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

[Compbio-allhands] PETER A. KOLLMAN LECTURESHIP - April 3, 2014
by Flowers, Nicole 01 Apr '14

01 Apr '14

THURSDAY, APRIL 3, 2014 AT 12:00 PM PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS LIBRARY 221 WEBCAST: Reception in Byers Hall 5th Floor Lounge at 3:30 Please see attached flyer. 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: Job offers at CRG-CNAG
by Tom Ferrin 17 Mar '14

17 Mar '14

-------- Original Message -------- Subject: Job offers at CRG-CNAG Date: Mon, 17 Mar 2014 15:32:34 +0100 From: Marc A. Marti-Renom <mmarti(a)pcb.ub.cat> To: Marc A. Marti-Renom <mmarti(a)pcb.ub.cat> Dear friends and colleagues (apologies for the mass posting), I would appreciate if you pass this e-mail to whom may be interested on working in 4D (structure and dynamics) genomics at the CRG and CNAG in Barcelona. Together with the Beato, Graf and Filion Labs, we have recently opened several positions to work on experimental and computational aspects of our ERC Synergy grant "/4DGenome: Dynamics of human genome architecture in stable and transient gene expression changes/". More details here for the four levels of expertise we seek: Postdocs http://www.nature.com/naturejobs/science/jobs/391399-for-postdoc-position Bioinformaticians http://www.nature.com/naturejobs/science/jobs/391401-for-bioinformatician-p… Technicianshttp://www.nature.com/naturejobs/science/jobs/391403-for-technic… PhDshttp://www.nature.com/naturejobs/science/jobs/391405-for-phd-position Many thanks in advance, Marc ... *Marc A. Marti-Renom, ICREA Research Professor* *Genome Biology Group Leader - CNAG - Centre Nacional d’Anàlisi Genòmica* *Structural Genomics Group Leader - CRG - Centre de Regulació Genòmica* Parc Científic de Barcelona – Torre I Baldiri Reixac, 4, 08028 Barcelona Tel +34 9340 33743 Email _mmarti(a)pcb.ub.cat <mailto:mmarti@pcb.ub.cat>_ Web _http://marciuslab.org_ - _http://cnag.cat_ - _http://crg.cat_ *** Consider the environment. Print responsibly. ***

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[Compbio-allhands] 3/13/14 Seminar with Tim Hughes
by Flowers, Nicole 07 Mar '14

07 Mar '14

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 Tim Hughes University of Toronto Kaleidoscopic evolution of C2H2 zinc finger DNA Binding March 13, 2014 N. Krogan, 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 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: Scientist - Molecular modeller/simulator position at Novozymes
by Jacobson, Matt 06 Mar '14

06 Mar '14

Begin forwarded message: From: "Wittmann, Torsten" <Torsten.Wittmann(a)ucsf.edu<mailto:Torsten.Wittmann@ucsf.edu>> Subject: Fwd: Scientist - Molecular modeller/simulator position at Novozymes Date: March 6, 2014 10:05:51 AM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> In case you have anyone looking for jobs. Sent from my iPhone Begin forwarded message: From: "JEIN (Jens Erik Nielsen)" <JEIN(a)novozymes.com<mailto:JEIN@novozymes.com>> Date: March 6, 2014, 12:27:26 AM PST To: "JEIN (Jens Erik Nielsen)" <JEIN(a)novozymes.com<mailto:JEIN@novozymes.com>> Subject: Scientist - Molecular modeller/simulator position at Novozymes Dear All Please see the job ad below. We are looking for a talented person with a molecular modelling/simulation background who will have a big impact on the protein engineering projects that will develop new products for the world’s largest producer of industrial enzymes. http://novozymes.com/en/careers/jobs/Pages/52705.aspx Best wishes Jens ------------------------------------- Jens Erik Nielsen Senior Manager Novozymes A/S Krogshoejvej 36 2880 Bagsvaerd Denmark Phone: +45 44461692 Mobile: +45 30771692 E-mail: jein(a)novozymes.com<mailto:jein@novozymes.com> Web: www.novozymes.com<http://www.novozymes.com/> Follow Novozymes on: LinkedIn<http://www.linkedin.com/company/novozymes/> | Twitter<https://twitter.com/Novozymes/> Novozymes A/S (reg. no.:10007127). Registered address: Krogshoejvej 36 DK-2880 Bagsvaerd, Denmark This e-mail (including any attachments) is for the intended addressee(s) only and may contain confidential and/or proprietary information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information herein is strictly prohibited. If you are not an intended recipient you should delete this e-mail immediately. Thank you. 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] Seminar - Friedrich Foerster, Max Planck Institute, March 11, 2014 - 10am - GH S261
by Hilary Mahon 05 Mar '14

05 Mar '14

--- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] Fwd: Job Postings for Life Scientists
by Jacobson, Matt 04 Mar '14

04 Mar '14

Begin forwarded message: From: "Lindstaedt, Bill" <Bill.Lindstaedt(a)UCSF.EDU<mailto:Bill.Lindstaedt@UCSF.EDU>> Subject: Job Postings for Life Scientists Date: March 4, 2014 9:52:56 AM PST To: <BPSTUDENTS(a)LISTSRV.UCSF.EDU<mailto:BPSTUDENTS@LISTSRV.UCSF.EDU>> Reply-To: "Lindstaedt, Bill" <Bill.Lindstaedt(a)UCSF.EDU<mailto:Bill.Lindstaedt@UCSF.EDU>> Bio-rad (note: 2 separate positions) (1) Sr. R&D Engineer, Microfluidics department Pleasanton, California Job Description<https://biorad-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.job…> The R&D engineer will design and build new instruments, and develop control and analytical software. You will develop mechatronics and optical systems as well as microfluidic devices. You will have the opportunity to develop these instruments from the research stage through product development. Required Skills • Hands-on working knowledge of microfluidics and automated fluidics instrumentation • Detailed understanding of laminar and liquid-liquid fluid flows • Experience manipulating microliter volumes of fluid • Experience in MEMS and/ or microfluidics fabrication • Proficient with SolidWorks • Proficient in programming in Python, MATLAB or C++ • Capable of developing and executing experimental protocols, and communicating findings clearly and concisely Required Experience • Degree in Mechanical Engineering, Chemical Engineering, or equivalent field • PhD and industrial experience, or MS or BS degree with equivalent research experience --- (2) Staff Scientist, Microfluidics department Pleasanton, California Job Description<https://biorad-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.job…> The staff scientist will help to lead the biology and biochemistry efforts in the group to develop the next generation of products. This is a multidisciplinary group and we will work on a multitude of systems from nucleic acids to proteins and cells. You will devise and develop assays and work intimately with the engineering group developing instrumentation. Finally, we are growing the Digital Biology Center to be the preeminent center for droplet microfluidics research. You will be a foundational member of the group and we look forward to your influence and creativity choosing future research directions. Required Skills • A proven track record of assay design, development and implementation. • Experience with NGS sample preparation methods • Familiarty with ELISA and other protein analysis methods • Experience developing and optimizing nucleic acids protocols, such as PCR. • Experience leading other scientists. • Excellence in written and oral communication. • PhD in biology, biochemistry, Chemical Engineering, or similar field • 3-5+ years experience in industry or academia post PhD or equivalent Apply online or contact Paul Korn paul_korn(a)bio-rad.com<mailto:paul_korn@bio-rad.com> at HR for questions. D. E. Shaw Research Postdoctoral Fellow New York, New York Job Description<https://careers.deshawresearch.com/recruit/JoiningDepartment.html>; or see attachment D. E. Shaw Research is seeking postdoctoral fellows of exceptional ability to join our New York-based team. This is a unique opportunity to develop and work with transformative technology in a dynamic, interdisciplinary environment. Candidates should have expertise in computational chemistry, biology, or physics, or in a relevant area of computer science or applied mathematics. Relevant areas of experience • the study of allosteric interactions or other functionally important conformational changes in biological molecules • structure prediction or design for proteins or RNA • the study of protein–protein or protein–nucleic acid interactions • force field improvement through detailed comparisons of simulation data with NMR measurements • development and implementation of new methodology (e.g., integrators, methods for enhanced sampling or free-energy calculations, or tools to efficiently analyze large simulation datasets). Application URL: http://www.deshawresearch.com/recruit/jobs/Oncampus/UCSF/PF Either apply online or send a CV or resume to Želimir Galjanić at Zelimir.Galjanic(a)career.DEShawResearch.com<mailto:Zelimir.Galjanic@career.DEShawResearch.com>. BioCentury Publications, Inc Senior Writer San Francisco, CA or Chicago, Illinois (See attachment) BioCentury Publications Inc. is widely known as the leading provider of business intelligence about the biotechnology and pharmaceutical industries through its high value-added newsletters, conferences and research services. The company currently has openings for Senior Writers to evaluate scientific developments, clinical research, regulatory and public policy developments for their healthcare, commercial and investment impact and write about them for our publications. Requirements • 4+ years work experience or other credentials to demonstrate advanced knowledge of the topics addressed by the company’s publications and services. • ability to write complex, multi-source articles of up to 3,000 words at least six times a year that identify emerging trends and engage in interpretative, forward-looking thinking. • expected to produce an average of at least two pages of published copy per week. • The ability to write clearly and accurately in English that is correct with respect to grammar, spelling and style, within the company’s deadlines. Fluency in a language other than English is highly desirable. • The ability to think analytically, to be able to evaluate the potential outcomes of actions or events, to communicate this reasoning in writing and, where appropriate, to provide supporting numerical analysis. Experience with financial modeling is highly desirable. • News judgment, i.e., the ability to prioritize news events in order of importance for the company’s audience, and to be able to explain the reasoning behind the ranking. Please contact Susan Morgan,smorgan(a)biocentury.com<mailto:smorgan@biocentury.com> Director of HR, BioCentury Publications, Inc. Bio-rad Scientist, BioEducation R&D Hercules, CA Job Description<https://biorad-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.job…> Bio-Rad believes that the biotechnology industry should play an integral role in supporting education, helping to develop today's students as tomorrow's scientists and problem solvers. Bio-Rad's Biotechnology Explorer program (www.explorer.bio-rad.com<http://www.explorer.bio-rad.com/>) has developed a line of laboratory kits which have provided millions of students around the world the opportunity to explore the fundamental techniques of genetic engineering, DNA fingerprinting, DNA amplification, protein expression and analysis, bioinformatics, and the creation of genetically modified organisms. Required Skills • The primary job responsibility is to develop hands-on biotechnology educational kits and activities for use in teaching labs at the high school, community college and university levels. • Performing the necessary laboratory work required to develop and validate new kits, and managing the project through the new product development process. • Technically support all existing products and be an expert source for technical questions related to all of our products for both internal and external inquiries. • Have an understanding of the education market and US educational system and participate in marketing activities and is expected to interact frequently with teachers and students. • Attend and support training workshops for teachers. The job requires 10-15% time traveling to tradeshows and customer visits. Education: MS (with industry work experience) or PhD in a life science discipline. Engineering, Bioinformatics, chemistry or environmental science background is a plus. The ideal candidate will minimally have completed a life science-based doctoral graduate program or have equivalent work experience. Required Experience • Passion for science education and be excited to work as part of a dynamic, fast paced, and highly motivated team. • Have balanced laboratory skills including molecular biology, protein biochemistry, and bioinformatics analysis. • Broad knowledge base of biology and science in general • Computer programming experience is a plus • Some teaching experience; experience working with teachers to deliver new classroom content are preferred. • Product development experience in industry are highly desirable. Bryony Ruegg, PhD Business Unit Manager Biotechnology Explorer Program Bio-Rad Laboratories, Inc. Email: bryony_ruegg(a)bio-rad.com<mailto:bryony_ruegg@bio-rad.com> Nodality (note: 2 separate positions) Nodality is a start-up biotechnology company with a unique technology that reveals biological function to enable better drug development, diagnostics and patient care. We are seeking qualified applicants for the position of Scientist I/II, Research. The scope of research will address the application of flow cytometric analysis to the interrogation of immune cell signaling in the context of development of therapeutic drugs and diagnostic tests for autoimmune disorders, cancer immunotherapy and hematologic malignancies. (1) Scientist I/II, Research South San Francisco, CA (See attachment) Functions: • Apply and further develop Nodality's SCNP technology to address clinically relevant questions addressing both disease biology and drug development. • Work effectively in multidisciplinary teams including clinical and computational sciences, addressing diverse scientific and clinical questions. • Apply understanding/knowledge of signaling biology to develop SCNP assays for continued expansion of biological scope and disease-based applications. • Effectively operate within multiple projects with varied objectives and timelines. Education and Experience: • PhD in a relevant discipline (or equivalent experience if all other criteria are met);minimal 2 yrs industry experience • Understanding / knowledge of signaling biology is essential and experience in cancer immunotherapy is a plus. • Knowledge of principles of flow cytometry is essential, hands-on experience is highly desirable. • Immunological background is preferred. • Excellent verbal and written communication skills are essential. --- (2) Scientist, Bioinformatics/Data Scientist South San Francisco, CA (See attachment) Responsibilities: • Work with biologists to design experiments to answer complex biological and clinical questions in oncology, autoimmunity, and immunology • Perform a variety of data analysis tasks ranging from exploring biology to developing and validating predictive models for clinical applications • Work in cross-functional teams with research biologists, technology experts, biostatisticians, clinical scientists, and computational scientists • Use your programming skills to efficiently manage experimental data and data workflows • Contribute to development of study protocols, statistical analysis plans and reports • Explore, evaluate, and implement novel approaches and data analysis methods for interpreting biological experiments and improving processes • Present proposals and findings within and beyond your team Job Requirements: • A PhD with strong background in computational biology, biostatistics, bioinformatics, computer science, data science or related field • Knowledge of molecular and cellular biology and experience working with biological data • Knowledge of statistical and machine learning techniques • Proficiency with popular statistical packages such as R • Proficiency with Python • Understanding of database systems (SQL, MongoDB, etc.) • Knowledge of web development languages and packages such as JavaScript, D3.js is a plus Please submit your resume with cover letter to jobs(a)nodalityinc.com<mailto:jobs@nodalityinc.com>. Nodality is an equal opportunity employer. -- Thi Nguyen, PhD Program Director, Career Development Graduate Students and Postdocs Office of Career and Professional Development Student Academic Affairs University of California, San Francisco 1675 Owens St, Ste 310 San Francisco, CA 94143 Phone: 415-514-4750 career.ucsf.edu<http://career.ucsf.edu> Please schedule meetings through Celestine Fry: 415-476-4986, ocpd(a)ucsf.edu<mailto:ocpd@ucsf.edu> --- Bill Lindstaedt, MS Director Office of Career and Professional Development Student Academic Affairs University of California, San Francisco 513 Parnassus Ave., Room S-140 San Francisco, CA 94143 Phone: 415-502-2422 career.ucsf.edu<http://career.ucsf.edu> Please schedule meetings through Celestine Fry: 415-476-4986, ocpd(a)ucsf.edu<mailto:ocpd@ucsf.edu> ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BPSTUDENTS&A=1> from this mailing list. 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: Postdoc Positions Available
by Jacobson, Matt 26 Feb '14

26 Feb '14

Begin forwarded message: From: Sharon Hammes-Schiffer <shs3(a)illinois.edu<mailto:shs3@illinois.edu>> Subject: Postdoc Positions Available Date: February 26, 2014 4:17:02 PM PST To: undisclosed-recipients:; Dear Colleague, I would appreciate your help in forwarding this e-mail to potential postdoc candidates. Best regards, Sharon POSTDOCTORAL POSITIONS AVAILABLE Several postdoctoral positions are currently available in my group at the University of Illinois at Urbana-Champaign. I am particularly seeking candidates interested in working on biologically oriented projects. These projects are focused on understanding the fundamental principles underlying enzyme and ribozyme catalysis, especially the roles of electrostatics, hydrogen bonding, and protein motion. One of the current projects centers on the use of nitrile probes placed at specific sites within an enzyme to examine the electrostatic and conformational changes along the catalytic cycle via the vibrational frequency shifts. Another current project uses mixed quantum mechanical/molecular mechanical (QM/MM) free energy methods to elucidate the mechanisms of several different ribozymes. Other projects focus on proton-coupled electron transfer (PCET) in enzymes. Two relevant papers are listed below, and additional information can be found on my group web site: http://www.scs.illinois.edu/schiffer/. Interested candidates should send a CV to me at shs3(a)illinois.edu<mailto:shs3@illinois.edu>. J. Layfield and S. Hammes-Schiffer, "Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding," J. Am. Chem. Soc. 135, 717-725 (2013). A. Ganguly, P. Thaplyal, E. Rosta, P. C. Bevilacqua, and S. Hammes-Schiffer, "Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme," J. Am. Chem. Soc. 136, 1483-1496 (2014). -- Sharon Hammes-Schiffer Swanlund Professor of Chemistry Department of Chemistry University of Illinois at Urbana-Champaign A410 Chemical & Life Sciences Laboratory 600 South Mathews Avenue Urbana, IL 61801-3364 Phone: (217) 300-0335 Fax: (217) 244-3186 e-mail: shs3(a)illinois.edu<mailto:shs3@illinois.edu> http://www.scs.illinois.edu/schiffer/ 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] Stefan Boresch talk today
by Jacobson, Matt 25 Feb '14

25 Feb '14

Noon, BH212 Stefan Boresch, U. Vienna "Free energy simulations: from boring methodological work to a promising novel approach for QM/MM" http://www.mdy.univie.ac.at/en/people/boresch/boresch.html 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] 2/27/14 Seminar with Bianxiao Cui
by Nicole Takesono Flowers 21 Feb '14

21 Feb '14

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 Bianxiao Cui Stanford Light-controlled intracellular signaling pathways in cell fate determination February 27, 2014 B. Huang, 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 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: Cool Kinase Talk (hastily scheduled!) tomorrow (Friday) - 4PM - BH212
by Jacobson, Matt 20 Feb '14

20 Feb '14

-- Matt Sent from my iPad Begin forwarded message: From: James Fraser <jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com>> Date: February 20, 2014 at 6:02:33 PM PST To: "Taunton, Jack (Jack.Taunton(a)ucsf.edu<mailto:Jack.Taunton@ucsf.edu>)" <Jack.Taunton(a)ucsf.edu<mailto:Jack.Taunton@ucsf.edu>>, "Kevan Shokat" <shokat(a)cmp.ucsf.edu<mailto:shokat@cmp.ucsf.edu>>, Natalia Jura <natalia.jura(a)ucsf.edu<mailto:natalia.jura@ucsf.edu>>, "Michael Grabe" <mdgrabe(a)pitt.edu<mailto:mdgrabe@pitt.edu>>, David Sivak <david.sivak(a)gmail.com<mailto:david.sivak@gmail.com>>, "Matthew Jacobson" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>>, Jim Wells <Jim.Wells(a)ucsf.edu<mailto:Jim.Wells@ucsf.edu>>, "Lim, Wendell" <Wendell.Lim(a)ucsf.edu<mailto:Wendell.Lim@ucsf.edu>>, Tanja Kortemme <kortemme(a)cgl.ucsf.edu<mailto:kortemme@cgl.ucsf.edu>>, "Fujimori, Danica" <Danica.Fujimori(a)ucsf.edu<mailto:Danica.Fujimori@ucsf.edu>>, Fletterick Robert <flett(a)msg.ucsf.edu<mailto:flett@msg.ucsf.edu>>, Agard Dave <agard(a)msg.ucsf.edu<mailto:agard@msg.ucsf.edu>>, Robert Stroud <stroud(a)msg.ucsf.edu<mailto:stroud@msg.ucsf.edu>>, Trever Bivona <TBivona(a)medicine.ucsf.edu<mailto:TBivona@medicine.ucsf.edu>>, Mark von Zastrow <vonzastrow(a)gmail.com<mailto:vonzastrow@gmail.com>>, "Jeff Cox" <jeffery.cox(a)ucsf.edu<mailto:jeffery.cox@ucsf.edu>> Subject: Cool Kinase Talk (hastily scheduled!) tomorrow (Friday) - 4PM - BH212 Matthew Young (Prof at UMichigan, was a postdoc once upon a time with John Kuriyan) was in town for BPS. He has some cool new mechanistic stories on Kinase regulation (and also some new directions on deubiquitinase inhibitors) that you all might be interested in! The seminar will be at 4PM Friday (tomorrow) in BH212. Please forward to your labs! https://dl.dropboxusercontent.com/u/7403581/matt_young.pdf If you want to meet with Matt, let me know, he'll get to campus around 2:30-3 and be free until 4. I'm happy to direct him your way - first come first served! The plan was to grab a beer after the talk at Terzetto, to which everyone is invited. Hope to see you there! And apologies for the last minute nature of the invite, Jaime ABSTRACT: Matthew Young - University of Michigan Allosteric Regulation Of Protein Kinase Enzymes Via An Electrostatic Switch That Modulates Active Site Dynamics Protein kinase (PK) enzymes are a large family of signaling proteins that play a central role in signal transduction pathways. Robust regulation of their catalytic activity is critical, and many oncogenes harbor mutations that result in misregulated PK activity. The chemical basis for how some PK regulatory factors ultimately affect the rate of chemistry is still not completely understood. We have identified a long-range electrostatic switch that we believe is used by allosteric PK regulatory factors to modulate the rate of chemistry by tuning active-site dynamics. We applied a combination of crystallography, kinetics, and molecular dynamics to determine the chemical kinetic basis for how this electrostatic switch, toggled by regulatory subunit binding, affects each step of the catalytic cycle of CDK2 kinase. We engineered point mutants to deconstruct the kinetic, dynamic, and thermodynamic consequences of the switch. We also evaluated other PKs and find that, although it has evolved to be triggered in different ways by diverse PK regulatory factors, the mechanics of this switch can be conserved. We demonstrate that a key component of the switch is that it affects a significant change in the electrostatic potential within the ATP*Mg binding site of the enzyme. This electrostatic effect is propagated through the low-dielectric protein interior and directly affects the two dominant rate-determining steps of catalysis: attenuating both the recruitment of catalytically essential Mg cofactors (affecting both kcat and KM) as well as the release of the ADP product. Conclusion: We present a chemical hypothesis that provides a mechanistic explanation for one way that a large-scale conformation transition, observed in diverse PK family members, is able to significantly affect the rate of chemistry by acting at a distance from the active site. -- -- James Fraser, PhD Assistant Professor Department of Bioengineering and Therapeutic Sciences Office: N212C Genentech Hall, Lab: N216 Genentech Hall james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu> // jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com> (415) 493-8421 http://www.fraserlab.com

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[Compbio-allhands] Biomolecular Discovery Dome - TODAY ONLY 11:30-1:30 Byers Hall 2nd floor atrium
by Tom Ferrin 20 Feb '14

20 Feb '14

If you didn't get a chance to experience the 3D Biomolecular Discovery Dome this week at the Biophysical Society annual meeting, you've still got a chance to see it. The dome will be running in the 1st floor atrium area of Genentech Hall TODAY Feb 20th between noon and 3pm. Short videos that examine macromolecular complexes and explore datasets from electron microscopy will be shown. Co-sponsored by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI).

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[Compbio-allhands] 2/20/14 Seminar with Claudio Joazeiro
by Nicole Takesono Flowers 14 Feb '14

14 Feb '14

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 Claudio Joazeiro Scripps Listerin/Ltn1 links Co-translational Protein Quality Control and Neurodegeneration. February 20, 2014 J. Weissman, 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 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: Postdoc opportunity: design of HIV entry inhibitors
by Andrej Sali 31 Jan '14

31 Jan '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: Cameron Abrams <cfa22(a)drexel.edu> > Subject: Postdoc opportunity: design of HIV entry inhibitors > Date: January 31, 2014 at 7:49:20 AM PST > To: sali(a)salilab.org > > Dear Andrej, > > My name is Cameron Abrams and I am the director of the computational core of an NIH-P01 program project entitled "Structure-based antagonism of HIV-1 envelope function in cell entry". I have immediate need to hire a postdoc with experience in docking calculations and molecular dynamics. I have attached a description of the position to this email. I would very much appreciate it if you could let me know if any members of your group would be interested in learning more about this position. > > Thanks in advance, > Cameron > ---- > Cameron F Abrams, Professor > Department of Chemical and Biological Engineering > Drexel University, Philadelphia, Pennsylvania > t 215-895-2231

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[Compbio-allhands] 2/13/14 Seminar with Benjamin Cravatt
by Nicole Takesono Flowers 31 Jan '14

31 Jan '14

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 Benjamin Cravatt Scripps Activity-based proteomics- applications for enzyme and inhibitor discovery. February 13, 2014 C. Fitzsimmons & R. Levin, Hosts 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 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: Astex Postdoctoral Training Program
by Brian Shoichet 29 Jan '14

29 Jan '14

FYI ---------- Forwarded message ---------- From: Marcel Verdonk <Marcel.Verdonk(a)astx.com> Date: Wed, Jan 29, 2014 at 10:48 AM Subject: Astex Postdoctoral Training Program To: "bshoichet(a)gmail.com" <bshoichet(a)gmail.com> Dear Brian, I hope you are well! I wanted to bring to your attention that Astex is starting a Postdoctoral Training Program this year. This will involve a number of postdocs each year, working in and across a range of disciplines, doing cutting edge science. These are fully industrial postdocs, based at the Astex site in Cambridge, UK, with supervision provided by Astex scientists. Assuming we can get a candidate of high enough calibre, one of these postdocs will be working with me in the Astex Computational Chemistry group. We have posted an advert on the CCL web site describing the Postdoctoral Training Program, and a little bit about a possible project in computational structure-based design: http://www.ccl.net/cca/jobs/joblist/mess0028548.shtml We are looking for outstanding young scientists with a background in computational chemistry, preferably with an expertise in structure-based methods. Given your outstanding work in Computational Chemistry I wondered if you were aware of a potential candidate in your group or department who might be suitable, and to whom you could pass on this message? Best wishes, Marcel _______________________________ *Marcel Verdonk, PhD* Director, Computational Chemistry & Informatics Astex Pharmaceuticals 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 226206 Fax: +44(0)1223 226201 marcel.verdonk(a)astx.com <m.verdonk(a)astex-therapeutics.com> www.astx.com <http://www.astex-therapeutics.com> _______________________________ This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. -- Brian Shoichet, Professor http://www.uoft.bkslab.org/ University of Toronto, Leslie Dan Faculty of Pharmacy Donnelly Centre Room 604 (416) 978-7224 University of California, San Francisco Dept. of Pharmaceutical Chemistry

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[Compbio-allhands] Fwd: Group leader search FMI
by Jacobson, Matt 28 Jan '14

28 Jan '14

Begin forwarded message: From: "Gasser, Susan" <susan.gasser(a)fmi.ch<mailto:susan.gasser@fmi.ch>> Subject: Group leader search FMI Date: January 28, 2014 6:28:00 AM PST To: "'matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>'" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Cc: _DS directors office <directors.office(a)fmi.ch<mailto:directors.office@fmi.ch>> Dear Matthew, I am writing to ask your help in identifying promising candidates for tenure-track group leader positions at the Friedrich Miescher Institute in Basel, Switzerland. As you know, the FMI pursues biomedical research of a basic nature, being particularly strong in the study of neuronal circuits, epigenetics (both chromatin and small RNAs) and in mechanisms that signal and determine cell fate. With the impending retirements of two senior scientists, we have decided to expand into a new area – that of quantitative cell biology. This means we are looking for individuals trained in either physics, math or computational sciences, who address basic biological questions both computationally and experimentally. Of course, we also accept applications from biologists, but we are particularly interested in attracting persons who will probe cell physiology quantitatively, such that they can propose and test models of complex cell and/or organismal function. The research environment at the FMI is outstanding. Young group leaders are given up to 6 years before tenure evaluation, and they have a large range of efficient core facilities at their disposal. They will have sufficient funding to run a group of 4-5 scientists without raising external support. The language of the institute is English and Basel has a lively biomedical research community. The exact research topic is less critical than the energy and enthusiasm with which the candidates address their question, and their willingness to interact with other FMI research teams. The deadline for application is April 15, 2014. Applications should be submitted online at www.fmi.ch/gl_search<http://www.fmi.ch/gl_search> and enquiries can be sent to Dirk Schuebeler (dirk(a)fmi.ch<mailto:dirk@fmi.ch>) or to me. We would be grateful if you could distribute the attached flyer in your institute and among promising scientists in your field. Best wishes, Susan Professor S. M. Gasser Director of the Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 CH-4058 Basel Switzerland tel +41 61 697 7255 (assistant) tel +41 61 697 5025 (direct) fax +41 61 697 3976 susan.gasser(a)fmi.ch<mailto:susan.gasser@fmi.ch> http://www.fmi.ch/<http://www.fmi.ch%3chttp:/www.fmi.ch/> 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] 1/30/14 Seminar with Kate Carroll
by Nicole Takesono Flowers 24 Jan '14

24 Jan '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursday, 1 pm CVRI 159 **PLEASE NOTE THE TIME AND ROOM CHANGE** Kate Carroll Scripps Painting the Cysteine Chapel: New Tools to Probe Oxidation Biology January 30, 2014 B. DeGrado, Host **PLEASE NOTE THE TIME AND ROOM CHANGE** This seminar is sponsored by Novartis. 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: Grabe lab post-doc candidate
by Jacobson, Matt 22 Jan '14

22 Jan '14

-- Matt Sent from my iPhone Begin forwarded message: From: "Grabe, Michael" <Michael.Grabe(a)ucsf.edu<mailto:Michael.Grabe@ucsf.edu>> Date: January 22, 2014, 4:02:52 PM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: Grabe lab post-doc candidate Hi Matt, I have a post-doc candidate, David Argudo, interviewing this Friday from Penn. His background is in the mechanical behavior of DNA under force. Please feel free to share the information on his talk with your group - they are more than welcome to attemd if the topic is of any interest. Cheers, Michael Speaker: David Argudo, University of Pennsylvania, Department of Mechanical Engineering (post-doc candidate in Grabe Lab) Presentation Title : "The Mechanical Response of DNA: Twisting the Molecule" Time: 10:30 am Friday January 24th, 2014 Room: 342 Smith Building (3rd floor) Abstract: Since the structure of double stranded DNA was discovered about six decades ago, there have been great developments in the fields of biology, genetic engineering, molecular biology, biophysics and numerous others. It is the objective of our work to carry on with these developments by providing new insights and understanding of DNA behavior/function using mechanics as our primary tool. To achieve this goal we focus on building analytical models for DNA molecules using rod theory and statistical mechanics. We model a key experiment in which a tensile force is applied on the DNA while simultaneously twisting it using optical or magnetic tweezers. In these experiments, DNA has been seen to form helical structures (supercoils), collapse into tightly condensed structures (toroids) and undergo structural changes (phase transitions). Our work focuses on studying all these phenomena by accounting for DNA elasticity, entropic effects due to thermal fluctuations and electrostatics. ------------------------------------------------------------------- Michael Grabe Associate Professor University of California, San Francisco Cardiovascular Research Institute Department of Pharmaceutical Chemistry 555 Mission Bay Blvd South, Room 452T, MC 3122 San Francisco, California 94158-9001

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[Compbio-allhands] Fwd: 5 year post-doctoral fellowship in Medical Image Analysis
by Tom Ferrin 21 Jan '14

21 Jan '14

-------- Original Message -------- Subject: 5 year post-doctoral fellowship in Medical Image Analysis Date: Tue, 21 Jan 2014 23:58:17 +0000 From: Bob Fisher <rbf(a)inf.ed.ac.uk> To: tef(a)cgl.ucsf.edu 5 year post-doctoral fellowship in Medical Image Analysis The University of Edinburgh is advertising a number of 5 year fellowships that are expected to evolve into open ended tenured positions. Of particular interest to this email are applicants in Medical Image Analysis However, the School of Informatics is also looking for applicants in Algorithms for Big Data and distributed Systems, Cryptography, Automated reasoning, Cyber-security, Robotic hardware control, Geo-location and modelling of natural systems, Data-intensive biomedicine, Analysis of gene regulation data and data-driven modelling of gene networks controlling neural development, Design with data, Data-intensive social systems The advertisement is below. Closing date 7 February 2014 (5pm). Candidates likely to be considered for interview will already have a PhD and several publications in quality journals or top conferences. Best wishes, Bob ================================================================ Chancellor's Fellowships: Informatics University of Edinburgh - School of Informatics 37,756 - 45,053 GBP College of Science and Engineering The University of Edinburgh, a global top 20 University located in one of the world`s finest cities, continues to invest in the future of its academic staff with the appointment of a cohort of 50 tenure-track Chancellor's Fellowships across all disciplines. These 5-year Fellowships are intended to support candidates at the start of their independent academic careers. Subject to satisfactory review at the end of year 3, the Fellow will then move to a standard University academic open-ended contract. It is anticipated that most appointees will be successful in obtaining an open ended contract. Our people have been making their mark on the world for more than four centuries. They've explored space, revolutionised surgery, won Nobel Prizes, published era-defining books, paved the way for life-saving medical breakthroughs and laid the foundations for solving the mysteries of the universe. We are looking for highly talented academics who will contribute to our continued achievement of excellence in research. Colleagues addressing data intensive research are encouraged. You will already be working in an independent research capacity and will be developing your reputation for high quality research. Chancellor's Fellows also make an important contribution to enriching student learning experiences through their research, teaching and personal tutoring. You will concentrate on research initially, but will be trained in teaching skills and progressively take up this core academic activity. As we are a global University, we are interested in candidates from any location and we can offer relocation support. The culture of the University is open and diverse and we strive to replicate that in our appointments. Whilst we are proud of our rich heritage, we are a University that looks to the future. We are a global University with world leading interdisciplinary research capability, ideal for collaborative work as required. By joining our research-led community of international academics you will enjoy excellent career opportunities and support. Appointment will normally be made on the Grade 8 Academic scale (37,756-45,053 GBP), dependent on experience. In exceptional circumstances a more senior appointment may be made. This is an excellent opportunity to be part of one of the world's top Universities where you will develop your career in a stimulating, friendly and diverse environment that nurtures talent and rewards success. We welcome applications from everyone irrespective of gender or ethnic group. As women and members of ethnic minorities are currently under-represented in posts at this level we particularly encourage applications from members of these groups. For more information visit our website https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.disp… Closing date: 7 February 2014 (5pm). Committed to Equality and Diversity The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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[Compbio-allhands] Fwd: Novartis Symposium on Novel Approaches to Therapeutics and Targets - January 30th
by Jacobson, Matt 21 Jan '14

21 Jan '14

-- Matt Sent from my iPhone Begin forwarded message: From: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Date: January 21, 2014, 11:55:41 AM PST To: <BBCFACULTY(a)LISTSRV.UCSF.EDU<mailto:BBCFACULTY@LISTSRV.UCSF.EDU>> Subject: Novartis Symposium on Novel Approaches to Therapeutics and Targets - January 30th Reply-To: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Please join us for the Novartis Symposium on Novel Approaches to Therapeutics and Targets. Speakers include Eric Martin and Cindy Shafer of Novartis and Kate Carroll from the Scripps Research Institute. See the attached flyer for more details. Thursday, January 30th 9:00 am - 2:00 pm Smith Cardiovascular Research Building Room 159 **Please note, Kate Carroll’s BBC Seminar Series talk will be from 1-2pm in CVRI Rm 159 and NOT in Byers Auditorium at 12pm. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ About the invited speakers: Eric Martin is Director of Computational Chemistry at Novartis. He is credited with having started the field of combinatorial library design in the early 90s. Over the past 25 years he has worked in computational chemistry, analytical instrument development, environmental-fate modeling, drug design and herbicide design. His recent research includes the development of three novel kinase virtual screening methods, which he has combined with experimental IC50 and structural data to screen 4 million compounds across the entire kinome achieving unprecedented speed and accuracy. Cindy Shafer is a Project Leader in the Global Discovery Chemistry Group at Novartis. While at Novartis, she has worked on oncology, diabetes and anti-viral programs from the hit-to-lead stage through lead optimization. Several of these programs have progressed to the clinic including TKI258/dovitinib (Ph III), HSP990 and the mutant-b-Raf inhibitors RAF265 and LGX818 (Ph III). In addition, she has led several early stage programs to develop tool compounds to further elucidate the biological relevance in oncology settings. Kate Carroll is an Associate Professor of Chemistry at The Scripps Research Institute, Florida Campus. Her research focuses on the role of oxidative thiol modifications in the dynamic regulation of signaling pathways and physiological processes. Her work includes the development of chemical probes and proteomic technologies for the dissection of redox signaling pathways. Recently she has applied these tools to the global analysis of sulfenic acid modified proteins for the identification of signaling networks regulated by cysteine oxidation. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We thank Novartis, CVRI and UCSF BBC Graduate Groups for their participation and generous financial support. Julia Molla UC San Francisco Program Coordinator, Biological& Medical Informatics and Chemistry& Chemical Biology 600-16th St. MC2280 San Francisco, CA 94158-2517 415-476-1914 phone ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BBCFACULTY&A=1> from this mailing list.

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[Compbio-allhands] Fwd: Post-doc with Rhoades and Miranker
by Andrej Sali 20 Jan '14

20 Jan '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: Andrew Miranker <Andrew.Miranker(a)YALE.EDU> > Subject: Post-doc with Rhoades and Miranker > Date: January 20, 2014 at 8:37:04 AM PST > To: Andrej Sali <sali(a)salilab.org> > > Dear Andrej, > > I am looking to recruit a post-doc in the near future for a position joint between myself and the lab of > Prof Liz Rhoades. I've attached a job-ad below. > Please encourage your graduating students to send me an application and/or come find Prof Rhoades > or myself at the Biophysical Society Meeting next month. > > Sincerely, > > Andrew > > > Andrew Miranker > Professor | Office: (203) 432-8954 > Dept of Molecular Biophysics & Biochemistry | Lab: (203) 432-5563 > Yale University | Assistant: (203) 432-5708 > 266 Whitney Avenue / Bass 318 | Fax: (203) 432-8492 > PO Box 208114 | Email: andrew.miranker(a)yale.edu > New Haven, CT 06520-8114 | Web: www.yale.edu/miranker/ > > **Please note. This is my professional email address and as such is read and > managed by my assistant, Lisa Adams (lisa.adams(a)yale.edu) >

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[Compbio-allhands] postdoc jobs ad in Singapore
by Andrej Sali 17 Jan '14

17 Jan '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

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[Compbio-allhands] Fwd: Reminder for TDT competition
by Jacobson, Matt 12 Jan '14

12 Jan '14

-- Matt Sent from my iPhone Begin forwarded message: From: Hanneke Jansen <hanneke(a)tdti.org<mailto:hanneke@tdti.org>> Date: January 12, 2014, 3:10:08 PM PST To: "'Jacobson, Matt'" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: Reminder for TDT competition Dear Matt, A quick reminder that the deadline for the second round of the TDT competition is coming up! There are four exciting challenges that focus on developing and disseminating computational workflows for drug discovery of neglected diseases with a premium on reproducibility (use freely available software tools!). Note that one of these challenges is an open innovation challenge which is a great place to submit truly novel workflows that can be exemplified on any publicly available dataset. The other three challenges are structured around specific questions with held-out test data to compare across the various submissions. Three cash prizes - plus partial reimbursement of travel - will be awarded! Winners are required to present their work at the TDT Award symposium during the Fall 2014 ACS National Meeting in San Francisco, California. Detailed information about the 2014 Competition can be found here: http://www.TDTproject.org/2014-competition.html Submissions deadline is February 3, 2014. Please remind people in your group and let me know if there are any questions. Ciao, Hanneke ++++++++++++++++++++++++++ Hanneke Jansen Hanneke(a)TDTi.org<mailto:Hanneke@TDTi.org> 415.336.3036 (cell)

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[Compbio-allhands] 1/16/14 Seminar with Kevin Healy
by Flowers, Nicole 10 Jan '14

10 Jan '14

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 Kevin Healy UC Berkeley Disease-Specifric Microphysiological Human Organ Models: the Future of Personalized Medicine? January 16, 2014 B. Conklin, 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: Very Exciting Postdoctoral Position Available
by Andrej Sali 09 Jan '14

09 Jan '14

Sent from my iPhone Begin forwarded message: > From: Klaus Schulten <kschulte(a)ks.uiuc.edu> > Date: January 9, 2014 at 1:25:50 PM PST > To: mike.himmel(a)nrel.gov, michael.crowley(a)nrel.gov, smithjc(a)ornl.gov, rwoods(a)ccrc.uga.edu, fsl+3(a)psu.edu, skaf(a)iqm.unicamp.br, ipolikarpov(a)ifsc.usp.br, pascutti(a)biof.ufrj.br, olson(a)scripps.edu, ramaro(a)ucsd.edu, jmccammon(a)ucsd.edu, sali(a)salilab.org, daggett(a)uw.edu, jonuchic(a)rice.edu, tolya(a)rice.edu, jpma(a)bcm.tmc.edu, cecilia(a)rice.edu, mpettitt(a)utmb.edu, brookscl(a)umich.edu, brb(a)mail.nih.gov, feig(a)msu.edu, tom.cheatham(a)pharm.utah.edu, case(a)biomaps.rutgers.edu, mlklein(a)temple.edu, twoolf(a)jhu.edu, thirum(a)umd.edu, pande(a)stanford.edu, haw2002(a)med.cornell.edu, Elizabeth.rhoades(a)yale.edu, tieleman(a)ucalgary.ca, treptow(a)unb.br, s.j.marrink(a)rug.nl, mv245(a)cam.ac.uk, g-schatz(a)northwestern.edu, bahar(a)pitt.edu, jerome.henin(a)ibpc.fr, david.perahia(a)lbpa.ens-cachan.fr, grace.brannigan(a)rutgers.edu, matteo.dalperaro(a)epfl.ch, wah(a)bcm.edu, roberto.lins(a)ufpe.br, thereza.soares(a)ufpe.br, mark.sansom(a)bioch.ox.ac.uk, cui(a)chem.wisc.edu, hgrubmu(a)gwdg.de, laio(a)sissa.it, dennis.salahub(a)ucalgary.ca, modesto.orozco(a)irbbarcelona.org, straub(a)bu.edu, itamar(a)ime.eb.br, schlick(a)nyu.edu, amackere(a)rx.umaryland.edu, rbb24(a)cam.ac.uk, pastorr(a)nhlbi.nih.gov, ddmmzz(a)pitt.edu, andricio(a)umich.edu, cbp(a)purdue.edu, roux(a)uchicago.edu, dinner(a)uchicago.edu, gavoth(a)uchicago.edu, vandervaart(a)asu.edu, chapmami(a)ohsu.edu, dabaker(a)uw.edu, gianni.defabritiis(a)upf.edu, p.g.bolhuis(a)uva.nl, christoph.dellago(a)univie.ac.at, erik.lindahl(a)scilifelab.se, Lennart.Nilsson(a)ki.se, stefan.fischer(a)iwr.uni-heidelberg.de, bgroot(a)gwdg.de, gerhard.hummer(a)biophys.mpg.de, caflisch(a)bioc.uzh.ch, takada(a)biophys.kyoto-u.ac.jp > Subject: Very Exciting Postdoctoral Position Available > > Dear Colleagues, > > > The Theoretical and Computational Biophysics Group of the University of Illinois is seeking applications for a postdoctoral research associate position in theoretical biophysics. > > The position is funded by the Energy Biosciences Institute (www.energybiosciencesinstitute.org) to guide through molecular dynamics simulations the development of enzymes needed in second generation biofuel production. These biofuels are made from degradation of agricultural waste, e.g., of wood chips, a process which involves use of redesigned bacterial enzymes. The redesign aims at preventing inhibition of the used enzymes by process products and at enhancing efficiency. The work will be performed in collaboration with experimentalists both at the University of California – Berkeley and at the University of Illinois Urbana-Champaign. The postdoc will interact with first rate researchers in polymer science, bacteriology, plant science and bioengineering and be involved in starting an exciting, completely new research area. Pursuing in connection with biofuel studies bacterial degradation of biomass in general will be encouraged. The new postdoc will join another Energy Biosciences Institute postdoc in my group and will enjoy a well equipped research laboratory and intense research team. > > More information is available in our website (http://tcbg.illinois.edu) and also in the attached announcement. > > Please feel free to share this announcement. > > Best regards, > > Klaus Schulten >

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[Compbio-allhands] Fwd: Happy New Year and hiring at new company
by Jacobson, Matt 09 Jan '14

09 Jan '14

Job opportunity ... Begin forwarded message: I’ve recently moved from Amazon because this is a compelling opportunity. IO is the global leader in software-defined data centers, and has pioneered the next-generation of data center infrastructure technology and Intelligent Control. We are a mature startup with over 600 clients, including for example Goldman Sachs. The Applied Intelligence team in San Francisco uses predictive modeling, analytics and simulation to impact both design and intelligent control. Are there any great people that spring to mind? I will attach the two job descriptions and may I ask you to let people know about the opportunity? Thank you and I’d love to catch up soon, Jim James Arnold, Ph.D. | Director Applied Intelligence Software M +1.415.216.5655 E jarnold(a)io.com<mailto:jarnold@io.com> | www.io.com<http://www.io.com> The communication contained in this e-mail is confidential and is intended only for the named recipient(s) and may contain information that is privileged, proprietary, attorney work product or exempt from disclosure under applicable law. If you have received this message in error, or are not the named recipient(s), please note that any form of distribution, copying or use of this communication or the information in it is strictly prohibited and may be unlawful. Please immediately notify the sender of the error, and delete this communication including any attached files from your system. Thank you for your cooperation. 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: Lunenfeld Tanenbaum Research Institute PI Search
by Andrej Sali 08 Jan '14

08 Jan '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: Donna Doherty <doherty(a)lunenfeld.ca> > Subject: Lunenfeld Tanenbaum Research Institute PI Search > Date: January 8, 2014 at 11:30:30 AM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Professor Sali, > > Please find enclosed information related to recruitment of scientists at the Lunenfeld Tanenbaum Research Institute at Mt. Sinai Hospital. Please feel free to forward this information to your colleagues. > > Sincerely, > > > Donna Doherty on behalf of Professors Jim Woodgett, Dan Durocher, and Daniel Drucker >

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[Compbio-allhands] 1/9/14 Seminar with Wah Chiu
by Nicole Takesono Flowers 06 Jan '14

06 Jan '14

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 Wah Chiu Baylor College of Medicine Structures of Viruses Inside and Outside the Host Cells January 9, 2014 Y. Cheng, 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] Mini-course: Information Theory and Biology
by David Sivak 03 Jan '14

03 Jan '14

Hi. You ever noticed how people around here use the word "Information" like it's going out of style? You ever wondered what's the big deal? We (David Sivak, Raj Bhatnagar, Michael Chevalier) plan on getting to the heart of all that in a mini-course at Mission Bay this spring on "Information Theory and Biology." If you have any interest in possibly taking this mini-course, please help us get a sense of numbers and backgrounds by sharing a little information [sorry] about yourself at: https://docs.google.com/forms/d/1HtENxOKiXyZXyzq9-4zoK0qWpTklQHLPpZC-UKqQYA… Feel free to pass along to other interested parties. Apologies for any mailing list duplication... Thanks, David -- David Sivak Systems Biology Fellow University of California, San Francisco david.sivak(a)gmail.com davidsivak.com 510-541-9006

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[Compbio-allhands] SAVE THE DATE- PETER A. KOLLMAN LECTURESHIP - April 3, 2014
by Nicole Takesono Flowers 20 Dec '13

20 Dec '13

SAVE THE DATE- THURSDAY, APRIL 3, 2014 AT 12:00 PM PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS LIBRARY 221 Reception in Byers Hall 5th Floor Lounge at 3:30 Please see attached flyer. 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] Peter Kolb Seminar - Thursday, Dec. 12 - 10am - Byers Hall 212
by Hilary Mahon 10 Dec '13

10 Dec '13

Please see attached. Thank you. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] BBC Seminar Speaker David Allis Talk CANCELLED
by Nicole Takesono Flowers 05 Dec '13

05 Dec '13

Please note that Dr. Allis had to cancel his previously scheduled talk (1/16/14) for the BBC Seminar Series. 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] Janet Thornton Seminar: Thurs., Dec. 5
by Patsy Babbitt 01 Dec '13

01 Dec '13

Please add to your calendars a special seminar by Janet Thornton: "The Evolution of Enzyme Mechanisms and Functional Diversity" Thursday, December 5th, 2013 3:00 – 4:00 PM Genentech Hall Auditorium Professor Dame Janet Thornton is the Director of the European Molecular Biology Laboratory — European Bioinformatics Institute (EMBL-EBI). She has been a leader in computational biology and bioinformatics throughout her career and has be awarded many honors, among them her election as a Fellow of the Royal Society and as a foreign associate of the National Academy of Sciences. >From her biography on Wikipedia, she is rightfully described as "one of the world’s leading researchers in structural bioinformatics, using computational methods to understand protein structure and function." Don't miss it! (Hosted by Patsy Babbitt) -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences 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] Fwd: Faculty positions in computational biology at the University of Rochester
by Jacobson, Matt 23 Nov '13

23 Nov '13

-- Matt Sent from my iPad Begin forwarded message: From: Sina Ghaemmaghami <sghaemma(a)bio.rochester.edu<mailto:sghaemma@bio.rochester.edu>> Date: November 22, 2013 9:18:43 AM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: Faculty positions in computational biology at the University of Rochester Dear Matt, I hope everything is going well with you. At the University of Rochester, we have undertaken a Data Science initiative. As part of that initiative, we are having tenure track job searches this year for individuals using computational approaches to investigate cross-disciplinary topics. One of the identified target areas is Computational Biology and Computational Bioengineering, e.g. functional and evolutionary genomics, proteomics and protein folding, systems biology, multi-scale modeling in bioengineering, or multimodal bio-imaging informatics. I am contacting you to see if you know of candidates on the job market (e.g. promising postdocs or already established researchers) who you could recommend, or let them know about this job search. An emphasis here would be on individuals for whom computational approaches are a key part of their research. Attached is the job description with information on how to apply, and please feel free to circulate this among your colleagues. Further information on the Data Science initiative and instructions for this search can be found at: http://www.rochester.edu/rocdata/recruit/interdisciplinary.html. The search is open to senior level candidates. So, if you know of someone who may be interested, please let me know. Sincerely, Sina Ghaemmaghami Department of Biology, University of Rochester 326 Hutchison Hall Rochester NY 14627 Tel (office): 585-275-4829 Tel (cell): 415-992-2594

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[Compbio-allhands] from Hanneke Jansen
by Jacobson, Matt 20 Nov '13

20 Nov '13

Forwarding ... ------------ Teach-Discover-Treat (TDT) is excited to announce our 2014 Competition. We have four exciting challenges that focus on developing and disseminating computational workflows for drug discovery of neglected diseases with a premium on reproducibility. Three cash prizes - plus partial reimbursement of travel - will be awarded! Winners are required to present their work at the TDT Award symposium during the Fall 2014 ACS National Meeting in San Francisco, California. Create and submit computational workflows that inspire drug discovery activities using freely available software tools. Detailed information about the 2014 Competition can be found here: http://www.TDTproject.org/2014-competition.html Submissions deadline is February 3, 2014. The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell, Patrick Walters and Emilio Xavier Esposito www.TDTproject.org<http://www.tdtproject.org/> twitter.com/TeachDiscoTreat<http://twitter.com/TeachDiscoTreat>

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[Compbio-allhands] Fwd: FINAL CALL: Faculty positions in Bioinformatics/Computational Biology in the Crick at LRI
by Andrej Sali 17 Nov '13

17 Nov '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: Nicholas Luscombe <nick(a)valleyofpigs.org> > Subject: FINAL CALL: Faculty positions in Bioinformatics/Computational Biology in the Crick at LRI > Date: November 15, 2013 at 2:40:52 AM PST > To: Paul Nurse <paul.nurse(a)royalsociety.org> > Cc: Richard Treisman <richard.treisman(a)cancer.org.uk>, Jim Smith <director(a)nimr.mrc.ac.uk>, Paul Nurse <paul.nurse(a)royalsociety.org> > > Dear Colleagues, > > Thank you for your help in circulating information about the Bioinformatics/Computational Biology position at the Crick@LRI. We’ve had a lot of interest and we’re hoping that many will result in applications! > > I would like to remind you that the deadline is 22 November 2013; I should be grateful if you would continue to spread the word. > > With many thanks for your support, > > Nick Luscombe > > > Website: http://tinyurl.com/ohgnxw8 > Application deadline: 22 November 2013 > Informal enquiries may be made by e-mail to nicholas.luscombe(a)cancer.org.uk > > --- > > Faculty positions for Bioinformatics and Computational Biology > Francis Crick Institute group leaders at the CRUK London Research Institute > > An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis. > > The Francis Crick Institute http://www.crick.ac.uk > The Francis Crick Institute will open at St Pancras in central London in 2015. Its research will use interdisciplinary approaches to investigate the biology of human health and disease, supported by core funding from CRUK, the MRC, and the Wellcome Trust, and by grants from UK and international funding agencies. > > The Crick is expanding Computational Biology research as a key component of its scientific strategy. The institute will offer an outstanding environment for computational research, with excellent opportunities for wet/dry collaborations across the range of biomedical and clinical research disciplines, supported by a strategic alliance with the Wellcome Trust Sanger Institute. The new Crick laboratories will feature excellent computational facilities including a state-of-the-art data centre. > > The London Research Institute http://www.london-research-institute.org.uk > The London Research Institute (LRI) is the largest Cancer Research UK research institute, with 40 research groups focusing on fundamental cancer biology. The Institute is based in well-equipped laboratories at Lincoln's Inn Fields in central London, and at Clare Hall in Hertfordshire. > > Computational Biology in Cancer http://tinyurl.com/ohgnxw8 > An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis. The LRI recruitment process for 2013 will carried out jointly with the Crick Institute. We shall appoint outstanding scientists seeking to establish independent and innovative research programmes focussed on: > > Newly appointed group leaders will receive core funding for research personnel, travel and consumables, and access to the Institute's comprehensive computational core facilities, backed by competitive employment terms. The new group leaders will move to the Crick laboratories in 2015. > > Website: http://tinyurl.com/ohgnxw8 > Application deadline: 22 November 2013 > Informal enquiries may be made by e-mail to nicholas.luscombe(a)cancer.org.uk > > > --- > Check out our new website: www.luscombelab.org > > Nicholas M LUSCOMBE, Professor of Computational Biology > > University College London (joint appointment) > UCL Genetics Institute, Dept of Genetics, Evolution & Environment, > University College London, Gower Street, London WC1E 6BT, UK > > Cancer Research UK London Research Institute (joint appointment) > 44 Lincoln's Inn Fields, London WC2A 3LY, UK > > Okinawa Institute of Science & Technology (adjunct faculty) > 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan > > > > > >

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[Compbio-allhands] 11/21/13 Seminar with Dana Pe'er
by Nicole Takesono Flowers 15 Nov '13

15 Nov '13

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 Dana Pe'er Columbia What can you do with 40 dimensions in single cells, mapping development, signal processing and disease? November 21, 2013 W. 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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[Compbio-allhands] Fwd: Computational and Systems Biology Positions at the Genome Institute of Singapore
by Tom Ferrin 14 Nov '13

14 Nov '13

-------- Original Message -------- Subject: Computational and Systems Biology Positions at the Genome Institute of Singapore Date: Thu, 14 Nov 2013 19:15:30 +0800 From: Tara Leah HUBER (GIS) <hubertl(a)gis.a-star.edu.sg> CC: Shyam PRABHAKAR (GIS) <prabhakars(a)gis.a-star.edu.sg>, Niranjan NAGARAJAN (GIS) <nagarajann(a)gis.a-star.edu.sg> Dear Colleague, We have some immediate Faculty openings in Computational and Systems biology at the Genome Institute of Singapore. Applicants with computational expertise in all areas and at all levels are welcome; areas of particular interest include: Regulatory Genomics and Epigenomics, Microbial Evolution and Metagenomics, Systems Biology and Cancer Genomics. Applicants should submit a CV, a statement of research interests and the names of three references by email (with job code "CSB-I" in the subject line) to: gisrecruit(a)gis.a-star.edu.sg <mailto:gisrecruit@gis.a-star.edu.sg> We are seeking outstanding researchers with the potential to establish impactful, independent and creative research programs at the GIS. Candidates are expected to have significant experience in the analysis of genome-wide/cell-wide biological datasets and to have demonstrated exceptional originality and excellence in their work. We would appreciate if you would share this information with your colleagues and bring it to the attention of any qualified candidate for these positions. With best regards, Niranjan and Shyam Niranjan Nagarajan Group Leader Associate Director, Computational and Systems Biology Shyam Prabhakar Group Leader Associate Director, Integrative Genomics Genome Institute of Singapore 60 Biopolis Street, #02-01 Genome, Singapore 138672 Tel: +65 6808 8071 (Niranjan Nagarajan) +65 6808 8046 (Shyam Prabhakar) http://www.gis.a-star.edu.sg ------------------------------- This e-mail and any attachments are only for the use of the intended recipient and may be confidential and/or privileged. If you are not the recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person as it may be an offence under the Official Secrets Act. -------------------------------

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[Compbio-allhands] Fwd: Institute for Genomic Biology Fellowship
by Andrej Sali 13 Nov '13

13 Nov '13

Begin forwarded message: > From: Taekjip Ha <TaekjipHa(a)mx.uillinois.edu> > Subject: Institute for Genomic Biology Fellowship > Date: November 13, 2013 at 10:03:13 AM PST > > > Dear colleagues, > > I wanted to bring to your attention an exciting postdoctoral fellows program at the University of Illinois at Urbana-Champaign. The Institute of Genomic Biology (IGB) opened its $70 M building in 2007 and is research home to dozens of world-class scientists. The IGB Fellows program appoints several new fellows each year through theme-based competition. For the Cellular Decision Making in Cancer Theme that I am involved with, the first two fellows became professors in Princeton and UIUC, both winning the NIH new innovators awards, just to give you some examples of the excellence of the program. This year’s application deadline is December 1st and I am attaching an ad that ran on Science magazine. The link below points to the application site which also shows a nice video about the virtue of living in Champaign-Urbana among other things. Please share this exciting opportunity with your young colleagues. > > http://www.igb.illinois.edu/education/igb-fellows > > Best wishes, > Taekjip Ha

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[Compbio-allhands] Fwd: Two junior group leader positions at the CRG (Barcelona)
by Andrej Sali 09 Nov '13

09 Nov '13

Sent from my iPhone Begin forwarded message: > From: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Date: November 9, 2013 at 8:11:26 AM PST > To: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Cc: Juan Valcarcel Juarez <juan.valcarcel(a)crg.eu> > Subject: Two junior group leader positions at the CRG (Barcelona) > > Dear friends, > > I would appreciate if you could forward this e-mail to whom you may think could be interested in a Junior Group Leader position at CRG in Barcelona. > > Additional information in the attached PDF. > > Many thanks in advance, > Marc > > > > ... > Marc A. Marti-Renom, ICREA Research Professor > Genome Biology Group Leader - CNAG - Centre Nacional d’Anàlisi Genòmica > Structural Genomics Group Leader - CRG - Centre de Regulació Genòmica > Parc Científic de Barcelona – Torre I > Baldiri Reixac, 4 > 08028 Barcelona > Tel +34 9340 33743 > Email mmarti(a)pcb.ub.cat > Web http://marciuslab.org - http://cnag.cat - http://crg.cat > > *** Consider the environment. Print responsibly. *** >

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[Compbio-allhands] Fwd: Postdoctoral opportunities at Princeton
by Andrej Sali 07 Nov '13

07 Nov '13

Sent from my iPhone Begin forwarded message: > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Date: November 7, 2013 at 1:47:15 PM PST > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Subject: Postdoctoral opportunities at Princeton > > Dear Colleagues, > > In an effort to attract the strongest possible candidates, we are extending our annual search for young theorists interested in problems at the interface of physics and biology, broadly interpreted. Princeton offers a very interactive community, with a nearly unique combination of theoretical mentors and friendly experimental collaborators. We have been fortunate so far in attracting a steady stream of wonderful postdoctoral scholars. We would like to continue this pattern, and ask for your further help in pointing a few more excellent new candidates in our direction. Thank you in advance for your willingness to contribute to this effort. > > We have extended the deadline for applications and letters another week, to November 15th. > > For more details, please see http://www.princeton.edu/physics/about/employment/biophysics/index.xml > > Best wishes, > > William Bialek > Chase Broedersz > Curtis Callan > Benjamin Machta > 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: POSTDOCTORAL POSITION IN COMPUTATIONAL NEUROSCIENCE AT ENS, PARIS
by Andrej Sali 07 Nov '13

07 Nov '13

Sent from my iPhone Begin forwarded message: > From: "Rava A. da Silveira" <rava(a)ens.fr> > Date: November 6, 2013 at 9:27:17 PM CST > To: "Rava A. da Silveira (Me)" <rava(a)ens.fr> > Subject: POSTDOCTORAL POSITION IN COMPUTATIONAL NEUROSCIENCE AT ENS, PARIS > > Dear colleague, > > Would you be so kind as to forward the postdoc ad pasted below to > potential candidates? > > Many thanks, and best regards, > > Rava > (Apologies for multiple postings.) > > ********* > > POSTDOCTORAL POSITION available in the group of RAVA AZEREDO DA > SILVEIRA at the ECOLE NORMALE SUPERIEURE, Paris > > This position will be devoted, in part, to the analysis and modeling > of exciting retina data sets from the labs of Botond Roska (FMI) and > Andreas Hierlemann (ETH). Experience with data analysis and > proficiency with numerical methods and programming, in addition to > familiarity with neuroscience topics and mathematical and statistical > methods, are desirable. In addition, research may be pursued on > problems of single-cell and network dynamics, neural coding, or > cognitive and behavioral modeling (inference, sensory integration, > decision making, etc), with more or less connection with data > depending upon the specific problem. Thus, a spirit of intellectual > adventure and eagerness is at least as desirable. > > The ENS, together with a number of neighboring institutions (College > de France, Institut Curie, ESPCI, Universités Paris 5, 6, and 7, and > Institut Pasteur), offers a rich scientific and intellectual > environment, with a strong representation in computational > neuroscience and related fields. Furthermore, as far as cities go, > Paris is not bad. > > The postdoctoral salary will be supplemented by travel and equipment funds. > > To apply, please send a letter of motivation and statement of > research, a curriculum vitae, a list of publication, and arrange for > three letters of recommendations to be sent, to rava(a)ens.fr. Reviewing > of the applications with start on 25 November 2013.

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[Compbio-allhands] Fwd: opening at Principia Biopharma
by Jacobson, Matt 05 Nov '13

05 Nov '13

Begin forwarded message: From: Ken Brameld <ken.brameld(a)principiabio.com<mailto:ken.brameld@principiabio.com>> Subject: opening at Principia Biopharma Date: November 5, 2013 10:31:24 AM PST To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, We met briefly at the Frontiers in Medicinal Chemistry meeting this past June. Things continue to go will at Principia and we are expanding. I have an opening for a recent PhD or postdoc in comp chem/chem informatics. The ideal candidate will be an enthusiastic and self-motivated individual who is seeking a position with the potential to broadly influence the efficiency and outcome of discovery research at Principia. The job description is attached. Would you mind circulating this to your group or to anyone you feel may be interested and qualified? Kind regards, -Ken Ken Brameld, Ph.D. Executive Dir., Research Technologies Principia Biopharma 650-416-7714 ken.brameld(a)principiabio.com<mailto:ken.brameld@principiabio.com> This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto. 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] Dr. James Petersson Talk, 11/5/13 10:00 am
by Flowers, Nicole 04 Nov '13

04 Nov '13

Dr. James Petersson, University of Pennsylvania, Department of Chemistry Tuesday, November 5 – 10 AM, RH-102, Pottruck Auditorium Thioamides: Minimalist chromophores for monitoring protein folding and stability Abstract: Our laboratory is developing new tools to understand protein folding, conformational changes, and proteolysis. We have recently shown that the thioamide - a single-atom substitution of the peptide backbone - can be used as a probe to monitor structural changes in proteins by quenching fluorophores, including the natural amino acids tryptophan and tyrosine, and several unnatural amino acids. We have developed methods for incorporating the thioamides into full-sized proteins by chemically synthesizing peptides containing the thioamides, and ligating them to proteins expressed in E. coli cells. Donor fluorophores can be incorporated into the cellularly-expressed fragment using unnatural amino acid mutagenesis or post-expression labeling, so that double-labeled proteins can be generated with a minimum of unnecessary peptide synthesis. Development of these methods allows us to begin study of the role of protein motion in processes such as cell signaling and amyloid diseases. We have alsoadapted our fluorophore/thioamide pairs to make probes of proteolysis, using the minimally-perturbing nature of the thioamide to investigate cleavage at specific sequences. We have used these tools in vitro, and we are working to extend them to use in lysates and living cells. 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] FREE Laser Toner Cartridges
by babbitt 28 Oct '13

28 Oct '13

The Babbitt lab is giving away four unused toner cartridges: HP-96A (part #C4096A). These cartridges fit HP LaserJet Series 2100/2200* (really old) printers. Please contact Joslyn Polzien atjoslyn.polzien(a)ucsf.edu<mailto:%20joslyn.polzien@ucsf.edu> if you are interested in some or all of them. *2100, 2100EP, 2100M, 2100SE, 2100TN, 2100XI, 2200, 2200D, 2200DN, 2200DT, 2200DSE, 2200DTN -- Patricia Babbitt, Professor Dept. of Bioengineering & Therapeutic Sciences 1700 4th Street, MC2550 University of California San Francisco, CA 94158 Phone: 1-415-476-3784 Email: babbitt(a)cgl.ucsf.edu Assistant: Ms. Joslyn Polzien Email: Joslyn.Polzien(a)ucsf.edu 8 AM – 12 PM: (415) 514-1214 1 PM – 5 PM: (415) 514-4861

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[Compbio-allhands] Fwd: ignite Bay Area (protein) Dynamics - November 5th
by Flowers, Nicole 28 Oct '13

28 Oct '13

Want to get together and talk science with other Bay Area researchers interested in the ways macromolecules move? Come to ignite Bay Area Dynamics (iBAD) on November 5th. Absolutely everyone is invited, from student to professor and academia to industry. Hear the latest work on dynamics in a fast, pithy form: Ignite talks are only five minutes apiece, with auto-advancing slides! Refreshments are provided and there will be plenty of time to chat with colleagues and speakers. Speakers: Susan Marqusee (Berkeley) Vijay Pande (Stanford) Jacob Corn (Genentech) Gira Bhabha (UCSF) November 5th, 2013 - 7 PM UCSF - Mission Bay Campus Byers Hall 212 More info: http://www.fraserlab.com/ibad or email Jaime Fraser (james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu>) or Jacob Corn (corn.jacob(a)gene.com<mailto:corn.jacob@gene.com>) Sponsored by the Protein Society (Society membership not required to attend). James Fraser, PhD Assistant Professor Department of Bioengineering and Therapeutic Sciences Office: N212C Genentech Hall, Lab: N216 Genentech Hall james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu> // jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com> (415) 493-8421 http://www.fraserlab.com 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: Protein Society Sponsored Dynamics Meeting - Tuesday November 5th 7PM at UCSF
by Jacobson, Matt 27 Oct '13

27 Oct '13

-- Matt Sent from my iPad Begin forwarded message: From: James Fraser <jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com>> Date: October 27, 2013 12:58:39 PM PDT To: Mark Kelly <mark.kelly(a)ucsf.edu<mailto:mark.kelly@ucsf.edu>>, Tanja Kortemme <kortemme(a)cgl.ucsf.edu<mailto:kortemme@cgl.ucsf.edu>>, Agard Dave <agard(a)msg.ucsf.edu<mailto:agard@msg.ucsf.edu>>, Robert Stroud <stroud(a)msg.ucsf.edu<mailto:stroud@msg.ucsf.edu>>, Fletterick Robert <flett(a)msg.ucsf.edu<mailto:flett@msg.ucsf.edu>>, Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>>, Jim Wells <Jim.Wells(a)ucsf.edu<mailto:Jim.Wells@ucsf.edu>>, Jack Taunton <taunton(a)cmp.ucsf.edu<mailto:taunton@cmp.ucsf.edu>>, Patsy Babbitt <babbitt(a)cgl.ucsf.edu<mailto:babbitt@cgl.ucsf.edu>>, Charles Craik <Charles.Craik(a)ucsf.edu<mailto:Charles.Craik@ucsf.edu>>, "Danica Fujimori" <fujimori(a)cmp.ucsf.edu<mailto:fujimori@cmp.ucsf.edu>>, Natalia Jura <natalia.jura(a)ucsf.edu<mailto:natalia.jura@ucsf.edu>>, "Degrado, William" <Bill.DegRado(a)ucsf.edu<mailto:Bill.DegRado@ucsf.edu>>, "England, Pamela" <Pamela.England(a)ucsf.edu<mailto:Pamela.England@ucsf.edu>>, John Gross <jdgross(a)cgl.ucsf.edu<mailto:jdgross@cgl.ucsf.edu>>, Bo Huang <bo.huang(a)ucsf.edu<mailto:bo.huang@ucsf.edu>>, Xiaokun Shu <xiaokun.shu(a)ucsf.edu<mailto:xiaokun.shu@ucsf.edu>>, Susan Miller <smiller(a)cgl.ucsf.edu<mailto:smiller@cgl.ucsf.edu>>, "Gestwicki, Jason" <Jason.Gestwicki(a)ucsf.edu<mailto:Jason.Gestwicki@ucsf.edu>>, "Cheng, Yifan" <YCheng(a)ucsf.edu<mailto:YCheng@ucsf.edu>>, Alan Frankel <frankel(a)cgl.ucsf.edu<mailto:frankel@cgl.ucsf.edu>>, "Narlikar, Geeta" <geeta.narlikar(a)ucsf.edu<mailto:geeta.narlikar@ucsf.edu>>, "Lim, Wendell" <Wendell.Lim(a)ucsf.edu<mailto:Wendell.Lim@ucsf.edu>>, <Shawn.Douglas(a)ucsf.edu<mailto:Shawn.Douglas@ucsf.edu>>, Chris Waddling <waddling(a)msg.ucsf.edu<mailto:waddling@msg.ucsf.edu>>, Ajay Jain <ajain(a)jainlab.org<mailto:ajain@jainlab.org>>, Adam Abate <arabate(a)gmail.com<mailto:arabate@gmail.com>>, Michael Fischbach <fischbach(a)fischbachgroup.org<mailto:fischbach@fischbachgroup.org>>, "John Kuriyan" <kuriyan(a)berkeley.edu<mailto:kuriyan@berkeley.edu>>, Jamie Cate <jcate(a)lbl.gov<mailto:jcate@lbl.gov>>, <doudna(a)berkeley.edu<mailto:doudna@berkeley.edu>>, Bryan Krantz <bakrantz(a)berkeley.edu<mailto:bakrantz@berkeley.edu>>, David Wemmer <DEWemmer(a)lbl.gov<mailto:DEWemmer@lbl.gov>>, Andreas Martin <a.martin(a)berkeley.edu<mailto:a.martin@berkeley.edu>>, Judith Klinman <klinman(a)berkeley.edu<mailto:klinman@berkeley.edu>>, <jfkirsch(a)berkeley.edu<mailto:jfkirsch@berkeley.edu>>, Ron Vale <vale(a)cmp.ucsf.edu<mailto:vale@cmp.ucsf.edu>>, James Partridge <partridge.james(a)gmail.com<mailto:partridge.james@gmail.com>>, David Sivak <david.sivak(a)gmail.com<mailto:david.sivak@gmail.com>> Cc: Jacob Corn <corn.jacob(a)gene.com<mailto:corn.jacob@gene.com>> Subject: Protein Society Sponsored Dynamics Meeting - Tuesday November 5th 7PM at UCSF Want to get together and talk science with other Bay Area researchers interested in the ways macromolecules move? Come to ignite Bay Area Dynamics (iBAD) on November 5th. Absolutely everyone is invited, from student to professor and academia to industry. Hear the latest work on dynamics in a fast, pithy form: Ignite talks are only five minutes apiece, with auto-advancing slides! Refreshments are provided and there will be plenty of time to chat with colleagues and speakers. Speakers: Susan Marqusee (Berkeley) Vijay Pande (Stanford) Jacob Corn (Genentech) Gira Bhabha (UCSF) November 5th, 2013 - 7 PM UCSF - Mission Bay Campus Byers Hall 212 More info: http://www.fraserlab.com/ibad or email Jaime Fraser (james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu>) or Jacob Corn (corn.jacob(a)gene.com<mailto:corn.jacob@gene.com>) Sponsored by the Protein Society (Society membership not required to attend). -- -- James Fraser, PhD Assistant Professor Department of Bioengineering and Therapeutic Sciences Office: N212C Genentech Hall, Lab: N216 Genentech Hall james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu> // jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com> (415) 493-8421 http://www.fraserlab.com

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[Compbio-allhands] Fwd: Postdoctoral Fellow Position - The Rockefeller University
by Jacobson, Matt 25 Oct '13

25 Oct '13

-- Matt Sent from my iPad Begin forwarded message: From: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Date: October 25, 2013 11:17:43 AM PDT To: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Subject: Postdoctoral Fellow Position - The Rockefeller University We would greatly appreciate sharing the attached position within your graduate students and postdocs. Best regards, Melanie J. Lee Administrative Assistant Center for Studies in Physics and Biology The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: 212-327-8636 Fax: 212-327-8544 http://www.rockefeller.edu/research/intercenter/cenphysics

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[Compbio-allhands] 10/31/13 Seminar with Erin Carlson
by Nicole Takesono Flowers 24 Oct '13

24 Oct '13

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 Erin Carlson Indiana Chemical Probes to Explore and Inhibit Bacterial Pathogenesis October 31, 2013 D. 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] 10/24/13 Seminar with David Bartel
by Nicole Takesono Flowers 18 Oct '13

18 Oct '13

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 David Bartel MIT MicroRNAs and a developmental switch in the nature of translational control. October 24, 2013 H. Madhani, 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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