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

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

27 Apr '12

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

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

26 Apr '12

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

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

25 Apr '12

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

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

24 Apr '12

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

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

20 Apr '12

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

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

18 Apr '12

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

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

17 Apr '12

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

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

13 Apr '12

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

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

12 Apr '12

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

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

11 Apr '12

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

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compbio-allhands April 2012