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

[Compbio-allhands] Fwd: DBDS Faculty Search
by Patricia C. Babbitt 09 Nov '15

09 Nov '15

-------- Forwarded Message -------- Subject: DBDS Faculty Search Date: Mon, 9 Nov 2015 17:39:40 +0000 From: Laura Dunkin-Hubby <lhubby(a)stanford.edu> To: babbitt(a)cgl.ucsf.edu <babbitt(a)cgl.ucsf.edu> Dear Dr. Babbitt, I am writing on behalf of Dr. Carlos Bustamante to ask your help in identifying candidates for an Assistant, Associate or Full Professor position in the new Department of Biomedical Data Science (DBDS) at the Stanford University School of Medicine. This appointment will be in the University Tenure Line (UTL). The predominant criterion for appointment in the University Tenure Line is a major commitment to research and teaching. We define biomedical data science as the study of biomedical data and information, of how such data and information may be structured, and of how analysis and processing of biomedical data and information will lead to new discoveries and to advances in health and healthcare. We are particularly interested in candidates dedicated to the development of novel computational and statistical methods for acquiring, representing, storing, analyzing, and applying biological and clinical data at all scales, who can apply their expertise in biomedical informatics and/or biostatistics to meet departmental goals. Further information on the Department of Biomedical Data Science can be found at[dbds.stanford.edu]dbds.stanford.edu. Applicants should have demonstrated strong ability and interest in conducting both methodological and collaborative research, and in teaching. We expect the successful candidate to conduct a vigorous, independent research program, to advise students, and to assist in program administration. Formal teaching in the classroom will be encouraged. An MD, MD/PhD, or PhD in biostatistics, statistics, biomedical informatics, computer science, biomedical engineering or a related area is required. Faculty rank will be determined by the qualifications and experiences of the successful candidate. Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty. It welcomes nominations of and applications from women, members of minority groups, protected veterans and individuals with disabilities, as well as from others who would bring additional dimensions to the university's research, teaching and clinical missions. I would appreciate your forwarding this announcement to individuals whom you feel would be particularly suited for this position. Interested candidates should send a copy of their curriculum vitae, a brief letter outlining their research and teaching interests, and arrange for three letters of reference to be submitted to: Euan Ashley, MD, PhD and Daniel Rubin, MD, MS Search Committee Co-Chairs Department of Biomedical Data Science Stanford University School of Medicine DBDSjobs_SOM(a)stanford.edu<mailto:DBDSjobs_SOM@stanford.edu> Applications will continue to be accepted and considered until the opening is filled. Sincerely yours, Carlos D. Bustamante, PhD Chair, Department of Biomedical Data Science Stanford University School of Medicine - Laura Dunkin-Hubby Administrative Assistant to Dr. Carlos Bustamante Stanford Center for Computational, Evolutionary and Human Genomics T 650.725.5067<file://localhost/tel/+1-650-723-2643> * cehg.stanford.edu -- 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 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Josel Tongson, +1 415-514-1214, 415-514-4861 GraciaJoselina.Tongson(a)ucsf.edu

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[Compbio-allhands] 11/12/15 Seminar with Xuewu Zhang
by Flowers, Nicole 06 Nov '15

06 Nov '15

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 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Xuewu Zhang UT Southwestern Regulation mechanisms of the neuronal axon guidance receptor plexin November 12, 2015 N. Jura, 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, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: potential comp chem position at Merck
by Jacobson, Matt 30 Oct '15

30 Oct '15

- Matt Begin forwarded message: From: "McMasters, Daniel R" <daniel_mcmasters(a)merck.com<mailto:daniel_mcmasters@merck.com>> Subject: RE: potential comp chem position at Merck Date: October 30, 2015 at 5:59:45 AM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, Thanks! Any help getting the word out to potential candidates is appreciated. We actually have two openings for computational chemists, one each in Boston and West Point, PA (Philadelphia area). There is also an opening for a cheminformatician/comp tox as well as one for a crystallographer. Here are the links for applicants to apply, and of course anyone can feel free to email me at any time. -Daniel Computational chemistry: https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft… Cheminformatics & computational toxicology: https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft… Crystallography: https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft…

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[Compbio-allhands] Fwd: Still open places for our course on modeling 3D genomes and genomic domains
by Andrej Sali 30 Oct '15

30 Oct '15

-- 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 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > Date: October 30, 2015 at 11:27:49 AM PDT > To: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > Subject: Still open places for our course on modeling 3D genomes and genomic domains > > Dear Friends and Colleagues, > > Apologies for the mass posting. > > We still have open positions for people who may be interested in our TADbit Course at the Gulbenkian Institute in Oeiras (near Lisbon) in Portugal. > > See the details here http://gtpb.igc.gulbenkian.pt/bicourses/CSDM15/ <http://gtpb.igc.gulbenkian.pt/bicourses/CSDM15/> or in the attached poster. > > Pass it along to whom you may think could be interested. > > Thanks in advance! > Marc A. Marti-Renom > > > > > ... > Marc A. Marti-Renom, ICREA Research Professor > Structural Genomics Group Leader > Centre Nacional d’Anàlisi Genòmica - Centre de Regulació Genòmica (CNAG-CRG) > Parc Científic de Barcelona – Torre I (10th floor) > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email: martirenom(a)cnag.crg.eu <mailto:martirenom@cnag.crg.eu> > Web: http://marciuslab.org <http://marciuslab.org/> · http://cnag.crg.eu <http://cnag.crg.eu/> · http://crg.cat <http://crg.cat/> > > *** Consider the environment. Print responsibly. *** > > CRG/”la Caixa” – Severo Ochoa FELLOWSHIPS AVAILABLE TO CARRY OUT PhD > STUDIES AT THE CENTER FOR GENOMIC REGULATION (CRG), BARCELONA > MORE INFORMATION AND ONLINE APPLICATION AT: http:// <http://www.crg.eu/lacaixa_fellowships>www.crg.eu/lacaixa_fellowships <http://www.crg.eu/lacaixa_fellowships> > > > > > > > > > > > > > >

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[Compbio-allhands] Fwd: The Rockefeller University - Fellow Position
by Jacobson, Matt 30 Oct '15

30 Oct '15

- Matt 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 30, 2015 at 9:44:01 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 2016. 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

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[Compbio-allhands] Fwd: open CC position
by Jacobson, Matt 29 Oct '15

29 Oct '15

- Matt Begin forwarded message: From: "Lexa, Katrina W" <katrina.lexa(a)merck.com<mailto:katrina.lexa@merck.com>> Subject: open CC position Date: October 29, 2015 at 1:45:42 PM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, Another comp chemist job ad went up for the Structural Chemistry dept – they are looking primarily for people coming out of a postdoc. https://taleo.msd.com/careersection/merck_external_career_section/jobdetail… They are hoping to fill several slots, so please pass along. Thanks! ------------------------------- Katrina Lexa Merck & Co., Inc. 126 East Lincoln Ave RY800-C364 Rahway, NJ 07065 phone: (732) 594-7058 office: RY800-D365 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), 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.

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[Compbio-allhands] Volunteers needed to help with upcoming Software Carpentry workshops at UCSF on R and Python
by Patricia C. Babbitt 28 Oct '15

28 Oct '15

Hi all, The UCSF Institute for Computational Health Sciences and the UCSF Library have set up a collaboration to bring in Software Carpentry to teach two bootcamp workshops, one an R and the other on Python on Nov. 20 and 21. The content is geared to grad students and postdocs who want to develop basic skills with these tools. Both will run for two days, 9 am to 5 pm. Volunteers are needed to help the Software Carpentry Instructors in providing assistance to workshop learners during practical sessions. While not a paid gig, breakfast and coffee/snacks will be offered in the afternoon of each day. You will be listed on the workshop materials and website as helpers and you can put this effort on your CV as service to the UCSF community and to show you have teaching experience in these areas. You can check out a similar recent boot camp to get a feel for the content and whether your expertise is a good fit: https://richford.github.io/2015-10-22-uw/ The roles for the helpers are described at https://software-carpentry.org/workshops/checklists/helpers.html If you're interested in doing this, please send an email to babbitt(a)cgl.ucsf.edu. I'm happy to answer questions you may have before deciding if you want to sign up for this. We'll take folks who are a fit on a first come, first served basis. If you decide to participate, we will also ask for your feedback on the experience, as having some expert eyes on the content and format of the boot camps and syllabi will be helpful for future workshops we want to mount on biostats and bioinformatics for the broad UCSF community. Getting your opinions about how best to do that would be helpful to us. If you're interested in participating as instructors in some of these later workshops, please let me know that as well. Thanks. Patsy Babbitt -- 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 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Josel Tongson, +1 415-514-1214, 415-514-4861 GraciaJoselina.Tongson(a)ucsf.edu

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[Compbio-allhands] Fwd: Tenure-Track Openings in Computational Biology at Carnegie Mellon University
by Jacobson, Matt 25 Oct '15

25 Oct '15

-- Matt Sent from my iPhone Begin forwarded message: From: "Robert F. Murphy" <murphy(a)cmu.edu<mailto:murphy@cmu.edu>> Date: October 25, 2015 at 5:15:54 PM PDT Subject: Re: Tenure-Track Openings in Computational Biology at Carnegie Mellon University ======================================== Tenure-track Faculty Positions Available We seek outstanding researchers who are developing and applying rigorous computational methods in all areas of biology for tenure-track positions in the Computational Biology Department within the School of Computer Science. We especially seek candidates working on automated analysis and modeling of biological and medical images, and those addressing problems in neurobiology using computational methods, although outstanding candidates from all areas will be enthusiastically considered. The department has extensive strengths in methods underlying genome-based personalized medicine (genome association for complex phenotypes, dynamic network models, efficient sequence analysis), bioimage informatics (analysis and modeling of cell and tissue organization, perturbation and differentiation), modeling and simulation of biological systems at various levels, and application of active machine learning to biological problems. A critical focus is that we do not simply build systems to reproduce or automate tasks that humans can do, but build machine learning and vision systems that answer questions and build models in ways well beyond human capabilities and that can be the driver behind choice of further experiments. Additional information on the department may be found at http://www.cbd.cmu.edu. We particularly encourage applications from candidates who have a demonstrated track record in mentoring and nurturing female and under-represented minority students. Appointments will be made either entirely in the Computational Biology Department or jointly with other departments in the University (as appropriate to the background and interests of the candidate and at a level commensurate with experience). New faculty members will be expected to both contribute to and benefit from the collaborative spirit that is a hallmark of Carnegie Mellon University and from opportunities to collaborate with other institutions in the Pittsburgh region. Applications should be submitted through the faculty application system at https://webapps.cs.cmu.edu/FacultyApplication/SCS/Welcome. Completed applications must be received by January 4, 2016. Carnegie Mellon is an EEO/Affirmative Action Employer - M/F/Disability/Veteran ======================= Robert F. Murphy, Ph.D. Ray and Stephanie Lane Professor of Computational Biology and Professor of Biological Sciences, Biomedical Engineering, and Machine Learning Head, Computational Biology Department, School of Computer Science, Carnegie Mellon University 7723 Gates and Hillman Centers, 5000 Forbes Ave., Pittsburgh, PA 15213 Phone: 412-268-3480, FAX: 412-268-2977, email: murphy(a)cmu.edu<mailto:murphy@cmu.edu>, Skype: rfmurphy1953 Personal Home Page: http://www.andrew.cmu.edu/user/murphy Honorary Professor, University of Freiburg and External Senior Fellow, Freiburg Institute for Advanced Studies

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[Compbio-allhands] 10/29/15 Seminar with Chris Garcia
by Flowers, Nicole 23 Oct '15

23 Oct '15

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 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Chris Garcia Stanford Turning cell surface receptor signaling through ligand engineering: Type I receptors versus GPCR October 29, 2015 J. Kung, 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, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 10/22/15 Seminar with Andrew Ward
by Flowers, Nicole 16 Oct '15

16 Oct '15

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 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Andrew Ward Scripps High-resolution cryoEM structures of viral glycoproteins and neutralizing antibodies October 22, 2015 W. DeGrado, 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, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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