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

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

16 Jan '13

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

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

16 Jan '13

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

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

16 Jan '13

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

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

15 Jan '13

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

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

14 Jan '13

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

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

14 Jan '13

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

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

13 Jan '13

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

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

11 Jan '13

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

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

09 Jan '13

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

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

04 Jan '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Susan Marqusee UC Berkeley Sequence Determinants of a Protein's Energy Landscape January 10, 2013 H. Lim, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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