January 2013 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] 2/7/13 Seminar with Jonathan Javitch
by Nicole Takesono Flowers 31 Jan '13

31 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 Jonathan Javitch Columbia A tale of two substrates: a novel mechanism for neurotransmiters:sodium symport February 7, 2013 R. Edwards, 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

1 0

[Compbio-allhands] Fwd: RE: employment offering in biotech
by Tom Ferrin 29 Jan '13

29 Jan '13

-------- Original Message -------- Subject: RE: employment offering in biotech Date: Mon, 28 Jan 2013 19:34:13 +0000 From: Petropoulos, Christos <Petropc(a)labcorp.com> To: Tom Ferrin <tef(a)cgl.ucsf.edu> CC: babbitt(a)cgl.ucsf.edu <babbitt(a)cgl.ucsf.edu> Thanks for your assistance Tom! I am attaching a job description if that helps? CJP -----Original Message----- From: Tom Ferrin [mailto:tef@cgl.ucsf.edu] Sent: Monday, January 28, 2013 10:04 AM To: Petropoulos, Christos Cc: babbitt(a)cgl.ucsf.edu Subject: Re: employment offering in biotech Christos, We have an email distribution list that I would be happy to forward your message to. --tom On 1/27/13 6:23 PM, Petropoulos, Christos wrote: > Dear Dr. Ferrin and Dr. Babbitt, > > > > I am the Chief Scientific Officer of Monogram Biosciences, a > biotechnology company located in South San Francisco. We have an > opening for a scientist in our bioinformatics group and are looking > for qualified candidates. I would like to know if there is a > mechanism for posting this position on your website or an appropriate UCSF website. > > > > Sincerely, > > > > Christos J Petropoulos, PhD > > Chief Scientific Officer, Monogram Biosciences > > Vice President, Laboratory Corporation of America > > > > -This e-mail and any attachments may contain CONFIDENTIAL information, > including PROTECTED HEALTH INFORMATION. If you are not the intended > recipient, any use or disclosure of this information is STRICTLY > PROHIBITED; you are requested to delete this e-mail and any > attachments, notify the sender immediately, and notify the LabCorp > Privacy Officer at privacyofficer(a)labcorp.com or call (877) 23-HIPAA / (877) 234-4722. > -This e-mail and any attachments may contain CONFIDENTIAL information, including PROTECTED HEALTH INFORMATION. If you are not the intended recipient, any use or disclosure of this information is STRICTLY PROHIBITED; you are requested to delete this e-mail and any attachments, notify the sender immediately, and notify the LabCorp Privacy Officer at privacyofficer(a)labcorp.com or call (877) 23-HIPAA / (877) 234-4722.

1 0

[Compbio-allhands] Fwd: [ISBRA-L] Full Professor - Bioinformatics
by Andrej Sali 27 Jan '13

27 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: ISBRA Mailing List <isbra-l(a)dna.engr.uconn.edu> > Subject: [ISBRA-L] Full Professor - Bioinformatics > Date: January 26, 2013 6:08:44 PM PST > To: <sali(a)salilab.org> > Reply-To: <isbrainfo(a)gmail.com> > > > The Department of Computer Science at Georgia State University invites > applications for an anticipated position of Full Professor in the > bioinformatics area beginning Fall Semester 2013, pending budgetary > approval. Earned Ph.D. in Computer Science or a related discipline is > required. An offer of employment will be conditional on background > verification. > > This position is part of a university-wide initiative that is seeking > to hire excellent faculty in several interdisciplinary areas. > Prospective candidates should demonstrate ability to bring national > and international recognition to the department as a center of > excellence for bioinformatics research and education. The hired > applicant is expected to to bring in major extramural funding, mentor > junior faculty, recruit top-quality Ph.D. students, and foster > interdisciplinary research collaborations among faculty in various > departments in GSU. > > Georgia State University, founded in 1913, is a Carnegie RU/VH > (Research University/Very High Research Activity) institution. Located > in the heart of downtown Atlanta, this major research university has > an enrollment of more than 30,000 undergraduate and graduate students > in eight colleges. Georgia State is the second-largest university in > the state, with students coming from every county in Georgia, every > state in the nation, and from over 145 countries. Georgia State > University is currently embarking on a record $1 billion campus > expansion. The Computer Science Department offers programs leading to > the B.S., M.S., and Ph.D. degrees in computer science. Currently, 20 > out of more than 60 Ph.D. students are involved in bioinformatics > research. They are supervised by 10 faculty members fully or > substantially involved in bioinformatics research through > collaboration with Computer Science and Biology faculty. Departmental > computing facilities for research and instruction include a > departmental network of PCs, Unix/Linux workstations, two > interconnected Beowulf clusters, and a 32-processor supercomputer. > The department?s faculty attracts substantial funding from many > federal agencies, including five NSF CAREER Awards. > > Women and minorities are particularly encouraged to apply. Applicants > should send letter of interest, C.V., and three letters of > recommendation to: > > Dr. Yi Pan, Chair > 2CI Bioinformatics > Department of Computer Science > Georgia State University > 34 Peachtree Street, Suite 1450 > Atlanta, Georgia 30303 > > Applications can also be sent via email to search4bio(a)cs.gsu.edu and > will be accepted until position is filled. > > > _______________________________________________ > To modify subscription preferences or unsubscribe from the ISBRA-L mailing list visit http://dna.engr.uconn.edu/cgi-bin/mailman/options/isbra-l/sali%40salilab.org

1 0

[Compbio-allhands] Fwd: Bioinformatics Requisition at ILMN San Diego
by Jacobson, Matt 18 Jan '13

18 Jan '13

Begin forwarded message: From: "Chorny, Ilya" <ichorny(a)illumina.com<mailto:ichorny@illumina.com>> Subject: Bioinformatics Requisition at ILMN San Diego Date: January 18, 2013 8:30:23 AM PST To: "babbitt(a)cgl.ucsf.edu<mailto:babbitt@cgl.ucsf.edu>" <babbitt(a)cgl.ucsf.edu<mailto:babbitt@cgl.ucsf.edu>>, "Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, "sali(a)salilab.org<mailto:sali@salilab.org>" <sali(a)salilab.org<mailto:sali@salilab.org>> Hi All, The group that I am in is opening up a requisition in the next week or so. If you know anyone that is interested in a genomic bioinformatics position at Illumina in San Diego please have them contact me. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist II Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com/> 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>

1 0

[Compbio-allhands] Fwd: looking for an associate
by Jacobson, Matt 18 Jan '13

18 Jan '13

Begin forwarded message: From: Tack <idkz(a)comcast.net<mailto:idkz@comcast.net>> Subject: Fwd: looking for an associate Date: January 18, 2013 9:53:08 AM PST To: Matt Jacobson <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, Brian Shoichet <bshoichet(a)gmail.com<mailto:bshoichet@gmail.com>>, Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>> Jose is a former UCSF/Kuntz Group graduate student who is a research analyst based in SF. tack Begin forwarded message: From: "Jose Haresco" <JHaresco(a)jmpsecurities.com<mailto:JHaresco@jmpsecurities.com>> Date: January 17, 2013 1:43:44 PM PST To: "'idkz(a)comcast.net<mailto:'idkz(a)comcast.net>'" <idkz(a)comcast.net<mailto:idkz@comcast.net>> Subject: looking for an associate Hi Tack, I hope this reaches you well. I was wondering if you could pass this on to any late-stage grad students. I'm looking for an associate. Our firm is on a growth trajectory and we are expanding the group. The job description is below. Interested applicants can contact me directly. Sincerely, Jose Title: Associate Equity Research Analyst, Medical-Devices and Molecular Diagnostics Location: San Francisco Keywords: equity analyst, medical devices, sell-side, buy-side, equity research The incumbent will support senior Equity Research Analysts by compiling data and formulating analysis and opinions to be used in buy/sell/hold recommendations. Specific responsibilities include financial model building, competitive analysis, market research, and company research. Candidate must be knowledgeable and proficient in working with clinical trials, researching and summarizing academic journal articles, analyzing scientific data, as well as creating comprehensive financial statements and have the ability to construct bottom-up income statements, balance sheets, and statements of cash flow. Ideally, the candidate will have experience in relevant to the medical device industry. Essential Function/Duties: 1. Develop financial models to forecast growth and profitability opportunities for publicly traded equity investments. This includes financial statement analysis, historical and projected, profitability metrics, margin analysis, and various ratio analyses. Perform valuation analysis such as discounted cash flow analysis, discount models, and other valuation calculations including, but not limited to, earnings, sales, cash flow and tangible book. 2. Assist Analysts with compilation and evaluation of all relevant research and information pertaining to equity investment ideas, their respective markets and their competitors, customers, suppliers and any other entities which might have a meaningful impact on a company’s financial outcomes. Relevant research and information comes from a variety of sources including scientific literature, industry conferences, company filings and meetings with company management, independent research firms, financial news sources and government and industry organizations. 3. Maintain and ensure accuracy of financial models, analyses and archives. Compile clinical research data across specific indications. Synthesize and summarize scientific publications. Provide summary of earnings conference calls to Analysts to assist in evaluating recent company performance. Disseminate information to internal departments as applicable. Minimum Qualifications: • Master's Degree in Bioengineering, Genetics, Nursing, Biostatistics, or a related life science field. Bachelor's degree may be considered if candidate has exceptional work experience in the field of healthcare equity research, clinical research, management consulting, or business development/marketing in healthcare fields • Position requires demonstration of excellent quantitative and analytical skill. While formal training in accounting or finance is not required, the applicant must have substantial experience using Microsoft Excel. • Advanced computer skills using Microsoft Office, with particular expertise in Excel, Word, & Powerpoint Programming experience with C++, Visual Basic, or Python helpful, but not required. • Strong verbal and writing skills. A writing sample will be required Visit us at http://www.jmpsecurities.com<http://www.jmpsecurities.com/> IMPORTANT NOTICES: This message is intended only for the addressee. If you are not the intended recipient, please notify the sender by e-mail reply. Additionally, you may not copy, disclose, distribute or otherwise make use of this message or its contents for yourself or for any other person as that action may be unlawful. ORDERS AND INSTRUCTIONS: JMP Securities ("JMP") does not accept action oriented, time sensitive instructions or transactions orders via e-mail. Such orders and/or instructions will not be accepted by JMP, and JMP will not be responsible for carrying out such orders or instructions, including orders to purchase and sell securities. CONFIDENTIALITY AND PRIVACY: JMP reserves the right to monitor and review the content of all e-mail communications sent and/or received by its employees. 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>

1 0

[Compbio-allhands] 1/24/13 Seminar with Wenying Shou
by Nicole Takesono Flowers 18 Jan '13

18 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 Wenying Shou Fred Hutchinson Cancer Center War and Peace: a biological basis for population segregation and mixing January 24, 2013 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

1 0

[Compbio-allhands] Fwd: Bioinformatics Requisition at ILMN San Diego
by Andrej Sali 18 Jan '13

18 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: "Chorny, Ilya" <ichorny(a)illumina.com> > Subject: Bioinformatics Requisition at ILMN San Diego > Date: January 18, 2013 8:30:23 AM PST > To: "babbitt(a)cgl.ucsf.edu" <babbitt(a)cgl.ucsf.edu>, "Matt.Jacobson(a)ucsf.edu" <Matt.Jacobson(a)ucsf.edu>, "sali(a)salilab.org" <sali(a)salilab.org> > > Hi All, > > The group that I am in is opening up a requisition in the next week or so. If you know anyone that is interested in a genomic bioinformatics position at Illumina in San Diego please have them contact me. > > Thanks, > > Ilya > > > Ilya Chorny Ph.D. > Bioinformatics Scientist II > Illumina, Inc. > 9885 Towne Centre Drive > San Diego, CA 92121 > Work: 858.202.4582 > Email: ichorny(a)illumina.com > Website: www.illumina.com > >

1 0

[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

1 0

[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.

1 0

[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>

1 0