mittag, PhD, Noon
by Flowers, Nicole 08 Apr '22

08 Apr '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF Tanja Mittag, PhD St. Jude Children's Research Hospital Protein disorder, multivalency and phase separation: Implications for biological function and disease April 14, 2022 W. Weiss, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Check Out the Spring Line Up for the Gladstone Data Science Training Program
by Zainab Yusufsada 06 Apr '22

06 Apr '22

The Gladstone Data Science Training Program <https://gladstone.org/events?series=data-science-training-program> provides you with learning opportunities and hands-on workshops to improve your skills in bioinformatics and computational analysis. Join one of these upcoming workshops to gain new skills and get support with your data. Spring 2022 Series All workshops are virtual! Single Cell RNA-Seq Analysis April 15-19, 2022 Register <https://gladstone.org/events/single-cell-rna-seq-analysis-2> Statistics of Enrichment Analysis April 22, 2022 Register <https://gladstone.org/events/statistics-enrichment-analysis-0> Introductory Machine Learning for Biologists May 3, 2022 Register <https://gladstone.org/events/introductory-machine-learning-biologists-2> Advanced Cytoscape Automation May 10, 2022 Register <https://gladstone.org/events/advanced-cytoscape-automation-0> Cordially, *Zainab Yusuf Sada* | Administrative Specialist Gladstone Institute of Data Science & Biotechnology 1700 Owens Street, San Francisco, CA 94518 T 415.734.4827|zainab.yusufsada(a)gladstone.ucsf.edu

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[Compbio-allhands] Fwd: Assistant Professor position Baylor College of Medicine
by Brian Shoichet 04 Apr '22

04 Apr '22

FYI ---------- Forwarded message --------- From: Palzkill, Timothy Gerald <timothyp(a)bcm.edu> Date: Mon, Apr 4, 2022 at 8:42 AM Subject: Assistant Professor position Baylor College of Medicine To: shoichet(a)cgl.ucsf.edu <shoichet(a)cgl.ucsf.edu> Dear Brian, I hope all is well with you. My department has a tenure track Assistant Professor position available. Our specific areas of interest for this position include computer-aided drug design (CADD), molecular dynamics (MD) simulations, protein design and folding prediction, application of machine learning and artificial intelligence (AI) to improve the target identification and drug discovery process. If your trainees are in the market for a faculty job, please pass this information along. They can find more detailed info and apply via this link https://bit.ly/36oTHSp or email directly to pharmacology(a)bcm.edu . Thanks, Tim Timothy Palzkill, Ph.D. Cullen Trust for Higher Education Chair Professor and Chair Department of Pharmacology and Chemical Biology Baylor College of Medicine -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] 4/7/22 Braisted Lecture with Alanna Schepartz
by Flowers, Nicole 01 Apr '22

01 Apr '22

UCSF-UCB Andrew Braisted Award Lectureship Livestream: http://tiny.ucsf.edu/Y5D1RO Alanna Schepartz, Ph.D. UC Berkeley Reimagining the Definition of a Protein Thursday, April 7, 2022 4 pm Genentech Hall Byers Auditorium UCSF Mission Bay Campus Contact: Charles Craik Sponsor: The Andrew Braisted Lecture Fund

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[Compbio-allhands] Check Out the Spring Line Up for the Gladstone Data Science Training Program
by Zainab Yusufsada 28 Mar '22

28 Mar '22

The Gladstone Data Science Training Program <https://gladstone.org/events?series=data-science-training-program> provides you with learning opportunities and hands-on workshops to improve your skills in bioinformatics and computational analysis. Join one of these upcoming workshops to gain new skills and get support with your data. Spring 2022 Series All workshops are virtual! Single Cell RNA-Seq Analysis April 15-19, 2022 Register <https://gladstone.org/events/single-cell-rna-seq-analysis-2> Statistics of Enrichment Analysis April 22, 2022 Register <https://gladstone.org/events/statistics-enrichment-analysis-0> Introductory Machine Learning for Biologists May 3, 2022 Register <https://gladstone.org/events/introductory-machine-learning-biologists-2> Advanced Cytoscape Automation May 10, 2022 Register <https://gladstone.org/events/advanced-cytoscape-automation-0> Cordially, *Zainab Yusuf Sada* | Administrative Specialist Gladstone Institute of Data Science & Biotechnology 1700 Owens Street, San Francisco, CA 94518 T 415.734.4827|zainab.yusufsada(a)gladstone.ucsf.edu

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[Compbio-allhands] Fwd: Opportunities at Schrödinger - Protein Structure Prediction/Optimization Scientist (Dynamics Simulations/Enhanced Sampling)
by Brian Shoichet 24 Mar '22

24 Mar '22

FYI ---------- Forwarded message --------- From: Annabel Cook <annabel.cook(a)schrodinger.com> Date: Wed, Mar 23, 2022 at 10:09 AM Subject: Opportunities at Schrödinger - Protein Structure Prediction/Optimization Scientist (Dynamics Simulations/Enhanced Sampling) To: <bshoichet(a)gmail.com> Dear Prof Shoichet, My name is Annabel Cook and I work in the Strategic Growth team at Schrödinger, Inc. Following our recent acquisition of XTAL BioStructures in Natick, MA, we are significantly expanding our structural biology capabilities, and are seeking scientists with expertise in structural biology, and protein structure prediction, optimization, and refinement. One of several roles we are looking to fill is a Protein Structure Prediction/Optimization Scientist (Dynamics Simulations/Enhanced Sampling) position, and I thought you may have some current or former group members who would be interested in hearing about the role. If so, please feel free to forward my contact information. I have included the specifics of the role below and applicants may apply directly here <https://grnh.se/a34dade13us>. Thank you in advance for your help. Do not hesitate to contact me if you have any questions! Kind regards, Annabel Protein Structure Prediction/Optimization Scientist (Dynamics Simulations/Enhanced Sampling) We’re seeking a Protein Structure Prediction/Optimization Scientist to join us in our mission to improve human health and quality of life through the development, distribution, and application of advanced computational methods! As a member of our Desmond (Molecular Dynamics) team, you’ll facilitate the refinement and optimization of predicted structures (homology models or AlphaFold V2) and validate these models in predictive free energy calculations for lead optimization. By advancing our methodology and immediately applying it to both our and our customers’ drug-discovery platforms, you’ll help tackle diseases that have been recalcitrant to structure-based drug design in the past. Schrödinger’s recent acquisition of XTAL BioStructures puts us in a unique position to advance the state of the art in protein structure prediction and refinement with experimental validation and support. We have other openings in this area that require slightly different skill sets. Please see our posts for Protein Structure Prediction/Optimization Scientist (Machine Learning) <https://grnh.se/e759b1a83us> and Protein Structure Prediction/Optimization Scientist (Core Homology) <https://grnh.se/aa293f6b3us>. Who will love this job: - A computational chemist with experience in biomolecular simulation, enhanced sampling, and free energy calculations - A passionate scientist who loves to push the boundaries of existing technology and creatively comes up with new ideas to address important problems - A methods developer who can implement a prototype using modern coding practices What you’ll do: - Identify problems in predicted structures from homology models or AlphaFold and develop strategies for refinement - Collaborate with scientists in other teams, including Machine Learning and Prime (Protein Structure Prediction), to exploit new developments and iteratively refine our strategy to improve the quality of predicted structures - Work with our drug discovery group to deploy new technologies in active projects and realize real-world impact What you should have: - PhD in computational chemistry, biochemistry, biophysics, or a related field, with a robust track record of publications in biomolecular simulations or enhanced sampling techniques - Proficiency in building complex workflows with Python - Experience with pharmaceutically relevant proteins, such as kinases, GPCRs, proteases, transferases, and/or ion channels is a plus Pay and perks: Schrödinger understands it’s people that make a company great. Because of this, we’re prepared to offer a competitive salary, stock options, and a wide range of benefits that include healthcare (with dental and vision), a 401k, pre-tax commuter benefits, a flexible work schedule, and a parental leave program. We have catered meals in the office every day, a company culture that is relaxed but engaged, and over a month of paid vacation time. Our Administrative and Human Resources departments also plan a myriad of fun company-wide events. New York is home to our largest office, but we have teams all over the world. Schrödinger is honored to have been selected as one of Crain's New York Best Places to Work for the past three years running. -- *Annabel Cook, PhD* | Principal Associate, Strategic Growth [image: Schrödinger, Inc.] <https://schrodinger.com> Schrödinger is hiring! Check out our careers page <https://www.schrodinger.com/careers> Our transparency document according to article 13 and 14 GDPR is available here <https://schrodinger.com/transparencydocinc>. -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] 3/31/22 BBC Seminar with Joanna Wysocka
by Flowers, Nicole 24 Mar '22

24 Mar '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Genentech Hall Auditorium Livestream: http://tiny.ucsf.edu/Y5D1RO Co-sponsored by the [cid:705c2812-9d04-4873-93a4-a6d52e62f537] Joanna Wysocka, PhD Stanford University Transcriptional regulation and emergence of form and function during development and evolution Marh 31, 2022 L. Weinberger, host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Spring 2022 BBC Seminar Schedule
by Flowers, Nicole 18 Mar '22

18 Mar '22

Attached, please find the schedule of speakers for BBC Seminar Series spring quarter. Thank you! Nicole Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94158-2517 Phone: (415) 502-6518

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[Compbio-allhands] Canceled: 3/17/22 BBC Seminar with Squire Booker, PhD, Noon
by Flowers, Nicole 14 Mar '22

14 Mar '22

Unfortunately, Dr. Booker has a family emergency and will not be able to deliver his lecture. This seminar has been cancelled.

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[Compbio-allhands] Fwd: data science job posting at Novartis Emeryville
by Andrej Sali 10 Mar '22

10 Mar '22

Sent from my iPhone Begin forwarded message: > From: Dave Barkan <davebarkan(a)gmail.com> > Date: March 10, 2022 at 10:42:27 AM PST > To: Andrej Sali <sali(a)salilab.org> > Subject: data science job posting at Novartis Emeryville > > > Hi Andrej, > > Hope everything is going well. We have a new Structural Bioinformatician position opening in our Data Science group in Emeryville and I was wondering if you could circulate this link across relevant labs and graduate programs. This is a great opportunity for new PhDs and post-docs to get into the biotech industry while still working in an environment that emphasizes scientific curiosity. > > https://www.novartis.us/careers/career-search/job-details/339342BR > > Thanks, > Dave Barkan

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[Compbio-allhands] 3/17/22 BBC Seminar with Squire Booker, PhD, Noon
by Flowers, Nicole 24 Feb '22

24 Feb '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF Squire Booker, PhD Pennsylvania State University Moving beyond methionine synthase: New insight into cobalamin-dependent methylation reactions Marh 17, 2022 D. Fujimori, host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Fwd: Job at EMBL Hamburg - Senior Scientific Software Engineer: New Methods for Structural Modeling
by Andrej Sali 22 Feb '22

22 Feb '22

> Begin forwarded message: > > From: Jan Kosinski <jan.kosinski(a)embl.de> > Subject: Job at EMBL Hamburg - Senior Scientific Software Engineer: New Methods for Structural Modeling > Date: February 22, 2022 at 6:39:11 AM PST > To: Andrej Sali <sali(a)salilab.org> > > Dear Andrej, > > We are having the below job opening, and I would be grateful if you could forward it to anyone who might be interested: > > We are seeking to recruit a Senior Scientific Software Engineer: New Methods for Structural Modeling, to develop and apply computational methods for modeling based on electron microscopy and other data, with the particular focus on using recent Artificial Intelligence-based modeling tools like AlphaFold and RoseTTAfold. Three years contract with possibility of extension. > > More information and application form: https://www.embl.org/jobs/position/HH00209 <https://www.embl.org/jobs/position/HH00209> > Closing date: 27 March 2022 > > Please check more about our lab <https://www.embl.org/groups/kosinski/> and our publications <https://www.embl.org/groups/kosinski/publications/>. > > We offer access to superb computational infrastructure, experimental data from electron microscopy and other techniques, competitive salaries, and excellent working conditions. > > Best, > Jan > > -- > Group leader at European Molecular Biology Laboratory (EMBL) Hamburg > Joint appointment Structural and Computational Biology Unit EMBL Heidelberg > Group leader at Centre for Structural Systems Biology (CSSB) > > c/o DESY, Building 15 (CSSB), Room 02.247 > Notkestraße 85 > 22607 Hamburg, Germany > Phone: +49(0)40 8998-87573 > https://www.embl.org/kosinski/ <https://www.embl.org/kosinski/> > https://www.cssb-hamburg.de/research/research_groups/kosinski_group/index_e… <https://www.cssb-hamburg.de/research/research_groups/kosinski_group/index_e…> > > Twitter: @jankosinski >

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[Compbio-allhands] Fwd: in silico modeling expert
by Brian Shoichet 15 Feb '22

15 Feb '22

FYI ---------- Forwarded message --------- From: Joseph Wu <joewu(a)stanford.edu> Date: Tue, Feb 15, 2022 at 9:39 PM Subject: RE: in silico modeling expert To: Brian Shoichet <bshoichet(a)gmail.com> Dear Brian, I hope all is well. I recently started a startup company using clinical genomics, AI/ML, and patient-specific iPSCs to accelerate drug discovery. I wonder if you know of any graduates in your program or department who may be interested in joining our company. The expertise would be as follow: 1.) Computational ligand screening (e.g. docking) for hit identification 2.) Hit-to-lead optimization for establishing quantitative structure-activity-relationship (QSAR) 3.) Computational protein modeling, e.g. homology modeling. If yes, please feel free to introduce me to him/her and I’ll be happy to set up a zoom call. Thank you in advance. Best wishes, Joe Joseph C. Wu, MD, PhD Director, Stanford Cardiovascular Institute Simon H. Stertzer, MD, Professor of Medicine & Radiology Stanford University School of Medicine 265 Campus Drive, Rm G1120B Stanford, CA 94305-5454 Ph: 650-736-2246; Fax: 650-736-0234 Email: joewu(a)stanford.edu Lab: http://wulab.stanford.edu Stanford CVI: http://med.stanford.edu/cvi <http://med.stanford.edu/cvi.html> [image: cid:image001.jpg@01D58538.54058B90] <http://med.stanford.edu/cvi.html> [image: cid:ff7027d6-b10c-47d4-9a0c-6aac03848d78] <https://twitter.com/Joseph_C_Wu> *From:* Brian Shoichet <bshoichet(a)gmail.com> *Sent:* Wednesday, November 3, 2021 11:19 AM *To:* Hao Zhang <zhanghao(a)stanford.edu> *Cc:* Stefan Gahbauer <steffgahbauer(a)gmail.com>; Joseph Wu < joewu(a)stanford.edu> *Subject:* Re: Mentor team for my career development grant (in collaboration with Stefan) Hi Hao, Yes, I'd be willing to do it. Brian On Wed, Nov 3, 2021 at 8:06 AM Hao Zhang <zhanghao(a)stanford.edu> wrote: Dear Brian, I hope you are doing well. In the past few months, Stefan and I have been working together to design novel compounds aiming to eliminate neurological off-target effects in CGS15943, a non-selective adenosine antagonist for antifibrotic therapy. Stefan and I had many discussions, in which he taught me the strategy for in-silico drug development, including ligand-receptor docking, protein homology prediction, and polarized side-chain design. The new design compound is being synthesized, and we will test the effects soon. I am writing a career development grant for the American Heart Association. As "in-silico based drug development" takes a major part of my proposal. I wonder if you would like to join my mentor team, responsible for the drug design. Our chemistry department or CRO is responsible for the chemical synthesis with your supervision. I can draft the mentor letter with your approval. Thanks for your consideration. Best wishes, Hao -- Brian Shoichet, Professor, UCSF latest science from the lab: *http://www.bkslab.org/ <http://www.bkslab.org/contact.php>* -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] Fwd: Searching for Postdoc Candidate in AI/ML and mathematical methods for Biology @ IBM Almaden
by Andrej Sali 15 Feb '22

15 Feb '22

> Begin forwarded message: > > From: Sara CAPPONI <Sara.CAPPONI(a)ibm.com> > Subject: Searching for Postdoc Candidate in AI/ML and mathematical methods for Biology @ IBM Almaden > Date: February 12, 2022 at 4:24:23 PM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Andrej, > > I hope that this email finds you well! > > I am reaching out because I was awarded as IBM PI of the NSF Center for Cellular Construction grant and I am looking for a postdoctoral researcher willing to work using advanced AI/ML methods for Biology. I am wondering if you are aware of someone looking for such position, e. g. a student in the final year of Ph.D. training or a postdoc at the end of the contract. If so, maybe you can point this person to me (sara.capponi(a)ibm.com <mailto:sara.capponi@ibm.com>). > > Also, I would appreciate if you could forward this email to anyone who might be interested in applying to this position. The postdoc ad is at the bottom of the email. > > Thanks for your time! > > Best, > Sara > > --------------- > > Postdoctoral Research Scientist in Cellular Engineering at IBM Almaden Research Center > > The Cellular Engineering laboratory at IBM Almaden Research Center is looking for a postdoctoral research scientist. The position is slated to begin immediately. The candidate is expected to apply advanced AI/ML methods in cellular engineering and synthetic biology to understand biological systems and cellular dynamics. > > The Cellular Engineering laboratory integrates multidisciplinary methods to understand the basic principles underlying cell functions in order to modify and build cells with designed activity. For this purpose, we have access to several IBM supercomputers, which are among the fastest in the world. The laboratory is part of the NSF Center for Cellular Construction in partnership with UC San Francisco, UC Berkeley, Stanford University, SF State University, and the SF Exploratorium. The overall goal of the Center is to develop an engineering discipline to design cells. The candidate will work in close collaboration with world known scientists. > > Our focus is to leverage AI/ML methods for harnessing the power of cells and develop powerful predictive models of cellular structure and function. The candidate is expected to integrate and develop novel AI/ML algorithms to understand the basic principles underlying cell functions in order to modify and build cells with designed activity. The ideal candidate should have strong background in computational biology and modeling, biophysics, AI/ML methods for biological system analysis and cellular dynamics. Relevant areas of expertise might include direct application of machine learning methods to cellular systems. > > Interested candidates should contact Sara Capponi, PhD, (sara.capponi(a)ibm.com <mailto:sara.capponi@ibm.com>) with a brief statement of research interest/cover letter, a CV, and contact information of 2-3 references. Students in their final year of Ph.D. training are encouraged to apply. > > > Qualifications: > > • PhD in Computational Biology, Computational Biophysics, Physics, Bioengineering or related field. > • Experience in chemistry, physics, engineering, computer science, computational biology, or related fields. > • Experience in computational modeling methods. > • Experience in machine learning, deep learning packages. > • Proven experience with python programming. > • Excellent English (oral and written) and good communication skills are necessary.

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[Compbio-allhands] Fwd: New position in computational chemistry, Pfizer Cambridge, MA
by John Irwin 15 Feb '22

15 Feb '22

Computational chemistry job at Pfizer in Cambridge. John Irwin UCSF Pharmaceutical Chemistry http://irwinlab.compbio.ucsf.edu ---------- Forwarded message --------- From: Mathiowetz, Alan M <alan.m.mathiowetz(a)pfizer.com> Date: Tue, Feb 15, 2022 at 10:53 AM Subject: New position in computational chemistry, Pfizer Cambridge, MA To: John Irwin <jir322(a)gmail.com> Hi, John- I wanted to let you know that we have a new opening for a computational chemist in my group at Pfizer, located in Cambridge, MA. The work primarily involves small molecule drug discovery in the therapeutic areas of Inflammation, Immunology, and Rare Diseases. If you know of a current or recent Ph.D. student or postdoc who is looking for such a position, please share the following link with them: Senior Scientist, Computational Chemistry Thank you and best regards, Alan

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[Compbio-allhands] Check Out the Winter Line Up for the Gladstone Data Science Training Program
by Zainab Yusufsada 12 Feb '22

12 Feb '22

The Gladstone Data Science Training Program <https://gladstone.org/events?series=data-science-training-program> provides you with learning opportunities and hands-on workshops to improve your skills in bioinformatics and computational analysis. Join one of these upcoming workshops to gain new skills and get support with your data. Winter 2022 Series All workshops are virtual this winter! Unix Command Line February 14, 2022 Register <https://gladstone.org/events/unix-command-line> Introduction to Statistics and Experimental Design February 22, 2022 Register <https://gladstone.org/events/introduction-statistics-and-experimental-desig…> Introduction to RNA-Seq, Sessions 1- 2 March 10–11, 2022 Register <https://gladstone.org/events/introduction-rna-seq-analysis-2> Intermediate RNA Seq Analysis Using R March 21, 2022 Register <https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-0> Cordially, *Zainab Yusuf Sada* | Administrative Specialist Gladstone Institute of Data Science & Biotechnology 1700 Owens Street, San Francisco, CA 94518 T 415.734.4827|zainab.yusufsada(a)gladstone.ucsf.edu

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[Compbio-allhands] 2/17/22 BBC Seminar with David Baker, PhD, Noon
by Flowers, Nicole 11 Feb '22

11 Feb '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF David Baker, PhD University of Washington Protein design using deep learning February 17, 2022 C. Bracken & P. Burroughs, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] 2/10/22 BBC Seminar, HARC Lecture with Greg Towers, PhD, Noon, IN PERSON
by Flowers, Nicole 10 Feb '22

10 Feb '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursday, Noon Genentech Hall Byers Auditorium- IN PERSON Livestream: http://tiny.ucsf.edu/Y5D1RO HARC Speaker Greg Towers, Ph.D. University College London What's so special about pandemic viruses? HIV and SARS-CoV-2 vs. Innate Immunity February 10, 2022 N. Krogan, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Check Out the Winter Line Up for the Gladstone Data Science Training Program
by Zainab Yusufsada 01 Feb '22

01 Feb '22

The Gladstone Data Science Training Program <https://gladstone.org/events?series=data-science-training-program> provides you with learning opportunities and hands-on workshops to improve your skills in bioinformatics and computational analysis. Join one of these upcoming workshops to gain new skills and get support with your data. Winter 2022 Series All workshops are virtual this winter! Introduction to R for Data Analysis February 4, 2022 Register <https://gladstone.org/events/introduction-r-data-analysis-2> Intermediate Cytoscape: Networks and Omics Data Visualization February 7, 2022 Register <https://gladstone.org/events/intermediate-cytoscape-networks-and-omics-data…> Unix Command Line February 14, 2022 Register <https://gladstone.org/events/unix-command-line> Introduction to Statistics and Experimental Design February 22, 2022 Register <https://gladstone.org/events/introduction-statistics-and-experimental-desig…> Introduction to RNA-Seq, Sessions 1- 2 March 10–11, 2022 Register <https://gladstone.org/events/introduction-rna-seq-analysis-2> Intermediate RNA Seq Analysis Using R March 21, 2022 Register <https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-0> Cordially, *Zainab Yusuf Sada* | Administrative Specialist Gladstone Institute of Data Science & Biotechnology 1700 Owens Street, San Francisco, CA 94518 T 415.734.4827|zainab.yusufsada(a)gladstone.ucsf.edu

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[Compbio-allhands] 2/3/22 BBC Seminar with Vanessa Ruta, PhD, Noon
by Flowers, Nicole 28 Jan '22

28 Jan '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF Vanessa Ruta, PhD Rockefeller University Sensing the scents: the structural and circuit mechanisms of olfaction February 3, 2022 A. Manglik, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] 1/27/22 BBC Seminar with Negar Rostamzadeh, PhD, Noon
by Flowers, Nicole 21 Jan '22

21 Jan '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF Negar Rostamzadeh, PhD Google Rethinking Values in Machine Learning Research and Practice January 27, 2022 H. Goodarzi, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] a job at Interline Therapeutics
by Andrej Sali 18 Jan '22

18 Jan '22

https://pro.snaphire.com/interlinetx-careers/jobdetails/ajid/dgVJ7/Scientis… -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] 1/13/22 BBC Seminar with Aaron Ring, MD, PhD, Noon
by Flowers, Nicole 07 Jan '22

07 Jan '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF Aaron Ring, MD, PhD Yale Targeting the immune exoproteome January 13, 2022 C. Bracken & S. Elledge, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Winter 2022 BBC Seminar Schedule
by Flowers, Nicole 06 Jan '22

06 Jan '22

Happy New Year! Attached, please find the calendar for the Winter 2022 BBC Seminar Series. Note that some seminars are remote and some are planned as in-person. Our first seminar of the quarter is today at noon over zoom with Dr. Feng Zhang of MIT. Thank you, Nicole Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94158-2517 Phone: (415) 502-6518

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