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

[Compbio-allhands] 11/20/14 Seminar with Molly Przeworski
by Flowers, Nicole 14 Nov '14

14 Nov '14

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 Molly Przeworski University of Chicago An evolutionary perspective on the human germ line mutation rate November 20, 2014 T. Friedrich, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, & 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] SEMINAR ANNOUNCEMENT: Bill Pearson, Nov. 11, 1 pm, BH-212
by Patsy Babbitt 11 Nov '14

11 Nov '14

Seminar notice: Bill Pearson, Univ. of VA School of Medicine Friday, Nov. 14, 1:00 BH-212 Bill works in the areas of computational biology and protein evolution. One of the founders of the field of sequence analysis and its applications for functional inference, he serves on many advisory boards, including that for European Bioinformatics Institute's UniProt, one of the two (with Genbank) primary public database for sequence information and annotation. He wrote the FASTA algorithm, one of the first widely used computer programs for identifying distantly related protein sequences. His approach is widely used to annotate newly sequenced genomes. His current research focuses on improving functional predictions for proteins by integrating annotation and variation information with sequence alignments. Title and abstract: Alignments with Annotations – providing functional information with similarity search Similarity searching with sequence alignment is the most reliable method for characterizing genomes and meta-genomes; sequence alignment algorithms may now be the major consumer of compute cycles in the life sciences. While similarity searching has become dramatically more sensitive over the past 25 years, and the number and diversity of sequences has increased by orders of magnitude, the display of sequence alignments is essentially unchanged. Despite the explosive growth of sequence, variation, and annotation data, and the hyper-connectedness of sequence and annotation databases, popular search programs show the same alignment information that was displayed in 1985. The FASTA search and alignment programs can incorporate functional site annotations, variation data, and domain boundaries Variant annotation allows the alignment score to improve; the domain annotation strategy partitions the alignment score across the annotated domains, reducing the problem of homologous over-extension. Annotation of functional sites allows exploration of the relationship between sequence similarity, active-site conservation, and functional similarity -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94158-2330, USA (CA 94158 for direct delivery by courier) Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Joslyn Polzien, +1 415-514-1214, 415-514-4861 Joslyn.Polzien(a)ucsf.edu

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[Compbio-allhands] 11/13/14 Seminar with Jeff Gore
by Flowers, Nicole 07 Nov '14

07 Nov '14

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 Jeff Gore MIT Cooperation, cheating, and collapse in microbial populations November 13, 2014 M. Thomson, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, & 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] 11/6/14 Braisted Lecture with Laura Kiessling
by Flowers, Nicole 06 Nov '14

06 Nov '14

UCSF-UCB Andrew Braisted Award Lectureship Lauraq Kiessling, Ph.D. Professor and MacArthur Foundation Fellow University of Wisconsin-Madison Us Versus Them: Cell Surface Glycans to Distinguish Human and Microbial Cells Thursday, November 6, 2014 4 pm Genentech Hall Byers Auditorium UCSF Mission Bay Campus Simulcast to Parnassus, Room 161 Reception in 1st Floor Atrium following talk Contact: Jim Wells, Charles Craik Sponsor: The Andrew Braisted Lecture Fund Nicole Takesono Flowers BMI, BP, & 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] SAVE THE DATE- PETER KOLLMAN LECTURESHIP- JANUARY 8, 2015
by Flowers, Nicole 04 Nov '14

04 Nov '14

SAVE THE DATE- THURSDAY, January 8, 2015 AT 12:00 PM Mark Murcko Disruptive Biomedical PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS S-161 Reception in Byers Hall 5th Floor Lounge at 3:30 Nicole Takesono Flowers BMI, BP, & 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: Faculty search at Ohio State University in theoretical/computational chemistry
by Andrej Sali 04 Nov '14

04 Nov '14

Sent from my iPhone Begin forwarded message: > From: "Herbert, John" <herbert(a)chemistry.ohio-state.edu> > Date: November 4, 2014 at 8:10:10 AM PST > To: "Herbert, John" <herbert(a)chemistry.ohio-state.edu> > Cc: "Herbert, John" <herbert(a)chemistry.ohio-state.edu> > Subject: Faculty search at Ohio State University in theoretical/computational chemistry > Reply-To: "Herbert, John" <herbert(a)chemistry.ohio-state.edu> > > Colleague, > I wish to draw your attention to a theoretical chemistry faculty search in my department, which is part of a larger “Data Analytics” initiative on campus, into which the University has committed significant resources. Because of the broader tie-in and the attendant layers of bureaucracy, the approval to search came relatively late, so I am sending out this blanket email. Please note that we will begin reviewing applications immediately, but the final deadline for applications is Dec. 1. > > The text of the advertisement is pasted at the end of this email. Please forward this email to your postdocs or former students who are looking for academic jobs. > > Thanks in advance, and best regards. > John Herbert > > > ================================== > John M. Herbert, Professor > Dept. of Chemistry & Biochemistry > The Ohio State University > 100 W. 18th Ave., Columbus, OH 43210 > Office: 2114 Newman & Wolfrom > (614) 292-6851 (voice) > (614) 292-1685 (fax) > http://www.chemistry.osu.edu/~herbert > ================================== > > > The College of Arts and Sciences at The Ohio State University seeks applications to fill a tenure-track faculty position in Data Analytics at the Assistant Professor level within the Department of Chemistry and Biochemistry. The successful applicant will develop and apply novel computational methods to guide discovery of new functional materials or molecules, and/or understand the properties of complex systems. The search will consider outstanding candidates in all areas of computational chemistry, but greatest needs exist in either (i) electronic structure theory and dynamics, or (ii) computational structural biology. Ideal candidates in area (i) would address fundamental questions to enable rational design of new materials with possible applications in energy harvesting and storage, novel electronic devices, catalysis, or sensing. The ideal candidate in area (ii) would complement and extend existing and emerging experimental methods in biomolecular structure and function, with possible applications in de novo structure prediction, molecular design, or macromolecule-ligand interactions. Successful candidates will demonstrate the potential to be leaders in methods development, but also have strong ties to experiment. Ohio State has a strong tradition in theoretical and computational chemistry, with access to excellent computing resources through the Ohio Supercomputer Center (www.osc.edu) A doctoral degree in Chemistry or Biochemistry is required at the time of application. This position is partially funded by Ohio State's Discovery Themes Initiative, a significant faculty hiring investment in key thematic areas in which the university can build on its culture of academic collaboration to make a global impact. > > The Ohio State University, Ohio’s flagship institution of higher education, is located in Columbus, a growing and affordable metropolitan area of ~1.5 million people with a stable and diversified economy. Columbus is consistently ranked as one of the most attractive cities in which to live and work. General information about the University, College, and community is available through links at: http://www.osu.edu. A curriculum vitae, a description of research experience and future plans, a description of teaching interests, a list of publications, and 3 letters of recommendation should be submitted to https://academicjobsonline.org/ajo/jobs/5049. Applications will be accepted and reviewed continuously, but to ensure a full review the application materials should be received no later than December 1, 2014. > > The Ohio State University is committed to establishing a culturally and intellectually diverse environment, encouraging all members of our learning community to reach their full potential. We are responsive to dual-career families and strongly promote work-life balance to support our community members through a suite of institutionalized policies. We are an NSF Advance Institution and a member of the Ohio/Western Pennsylvania/West Virginia Higher Education Recruitment Consortium (HERC). > > The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status. Ohio State is an NSF Advance Institution. > > >

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[Compbio-allhands] Fwd: Tenure Track Position in Systems Biology and Microbiology
by Andrej Sali 03 Nov '14

03 Nov '14

-- 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: Thibault Mayor <mayor(a)mail.ubc.ca> > Date: November 3, 2014 at 11:14:27 PM PST > Subject: Tenure Track Position in Systems Biology and Microbiology > To: Thibault Mayor <mayor(a)mail.ubc.ca> > > Dear colleague, > > The Centre of High-Throughput Biology and the Department of Microbiology and Immunology of the University of British Columbia are seeking a new Faculty applicant for a tenure-track position. More specifically, we are looking for an applicant with expertise in Microbiology and Systems Biology, and we would be grateful if you could bring this opening to the attention of potential candidates. > > Thank you on the behalf of the Search Committee > > Very Best, > > Thibault > > > Thibault Mayor, Ph.D. > Associate Professor > CHiBi - Centre for High-Throughput Biology > Department of Biochemistry and Molecular Biology > University of British Columbia > 2125 East Mall - Room 306 > Vancouver - BC - V6T 1Z4 - Canada > > office: 604 822 5144 > lab: 604 822 5259 > fax: 604-822-9126 > email: mayor(a)mail.ubc.ca <mailto:mayor@mail.ubc.ca> > web : www.chibi.ubc.ca/faculty/mayor/labhome <http://www.chibi.ubc.ca/faculty/mayor/labhome> > > > > > www.hupo2015.com <http://www.hupo2015.com/> > > > > > > > > > >

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[Compbio-allhands] Fwd: Merck Postdoctoral Research Fellow - Computational Chemistry POS000146
by Jacobson, Matt 03 Nov '14

03 Nov '14

Begin forwarded message: From: "Guo, Zhuyan" <zhuyan.guo(a)merck.com<mailto:zhuyan.guo@merck.com>> Subject: Merck Postdoctoral Research Fellow - Computational Chemistry POS000146 Date: November 3, 2014 8:34:46 AM PST To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Prof. Jacobson, By means of this email, I would like to reach out to you and your group about a postdoc opening in computational chemistry at Merck in New Jersey. The link below will lead directly to the job description on the Merck careers page. If you have students that are finishing up in the next 6 months or postdocs who might be interested in doing a postdoc in pharma for a couple years, please encourage them to apply. Link to the position: https://merck.taleo.net/careersection/merck_external_career_section/jobdeta… I also attached a pdf flyer for general information about the Merck postdoc program. I’ll be happy to answer any questions or provide additional information. So please do not hesitate to contact me. Best regards, Zhuyan Guo, Ph.D Department of Structural Chemistry Merck Research Laboratories Kenilworth, NJ 07033 Tel. 908-740-3796 Email: Zhuyan.Guo(a)merck.com<mailto:Zhuyan.Guo@merck.com> Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. 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] Fwd: Postdoctoral opportunities in theoretical biological physics at Princeton University
by Andrej Sali 29 Oct '14

29 Oct '14

> Begin forwarded message: > > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Cc: "Wingreen, Ned S." <wingreen(a)Princeton.EDU> > Subject: Postdoctoral opportunities in theoretical biological physics at Princeton University > Date: October 29, 2014 at 2:17:43 PM EDT > > Dear Colleague, > > We are following up to remind you of the existence at Princeton of several > openings for recent PhDs in theoretical physics who wish to pursue a > career in theoretical biological physics. As we hope you know, we have > been building a group in this area at Princeton over the last decade, and > we now have a robust activity that involves students, postdocs and faculty > from several departments. We are actively recruiting postdocs to join this > group, and we hope that you will urge any outstanding prospective or > recent PhD students of your acquaintance to apply to any of the following > positions for which they might be eligible (please note and do point out that > the mid-October application deadlines for all positions have been extended > to November 15!). > > 1. Postdoctoral Associate in our group. This is a regular Physics > postdoctoral position, but one in which the incumbent has great freedom to > choose projects, and can benefit from the mentorship of any of the senior > members of our group (or linear combinations thereof). Past holders of > this position have had a remarkable record of success in landing > next-level positions in the field of biophysics. Please direct your > students to the following link for more information: > https://www.princeton.edu/physics/about/employment/biophysics/index.xml <https://www.princeton.edu/physics/about/employment/biophysics/index.xml> > > 2. Postdoctoral Fellow of the Princeton Center for Theoretical Science > (PCTS). The PCTS sponsors interdisciplinary research based in theoretical > physics and the PCTS Faculty Fellows select three new Fellows each year > from a pool of candidates in all fields of theory. The PCTS provides a > unique environment for exceptional recent PhDs in theoretical physics, > broadly construed, to broaden their horizons and explore new fields. > Candidates must be nominated by senior scientists. Nominations of > biological physicists are encouraged, and Fellows with such interests > would be welcomed as participants in our group. Appointments to this > position are at the level of Associate Research Scholar. Please consult > http://pcts.princeton.edu/pcts <http://pcts.princeton.edu/pcts> for more information. > > 3. Lewis-Sigler Theory Fellow. The Lewis-Sigler Institute (LSI), a joint > venture of the Physics and Molecular Biology (and other) departments, > offers five-year positions at the level of Associate Research Scholar that > carry extra resources and the opportunity to teach in innovative > undergraduate programs. These positions are appropriate for exceptional newly- > minted PhD’s who are ready to lead their own group. LSI Theory Fellows are > selected by the full LSI faculty, but typically work very closely with our > group. Application procedures will be described on the LSI website. Applicants > to (1) who wish to also be considered as Lewis-Sigler Theory Fellows should so > indicate in their cover letter. > > We emphasize that we are interested in applications from students > with exceptional theoretical skills and a strong motivation to use > these skills to pursue biological problems, independent of the depth of their > research experience in biology. Many of our most successful postdocs have > learned their biology "on the job", and we think that we provide an > outstanding environment for such learning. Your assistance in encouraging > strong candidates for any of these positions to apply would be appreciated. > > Bill Bialek, Curt Callan and Ned Wingreen > > > Lee Morgan > 257 Carl Icahn Laboratory > Lewis-Sigler Institute of Integrative Genomics > Princeton University > Princeton, NJ 08544 > 609-258-0859

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[Compbio-allhands] Fwd: The Rockefeller University - Fellow Position
by Jacobson, Matt 24 Oct '14

24 Oct '14

Begin forwarded message: From: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Subject: The Rockefeller University - Fellow Position Date: October 24, 2014 10:54:48 AM PDT To: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Dear Colleague: The Center for Studies in Physics and Biology, at The Rockefeller University, expects to have a small number of postdoctoral fellowships available for appointments in September 2015. We are seeking theoretical physicists, mathematicians and computer scientists with a demonstrable interest in the interface between their discipline and biology. The Fellows are to be at that stage of career as to function as independent members of the Center, free to work alone or in collaboration with any members of The Rockefeller University faculty. Would you be so kind as to post the attached notice, and share this within your department and with your peers and colleagues. Many thanks! Melanie J. Lee Administrative Assistant Center for Studies in Physics and Biology Rockefeller University 1230 York Avenue New York, NY 10065-6399 Tel: 212-327-8636 Fax: 212-327-8544 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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