- 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 06 Mar '14

06 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 27 Feb '14

27 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 21 Feb '14

21 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 01 Feb '14

01 Feb '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 23 Jan '14

23 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 22 Jan '14

22 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 04 Jan '14

04 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 28 Oct '13

28 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 26 Oct '13

26 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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[Compbio-allhands] Fwd: Dr. Nicholas Furnham Seminar -- Thursday, October 24th
by Flowers, Nicole 17 Oct '13

17 Oct '13

Please join Patsy Babbitt on Thursday, October 24th, 2013 3:00 – 4:00 PM Byers Hall, Room BH-215 for a talk by visiting speaker Nick Furnham, PhD Postdoctoral Fellow, Thornton Research Group EMBL-EBI (European Molecular Biology Laboratory — European Bioinformatics Institute) on Automatically Cataloguing Changes in Enzyme Chemistry with Changes in Protein Evolution for 380 Domain Superfamilies --- Joslyn Polzien Assistant to Drs. Patricia Babbitt & Tanja Kortemme Dept. of Bioengineering & Therapeutic Sciences University of California, San Francisco 8 AM – 12 PM: (415) 514-1214 1 PM – 5 PM: (415) 514-4861 joslyn.polzien(a)ucsf.edu<mailto:joslyn.polzien@ucsf.edu> 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: Assistant Professor Position in Biochemistry CU Boulder
by Brian Shoichet 14 Oct '13

14 Oct '13

---------- Forwarded message ---------- From: Brian Shoichet <bshoichet(a)gmail.com> Date: Mon, Oct 14, 2013 at 11:56 AM Subject: Fwd: Assistant Professor Position in Biochemistry CU Boulder To: Ryan Coleman <ryan.g.coleman(a)gmail.com> FYI. Brian ---------- Forwarded message ---------- From: Amy E Palmer <amy.palmer(a)colorado.edu> Date: Mon, Oct 14, 2013 at 11:45 AM Subject: Assistant Professor Position in Biochemistry CU Boulder To: Amy E Palmer <amy.palmer(a)colorado.edu> Dear Colleagues I am writing to request your help in identifying candidates for a *faculty position in Biochemistry at the Assistant Professor* level at the *University of Colorado, Boulder*. In addition to establishing a vigorous research program, the new faculty will participate in teaching biochemistry or chemistry at the undergraduate and graduate levels. Candidates working in all areas of research will be considered. We have a healthy graduate program with each faculty member taking about one new graduate student a year, as well as excellent support facilities and a large amount of shared research equipment. Because the Biochemistry Program is situated within the Department of Chemistry & Biochemistry, there are many opportunities to interact with chemistry faculty, some of whom have considerable interest in biochemistry. We also have a joint graduate program with the Department of Molecular, Cellular, and Developmental Biology, located on campus, thus there are excellent interactions with molecular biologists and geneticists. There are strong connections between biochemistry and the physical sciences, and these connections are supported by an NIH-funded training program in Biophysics. Finally, we moved into a new state of the art Jennie Smoley Caruthers Biotechnology Building about 1 year ago which also houses the Department of Chemical and Biological Engineering and the BioFrontiers Institute, providing ample opportunity for cross-disciplinary and interdisciplinary interactions. The University has a strong interest in recruiting minority and women for faculty positions. There is a general feeling that simply stating in advertisements that "The University of Colorado is an Affirmative Action/Equal Opportunity Institution" is not enough. We would like to maximize chances of identifying all minorities and women who would be appropriate candidates for present and future openings in the Biochemistry Program. We would greatly appreciate it if you would bring this opening to the attention of candidates you feel are suitable. Enclosed is a copy of our position announcement. The position is advertised in Sciencejobs and Naturejobs.**** Sincerely,**** Amy Palmer ************************************ Associate Professor Department of Chemistry and Biochemistry BioFrontiers Institute UCB 596 3415 Colorado Ave Univesity of Colorado Boulder, CO 80303 303-492-1945 http:/Chem.colorado.edu/palmergroup -- 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 -- 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] 10/17/13 Seminar with Richard Bonneau
by Nicole Takesono Flowers 11 Oct '13

11 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 Richard Bonneau NYU Integrative computational methods for learning dynamic regulatory models: application to T-cell differentiation and function October 17, 2013 A. Sczesnak, 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: Group leader in Computational Biology at EMBL Heidelberg
by Andrej Sali 10 Oct '13

10 Oct '13

Sent from my iPhone Begin forwarded message: > From: Christoph Mueller <cmueller(a)embl.de> > Date: October 10, 2013 at 6:30:23 AM PDT > To: sali(a)salilab.org > Subject: Group leader in Computational Biology at EMBL Heidelberg > > Dear Andrej, > > We are seeking to recruit a group leader/teamleader in Computational Biology/Bioinformatics at EMBL Heidelberg. > > Although the call is deliberately broad structural bioinformatics (e.g. modelling of protein complexes and their interactions and/or dynamics in a cellular context), image analysis/visualisation (e.g. reading out data from GFP screens, E-tomograms or visualising a virtual cell atlas) is one of the topics. I would be grateful if you could forward the attached advert to suitable candidates! > > Thanks for your help! > Christoph > -- > ---------------------------------------------------------------------------- > Dr. Christoph W. Müller > Joint Head of Structural and Computational Biology Unit > > EMBL > Meyerhofstrasse 1 > 69117 Heidelberg, Germany > > email: cmueller(a)embl.de > phone: 0049-6221-387-8320 > fax: 0049-6221-387-519 > http://www.embl.de > ----------------------------------------------------------------------------- > > > >

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[Compbio-allhands] Fwd: Listservs: Business Careers for Scientists: considering the options
by Jacobson, Matt 07 Oct '13

07 Oct '13

Begin forwarded message: From: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Subject: Fwd: Listservs: Business Careers for Scientists: considering the options Date: October 7, 2013 10:45:48 AM PDT To: <BPSTUDENTS(a)LISTSRV.UCSF.EDU<mailto:BPSTUDENTS@LISTSRV.UCSF.EDU>> Reply-To: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Hi everyone, The Business Club at UCSF invites you to our first event this academic year, Business Careers for Scientists: Considering the Options. Dr. Jenny Rooke will give an overview of business careers for scientists from her own experience. Dr. Jenny Rooke drives innovation in the life sciences through investing and business building around brilliant scientists and engineers with novel technologies. Her investing experience includes roles at the Bill & Melinda Gates Foundation and at Fidelity Biosciences, a healthcare venture capital firm. Dr. Rooke held multiple executive roles at U.S. Genomics, a venture-backed biotech start-up advancing single molecule detection technologies for diagnostics, biodefense, and research tools. Previously, Dr. Rooke was a management consultant with McKinsey & Co., where she advised leading pharmaceutical and biotech companies on business strategy. Dr. Rooke earned her PhD in genetics from Yale University and her BS in physics from Georgia Tech. When: 5:30PM, 10/9/2013 Where: Byer Hall 212, UCSF Mission Bay Campus --------------------------------------------------------------- Business Club at UCSF<http://www.businessatucsf.org/>, join us on LinkedIn<http://www.linkedin.com/groups?gid=4111410> 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=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: FACULTY POSITIONS OPEN--Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
by Jacobson, Matt 03 Oct '13

03 Oct '13

Begin forwarded message: From: imbwww <imbwww(a)imb.sinica.edu.tw<mailto:imbwww@imb.sinica.edu.tw>> Subject: FACULTY POSITIONS OPEN--Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan Date: October 2, 2013 6:26:31 PM PDT To: Undisclosed recipients:; Dear colleagues, The Institute of Molecular Biology (Academia Sinica, Taiwan) is recruiting young and talented faculty to join the research groups. We would like to seek your help in distributing this advertisement to potential candidates in your laboratory or to those who you think might be interested in. Your kind assistance is highly appreciated. Best regards, ************************ The recruitment committee Institute of Molecular Biology Academia Sinica, Taipei, Taiwan 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: Opportunity at start up
by Jacobson, Matt 26 Sep '13

26 Sep '13

-- Matt Sent from my iPhone Begin forwarded message: From: Kathy Young <kathy(a)hertzfoundation.org<mailto:kathy@hertzfoundation.org>> Date: September 26, 2013, 2:04:55 PM PDT To: Katherine Young <kathy(a)hertzfoundation.org<mailto:kathy@hertzfoundation.org>> Subject: Opportunity at start up We are passing this opportunity along on behalf of Hertz Fellow Michael Schnall-Levin in case you, or someone you know, are interested in this opportunity. If this doesn't apply to you, please disregard. Thanks, Kathy Young Chief Operating Officer Fannie & John Hertz Foundation Dear Hertz Fellows and Alumni, We are an early-stage startup located in the SF bay area building a really exciting technology to revolutionize Next Generation Sequencing. Our company is truly multidisciplinary- together we have backgrounds in biochemistry, chemistry, microfluidics, engineering and computational biology. We are a young company but we are very ambitious and our leadership includes founders of the some of the biggest companies in Biotech. We are currently looking for a superstar in Computational Biology (see the attached job description), but are always interested in meeting talented people in any discipline. If you or anyone you know is interested, please reach out to me at mike(a)10xtechnologies.com<mailto:mike@10xtechnologies.com>. Michael Schnall-Levin (Hertz Fellow 2006 - 2011)

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[Compbio-allhands] Fwd: computational chemistry position for your students
by Brian Shoichet 25 Sep '13

25 Sep '13

FYI ---------- Forwarded message ---------- From: Kerry Boehner <kerry(a)kobsolutions.com> Date: Tue, Sep 24, 2013 at 11:03 AM Subject: computational chemistry position for your students To: bshoichet(a)gmail.com Hi Brian, My name is Kerry Boehner, and I’m a recruiter in the pharmaceutical and biotechnology fields. I’m recruiting for a Computational Chemist for a client in China & I thought one of your post-docs or students might be interested. I’ve included the description below. They are open to scientists coming straight from academia, as well as industry. My client offers a great compensation package, including relocation. Please don't hesitate to contact me if you need anything, and I appreciate your assistance! Kerry Kerry Boehner KOB Solutions, Inc. 412-851-9696 kerry(a)kobsolutions.com www.kobsolutions.com *Recruiting Solutions for Pharma, Biotech & Med Device* My client seeks a Computational Chemist for Computer-Aided Drug Design – the ideal candidate will take on the following responsibilities: --structure-based drug design --target identification and lead generation --assist project teams to answer key issues during hit-to-lead and lead optimization through techniques like protein/ligand analysis and simulation using MD and molecular docking. Requirements: --Ph.D. degree in computational chemistry, computational biology or a related field. --Familiarity with up-to-date biological screening paradigms. --A proven track record in leveraging in silico techniques to drive basic science projects or in impacting hit finding activities in a drug discovery environment. --Demonstrate the ability to work independently as effectively as being able to collaborate in multidisciplinary teams. --Strong analytical and problem-solving skills and scientific creativity are essential. --Excellent oral and written communication skills and organizational skills are required. -- 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: Attractive Statistical Genomics Faculty Position in Vancouver
by Andrej Sali 24 Sep '13

24 Sep '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: Jennifer Bryan <jenny(a)stat.ubc.ca> > Subject: Attractive Statistical Genomics Faculty Position in Vancouver > Date: September 23, 2013 4:54:11 PM PDT > To: Jennifer Bryan <jenny(a)stat.ubc.ca> > > The University of British Columbia has an exceptional opportunity for > a highly qualified researcher in the broad domain of statistical > genomics to launch a career as an Assistant Professor. As described > in the attached advertisement, this position is backed by a Canada > Research Chair for the early career, and is supported as a hard-money > position afterwards. The position is jointly backed by the > Departments of Statistics and Medical Genetics at UBC, and the > research would be based at the successful Centre for Molecular > Medicine and Therapeutics - a centre based on interdisciplinary > research collaboration. > > The search is open, with flexibility for the top candidate to build a > successful research program in the area of their interest. Research > space, training programs and computational resources are in place, > allowing the recruit to move rapidly. > > In short, this is a great position. We hope you will pass this > information along within the broad biostatistics community and > encourage top candidates to apply. > > I would be pleased to communicate with anyone having questions about > the position. > > Regards, > > Jenny Bryan > jenny(a)stat.ubc.ca > > P.S .The criteria for the Canada Research Chair restricts eligibility > to scientists within 10 years of receiving a Ph.D. As the position > will include some teaching within the Department of Statistics, > applications must indicate formal training in a field of statistics. > > Jennifer Bryan > Associate Professor > Department of Statistics and > the Michael Smith Laboratories > University of British Columbia > Vancouver, BC Canada >

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[Compbio-allhands] 9/26/13 Seminar with Laura Lavery
by Nicole Takesono Flowers 20 Sep '13

20 Sep '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 Laura Lavery Clements Lecture Molecular asymmetry provides new insights into Hsp90 mechanism September 26, 2013 D. Agard, 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: Faculty position in Theoretical Soft/Bio Physics
by Andrej Sali 20 Sep '13

20 Sep '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: "Mossman, Kaspar" <kaspar.mossman(a)qb3.org> > Subject: FW: Faculty position in Theoretical Soft/Bio Physics > Date: September 20, 2013 12:02:52 PM PDT > To: "SALI, ANDREJ" <sali(a)salilab.org> > > Hi Andrej, could you forward this to anyone who might be interested? and maybe if you know of relevant faculty w/ similar labs to yours, you could tell me who they might be? > > Thanks! > > Kaspar > > -----Original Message----- > From: Nancy Forde [mailto:nforde@sfu.ca] > Sent: Friday, September 20, 2013 11:37 AM > To: Mossman, Kaspar > Subject: Faculty position in Theoretical Soft/Bio Physics > > Dear Kaspar, > > I hope this message finds you well. If you are able to pass on this message and attached ad for a faculty position here at SFU to interested parties (i.e., theorists) at QB3, that would be great. > > SFU Physics is hiring a theorist in soft condensed matter or biological Physics. We are excited to be growing our complement of researchers in this area, and to further strengthen our already strong international reputation. Please help us to find the best candidate possible by forwarding the attached ad to outstanding theorists who would be interested in moving to beautiful Vancouver, British Columbia! Details are also available online at http://www.physics.sfu.ca/news/newsitem?id=79. > > Best wishes, > Nancy > > > -- > Nancy Forde > Associate Professor > Department of Physics > Simon Fraser University > 8888 University Dr. > Burnaby, BC V5A 1S6 > -- > nforde(a)sfu.ca > 778-782-3161; 778-782-3592 (fax) > http://www.sfu.ca/fordelab >

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[Compbio-allhands] Monica's thesis talk
by Jacobson, Matt 13 Sep '13

13 Sep '13

Reminder: Please join for Monica's Thesis Seminar! Monica Tremont (Jacobson Lab) Multiscale Models for Microtubule Assembly and Cytoplasmic Crowding Friday Sept 13, 2pm in GH Auditorium

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[Compbio-allhands] Fwd: POSTDOC OPPORTUNITY-PLEASE DISTRIBUTE
by Jacobson, Matt 05 Sep '13

05 Sep '13

Begin forwarded message: From: "Zachow, Christine A." <zachow2(a)llnl.gov<mailto:zachow2@llnl.gov>> Subject: POSTDOC OPPORTUNITY-PLEASE DISTRIBUTE Date: September 4, 2013 11:31:45 AM PDT To: Undisclosed recipients:; POSTDOC OPPORTUNITY-PLEASE DISTRIBUTE Lawrence Livermore National Laboratory is currently accepting applications for its prestigious Lawrence Fellowship. Applications can be submitted through our website: https://fellowship.llnl.gov/ They must be completed no later than November 1, 2013. The Lawrence Livermore National Laboratory’s prestigious Lawrence Fellowship is once again soliciting applications from your most promising rising postdocs. The fellowship was established to provide outstanding postdocs an opportunity to pursue cutting-edge science and stimulate cross-fertilization of ideas. The successful candidates have freedom to pursue world-class research with ample resources to support their efforts. The Fellows will interact with scientists with a wide range of expertise. The Laboratory is committed to making their experience at LLNL positive and rewarding. This three-year fellowship is awarded only to candidates with exceptional talent, credentials, scientific track records, and potential for significant achievements. Typically, two to four awards are given each year. After their three-year term, the Fellows may consider any career options, including employment at the Laboratory. Fellows will propose original and independent research in one or more aspects of science relevant to the mission and goals of LLNL. Research areas may include: * Atmospheric Science * Engineering * Biology * Environmental Science * Chemistry * Geoscience * Applied Mathematics * Lasers * Computer Science * Materials Science * Energy * Physics Further information is available at https://fellowship.llnl.gov/. You may contact me at zachow2(a)llnl.gov<x-msg://70/zachow2@llnl.gov> if you have any questions. Christine Zachow Program Administrator Lawrence Fellow & Lawrence Scholar Programs Lawrence Livermore National Laboratory 7000 East Ave. L-19 Livermore, CA 94550 925-423-0633 -- 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: Job Description
by Andrej Sali 12 Aug '13

12 Aug '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: "Mark Smythe" <m.smythe(a)protagonist-inc.com> > Subject: Job Description > Date: August 8, 2013 10:23:35 PM PDT > To: "'Andrej Sali'" <sali(a)salilab.org>, "'Charles Craik'" <Charles.Craik(a)ucsf.edu> > > Hi Andrej and Charly > Attached is the job description with a shorter version embeeded in this email. > If you have any comments/ammendments please let me know. > I will submit it to the web sites Andrej mentioned. > Please feel free to distribute. > Thanks for your help. > Mark > > Protagonist Therapeutics - Molecular Modeller /Computational Chemist / Bioinformatician > > Organisational Environment > Protagonist Therapeutics (www.protagonist-inc.com) is a US biotechnology company dedicated to the discovery of disulfide-rich peptides as well differentiated orally active peptides against those targets/diseases for which suitable small molecule or biologic options are not available. > > The work will be carried out at Menlo Park, California, USA. > > DUTY STATEMENT > > Primary Purpose of Position > Protagonist Therapeutics is seeking a talented and highly motivated scientist to join the drug design group. The candidate will use proprietary molecular modeling tools in combination with existing commercial software packages to design new compounds and optimize existing compounds. Protagonist is pursing the development of orally stable peptide derivatives for gastrointestinal diseases. > > The successful candidate will have a PhD in computational chemistry, bioinformatics or related discipline. The candidate will have previous involvement in all elements of molecular design impacting on IND candidate generation and proven ability to enhance peptide stability and permeability. In addition, the candidate will be familiar with molecular recognition and improving potency, be familiar with accessing public domain sequence, function, and structural information, has knowledge of disulfide rich peptides, macrocyles, clustering algorithm, molecular modeling packages, scripting/programming languages, with a preference for C++ and has worked in a Linux environment. The candidate well versed of the relevant literature, and have demonstrated hands on experience in structure based design. At least three years of industry experience is desirable. > > Duties > Duties and responsibilities include, but are not to: > • To be responsible for the structure-based drug design of one or more targets > • To optimize affinity of peptide-derivatives whilst maintaining and optimizing oral stability features > • To have up to date knowledge of the literature of one or more target > • The use of drug-design tools such as database searching, docking, scoring etc for the structure-based design of biologically active molecules > • To interpret and to use structural data, biological assay data, stability data, mutagenesis data, sequencing data, pharmacological data etc in the design of biological active molecules > > Reporting Relationships > The position reports to Dr Mark Smythe, VP Technology and Alliances for Protagonist Therapeutics. > > SELECTION CRITERIA > > Qualifications > The candidate will hold a Ph.D. in bioinformatics, computational chemistry or molecular modelling or related discipline, with significant research experience. Experiences in enhancing peptide affinity, stability and oral stability are essential. Project planning and meeting deadlines is an absolute advantage. Moreover, proven capacity and knowledge in deriving SAR of hit and lead candidates is highly desirable. > > Knowledge and Skills/Experience > Essential > • PhD in computational chemistry, bioinformatics or related discipline is required > • Proven translational experience towards IND candidates > • Knowledge of disulfide rich peptides and macrocycles > • Knowledge and practical experience in improving stability of peptides and macrocyles > • Previous experience in clustering > • Ability to program, preferably in C/C++ > • Working experience with pharmacophores > • Previous experience in structure-based drug design > • Thorough understanding of molecular recognition > • Thorough understanding of the drug design literature > • To have experience in scaffold hopping and peptide/protein engineering > • Develop and maintain integrated chemoinformatic database/registry > > Desirable > • Previous experience in database searching and docking > • Understanding of scoring functions > • Understanding of sequence search/alignment (Blast) > • Knowledge of SQL and Oracle Database > > Personal Qualities > Essential > • Ability to work in an efficient and well organized manner > • Ability to work collaboratively with internal and external team colleagues > • Ability to work with minimal supervision > • Ability to adhere to specific work schedules and meet deadlines > • Methodical approach to problem solving > • Excellent written and verbal communication skills > • Excellent interpersonal skills > • Sound problem-solving skills > > Remuneration: Protagonist Therapeutics provides competitive salary packages commensurate to experience to ensure that we are able to hire the best people from around the world. > > Closing Date: 21st August, 2013 > > Applications are to be sent to: > Human Resource Consultant > Email: hr(a)protagonist-inc.com > > >

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[Compbio-allhands] Fwd: 3 postdoc positions available immediately
by Jacobson, Matt 07 Aug '13

07 Aug '13

Begin forwarded message: From: <ealexov(a)clemson.edu<mailto:ealexov@clemson.edu>> Subject: 3 postdoc positions available immediately Date: August 7, 2013 6:18:02 AM PDT To: Undisclosed recipients:; Dear Colleagues, Just a quick announcement: 3 postdoctoral fellowships are immediately available here in Clemson (see below and the attached PDF file). Please, forward the announcement to all interested parties. I apologize to multiple copies of the ad that you may receive. Thank you in advance, Emil ================== Three post-doctoral fellowships in Biology of Human Diseases The Departments of Biological Sciences, Genetics and Biochemistry, and Physics at Clemson University are seeking three exceptionally talented new investigators, who hold a PhD in relevant fields. This unique opportunity exists for PhD graduates and postdoctoral fellows with a special interest in "The biology of human diseases: mechanisms, diagnosis, and personalized medicine", who aspire to become tenure track faculty in the near future. The fellows will be mentored by NIH funded researchers and trained in writing successful research grants, management of budgets and running a laboratory. We are especially looking for a computational biophysicist (3D structure modeling, energy calculations, MD and in silico virtual screening), an experimental biochemist (molecular cloning and protein purification, protein stability, enzyme activity, binding efficiency, enzyme kinetics, and structural determination) and an experimental biologist (cell and molecular biology/zebrafish model). These positions are part of the "Biology of Human Diseases" initiative at Clemson University to understand the molecular basis of human diseases and will provide the opportunity to development a pipe-line for diagnostics and treatment of genetic disorders. Postdoctoral fellows will have access to excellent experimental facilities and a supercomputer cluster. These positions are intended to act as a springboard for fast-track tenure track faculty positions and accepted post-doctoral fellows are required to submit a NIH Pathway to Independence Award (K99/R00). The positions are for an initial period of one year with possible appointment for an additional two years depending on satisfactory progress. The postdoctoral fellows will also help to train students in the participating departments. A competitive stipend inclusive of benefits and funding for research are offered according to field and experience. Interested candidates should send their CV, a statement of research and career objectives, and the names of at least three references in a single PDF to the following faculty: 1) Computational Biophysicist: Prof. Emil Alexov (ealexov(a)clemson.edu<mailto:ealexov@clemson.edu>) 2) Experimental Biochemist: Prof. Weiguo Cao (wgc(a)clemson.edu<mailto:wgc@clemson.edu>) 3) Experimental Biologist: Prof. Susan Chapman (SCHAPM2(a)clemson.edu<mailto:SCHAPM2@clemson.edu>) All application material received by September 1, 2013 will receive guaranteed consideration; however, applications will be accepted and evaluated until the positions are filled. 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 in Computational GPCR Ligand Design
by Brian Shoichet 28 Jun '13

28 Jun '13

FYI ---------- Forwarded message ---------- From: "David E. Gloriam" <david.gloriam(a)sund.ku.dk> Date: Jun 28, 2013 5:13 AM Subject: Postdoc in Computational GPCR Ligand Design To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu> Dear Brian, I have a computational chemistry postdoc opening in my group ( http://ccl.net/cca/jobs/joblist/mess0027098.shtml) I would be most grateful if you could please forward this mail to any interested person in your own group or network, that you think may be interested in a GPCR ligand design postdoc in Europe. Best Regards, David David Gloriam | Associate Professor Department of Drug Design and Pharmacology Faculty of Health And Medical Sciences University of Copenhagen T +45 35 33 61 62 | M +46 70 31 48 390

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[Compbio-allhands] Fwd: Job Opening for a Computational Chemist
by Jacobson, Matt 14 Jun '13

14 Jun '13

-- Matt Sent from my iPhone Begin forwarded message: From: "Demeter, David (DA)" <dademeter(a)dow.com<mailto:dademeter@dow.com>> Date: June 14, 2013, 12:44:50 PM PDT To: "kschulte(a)ks.uiuc.edu<mailto:kschulte@ks.uiuc.edu>" <kschulte(a)ks.uiuc.edu<mailto:kschulte@ks.uiuc.edu>>, "rod(a)ysbl.york.ac.uk<mailto:rod@ysbl.york.ac.uk>" <rod(a)ysbl.york.ac.uk<mailto:rod@ysbl.york.ac.uk>>, "brookscl(a)umich.edu<mailto:brookscl@umich.edu>" <brookscl(a)umich.edu<mailto:brookscl@umich.edu>>, "william.jorgensen(a)yale.edu<mailto:william.jorgensen@yale.edu>" <william.jorgensen(a)yale.edu<mailto:william.jorgensen@yale.edu>>, "shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>" <shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>>, "alex_tropsha(a)unc.edu<mailto:alex_tropsha@unc.edu>" <alex_tropsha(a)unc.edu<mailto:alex_tropsha@unc.edu>>, "pearlman(a)mail.utexas.edu<mailto:pearlman@mail.utexas.edu>" <pearlman(a)mail.utexas.edu<mailto:pearlman@mail.utexas.edu>>, "toprea(a)salud.unm.edu<mailto:toprea@salud.unm.edu>" <toprea(a)salud.unm.edu<mailto:toprea@salud.unm.edu>>, "carlos.simmerling(a)sunysb.edu<mailto:carlos.simmerling@sunysb.edu>" <carlos.simmerling(a)sunysb.edu<mailto:carlos.simmerling@sunysb.edu>>, "merz(a)qtp.ufl.edu<mailto:merz@qtp.ufl.edu>" <merz(a)qtp.ufl.edu<mailto:merz@qtp.ufl.edu>>, "nathan.baker(a)pnnl.gov<mailto:nathan.baker@pnnl.gov>" <nathan.baker(a)pnnl.gov<mailto:nathan.baker@pnnl.gov>>, "maxb(a)unc.edu<mailto:maxb@unc.edu>" <maxb(a)unc.edu<mailto:maxb@unc.edu>>, "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, "fetrowjs(a)wfu.edu<mailto:fetrowjs@wfu.edu>" <fetrowjs(a)wfu.edu<mailto:fetrowjs@wfu.edu>>, "ajain(a)jainlab.org<mailto:ajain@jainlab.org>" <ajain(a)jainlab.org<mailto:ajain@jainlab.org>>, "mgilson(a)ucsd.edu<mailto:mgilson@ucsd.edu>" <mgilson(a)ucsd.edu<mailto:mgilson@ucsd.edu>>, "jbriggs(a)uh.edu<mailto:jbriggs@uh.edu>" <jbriggs(a)uh.edu<mailto:jbriggs@uh.edu>>, "flbrown(a)chem.ucsb.edu<mailto:flbrown@chem.ucsb.edu>" <flbrown(a)chem.ucsb.edu<mailto:flbrown@chem.ucsb.edu>>, "carlsonh(a)umich.edu<mailto:carlsonh@umich.edu>" <carlsonh(a)umich.edu<mailto:carlsonh@umich.edu>>, "lybrand(a)structbio.vanderbilt.edu<mailto:lybrand@structbio.vanderbilt.edu>" <lybrand(a)structbio.vanderbilt.edu<mailto:lybrand@structbio.vanderbilt.edu>>, "madura(a)mail.cc.duq.edu<mailto:madura@mail.cc.duq.edu>" <madura(a)mail.cc.duq.edu<mailto:madura@mail.cc.duq.edu>>, "dmorikis(a)engr.ucr.edu<mailto:dmorikis@engr.ucr.edu>" <dmorikis(a)engr.ucr.edu<mailto:dmorikis@engr.ucr.edu>>, "pomes(a)sickkids.on.ca<mailto:pomes@sickkids.on.ca>" <pomes(a)sickkids.on.ca<mailto:pomes@sickkids.on.ca>>, "tps(a)pnl.gov<mailto:tps@pnl.gov>" <tps(a)pnl.gov<mailto:tps@pnl.gov>>, "Celia.Schiffer(a)umassmed.edu<mailto:Celia.Schiffer@umassmed.edu>" <Celia.Schiffer(a)umassmed.edu<mailto:Celia.Schiffer@umassmed.edu>>, "case(a)biomaps.rutgers.edu<mailto:case@biomaps.rutgers.edu>" <case(a)biomaps.rutgers.edu<mailto:case@biomaps.rutgers.edu>>, "pap4(a)uic.edu<mailto:pap4@uic.edu>" <pap4(a)uic.edu<mailto:pap4@uic.edu>>, "ramaro(a)mccammon.ucsd.edu<mailto:ramaro@mccammon.ucsd.edu>" <ramaro(a)mccammon.ucsd.edu<mailto:ramaro@mccammon.ucsd.edu>> Subject: Job Opening for a Computational Chemist Ladies & Gentlemen, Dow AgroSciences currently has a job opening for a Ph.D. computational chemist. An additional 2-5 years of post-doctoral and/or industrial experience in molecular modeling is preferred. If you know of anyone who is currently seeking such a position, I would appreciate it if you would pass along this information. We are currently collecting resume’s and would like to start phone interviews by mid July. A link to the job posting is included below. Thank you for your time. http://careers.dowagro.com/job/Indianapolis-Computational-Chemist-Discovery… Sincerely, David A. Demeter, Ph.D. Senior Research Scientist, R&D Chemistry / CAMD Dow AgroSciences LLC 9330 Zionsville Road, Bldg 306/D2-884 Indianapolis, IN 46268 Voice: 317-337-3413 Fax: 317-337-3215 E-mail: dademeter(a)dow.com<mailto:dademeter@dow.com> NOTICE: This e-mail message (including all attachments) from Dow AgroSciences LLC is for the sole use of the intended recipient(s). Any unauthorized review, use, disclosure or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message and any attachments.

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[Compbio-allhands] Dan Tawfik Seminar Announcement
by Flowers, Nicole 11 Jun '13

11 Jun '13

Please join Patsy Babbitt and Jaime Fraser on Thursday, June 20, 2013 12:00 – 1:00 PM Byers Auditorium, Genentech Hall for a talk by visiting seminar speaker Dan Tawfik, PhD Professor, Weizmann Institute of Science, Israel Department of Biological Chemistry on Enzyme Mechanism and Evolution --- Joslyn Polzien Assistant to Drs. Patricia Babbitt & Tanja Kortemme Dept. of Bioengineering & Therapeutic Sciences University of California, San Francisco 8 AM – 12 PM: (415) 514-1214 1 PM – 5 PM: (415) 514-4861 joslyn.polzien(a)ucsf.edu<mailto:joslyn.polzien@ucsf.edu> 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: Available Postdoctoral Positions in Computational Chemical Biology
by Jacobson, Matt 04 Jun '13

04 Jun '13

Begin forwarded message: From: David Minh <dminh(a)iit.edu<mailto:dminh@iit.edu>> Subject: Available Postdoctoral Positions in Computational Chemical Biology Date: June 4, 2013 9:40:56 AM PDT To: Undisclosed recipients:; Dear Colleagues, I am accepting applications for postdoctoral positions in my new research group at the Illinois Institute of Technology, located in Chicago. Please encourage interested and suitable candidates to apply. One position is available in Fall 2013 and potentially another in Summer 2014. Research will focus on developing and applying molecular docking algorithms based on implicit ligand theory, a new theoretical framework for binding free energies based on rigid receptor configurations (http://dx.doi.org/10.1063/1.4751284<http://link.aip.org/link/doi/10.1063/1.4751284>). Ideal candidates will have strong computer programming skills, a background in computational/theoretical chemistry or physics (especially statistical mechanics), and interest in chemical biology and drug discovery. A PhD is required prior to the start date. Interested candidates should submit a cover letter, CV, and contact information for 2-3 references to david.minh(a)iit.edu<mailto:david.minh@iit.edu>. For more information, see http://mccammon.ucsd.edu/~dminh/ Best regards, David Minh 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: superior CADD candidates
by Brian Shoichet 22 May '13

22 May '13

Dear Colleagues, This may interest some of you. Brian ---------- Forwarded message ---------- From: Herbertz, Torsten <therbertz(a)formatherapeutics.com> Date: Wed, May 22, 2013 at 12:51 PM Subject: superior CADD candidates To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu>, " klebe(a)staff.uni-marburg.de" <klebe(a)staff.uni-marburg.de>, " klebe(a)mailer.uni-marburg.de" <klebe(a)mailer.uni-marburg.de> Dear Prof. Shoichet & Klebe,**** ** ** I am reaching out to ask for your help in identifying exceptional candidates for open CADD positions at Forma Therapeutics ( http://formatherapeutics.com/) in the Boston area & making you aware that we would consider highly recommended post-docs in your labs.**** I made your acquaintance all the way back in 2002 at the Erice Gene-to-drugs xray crystallography conference and we have encountered each other on numerous occasions like the CADD GRC. Furthermore, I have been following your published work with much interest. Your laboratories produce very important results and insights that I attempt to apply & adapt to my own work, particularly here at Forma, where I have the privilege of leading a growing CompChem group (with 5 current members).**** We are mostly interested in candidates who have demonstrated small molecule drug discovery experience, a very sound understanding of medicinal chemistry and how to work with medchemists. Furthermore, good organic chemistry & biophysical chemistry are more important than method development, chemoinformatics, ….**** Forma is an oncology-focused relatively young (~5 years) and small (~110 people) company located in Watertown, MA.**** We are interested in many molecular target classes relevant to cancer biology, including cancer metabolism, epigenetics, protein-protein interactions and protein homeostasis to name a few.**** Computational chemistry is an integral part of our discovery paradigm; we generally only work on structure-enabled targets. Every project team includes a compchemists, who is invested as much as medicinal chemists, biologist and biochemists. In general, we follow two strategies in parallel: lead identification and chemical biology - in essence finding a tool compound for target validation. The hope is to push interesting chemical matter as far as we can toward pre-clinical development.**** This is a brief & simplified introduction to Forma and I hope that it convinces you that Forma is an exciting place to do drug discovery.**** I hope that you can provide interesting candidate leads for me to follow up. **** Any assistance that you can extend is deeply appreciated.**** ** ** Best regards,**** ** ** Torsten Herbertz, PhD**** Principal Scientist**** ** ** Forma Therapeutics, Inc.**** 500 Arsenal Street, Suite 100**** Watertown, MA 02472**** Email: therbertz(a)formatherapeutics.com <dmillan(a)formatherapeutics.com>**** Office: +1-857-209-2327**** www.formatherapeutics.com**** [image: Description: cid:image001.jpg@01CA92A2.4F452810]**** ** ** -- Brian Shoichet Professor University of California, San Francisco Dept. of Pharmaceutical Chemistry phone: 415-514-4126; fax: 415-514-4260 http://shoichetlab.compbio.ucsf.edu

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[Compbio-allhands] Fwd: UT Southwestern Seeks Research Scientists for Bioinformatics Initiative
by Tom Ferrin 21 May '13

21 May '13

-------- Original Message -------- Subject: UT Southwestern Seeks Research Scientists for Bioinformatics Initiative Date: Wed, 15 May 2013 19:37:33 +0000 From: Mack Dressler <Mack.Dressler(a)UTSouthwestern.edu> To: tef(a)cgl.ucsf.edu <tef(a)cgl.ucsf.edu> Dear Dr. Ferrin The Department of Clinical Sciences at the University of Texas Southwestern Medical Center is recruiting for its newly launched Translational Bioinformatics Initiative (http://tinyurl.com/UTSW-TBI) The Initiative is recruiting full-time bioinformatics researchers at all levels, including postdoctoral researchers and research scientists. Successful candidates will join an active and expanding bioinformatics research effort and will have the opportunity to collaborate with experimental and clinical researchers throughout UT Southwestern, the Department of Computer Science at UT Dallas, and the Texas Advanced Computing Center at UT Austin. Please share the attached posting with colleagues who might know of potential candidates, graduating students, and your institution’s career guidance center. Thank you for your consideration. If you would like additional information please contact me via e-mail or telephone (see below.) Sincerely, Lindsay G. Cowell, PhD Division of Biomedical Informatics Department of Clinical Sciences University of Texas Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-9066 phone: 214-648-2289 fax: 214-648-2064 Lindsay.Cowell(a)utsouthwestern.edu <mailto:Lindsay.Cowell@utsouthwestern.edu> ------------------------------------------------------------------------ UT Southwestern Medical Center The future of medicine, today.

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[Compbio-allhands] Fwd: Consulting Panel
by Jacobson, Matt 13 May '13

13 May '13

Begin forwarded message: From: "Brown, Rebecca" <Rebecca.Brown3(a)UCSF.EDU<mailto:Rebecca.Brown3@UCSF.EDU>> Subject: Consulting Panel Date: May 13, 2013 3:41:32 PM PDT To: <BPSTUDENTS(a)LISTSRV.UCSF.EDU<mailto:BPSTUDENTS@LISTSRV.UCSF.EDU>> Reply-To: "Brown, Rebecca" <Rebecca.Brown3(a)UCSF.EDU<mailto:Rebecca.Brown3@UCSF.EDU>> ----- Hi everyone, Are you interested in a career in consulting? The 2013 Consulting Panel is tomorrow! The panelists are: Cory Blaiss, Ph.D., Analyst at Kantar Health Leslie Waite, Ph.D., Senior Clinical Trainer at Genentech Neil Sheehy, Ph.D., Analyst at Prescient Life Sciences Networking reception afterward where the people can mingle and network. Time: 5/14/2013, 5:30PM Location: Mission Bay Helen Diller 160 For more information on the panelists, go to http://www.businessatucsf.org/<https://mail.ucsf.edu/owa/redir.aspx?C=Z06Py7uo7EelPdTT0oztNUEDQkWzI9AI17UG…> --------------------------------------------------------------- Business Club at UCSF<https://mail.ucsf.edu/owa/redir.aspx?C=Z06Py7uo7EelPdTT0oztNUEDQkWzI9AI17UG…>, join us on LinkedIn<https://mail.ucsf.edu/owa/redir.aspx?C=Z06Py7uo7EelPdTT0oztNUEDQkWzI9AI17UG…> and Consulting Club at UCSF<https://mail.ucsf.edu/owa/redir.aspx?C=Z06Py7uo7EelPdTT0oztNUEDQkWzI9AI17UG…> ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BMI_STUDENTS&A=1> from this mailing list. Rebecca Brown Biophysics Graduate Program Coordinator Genentech Hall S-406 600 16th St. Box 2240 University of California San Francisco San Francisco, CA 94158-2517 (415) 476-6671 (p) (415) 476-1902 (f) ________________________________ 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: Bill Eaton Visit today -- Seminar Room Change -- now in GH-N114
by Jacobson, Matt 09 May '13

09 May '13

Bill Eaton Seminar – “Transition paths in protein folding from theory, molecular dynamics simulations and single molecule fluorescence experiments" 1:30 PM, now in N114 Begin forwarded message: Hi all, Please see updated schedule for Bill. I would appreciate if you could forward to your labs -- the lunch with students and postdocs will still be in GH - S261, just the seminar room has changed. Thanks ! Hilary 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] 5/16/13 Seminar with Jeffrey Skolnick
by Nicole Takesono Flowers 09 May '13

09 May '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Jeffrey Skolnick Georgia Tech Interplay of physics and evolution in the likely origin of protein biochemical function May 16, 2013 P. Cimermancic, 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: Editorial position
by Brian Shoichet 29 Apr '13

29 Apr '13

For those interested in editor positions, this is a good group -- ---------- Forwarded message ---------- From: Sheppard, Terry <t.sheppard(a)us.nature.com> Date: Mon, Apr 29, 2013 at 9:40 AM Subject: Editorial position To: Brian Shoichet <shoichet(a)cgl.ucsf.edu> Hi Brian,**** I hope that you are well and that your transition to your new digs is proceeding smoothly.**** ** ** We are hiring a new Assistant Editor at *Nature Chemical Biology* and seek your help in getting the word out. You can see the advertisement here: http://www.nature.com/naturejobs/science/jobs/318829-Assistant-Editor. **** ** ** Please pass it along to colleagues and to any of your research associates who may be interested in applying. We have a slight preference for candidates whose backgrounds fall more on the biological side of chemical biology, but we are happy to see applications from scientists with training in any area of chemical biology.**** ** ** Many thanks,**** Terry**** ** ** Terry L. Sheppard, Ph.D.**** Editor, *Nature Chemical Biology***** ** ** -- Brian Shoichet Professor University of California, San Francisco Dept. of Pharmaceutical Chemistry phone: 415-514-4126; fax: 415-514-4260 http://shoichetlab.compbio.ucsf.edu

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[Compbio-allhands] 5/2/13 Seminar with Laura Kiessling
by Nicole Takesono Flowers 26 Apr '13

26 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Laura Kiessling University of Wisconsin-Madison Probing and Perturbing the Cell's Glycan Coat May 2, 2013 K. Shokat, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 5/2/13 Seminar with Laura Kiessling
by Nicole Takesono Flowers 26 Apr '13

26 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus HSW 303 Laura Kiessling University of Wisconsin-Madison Probing and Perturbing the Cell's Glycan Coat May 2, 2013 K. Shokat, 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: postdoc ad
by Tom Ferrin 23 Apr '13

23 Apr '13

Postdoc opportunity... -------- Original Message -------- Subject: postdoc ad Date: Sun, 21 Apr 2013 16:22:56 -0400 (EDT) From: Sarah Tishkoff <tishkoff(a)mail.med.upenn.edu> To: <tef(a)cgl.ucsf.edu> Dear Dr. Ferrin, I am currently advertising for postdoc position and would be very appreciative if you could send out this postdoc ad to graduate students in the bioinformatics program at UCSF. We have a FANTASTIC opportunity for creative and independent postdocs to work on some one-of-a-kind datasets that we are generating in the next year. There will definitely be opportunities for developing/applying novel methodology and for publishing high profile papers Thanks very much in advance. Best Regards, Sarah Sarah Tishkoff, Ph.D. David and Lyn Silfen University Professor Departments of Genetics and Biology University of Pennsylvania Tel: 215-746-2670 tishkoff(a)mail.med.upenn.edu http://www.med.upenn.edu/tishkoff/

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[Compbio-allhands] Fwd: Bioinformatics Summer Intern Posting_Ltr(2).docx
by Andrej Sali 23 Apr '13

23 Apr '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: Dan Hostetter <dan(a)cytomx.com> > Subject: Bioinformatics Summer Intern Posting_Ltr(2).docx > Date: April 22, 2013 4:29:09 PM PDT > To: Dave Barkan <davebarkan(a)gmail.com>, "sali(a)salilab.org" <sali(a)salilab.org> > Cc: Luc Desnoyers <luc(a)cytomx.com> > > Hi Dave and Andrej, > > Hope you are both doing really well! > > I’ve been having a great time applying my protease knowledge at CytomX . We have started our very first summer internship program and need bioinformatics expertise. I thought both of you would be a great resource for recommendations. > > CytomX has applied the pro-drug concept to antibody therapeutics to address toxicities that occur when antibodies bind to target in healthy tissue. We call our protease activated antibodies “Probodies”. Our technology leverages protease activity that is present in tumor tissue and not healthy tissue to activate our Probodies. We would love to mine RNA expression databases for targets that fit certain criteria such as (1) extracellular and therefore accessible to an antibody therapeutic and (2) a protease that can cleave our Probody is also expressed. The ideal candidate would be comfortable working with RNA expression databases and able to create filters based on the needs of our Probody platform. I’ve attached a description of the intern position to this email as a Word document. > > I’m copying Luc Desnoyers on this email. Luc is the head of our cell biology group and is a great mentor. The student intern would be working with Luc and someone in the cell biology group. I can vouch that everyone in Luc’s group is nice and all of them are patient teachers. > > If you have anyone in mind that would be a good fit, please let us know. I’m confident they would have a great experience at CytomX. > > Thanks guys! > > Best, > Dan

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[Compbio-allhands] 4/18/13 Seminar with Adrian Keatinge-Clay
by Nicole Takesono Flowers 19 Apr '13

19 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus HSW 303 Former Biophysics Student and Stroud Lab Post-doc, Adrian Keatinge-Clay University of Texas Visualizing and harnessing polyketide assembly lines April 25, 2013 R. Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 4/18/13 Seminar with Garry Nolan
by Nicole Takesono Flowers 19 Apr '13

19 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus HSW 303 Former Biophysics Student and Stroud Lab Post-doc, Adrian Keatinge-Clay University of Texas Visualizing and harnessing polyketide assembly lines April 25, 2013 R. Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Computational biologist position at Monsanto
by Jacobson, Matt 16 Apr '13

16 Apr '13

Begin forwarded message: From: "Groban, Eli" <EGroban(a)intrexon.com<mailto:EGroban@intrexon.com>> Subject: FW: Computational biologist position at Monsanto Date: April 16, 2013 11:33:58 AM PDT To: "matt(a)cgl.ucsf.edu<mailto:matt@cgl.ucsf.edu>" <matt(a)cgl.ucsf.edu<mailto:matt@cgl.ucsf.edu>> FYI. Thank you, Eli Groban, PhD Director, Metabolic Engineering and Systems Biology Industrial Products Division Intrexon Corporation 201 Industrial, Suite 450, San Carlos, CA 94070 p: 650.597.4026 | m: 415.971.7517 | egroban(a)intrexon.com<mailto:name@intrexon.com> www.dna.com<http://www.dna.com/> From: Kevin Costa <kcosta(a)berkeley.edu<mailto:kcosta@berkeley.edu>> Date: Tuesday, April 16, 2013 11:19 AM To: "all(a)synberc.org<mailto:all@synberc.org>" <all(a)synberc.org<mailto:all@synberc.org>> Subject: Computational biologist position at Monsanto Monsanto seeks a creative, mathematically-minded Computational Biologist to help us transform big data into higher yielding crops. In this role you role will support research across Monsanto Technology by integrating, modeling, and interpreting unprecedented genomic, transcriptomic, metabolic, phenotypic, population genetic, and geospatial data, all with the goal of driving interpretation into practical use. We aim to help feed the mid-21st century world using less water, less fertilizer, and less pesticide. https://monsanto.taleo.net/careersection/2/jobdetail.ftl?job=262740&lang=en… -- [cid:part2.03050501.00000805@berkeley.edu]<http://synberc.org/> Kevin Costa Administrative Director SynBERC - Synthetic Biology Engineering Research Center University of California, Berkeley 5885 Hollis Street, Room 4214, Mailcode 3224 Emeryville, CA 94608-2015 510-486-7568 510-432-7568 (cell) 510-486-4252 (fax) kcosta(a)berkeley.edu<mailto:kcosta@berkeley.edu> www.synberc.org<http://www.synberc.org/> ________________________________ CONFIDENTIAL TRANSMISSION - This message, including any attachments, is confidential and may be privileged. If you are not the intended recipient, please delete it without further distribution and reply to the sender that you have received the message in error. [cid:part2.03050501.00000805@berkeley.edu] 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] 4/18/13 Seminar with Garry Nolan
by Nicole Takesono Flowers 12 Apr '13

12 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Garry Nolan Stanford A structure for cancer and immunity at the single cell level by mass cytometry April 18, 2013 J. Rettenmaier, 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] 4/11/13 Seminar with Brenda Schulman
by Nicole Takesono Flowers 04 Apr '13

04 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Brenda Schulman St. Jude Children's Research Hospital Twists and Turns in Ubiquitin Conjugation Cascades April 11, 2013 J. Gross, 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: A summer intern position opening in computational chemistry at GlaxoSmithKline
by Jacobson, Matt 02 Apr '13

02 Apr '13

Begin forwarded message: From: Xuan Hong <xuan.2.hong(a)gsk.com<mailto:xuan.2.hong@gsk.com>> Subject: A summer intern position opening in computational chemistry at GlaxoSmithKline Date: April 2, 2013 8:21:56 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Matt, I am a computational chemist in GlaxoSmithKline and am based in the Upper Merion, PA site. I have a summer intern position open (June 3rd to August 31st). The intern would be looking into strengths and weaknesses of loop sampling methods. I am wondering if you know any students who might be interested? (Interested students could directly email their CVs to me.) Thank you so much. Kind regards, Xuan Xuan Hong, PhD Computational & Structural Chemistry GlaxoSmithKline Pharmaceuticals 709 Swedeland Road King of Prussia, PA 19406 Office: 610-270-5013 Email: Xuan.2.Hong(a)gsk.com<mailto:Xuan.2.Hong@gsk.com> Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] Seminar - Bill Eaton, NIH-Biophysical Chemistry Section - May 9, 2013, GH - S261
by Hilary Mahon 01 Apr '13

01 Apr '13

Please see attached. --- 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] 3/14/13 Seminar with Celeste Nelson
by Nicole Takesono Flowers 08 Mar '13

08 Mar '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Celeste Nelson Princeton Physical control of tissue morphogenesis March 14, 2013 Z. Gartner, 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] 3/7/13 Seminar with Michael Laub
by Nicole Takesono Flowers 04 Mar '13

04 Mar '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Michael Laub MIT Specificity and evolution of bacterial signaling pathways March 7, 2013 A. Shiver, 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: University of Calgary, Canada Research Chair-II Chair in Computational NanoBioMedicine
by Andrej Sali 01 Mar '13

01 Mar '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: Peter Tieleman <tieleman(a)ucalgary.ca> > Subject: University of Calgary, Canada Research Chair-II Chair in Computational NanoBioMedicine > Date: February 28, 2013 6:07:27 PM PST > To: "Prof. J. Andrew McCammon" <jmccammon(a)mail.ucsd.edu>, Ken Dill <dill(a)laufercenter.org>, "\"\"\"\"jonuchic\"@rice. edu"@guitar.compbio.ucsf.edu, "'Hue Sun Chan'" <chan(a)arrhenius.med.utoronto.ca>, Régis Pomès <pomes(a)sickkids.ca>, "'Gilles H. Peslherbe'\"" <Gilles.Peslherbe\"@Concordia.ca>, mgilson(a)ucsd.edu, mlklein(a)temple.edu, hgrubmu@��gwdg.de, Bert de Groot <bgroot(a)gwdg.de>, Erik Lindahl <lindahl(a)cbr.su.se>, Qiang Cui <cui(a)chem.wisc.edu>, Arun Yethiraj <yethiraj(a)chem.wisc.edu>, Marc Baaden <baaden(a)smplinux.de>, David Spoel <spoel(a)xray.bmc.uu.se>, Benoit Roux <roux(a)uchicago.edu>, g.gompper(a)fz-juelich.de, Sandeep Patel <spatel(a)mail.chem.udel.edu>, Edward Lyman <elyman(a)udel.edu>, sali(a)salilab.org, Mark Sansom <mark.sansom(a)bioch.ox.ac.uk>, Michael Feig <feig(a)msu.edu>, "Baker,"Nathan <Nathan.Baker"@pnnl.gov>, David Sept <dsept(a)umich.edu>, David Shaw <David.Shaw(a)DEShawResearch.com>, Simon Bernèche <simon.berneche(a)unibas.ch>, bb8(a)columbia.edu, amackere(a)rx.umaryland.edu, Thomas Cheatham III <tec3(a)utah.edu>, Ross Walker <ross(a)rosswalker.co.uk>, Bernard.Brooks2(a)nih.hhs.gov, Wilfred F. van Gunsteren <wfvgn(a)igc.phys.chem.ethz.ch>, Siewert Jan Marrink <S.J.Marrink(a)rug.nl>, hummer(a)helix.nih.gov, Christine Peter <peter(a)mpip-mainz.mpg.de>, "> > > Dear colleagues, > > Please bring the attached ad to the attention of potential candidates. We think this is a great opportunity for excellent younger scholars. > > With best regards, > > Peter > > -- > Dr. D. Peter Tieleman, Professor, AIHS Scientist > AITF Strategic Chair in (Bio)Molecular Simulation > Department of Biological Sciences, University of Calgary

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[Compbio-allhands] Invitae hiring multiple bioinformatics positions
by Alexandra Schnoes 28 Feb '13

28 Feb '13

BMI alum Lawrence Lee is now at Invitae and looking for multiple bioinformaticists (among other positions). Link to job postings below. Alex ---------- Forwarded message ---------- From: Lawrence Lee via LinkedIn <member(a)linkedin.com> Date: Thu, Feb 28, 2013 at 11:32 AM Subject: Lawrence shared a link with you To: Alexandra Schnoes <schnoes(a)gmail.com> LinkedIn MESSAGES *Lawrence Lee wrote:* Hey Alex! Hope all is well. We are hiring a lot of bioinformaticists right now. Perhaps you can pass this job posting along to near and recent grads? Thanks, Lawrence *Careers*<http://www.linkedin.com/e/63rla0-hdqb8faj-38/YpT4cyzc6TmEskh6Y1GeBi3Jj0B_/b…> invitae.com InVitae offers competitive compensation and full health benefits to our staff. If you are interested in applying to any of the following positions, please contact: InVitae-jobs(a)InVitae.com Customer Success (Client Services):... (See more articles »<http://www.linkedin.com/e/63rla0-hdqb8faj-38/tod/-1/INDUSTRY/industryNews/E…> ) View Article<http://www.linkedin.com/e/63rla0-hdqb8faj-38/YpT4cyzc6TmEskh6Y1GeBi3Jj0B_/b…>| -- Alexandra Schnoes schnoes(a)gmail.com

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[Compbio-allhands] 2/28/13 Seminar with David Liu
by Nicole Takesono Flowers 22 Feb '13

22 Feb '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 David Liu Harvard Small-molecule and macromolecule discovery driven by evolution February 28, 2013 Z. Gartner, 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: bioinformatics/programmer opening for BindingDB project
by John Irwin 22 Feb '13

22 Feb '13

FYI ---------- Forwarded message ---------- From: Michael K. Gilson <mgilson(a)ucsd.edu> Date: Fri, Feb 15, 2013 at 1:26 PM Subject: bioinformatics/programmer opening for BindingDB project To: John Irwin <jji(a)cgl.ucsf.edu> Dear John, I would be grateful if you could bring the following opportunity to the attention of suitable individuals who may be interested. Due to renewed NIH funding, the BindingDB project (www.bindingdb.org) has opportunities at the postdoctoral or staff levels, depending upon background and interests, to further the development and application of BindingDB. Potential directions included inventing, implementing and deploying new BindingDB functionalities; and making new scientific connections between BindingDB data and structural, genomic, pathway and/or clinical data. Relevant background and expertise includes chemistry, chemical informatics, biochemistry, systems biology, genomics, web application development (Java, Javascript, HTML 5, CSS, XML), IT (Tomcat, Apache, sysadmin), and relational databases. Contact: Mike Gilson, mgilson(a)ucsd.edu Please feel free to contact me if you have any questions. Thanks and best regards, Mike P.S. Are you staying at UCSF? -- Michael K. Gilson, M.D., Ph.D. Professor, Skaggs School of Pharmacy and Pharmaceutical Sciences Director, UCSD Drug Discovery Institute U. C. San Diego 9500 Gilman Drive Pharmaceutical Sciences Building, Room 3224 La Jolla, CA 92093-0736 Voice: 858-822-0622 Fax: 858-822-7726http://gilson.ucsd.eduhttp://www.bindingdb.orghttp://drugdiscov…

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[Compbio-allhands] Fwd: recruitment letter...
by Andrej Sali 22 Feb '13

22 Feb '13

Begin forwarded message: > From: Ram Samudrala <ram(a)compbio.washington.edu> > Subject: recruitment letter... > Date: February 21, 2013 4:31:36 PM PST > To: sali(a)salilab.org > Reply-To: ram(a)compbio.washington.edu > > Hi Andrej, I hope you are well. I am wondering if you could forward > this email around to your local CompBio groups? Thanks. > > --Ram > > > Postdoctoral opportunity in Translational Research Project at the Samudrala > Group in University of Washington, Seattle > > -- > > The Samudrala group at the University of Washington in Seattle is > seeking to recruit 2-3 postdoctoral fellows to work on the > Computational Analysis of Noval Drug Opportunities (CANDO) drug > discovery project funded by a 2012 NIH Director's Pioneer Award > (http://cando.compbio.washington.edu) The project goals are to screen > all human ingestible compounds against all proteins (primarily solved > protein structures) computationally to identify new uses for existing > drug compounds. Computational hits/leads are verified in vitro quickly > followed by clinical studies (since all compounds studied initially > are FDA approved drugs) for more than 30 indications with the aid of > numerous collaborations. > > The project has just begin its 3rd year, and an initial version of the > compound-protein matrix covering several thousand drugs (mostly FDA > approved drugs) vs. ~40,000 protein structures has been > completed. Bench studies are underway for two of the initial > indications we are going after (beta thalessemia major and multi-drug > resistant tuberculosis) and numerous other bench studies are soon to > follow. This is based on the multitargeting idea of how one compound > (or more) interacts with multiple proteins (all structures and > homologues) in a given system to produce a desired outcome (which is > how it happens in nature). More importantly, anything we find can be > directly evaluated by quick clinical study to demonstrate efficacy > since everything we'll initially focus on would've made it clinical > trials or through phase 2 testing at least. > > We are looking for individuals with the passion and skill set to help > us complete and deploy the pipeline for maximal benefit. Particularly > we are interested in a pipeline developer who would ideally be an > expert on machine learning techniques that will help integrate the > chem- and bioinformatic data with docking simulations, i.e., create a > more robust and automated pipeline that is adaptable to individual > indications and genotypes. We are also interested in a docking code > developer that will help implement the third version of the > fragment-based docking with dynamics protocol we have developed and > integrate the pipeline and docking methodology as a systems-based drug > discovery product. Another role which is part of the developer job > description is to work on a web application that can handle > personalisation and integrate it with our in-house cando database > API. This will finally give one-stop-shop-software to find putative > drugs for a particular indication of interest done using all the > proteins of the related organisms. So the final output of our > methodology is a drug-disease network which is linked back to > protein-compounds network, i.e. an atomistic description of all > existing and new drug prediction we are making. > > Gaurav Chopra, one of my postdocs and the overall project manager of > CANDO, will be attending CASP10 and is the person who you'd closely > work with should you accept this position. So please talk to him and > if you're interested in this position, and if you feel the project is > a good fit for you, send us both your CV and a brief statement of > interest to gaurav(a)compbio.washington.edu and > ram(a)compbio.washington.edu > > -- > > -- > > --- > You received this message because you are subscribed to the Google Groups "samudrala-compbio" group. > To unsubscribe from this group and stop receiving emails from it, send an email to samudrala-compbio+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > > > > --20cf306f722a5dcabe04d6442e13 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Hi = > George,<div> =3D"arial,helvetica,sans-serif"> </div><div> olor=3D"#000000">Here is th= > e email we sent out for CASP when I met people there. Please change as need= > ed and spread the word for recruiting two postdocs!</d= > iv> > > <div> "> </div><div> ace=3D"arial,helvetica,sans-serif">Thanks,</div><div><= > font color=3D"#000000">Gaur= > av</div> > > <div> "> </div><div> =3D"arial, helvetica, sans-serif">--</div><div> style-span" face=3D"arial, helvetica, sans-serif"> e-span" style=3D"border-collapse:collapse;color:rgb(34,34,34);font-family:a= > rial,sans-serif;font-size:13px"> > > Postdoctoral opportunity in Translational Research Project at the Samudrala= > Group in University of Washington, Seattle -- The Samudrala = > group at the University of Washington in Seattle is seeking to recruit 2= > -3 postdoctoral fellows to work on the > > Computational Analysis of Noval Drug Opportunities (CANDO) drug discover= > y project funded by a 2012 NIH Director's Pioneer Award (<a href=3D"= > http://cando.compbio.washington.edu/" target=3D"_blank" style=3D"color:rgb(= > 17,85,204)">http://cando.compbio.washington.edu</a>). The project goals are= > to screen > > all human ingestible compounds against all proteins (primarily solved pr= > otein structures) computationally to identify new uses for existing drug= > compounds. Computational hits/leads are verified in vitro quickly > followed by clinical studies (since all compounds studied initially > are FDA approved drugs) for more than 30 indications with the aid of num= > erous collaborations. The project has just begin its 3rd year, and a= > n initial version of the compound-protein matrix covering several thousa= > nd drugs (mostly FDA > > approved drugs) vs. ~40,000 protein structures has been completed. Bench= > studies are underway for two of the initial indications we are going af= > ter (beta thalessemia major and multi-drug resistant tuberculosis) and n= > umerous other bench studies are soon to > > follow. =A0This is based on the multitargeting idea of how one compound = > (or more) interacts with multiple proteins (all structures and homologue= > s) in a given system to produce a desired outcome (which is how it happe= > ns in nature). More importantly, anything we find can be > > directly evaluated by quick clinical study to demonstrate efficacy since= > everything we'll initially focus on would've made it clinical t= > rials or through phase 2 testing at least. We are looking for indivi= > duals with the passion and skill set to help > > us complete and deploy the pipeline for maximal benefit. Particularly we= > are interested in a pipeline developer who would ideally be an expert o= > n machine learning techniques that will help integrate the chem- and bio= > informatic data with docking simulations, i.e., create a > > more robust and automated pipeline that is adaptable to individual indic= > ations and genotypes. We are also interested in a docking code developer= > that will help implement the third version of the fragment-based dockin= > g with dynamics protocol we have developed and > > integrate the pipeline and docking methodology as a systems-based drug d= > iscovery product. Another role which is part of the developer job descri= > ption is to work on a web application that can handle personalisation an= > d integrate it with our in-house cando database > > API. This will finally give one-stop-shop-software to find putative drug= > s for a particular indication of interest done using all the proteins of= > the related organisms. So the final output of our methodology is a drug= > -disease network which is linked back to > > protein-compounds network, i.e. an atomistic description of all existing= > and new drug prediction we are making. Gaurav Chopra, one of my pos= > tdocs and the overall project manager of CANDO, will be attending CASP10= > and is the person who you'd closely > > work with should you accept this position. So please talk to him and if = > you're interested in this position, and if you feel the project is a= > good fit for you, send us both your CV and a brief statement of interes= > t to=A0<a href=3D"mailto:gaurav@compbio.washington.edu" style=3D"color:rgb(= > 17,85,204)">gaurav(a)compbio.washington.edu</a>=A0and > > <a href=3D"mailto:ram@compbio.washington.edu" style=3D"color:rgb(17,85,204)= > ">ram(a)compbio.washington.edu</a></div><div></div><div> lass=3D"Apple-style-span" color=3D"#222222" face=3D"arial, sans-serif"><spa= > n class=3D"Apple-style-span" style=3D"border-collapse:collapse"> > > </div><div> lvetica, sans-serif">--</div> > > > > -- >   > --- > You received this message because you are subscribed to the Google Groups &= > quot;samudrala-compbio" group. > To unsubscribe from this group and stop receiving emails from it, send an e= > mail to samudrala-compbio+unsubscribe(a)googlegroups.com. > For more options, visit <a href=3D"https://groups.google.com/groups/opt_out= > ">https://groups.google.com/groups/opt_out</a>. >   >   > > --20cf306f722a5dcabe04d6442e13-- -- 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] 2/21/13 Seminar with Bridget Carragher
by Nicole Takesono Flowers 15 Feb '13

15 Feb '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Bridget Carragher Scripps Investigating the dynamics of nanomachines using automated electron microscopy February 21, 2013 R. Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Informatics Positions at Janssen
by Andrej Sali 15 Feb '13

15 Feb '13

Sent from my iPhone Begin forwarded message: > From: "Stephens, Susan [JRDUS]" <sstephens1(a)its.jnj.com> > Date: February 15, 2013, 11:31:33 AM EST > To: "Stephens, Susan [JRDUS]" <sstephens1(a)its.jnj.com> > Subject: Informatics Positions at Janssen > > Janssen has a number of excellent positions open for individuals with strong informatics skills. The positions are within therapeutic areas, so individuals will have the ability to strongly impact the portfolio of drugs that we bring to market. > > Interested individuals should apply on J&J’s job Web site. > > Susie > > ___________________________________________________________________________________________ > 1088130206 PRINCIPAL SCIENTIST, COMPUTATIONAL BIOLOGIST - http://jobs.jnj.com/s/uNXQ58#.URkufVX9Qks.email > 1063130206 SENIOR SCIENTIST, COMPUTATIONAL BIOLOGIST - http://jobs.jnj.com/s/oAdSR4#.URkxIA12K8Y.email > 1339130206 SENIOR SCIENTIST, COMPUTATIONAL BIOLOGIST - http://jobs.jnj.com/s/OOTkcD#.URlfw9kwEto.email > 1302130206 SCIENTIST, COMPUTATIONAL BIOLOGIST - http://jobs.jnj.com/s/eQ7P7N#.URkv71XYu-0.email > 2216121206 SENIOR SCIENTIST, BIOMARKERS - http://jobs.jnj.com/job/Spring-House-SENIOR-SCIENTIST%2C-BIOMARKERS-Job-PA-… > >

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[Compbio-allhands] QB3 Informal Seminar: Dr. Jon Mason
by Yvonne Y. Munchua 14 Feb '13

14 Feb '13

Hello, everyone. Dr. Brian Shoichet will be hosting a QB3 Informal Seminar to be given by Dr. Jon Mason, Senior Research Fellow/Head of Computational Chemistry at Heptares Therapeutics. The event will be held tomorrow, Friday, February 15, from 9:30 am - 11:00 am RH-102 - Rock Hall Auditorium (please see attached flyer). The title of the presentation is, "SBDD for GPCRs: Driving druggability assessment, lead identification & optimization for potency & kinetics with receptor structure, including the use of new water network energetic analyses." Thank you, Yvonne Y. Munchua Asst. to Dr. Brian Shoichet UCSF Dept. of Pharm. Chem. 1700 4th Street, BH-508, Box 2550 San Francisco, CA 94158 P: (415) 514-4261 F: (415) 514-4260 yvonne.munchua(a)ucsf.edu

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[Compbio-allhands] Fwd: Open Positions: ELBE Postdoc Program in Dresden
by Andrej Sali 14 Feb '13

14 Feb '13

Begin forwarded message: > From: Gene Myers <myers(a)mpi-cbg.de> > Subject: Open Positions: ELBE Postdoc Program in Dresden > Date: February 14, 2013 7:48:29 AM PST > To: undisclosed-recipients:; > > Dear colleague, > > The Max-Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG) and the MPI for the Physics of Complex Systems (MPI-PKS) in Dresden have formed a new Systems Biology Center that is particularly focused on combining genomics, image-based, and bio-physical approaches. > We are beginning the next cycle of a fully-funded postdoctoral program and are seeking applicants. > > We kindly ask you to bring the attached one-page announcement to the attention of your students. > > Best regards, > Gene Myers > Founding Director, The Systems Biology Center at Dresden > > > Dr. Gene Myers, Director > Tschira Chair of Systems Biology > Max-Planck Institute of > Molecular Cell Biology & Genetics > Pfotenhauerstr. 108 > 01307 Dresden > > Tel: +49 351 210-1220 > Fax: +49 351 210-1209 > -- 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: Job Openings with the RCSB PDB in San Diego
by Andrej Sali 10 Feb '13

10 Feb '13

Sent from my iPhone Begin forwarded message: > From: Philip Bourne <bourne(a)sdsc.edu> > Date: February 9, 2013, 3:47:59 PM PST > To: Philip Bourne <bourne(a)sdsc.edu> > Cc: Philip Bourne <bourne(a)sdsc.edu> > Subject: Job Openings with the RCSB PDB in San Diego > > Folks: > > Excuse the intrusion, but I would very much appreciate you passing on the job opportunities (attached) with our group here in San Diego. In a nutshell we are looking for: > An outstanding Web developer to work on the next generation RCSB PDB interface > An outstanding database programmer to work on the next generation PDB RCSB data model and data warehouse > Thanks. > > Sincerely, > Phil > > Philip E. Bourne, Ph.D. > Associate Vice Chancellor for Innovation and Industrial Alliances, UCSD > Professor of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD > Associate Director, RCSB Protein Data Bank > Founding Editor in Chief, PLoS Computational Biology > Co-founder, SciVee Inc. www.scivee.tv > www.sdsc.edu/pb > +1 858 354 8301

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[Compbio-allhands] Peter A. Kollman Lectureship with Michael Levitt - February 14, 2013
by Nicole Takesono Flowers 08 Feb '13

08 Feb '13

Peter A. Kollman Lectureship Michael Levitt, Ph.D. Stanford Combinatorial Methods Solve a Difficult Structural Problem to Reveal How Chaperonins Work in Eukaryotes Thursday, February 14, 2013 12:00 PM J. Gross, Host Genentech Hall Byers Auditorium UCSF Mission Bay Campus Simulcast to Parnassus. Room S161 Reception in Byers Hall 5th Floor Lounge at 3:30 Sponsor: The Peter Kollman Fund 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: Post-doctoral positions available
by Andrej Sali 08 Feb '13

08 Feb '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: "Alan E. Mark" <a.e.mark(a)uq.edu.au> > Subject: Re: Post-doctoral positions available > Date: February 7, 2013 5:29:40 PM PST > To: Robert Best <robertbe(a)helix.nih.gov> > Cc: mlklein(a)temple.edu, dietmar.paschek(a)uni-rostock.de, marrink(a)chem.rug.nl, Ron Elber <ron(a)ices.utexas.edu>, jernigan(a)iastate.edu, dmz(a)ccbb.pitt.edu, Richard Lavery <richard.lavery(a)ibcp.fr>, kremer(a)mpip-mainz.mpg.de, Cecilia Clementi <cecilia(a)rice.edu>, Juan J de Pablo <depablo(a)engr.wisc.edu>, ftama(a)u.arizona.edu, Bruce Berne <bb8(a)columbia.edu>, David Coker <coker(a)chem.bu.edu>, Peter Rossky <rossky(a)mail.utexas.edu>, Dmitry Matyushov <dmitrym(a)asu.edu>, Kenneth Jordan <ken(a)visual1.chem.pitt.edu>, Doug Tobias <dtobias(a)uci.edu>, "Richard A. Friesner" <rich(a)chem.columbia.edu>, Bernhardt Trout <trout(a)mit.edu>, Karl Freed <k-freed(a)uchicago.edu>, Ken Dill <dill(a)maxwell.compbio.ucsf.edu>, David Reichman <reichman(a)chem.columbia.edu>, Jonathan Essex <J.W.Essex(a)soton.ac.uk>, bbagchi(a)sscu.iisc.ernet.in, gardes(a)rpi.edu, Jay Ponder <ponder(a)dasher.wustl.edu>, skolnick(a)gatech.edu, Andrei Tokmakoff <tokmakof(a)mit.edu>, Mark E Tuckerman <mark.tuckerman(a)nyu.edu>, pdebene(a)Princeton.EDU, william.jorgensen(a)yale.edu, lpratt(a)tulane.edu, aluzar(a)vcu.edu, bertil.halle(a)bpc.lu.se, Berend Smit <Berend-Smit(a)Berkeley.edu>, truskett(a)che.utexas.edu, Alexander Grosberg <ayg1(a)nyu.edu>, Barry Honig <bh6(a)columbia.edu>, Christopher Jarzynski <cjarzyns(a)umd.edu>, Eric Vanden-Eijnden <eve2(a)cims.nyu.edu>, Eugene Stanley <hes(a)bu.edu>, Felix Ritort <ritort(a)ffn.ub.es>, George Oster <goster(a)nature.berkeley.edu>, Hank Ashbaugh <hanka(a)tulane.edu>, Leonid Mirny <leonid(a)mit.edu>, Massimo Marchi <marchi(a)dsi.unimi.it>, Michael Shirts <michael.shirts(a)virginia.edu>, Michelle Parrinello <parrinello(a)phys.chem.ethz.ch>, Nicolae-Viorel Buchete <buchete(a)ucd.ie>, PieterRein tenWolde <tenwolde(a)amolf.nl>, Terry Hwa <hwa(a)ucsd.edu>, Thomas Miller <tfm(a)caltech.edu>, William Swope <swope(a)almaden.ibm.com>, "Wilfred F. van Gunsteren" <wfvgn(a)igc.phys.chem.ethz.ch>, "Alexandre M.J.J. Bonvin" <a.m.j.j.bonvin(a)uu.nl>, Xavier Daura <Xavier.Daura(a)uab.cat>, Helmut Grubmüller <hgrubmu(a)gwdg.de>, Daan Geerke <d.p.geerke(a)vu.nl>, David Smith <dsmith(a)irb.hr>, Christine Peter <peter(a)mpip-mainz.mpg.de>, Peter Tieleman <tieleman(a)ucalgary.ca>, "Megan O'Mara" <m.omara(a)uq.edu.au>, Alan Mark <a.e.mark(a)uq.edu.au>, David Fairlie <d.fairlie(a)imb.uq.edu.au>, Jennifer Martin <j.martin(a)imb.uq.edu.au>, Ricardo Mancera <R.Mancera(a)curtin.edu.au>, Durba Sengupta <d.sengupta(a)ncl.res.in>, Julian Gale <julian(a)ivec.org>, Irene Yarovsky <irene.yarovsky(a)rmit.edu.au>, jill.gready(a)anu.edu.au, Shin-Ho Chung <shin-ho.chung(a)anu.edu.au>, pande(a)stanford.edu, Ken Merz <merz(a)qtp.ufl.edu>, sali(a)salilab.org, Nilges Michael <nilges(a)pasteur.fr>, giorgio colombo <g.colombo(a)icrm.cnr.it>, lucy.forrest(a)biophys.mpg.de, ben.corry(a)anu.edu.au, Toby Allen <e88304(a)ems.rmit.edu.au>, dominik.marx(a)theochem.ruhr-uni-bochum.de, brookscl(a)umich.edu, roux(a)uchicago.edu, Rebecca Wade <rebecca.wade(a)h-its.org>, "michael.shirts(a)virginia.edu" <michael.shirts(a)virginia.edu>, Chandra Verma <chandra(a)bii.a-star.edu.sg>, "Dr M. Vendruscolo" <mv245(a)cus.cam.ac.uk>, Emanuele Paci <e.paci(a)leeds.ac.uk>, Chris Oostenbrink <chris.oostenbrink(a)boku.ac.at>, Bojan Zagrovic <bojan.zagrovic(a)univie.ac.at> > > Dear All, > > I would greatly appreciate it if you could pass the attached advertisement onto suitable post-doctoral candidates. I currently have two post-doctoral positions available funded by the Australian Health and Medical Research council (NHMRC) in my group at the University of Queensland, Australia. > > The specific projects focus on the use of molecular dynamics simulations to investigate the mechanism of action of ABC transporters and cytokine receptors as well as the interaction of small molecules and antimicrobial peptides with lipid bilayers. Applicants should hold or have recently submitted a PhD in computational chemistry or biophysics, or a related discipline. Experience in molecular dynamics simulations or related computational techniques, strong computational and programming skills are essential. Prior experience in free energy simulation techniques, simulations of membrane protein systems, or forcefield parameterisation will be an advantage. The University of Queensland (UQ) is located in sub tropical Brisbane on the east coast of Australia. UQ is one of the top research Universities in the Country and is consistently ranked within the top 50 Universities world wide. UQ was also one one of only two Institutions to receive a top ranking on Computational Chemistry in the most recent national research assessment. > > Interested applicants must apply online according to the instructions given in the attached file or see http://uqjobs.uq.edu.au/jobDetails.asp?sJobIDs=494312. > > If applicants have specific questions they can also contact me <a.e.mark(a)uq.edu.au> or Megan O'Mara <m.omara(a)uq.edu.au> directly. >> > Best wishes, > > Alan Mark > -- > -------------------------------------------------------------------- > This message was composed using voice recognition software. Please forgive any strange words I fail to correct. > ____________________________________________________________________ > Prof. Alan E. Mark > > BRISBANE > Molecular Dynamics Group > School of Chemistry and Molecular Biosciences (SCMB) > University of Queensland > Brisbane, QLD 4072, > Australia > > http://scmb.uq.edu.au/staff/alan-mark > http://compbio.biosci.uq.edu.au > > Physical address: > Rm 331 Level 3, Molecular Biosciences Building (#76) > > Email a.e.mark(a)uq.edu.au > Secretary: md.secretary(a)uq.edu.au > Phone: +61-7-3365 4180 > FAX: +61-7-3365 3872 > Secr: +61-7-3365 3821 > > Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland

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