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

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

30 Jan '12

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

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

25 Jan '12

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

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

20 Jan '12

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

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

19 Jan '12

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

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

18 Jan '12

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

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

18 Jan '12

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

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

11 Jan '12

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

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

09 Jan '12

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

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

04 Jan '12

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

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compbio-allhands January 2012