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

[Compbio-allhands] Fwd: The Rockefeller University - Fellow Position
by Jacobson, Matt 11 Oct '12

11 Oct '12

-- Matt Sent from my iPhone Begin forwarded message: From: Melanie Lee <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Date: October 11, 2012, 10:10:20 AM PDT To: Melanie Lee <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Subject: The Rockefeller University - Fellow Position Dear Colleague: The Center for Studies in Physics and Biology, at The Rockefeller University, expects to have a small number of postdoctoral fellowships available for appointments in September 2013. We are seeking theoretical physicists, mathematicians and computer scientists with a demonstrable interest in the interface between their discipline and biology. The Fellows are to be at that stage of career as to function as independent members of the Center, free to work alone or in collaboration with any members of The Rockefeller University faculty. Would you be so kind as to post the attached notice, and share this within your department and with your peers and colleagues. Many thanks! Melanie J. Lee Administrative Assistant Center for Studies in Physics and Biology Rockefeller University 1230 York Avenue New York, NY 10065-6399 Tel: 212-327-8636 Fax: 212-327-8544

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[Compbio-allhands] Fwd: AMMA: POSTDOCTORAL POSITIONS (3 at CSIRO and 1 at the University of Orléans, France)
by Andrej Sali 10 Oct '12

10 Oct '12

-- 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: Elizabeth Yuriev <Elizabeth.Yuriev(a)monash.edu> > Subject: AMMA: POSTDOCTORAL POSITIONS (3 at CSIRO and 1 at the University of Orléans, France) > Date: October 9, 2012 7:56:11 PM PDT > To: Undisclosed recipients: ; > > OCE POSTDOCTORAL POSITIONS in the VNLab at CSIRO > > 1. OCE Postdoctoral Fellow - Modelling of Graphene Oxide Nanostructures > Closing Date: Open until Filled > Reference: VIC12/03679, > Salary: AU$78K - $85K per annum plus up to 15.4% Superannuation > Duration: 36 months > > CSIRO Materials Science and Engineering is seeking to appoint a highly motivated graduate who will take a substantive role in developing a theoretical and computational framework for modelling the formation, structure, porosity, and properties of graphene oxide nanosheets and membranes. The Fellow will play an important role in the graphene capabilities in the Virtual Nanoscience Laboratory (VNLab), under the direction of Dr. Amanda Barnard, and in the collaboration with Dr Dan Li at Monash University. > > Specifically you will: > • Use an electronic structure simulation to determine the structure of graphene oxide nanosheets, and different types of sheet/sheet interactions; > • Use CSIRO’s in-house package for dynamical modelling of aggregation behaviour, to explore the self-assembly of ensembles of exemplary nanosheets as a function of time, temperature, solvation conditions and concentration; > • Develop a rigorous classification system or different types of graphene oxide nanostructure, based on their conditions of formation, and ultimate properties; > • Produce high quality scientific and technical outputs including journal articles, conference papers and presentations, patents and technical reports. > You will be mentored by senior scientists as part of CSIRO’s Postdoctoral Fellows Program which aims to train early career scientists for a research role. > > LINK: http://csiro.nga.net.au/?jati=215fcf62-0176-9bfe-d1a4-6e0cc642b3de > > > 2. OCE Postdoctoral Fellow - Zinc Oxide Nanostructures > Closing Date: 31 October 2012 > Reference: VIC12/03140, > Salary: AU$78K - $85K per annum plus up to 15.4% Superannuation > Duration: 36 months > > CSIRO Materials Science and Engineering is seeking to appoint a highly motivated PhD graduate who will take a substantive role in developing a theoretical and computational framework for modelling the nanomorphology, environmental stability, and surface properties of zinc oxide (ZnO) nanoparticles. The Fellow will play an important role in the oxide nanomaterials capabilities in the Virtual Nanoscience Laboratory (VNLab), under the direction of Dr. Amanda Barnard, and become an important advisor and partner to the experimental effort under the direction of Dr. Phil Casey (CSIRO). This project is part of a collaboration with Dr Michelle Spencer at La Trobe University, and the Fellow will be encouraged to engage in the University research activities and interact with graduate students. > > Specifically you will: > •Using electronic structure simulations to determine the equilibrium structure and chemical terminations of ZnO surfaces, based on crystallographic orientations and chemical configurations; > •Predict the relative stability of each configuration as a function of temperature and partial pressure (or chemical species) using ab initio thermodynamics to generated a sets of surface phase diagrams under environmentally and industrially relevant; > •Establish the equilibrium morphology of ZnO as a function size and thermochemical conditions, and the relative stability of non-equilibrium morphologies (based on observations of the research team); > •Develop a range of different structure/property maps predicting efficiency of different ZnO nanostructures, under different conditions > •Work collaboratively with scientists in different domains, including computational members of the Virtual Nanoscience laboratory, computational and experimental scientists within CSIRO, and computational colleagues at La Trobe University. > > LINK: http://csiro.nga.net.au/publicfiles/csiro/jobs/B852DE11-66E2-B439-7321-6DE4… > > > 3. OCE Postdoctoral Fellow - Modelling of Inhibitor/Surface Interactions > Closing Date: 31 October 2012 > Reference: VIC12/03140, > Salary: AU$78K - $85K per annum plus up to 15.4% Superannuation > Duration: 36 months > > CSIRO Materials Science and Engineering is seeking to appoint a highly motivated graduate who will take a substantive role in developing a fundamental understanding of the interaction of inhibitors ( both organic and inorganic) with metal surfaces. > > You will combine both modelling of inhibitor/surface interactions with a targeted experimental program to investigate specific elements of binding of inhibitors to the surface and their role in controlling the electrochemistry of the metal/oxide/liquid interface. You will benefit from the established molecular modelling techniques in Dr Barnard’s Virtual Nano-Science laboratory and from both the experimental techniques and extensive data base on inhibiting performance within Dr Cole’s Environmental Surface Design team. > > Specifically you will: > •Predict the interaction of inhibitor molecules with metal and metal oxide surfaces using density functional methodologies; > •Determine the effect of interfaces and features within the metal/metal oxide surface on the interaction with inhibitors ; > •Determine the effect of surface charge and potential variation and the associated double layer effects on surface/inhibitor effects; > •Carry out experimental studies (incl. Electrochemical and analytical approaches) to verify the nature of surface/inhibitor interactions; > •Produce high quality scientific and technical outputs including journal articles, conference papers and presentations; > •Work collaboratively with scientists in different domains, including both computational members of the, computational and experimental scientists within Environmental surface design and Virtual Nanoscience. > > LINK: http://csiro.nga.net.au/?jati=639BF3DD-1BC5-9B3D-7185-6DFB1675D727 > > -Amanda > > > Post-Doctoral position at the University of Orléans in Structural Bioinformatics & Chemoinformatics group – please see attached > > > > Cheers, > Elizabeth > > > ************ > Dr Elizabeth Yuriev > Secretary, > Association of Molecular Modellers of Australasia (AMMA) > > Senior Lecturer > Faculty of Pharmacy and Pharmaceutical Sciences > Medicinal Chemistry and Drug Action > Monash Institute of Pharmaceutical Sciences > Monash University (Parkville Campus) > 381 Royal Parade, Parkville VIC 3052, Australia > Tel: Int +61 3 9903 9611, Fax: +61 3 9903 9143 > E-mail: elizabeth.yuriev(a)monash.edu > www.pharm.monash.edu.au

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[Compbio-allhands] BBC Journal Club, October 16th, GH Auditorium
by Bass, Karche 10 Oct '12

10 Oct '12

[BBC Journal Club] [BP * BMI * CCB] [Tuesday, October 9- 10:45 am - GH Auditorium] Amy Jacobson Khare, S.D., et al. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat. Chem. Biol. 8, 294-300 (2012). Andrew VanBenschoten Wang L et.al. Allosteric control of the ribosome by small-molecule antibiotics. Nature Structural & Molecular Biology. 19:9 957-963. (2012) Karché K. Bass Karché K. Bass | Administrative Assistant Asst. to John D. Gross, Charles Craik, Susan Miller, Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0943 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Fwd: PI position
by Andrej Sali 05 Oct '12

05 Oct '12

Sent from my iPhone Begin forwarded message: > From: "Chandra, Verma" <chandra(a)bii.a-star.edu.sg> > Date: October 5, 2012, 4:27:22 PM PDT > To: sali(a)salilab.org > Subject: PI position > > dear prof sali > > we have an opening at a PI level for someone who has had at least 4-5 years postdoctoral experience in the field of biomolecular modelling and computational chemistry. if you do know of someone who may be interested I would be grateful if you could please ask them to contact me > > many thanks > > chandra verma > a*star, singapore >

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[Compbio-allhands] 10/11/12 Seminar with Caleb Bashor
by Nicole Takesono Flowers 05 Oct '12

05 Oct '12

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 Caleb Bashor Clements Lecture Modular strategies for reprograming signal transduction pathways: rewiring the yeast mating pathway October 11, 2012 Wendell 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] reminder
by Jacobson, Matt 04 Oct '12

04 Oct '12

Talk by David Shaw, in Genentech Hall, noon 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: multiple qBio positions at UCSD
by Andrej Sali 04 Oct '12

04 Oct '12

Begin forwarded message: > From: Terry Hwa <hwa(a)ucsd.edu> > Subject: multiple qBio positions at UCSD > Date: October 4, 2012 11:14:12 AM PDT > To: Terry Hwa <thwa(a)ucsd.edu> > > > Dear Colleagues, > > I am writing to tell you about some exciting opportunities at the interface of the physical and biological sciences at U.C. San Diego. This is the second year of a major campus-wide initiative in quantitative biology (qBio). Following five successful qBio hires last year, there will be another cluster of hirings conducted across biology, physics, chemistry, and bioengineering, as well as on-going searches for senior biophysics theory positions. We expect additional positions in complementary fields next year. > > It is our goal to use these positions to assemble a dream team in quantitative biology, building on the vast base of biological research in the La Jolla basin, and a well established tradition of collaboration between the physical and biological sciences at UCSD. We encourage you to pass this information to interested junior and senior colleagues to pursue these dreams together. > > thank you and best wishes, > > Terry Hwa > >

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[Compbio-allhands] BBC Journal Club, Tuesday, October 9th
by Bass, Karche 03 Oct '12

03 Oct '12

BMI ~ BP ~ CCB Tuesday, October 9th, 2012 10:45 am, GH Auditorium Thomas Stevens Santos, Silvia D M et al. Spatial Positive Feedback at the Onset of Mitosis. Cell 149.7 (2012): 1500-13. Marian Deuker A CXCL1 Paracrine Network Links Cancer Chemoresistance and Metastasis bioinformatics ~ biophysics ~ chemistry and chemical biology Karché K. Bass Karché K. Bass | Administrative Analyst Asst. to John D. Gross, Charles S. Craik, Susan Miller, and Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA *: 415-502-0523 | 7: | *: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Fwd: FACULTY POSITIONS OPEN--Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
by Jacobson, Matt 01 Oct '12

01 Oct '12

-- Matt Sent from my iPad Begin forwarded message: From: imbwww <imbwww(a)imb.sinica.edu.tw<mailto:imbwww@imb.sinica.edu.tw>> Date: September 30, 2012 7:27:36 PM PDT Cc: vivi chiang <vivi(a)imb.sinica.edu.tw<mailto:vivi@imb.sinica.edu.tw>> Subject: FACULTY POSITIONS OPEN--Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 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 potentialcandidates 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

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[Compbio-allhands] Seminar October 4, noon
by Jacobson, Matt 28 Sep '12

28 Sep '12

David Shaw will give a seminar at noon on Thursday, October 4, in Genentech Hall auditorium, entitled "Millisecond-long molecular dynamics simulations of proteins" http://www.deshawresearch.com/ Hope to see you there (No BBC seminar was scheduled for this date, so we are using that time slot for this somewhat impromptu seminar. I've included all the listservs that I have access to on this email, but feel free to forward.) -- Matt 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] BBC Journal Club, Tuesday, October 2- 10:45AM, GH Aud
by Bass, Karche 26 Sep '12

26 Sep '12

BMI ~ BP ~ CCB Tuesday, October 2nd 10:45 am, GH Auditorium Kyle Barlow, BMI Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748-1759 (2012). Noah Younger, CCB Illing PT et al. Immune self-reactivity triggered by drug-modified HLA-peptide repertoire. Nature. 2012; 486:554-558. bioinformatics ~ biophysics ~ chemistry and chemical biology Karché K. Bass Karché K. Bass | Administrative Analyst Asst. to John D. Gross, Charles Craik, Susan Miller, Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA •: 415-502-0943 | 7: | •: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

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[Compbio-allhands] Fwd: CADD position at BMS
by Jacobson, Matt 25 Sep '12

25 Sep '12

Begin forwarded message: From: "Johnson, Stephen" <stephen.johnson(a)bms.com<mailto:stephen.johnson@bms.com>> Subject: CADD position at BMS Date: September 25, 2012 2:30:27 PM PDT To: "Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Dear Professor Jacobson, Debbie Loughney and I were discussing our visit to UCSF earlier this year as we just recently opened a new position within the CADD group at BMS. In short, the scientist that fills the position will be expected to help us expand and extend our toolset for addressing off-target liabilities including both ADMET and selectivity issues. The scientist will be active in the development of new methodology and its application in discovery projects. As such, we’re hoping to find someone with reasonable programming skills, in addition to being a top-tier CADD scientist. I wonder if you might have any current or former students/postdocs that you think may be a good fit for the position? Anyone that is interested can view the position profile and apply here: https://bms.taleo.net/careersection/jobdetail.ftl?job=45378&lang=en&sns_id=… They are also welcome to email directly in addition to applying through the website. Regards, Steve ================= Stephen Johnson Sr. Principal Scientist, CADD Head, Molecular Analytics Bristol-Myers Squibb, Co. stephen.johnson(a)bms.com<mailto:stephen.johnson@bms.com> ________________________________ This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. 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] 9/27/12 Seminar with Sheng Zhong
by Nicole Takesono Flowers 21 Sep '12

21 Sep '12

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 Sheng Zhong University of Illinois Comparative Epigenomics: a case study of human, mouse and pig pluripotent stem cells. September 27, 2012 Bo Huang, 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: Postdoctoral opening
by Jacobson, Matt 20 Sep '12

20 Sep '12

As some of you know, I think very highly of Gilson's work Begin forwarded message: From: "Michael K. Gilson" <mgilson(a)ucsd.edu<mailto:mgilson@ucsd.edu>> Subject: Postdoctoral opening Date: September 20, 2012 1:56:32 PM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Dear Matt, I thought I would mention that there is a current opening for a postdoctoral position in my lab. It is posted here on the computational chemistry list: http://www.ccl.net/cca/jobs/joblist/mess0025099.shtml I would be grateful if you could pass this along to trainees who might be interested. Feel free to contact me if you would like any more information. All the best, Mike -- 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: 858-822-7726 http://gilson.ucsd.edu http://www.bindingdb.org http://drugdiscovery.ucsd.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] Fwd: Faculty position in medicinal/pharmaceutical chemistry preferrably with computational research emphasis
by Brian Shoichet 19 Sep '12

19 Sep '12

FYI ---------- Forwarded message ---------- From: Peter Oelschlaeger <poelschlaeger(a)westernu.edu> Date: Wed, Sep 19, 2012 at 11:53 AM Subject: Faculty position in medicinal/pharmaceutical chemistry preferrably with computational research emphasis To: Peter Oelschlaeger <poelschlaeger(a)westernu.edu> Dear Professors,**** ** ** I would like to let you know about a faculty position in medicinal/pharmaceutical chemistry (preferably with a computational research emphasis) that the Department of Pharmaceutical Sciences in the College of Pharmacy at Western University of Health Sciences is offering.*** * ** ** Could you please inform any postdocs or colleagues that might be interested in applying?**** A posting with job description and instructions on how to apply has been posted on Science Careers:**** http://scjobs.sciencemag.org/jobs/153661-91602/**** ** ** Thank you very much for your help,**** ** ** Peter**** ** ** ************************************************************* *Peter Oelschlaeger, PhD* *Assistant Professor* *Department of Pharmaceutical Sciences* *College of Pharmacy* *Western University of Health Sciences* *309 E. Second St., Pomona, CA 91766* *Phone: 909-469-8232 (office), 909-469-8234 (lab)* *Fax: 909-469-5600* *Email: poelschlaeger(a)westernu.edu* *http://www.westernu.edu/stp/bios.php?bio=poelschlaeger* ** ** ** ** -- 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] Informal Seminar: David Minh, "Molecular Docking: Foundations in Statistical Mechanics"; Friday, 10:30am, GH S204
by David Sivak 19 Sep '12

19 Sep '12

Informal Seminar: Friday, September 21, 10:30am, Genentech S204 Molecular Docking: Foundations in Statistical Mechanics David Minh (mccammon.ucsd.edu/~dminh/) I will describe implicit ligand theory, a new formalism for noncovalent binding free energies that separates the calculation into two simulation stages: (i) sampling receptor configurations and (ii) calculating the binding PMF - the affinity of a ligand to a rigid receptor - for each receptor snapshot. Molecular docking may be interpreted as applying a dominant state approximation to each stage. Implicit ligand theory provides a pathway for the improvement of scoring functions. Recommended reading: http://arxiv.org/abs/1208.4885 -- 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] Fwd: A postdoc to work with Peter Minary in Computer Science at Oxford University
by Andrej Sali 17 Sep '12

17 Sep '12

Begin forwarded message: > From: "Michael Levitt" <michael.levitt(a)stanford.edu> > Subject: A postdoc to work with Peter Minary in Computer Science at Oxford University > Date: September 17, 2012 1:20:07 PM PDT > To: "'Michael Levitt'" <michael.levitt(a)stanford.edu> > > Dear Colleague and Friend, > > I am writing to ask for your help in identifying suitable candidates for a postdoctoral fellow to collaborate with Dr. Peter Minary. Peter has moved from Stanford to an independent position in Computer Science at Oxford and I can recommend him to any person who would like to become an expert at the most amazing methods for sampling macromolecular conformations. > > Searching Pubmed (http://www.ncbi.nlm.nih.gov/pubmed?term=minary%20p) shows Peter recent publications. His program remarkable program MOSAICS is athttp://csb.stanford.edu/minary/MOSAICS.html/ . > > This position has been advertised in Nature and Science. I append the Science add here (http://www.2020science.net/news/fellowship-computational-biology ). > > So many thanks and with all best regards, > Michael > -- 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: Subject: Postdoc opportunities at Princeton
by Andrej Sali 17 Sep '12

17 Sep '12

Sent from my iPhone Begin forwarded message: > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Date: September 17, 2012 1:07:08 PM PDT > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Cc: William Bialek <wbialek(a)Princeton.EDU>, "Curtis G. Callan Jr." <ccallan(a)Princeton.EDU>, "Wingreen, Ned S." <wingreen(a)Princeton.EDU>, "Chase P. Broedersz" <cbroeder(a)Princeton.EDU>, "Ben Machta (ben.machta(a)gmail.com)" <ben.machta(a)gmail.com>, "Rava A. da Silveira (rava(a)ens.fr)" <rava(a)ens.fr> > Subject: Subject: Postdoc opportunities at Princeton > > Dear colleagues, > > We are searching for young theorists with interests at the interface of physics and biology, and hope that you will bring this opportunity to the attention of likely candidates. As described in the attached advertisement (also available at http://www.princeton.edu/physics/about/employment/biophysics/index.xml) problems of current interest in our group cover a wide range of topics, and we always welcome people who will bring new questions of their own devising. Our community is very interactive, with multiple opportunities for collaboration, both among theorists and with many friendly local experimentalists. > > Many thanks for your help, > > Bill, Chase, Curt, Ben, Rava, and Ned > > William Bialek > John Archibald Wheeler/Battelle Professor in Physics > > Chase P. Broedersz > Lewis-Sigler Theory Fellow > > Curtis G. Callan, Jr. > James S. McDonnell Distinguished University Professor of Physics > > Benjamin Machta > Lewis-Sigler Theory Fellow > > Rava A. da Silveira > Princeton Global Scholar > > Ned S. Wingreen > Howard A. Prior Professor in the Life Sciences > > >

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[Compbio-allhands] Fwd: AMMA: job and postdoc opportunities
by Andrej Sali 16 Sep '12

16 Sep '12

Begin forwarded message: > From: Elizabeth Yuriev <Elizabeth.Yuriev(a)monash.edu> > Subject: AMMA: job and postdoc opportunities > Date: September 16, 2012 6:01:13 PM PDT > To: Undisclosed recipients: ; > > 1. Postdoctoral Research Associate, University of Liverpool > > £31,020 - £31,948 pa > Faculty of Science and Engineering, School of Physical Sciences, Department of Chemistry > Location: Liverpool City Centre > Ref: R-580533/WWW > Closing date for receipt of applications: 5 October 2012 > Joining a team of five postdoctoral researchers to develop a lead candidate compound, you will form part of a joint collaborative programme between the Departments of Chemistry and Pharmacology in a programme funded by the Medical Research Council (MRC). You should have a MChem degree and a PhD (or about to be obtained) in molecular modelling or closely related area. > The project involves the rational design, via molecular modelling, of novel analgesic compounds and will focus on exploring the structure activity relationships of molecules, their isosteres and optimising pharmacokinetic properties. Crucial to the vision is the use of molecular modelling to lead laboratory synthesis and testing to achieve compounds that are fit for purpose. The post is available for 12 months in the first instance. > > http://www.liv.ac.uk/working/job_vacancies/research/R-580533.htm > > Dr Neil Berry > Department of Chemistry > University of Liverpool > Liverpool > L69 7ZD > Tel: +44(0)151 794 3877 > Fax: +44(0)151 794 3588 > http://www.liv.ac.uk/~ngberry > > > 2. Senior Software Developer, Lhasa Limited > > There is more than one post on offer. There is no set closing date at the moment – but applications to be made as soon as possible. > Anyone interested in the job should contact my colleague Menaz Tabassum, who is responsible for recruitment here at Lhasa. Menaz’s email address is:- > Menaz.tabassum(a)lhasalimited.org > > (please see attachment for details) > > > 3. Postdoc position on Computational Protein Design at LAAS-CNRS, Toulouse, France > > The Robotics and Interactions group at LAAS-CNRS (Toulouse, France) is seeking for a postdoctoral researcher to work in an interdisciplinary project on Computational Protein Design. The project, ProtiCAD, is funded by the French National Research Agency (ANR). It involves three research groups with expertise in computer science / robotics, computational biology and enzyme engineering, and a start-up company. The work will mainly involve the development of algorithms to efficiently explore very large state-spaces, which correspond to different sequences and conformations of a protein. > > Candidates should have strong background in search algorithms and combinatorial optimization methods, as well as excellent programming skills. > Research will be carried in close collaboration with people in the other laboratories; therefore, applicants should enjoy teamwork and have very good communication skills. > Good English level is mandatory and notions of French would be a plus. > Toulouse is a beautiful, dynamic and safe city situated in the South West of France, within only 1.5 hour drive from the Pyrenees and the Mediterranean Sea. Toulouse offers outstanding opportunities for culture, entertainment and outdoor activities. > The position is available from December 2012, for a duration of up to two years. > Applications, including a CV, a cover letter and contact information of at least two references, should be sent by email to Juan Cortés (juan.cortes(a)laas.fr) with subject: "ProtiCAD postdoc application". > > > > > > > > > > ************ > Dr Elizabeth Yuriev > Senior Lecturer > Faculty of Pharmacy and Pharmaceutical Sciences > Medicinal Chemistry and Drug Action > Monash Institute of Pharmaceutical Sciences > Monash University (Parkville Campus) > 381 Royal Parade, Parkville VIC 3052, Australia > Tel: Int +61 3 9903 9611, Fax: +61 3 9903 9143 > E-mail: elizabeth.yuriev(a)monash.edu > www.pharm.monash.edu.au > -- 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: New positions at Janssen
by Andrej Sali 13 Sep '12

13 Sep '12

Begin forwarded message: > From: "Szalma, Sandor [JRDUS]" <sszalma(a)its.jnj.com> > Subject: FW: New positions at Janssen > Date: September 13, 2012 12:15:23 PM PDT > To: <trey.ideker(a)gmail.com>, <pbourne(a)ucsd.edu>, <ajayr(a)us.ibm.com>, <sali(a)salilab.org>, <jmccammo(a)mccammon.ucsd.edu>, "Athey, Brian" <bleu(a)umich.edu>, <brookscl(a)umich.edu>, <case(a)rutgers.edu>, <eperakslis(a)gmail.com>, <eneumann(a)mindspring.com>, <gergely.toth(a)gmail.com>, <gyanbhanot(a)gmail.com>, "Jill P. Mesirov" <mesirov(a)broad.mit.edu>, <alb(a)neu.edu>, "Martin Leach" <mleach(a)broadinstitute.org>, <piotr_cieplak(a)yahoo.com>, "Meroueh, Samy" <smeroueh(a)iupui.edu>, <vajda(a)bu.edu>, <taisung(a)yahoo.com>, <taisung(a)gmail.com>, <zszallasi(a)chip.org>, <nanjie_deng(a)yahoo.com>, "John Vu" <johnvu(a)andrew.cmu.edu> > > Hi, > > Please find below a couple of new jobs posting from Janssen – feel free to forward. > > > Head, High Performance Computing: > http://jobview.monster.com/Head-of-High-Performance-Computing-HPC-Job-New-Y… > > Senior Scientist, High Performance Computing: > http://jobview.monster.com/Senior-Scientist-High-Performance-Computing-HPC-… > > Head, Computational & Systems Biology: > http://jobview.monster.com/Head-Computational-Systems-Biology-Job-New-York-… > > Senior Scientist, Computational & Systems Biology: > http://jobview.monster.com/Senior-Scientist-Computational-Systems-Biology-J… > > Thank you! > > Sándor > > > Dr. Sándor Szalma > > Senior Research Fellow & Head, External Innovation, R&D IT > > Janssen Research & Development, LLC > Adjunct Professor, Rutgers, The State University of New Jersey > > 3210 Merryfield Row #1624 > San Diego, CA 92121, USA > T: +1 858 320 3445 > C: +1 858 603 3441 > F: +1 858 458 3746 > E: sszalma(a)its.jnj.com > > This e-mail message is confidential and for the sole use of the intended recipient(s) and may contain privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not an intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. Thank you. > >

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[Compbio-allhands] Fwd: computational scientist for GBT
by Andrej Sali 13 Sep '12

13 Sep '12

Begin forwarded message: > From: Steve Gwaltney <sgwaltney(a)globalbloodtx.com> > Subject: computational scientist for GBT > Date: September 10, 2012 6:14:45 PM PDT > To: Matt Jacobson <matt.jacobson(a)ucsf.edu>, Andrej Sali <sali(a)salilab.org> > Cc: Brian Metcalf <bmetcalf(a)globalbloodtx.com>, Kathy Stafford <kstafford(a)globalbloodtx.com> > > Hi Matt and Andrej, > > I am looking to hire a computational scientist to help us with compound design, structural biology issues, predictive tools, etc. Please find attached a job description for this position. If you know of good scientists who are qualified, please forward this to them. > > Thank you, > Steve > > Stephen L. Gwaltney, II, PhD > Vice President, Chemistry > Global Blood Therapeutics > 455 Mission Bay Blvd South > Suite 575 > San Francisco, CA 94158 > 415-766-3626 >

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[Compbio-allhands] Fwd: seminar announcement
by Jacobson, Matt 11 Sep '12

11 Sep '12

From: Matthew Jacobson <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: seminar announcement Date: September 10, 2012 3:46:12 PM PDT To: <allhands(a)compbio.ucsf.edu<mailto:allhands@compbio.ucsf.edu>>, <BPSTUDENTS(a)LISTSRV.UCSF.EDU<mailto:BPSTUDENTS@LISTSRV.UCSF.EDU>> David Shaw will be giving a talk on October 4; there is no BBC seminar scheduled that day, so we will use the noon timeslot. I'll send out a title and a reminder later. Seminar: Thursday, October 4, 2012 from 12-1PM, Location: GH Auditorium For those who don't know him: http://www.deshawresearch.com/ -- Matt 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: Post-doctoral advert
by Andrej Sali 30 Aug '12

30 Aug '12

-- 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: "Prof. C.E. Rudd" <cer51(a)cam.ac.uk> > Subject: Post-doctoral advert > Date: August 31, 2012 9:38:55 AM GMT+12:00 > To: lavy(a)stevens.edu > Cc: caterina.strambio(a)unige.ch, sali(a)salilab.org > > > Dear Colleague > > Would it be possible to ask you to post this advert for a post-doctoral fellow position in Cambridge University? We recently uncovered a novel immune cell specific adaptor that binds to the cytoplasmic face of the NPC in T-cells and which regulates RanGAP activity. > > Thank you for your help with this. > > Chris > > > -- > Christopher E. Rudd, Ph.D, D.Sc. > Professor of Molecular Immunology > Head, Cell Signalling Section > Department of Pathology > University of Cambridge > Tennis Court Road > Cambridge, UK > CB2 1QP > Tel: 44 1223 765 661 > Fax: 44 1223 764 733 > and > Cambridge Institute of Medical Research > Hills Road, Cambs CB2 0XY > 01223-769087 (lab: 01223-769086) > > http://www.cimr.cam.ac.uk/investigators/rudd/index.html > http://www.path.cam.ac.uk/pages/rudd/ > > http://www.immunology.cam.ac.uk/directory/profile.php?cerudd > http://www.infectiousdisease.cam.ac.uk/directory/cer51@cam.ac.uk > > >

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[Compbio-allhands] Fwd: open positions
by Jacobson, Matt 30 Aug '12

30 Aug '12

position open just across the street from UCSF Begin forwarded message: From: Michael Gonzales <mgonzales(a)celgene.com<mailto:mgonzales@celgene.com>> Subject: open positions Date: August 30, 2012 12:18:23 PM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Matt, Hope all is going well with you. I'm wondering if you know anyone that might be a fit for a couple open positions that I have in my group. The positions are "contract" but I intend to make these full time after successful completion of the project. I'm looking for someone to essentially lead NGS analysis for my group. Specifically I need someone who is experienced in: - rigorous analysis of RNA-seq data (ideally from clinical samples) - GEP, mutations, splice form quantification, gene fusions, etc - putting together the infrastructure to analyze NGS data (db, algorithms, etc) Here's my wish list of qualifications: ============================= REQUIRED QUALIFICATIONS · Graduate-level degree (Ph.D. preferred) in a life science discipline (bioinformatics, biology, biochemistry, medicinal chemistry, bioengineering, etc.). Candidates with a degree in another natural science, computer science, information technology or a related discipline will also be considered but must have a track record of research experience in computational life science · Two years post-graduate work experience conducting computational biology research (academic, government, or industry) · Proven record of working with Next-Gen Sequence (NGS) analysis including RNA-seq, ChIP-seq, whole genome assembly. · Extensive experience with large genomic data sets, as exemplified by the following areas: microarray analysis, high-throughput sequence analysis, automated annotation, gene prediction, population genomics, quantitative genetics, comparative genomics · Experience working in a command line environment including compiling and configuring bioinformatics software · Experience with extracting, manipulating, and integrating data from public biological data repositories (e.g. NCBI, Ensembl, UCSC). · Proficient programming skills with at least one scripting language (Perl, R, Python, Ruby, etc) · Strong interest in science and technology and ability to rapidly adopt and adapt to leading edge technologies · Excellent oral presentation and communications skills · Advanced ability to work independently under established deadlines and as part of a team PREFERRED QUALIFICATIONS · Demonstrated success in publishing computational science results and in presenting data to senior management · Experience managing projects involving advanced computing and information technologies used in life science research in academia, government laboratories, and/or industry · Proven ability to promote and support the use of computing, visualization, networking, and massive data storage systems to scientists to expand their research impact ============================= ------------------------------------------------------- Michael B. Gonzales, Ph.D. Director, Computational Biology Celgene Corporation 1500 Owens Street, Suite 600 San Francisco, CA 94158 T: 415.839.7113 │ F: 415.839.7011 ********************************************************* THIS ELECTRONIC MAIL MESSAGE AND ANY ATTACHMENT IS CONFIDENTIAL AND MAY CONTAIN LEGALLY PRIVILEGED INFORMATION INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR INDIVIDUALS NAMED ABOVE. If the reader is not the intended recipient, or the employee or agent responsible to deliver it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please reply to the sender to notify us of the error and delete the original message. 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] Fwd: Research Fellow in Computational Structural Biology
by Andrej Sali 30 Aug '12

30 Aug '12

Begin forwarded message: > From: Jennifer Wilkinson <jennifer.wilkinson(a)cs.ox.ac.uk> > Subject: Research Fellow in Computational Structural Biology > Date: August 30, 2012 9:40:21 PM GMT+12:00 > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Dr. Sali, > > We currently are advertising a research fellowship vacancy in Oxford, and would be grateful if you could distribute details to anyone who may be interested within your group. I have pasted details of the position below. > > Many thanks, > > Jennifer > > Research Fellow in Computational Structural Biology > > Grade 7: Salary £29,249-£35,938 (with a discretionary range to £39,257) > Fixed term contract for up to 2 years duration > > We are looking for a highly motivated researcher with a documented track record of successful research projects and a desire to do interdisciplinary research. This 24 month post-doctoral position will focus on the development and application of new methods in structure-based modelling and bioinformatics. The research will be carried out under the supervision of Prof. Charlotte Deane and Dr. Peter Minary in collaboration with the Structural Genomics Consortium and the EPSRC funded2020 Science programme. > > Candidates who have a doctorate in a relevant discipline and experience in scientific computing, software development and structural biology are particularly sought; however, exceptional candidates in all areas will be considered. Excellent programming and statistical skills are essential, as is experience of working with large-scale data sets. You will be expected to produce leading scientific research, publish results in top scientific journals, and interact closely with other members of the group and group collaborators. > > The post is available for up to 2 years, has a salary on the University grade 07S scale (currently £29,249 to £35,938), includes membership of the University pension scheme and has an annual leave entitlement of 38 days per year (inclusive of all public holidays and university closed periods). Requests to work on a part time or flexible basis will be considered. > > In addition candidates should arrange for the two letters of reference to be sent directly to the Administration Department (Vacancies), 1 South Parks Road, Oxford, OX1 3TG, email: jobs(a)stats.ox.ac.uk, before the closing date (a letter by email is sufficient). > > Please direct informal enquiries to the Administrator (email: jobs(a)stats.ox.ac.uk) Please quote reference: 104157 on all correspondence. > > To apply for this role and for further details, including the job description and selection criteria, please click here. All applications for this vacancy are to be made online > > Only applications received before the closing date 12 noon (UK time) Monday 1 October, 2012, can be considered. > > > > Jennifer Wilkinson > Project Manager > ___________ > University of Oxford > Department of Computer Science > Wolfson Building > Parks Road > Oxford OX1 3QD > > +44(0)1865 610782 > > *Please note, I am only in the office on Thursdays and Fridays. > > http://www.2020science.net >

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[Compbio-allhands] Fwd: Of Interest?
by Andrej Sali 28 Aug '12

28 Aug '12

-- 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: "Gregory A. Voth" <gavoth(a)uchicago.edu> > Subject: Of Interest? > Date: August 29, 2012 9:20:18 AM GMT+12:00 > To: "cgtheory(a)vothgroup.uchicago.edu" <cgtheory(a)vothgroup.uchicago.edu> > > > Dear Colleagues, > > The attached add is for a postdoc position at Genentech. Someone in your group may be interested in it so please pass it on. The email address to apply is on the add. The work is in part to be done in collaboration with my group (see attached). > > Best wishes, > Greg Voth > > __________________________________________________________________ > > Gregory A. Voth, Ph.D. > Haig P. Papazian Distinguished Service Professor > Department of Chemistry, The James Franck Institute, and > The Institute for Biophysical Dynamics > Senior Fellow, Computation Institute > Senior Scientist, Argonne National Laboratory > > Department of Chemistry > The University of Chicago > 5735 S. Ellis Avenue > Chicago, Illinois 60637 > Phone: 773-702-9092 > Fax: 773-795-9106 > Administrative Assistant: 773-702-9096 > Email: gavoth(a)uchicago.edu > Office: 231 Searle > Admin Office: 233 Searle > ___________________________________________________________________ > > > _______________________________________________ > Cgtheory mailing list > Cgtheory(a)vothgroup.uchicago.edu > http://vothgroup.uchicago.edu/cgi-bin/mailman/listinfo/cgtheory

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[Compbio-allhands] Fwd: Of Interest?
by Jacobson, Matt 28 Aug '12

28 Aug '12

Begin forwarded message: From: "Gregory A. Voth" <gavoth(a)uchicago.edu<mailto:gavoth@uchicago.edu>> Subject: Of Interest? Date: August 28, 2012 2:24:12 PM PDT To: "proteins(a)vothgroup.uchicago.edu<mailto:proteins@vothgroup.uchicago.edu>" <proteins(a)vothgroup.uchicago.edu<mailto:proteins@vothgroup.uchicago.edu>> Dear Colleagues, The attached add is for a postdoc position at Genentech. Someone in your group may be interested in it so please pass it on. The email address to apply is on the add. The work is in part to be done in collaboration with my group (see attached). My apologies for any duplicate email you may receive on this. Best wishes, Greg Voth __________________________________________________________________ Gregory A. Voth, Ph.D. Haig P. Papazian Distinguished Service Professor Department of Chemistry, The James Franck Institute, and The Institute for Biophysical Dynamics Senior Fellow, Computation Institute Senior Scientist, Argonne National Laboratory Department of Chemistry The University of Chicago 5735 S. Ellis Avenue Chicago, Illinois 60637 Phone: 773-702-9092 Fax: 773-795-9106 Administrative Assistant: 773-702-9096 Email: gavoth(a)uchicago.edu<mailto:gavoth@uchicago.edu> Office: 231 Searle Admin Office: 233 Searle ___________________________________________________________________ _______________________________________________ Proteins mailing list Proteins(a)vothgroup.uchicago.edu<mailto:Proteins@vothgroup.uchicago.edu> http://vothgroup.uchicago.edu/cgi-bin/mailman/listinfo/proteins 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] FW: Sr. Bioinformatics Scientist - SF - Position Details
by Schnoes, Alexandra 22 Aug '12

22 Aug '12

They are aggressively trying to staff 2 positions, looking for people who know RNA-seq and R. This is for a biotech based inside SF. Feel free to pass around. REQUIRED QUALIFICATIONS * Graduate-level degree (Ph.D. preferred) in a life science discipline (bioinformatics, biology, biochemistry, medicinal chemistry, bioengineering, etc.). Candidates with a degree in another natural science, computer science, information technology or a related discipline will also be considered but must have a track record of research experience in computational life science * Two years post-graduate work experience conducting computational biology research (academic, government, or industry)* Proven record of working with Next-Gen Sequence (NGS) analysis including RNA-seq, ChIP-seq, whole genome assembly. * Extensive experience with large genomic data sets, as exemplified by the following areas: microarray analysis, high-throughput sequence analysis, automated annotation, gene prediction, population genomics, quantitative genetics, comparative genomics * Experience working in a command line environment including compiling and configuring bioinformatics software * Experience with extracting, manipulating, and integrating data from public biological data repositories (e.g. NCBI, Ensembl, UCSC). * Proficient programming skills with at least one scripting language (Perl, R, Python, Ruby, etc) * Strong interest in science and technology and ability to rapidly adopt and adapt to leading edge technologies * Excellent oral presentation and communications skills * Advanced ability to work independently under established deadlines and as part of a team PREFERRED QUALIFICATIONS * Demonstrated success in publishing computational science results and in presenting data to senior management * Experience managing projects involving advanced computing and information technologies used in life science research in academia, government laboratories, and/or industry * Proven Appreciate you reaching out to you network!! Cheers, Amanda Amanda McDermott Consultant, Bioinformatics and Genomics Real Staffing Group One Sansome Street, San Francisco, CA 94101 ------------------------------------------------ T: 415-796-8050 E. a.mcdermott(a)realstaffing.com<mailto:a.mcdermott@realstaffing.com> Global Village: 232 7038 ------------------------------------------------ www.realstaffing.com<http://www.realstaffing.com> [Picture (Metafile)] Join my LinkedIn network<http://www.linkedin.com/in/amandamcdermottbioinformatics> [Picture (Metafile)]We want to provide you with the best service possible - click here<http://www.keysurvey.co.uk/f/444734/26ec/> to submit your feedback You can view our privacy statement at http://www.realstaffing.com/page/privacy_policy. If you do not wish to receive future electronic e-mails from us about our service please email: data-protection(a)realstaffing.com<mailto:data-protection@realstaffing.com> This electronic transmission is confidential and intended solely for the addressee(s). If you are not an intended addressee, you must not disclose, copy, distribute or take any action in reliance upon this transmission. If you have received this transmission in error, please notify Real Staffing Group, http://www.realstaffing.com/page/registration_details

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[Compbio-allhands] Juergen Haas Seminar -- ROOM CHANGE TODAY -- new room GH S204 -- 11AM TODAY, AUG. 10
by Hilary Mahon 10 Aug '12

10 Aug '12

--- 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: Two postdoctoral positions available
by Andrej Sali 02 Aug '12

02 Aug '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at 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: Patrick Aloy <paloy(a)irbbarcelona.org> > Subject: Two postdoctoral positions available > Date: August 2, 2012 7:19:18 AM PDT > To: undisclosed-recipients:; > > Dear friends and colleagues, > > we have two open postdoctoral positions in the group, one computational and one experimental, and I should be grateful if you could advertise them in your institutes and forward the message to people that might be interested (job adverts attached). Despite everything you might read on the newspapers, Barcelona is still an attractive place for research ;-) > > Best, > > PTCK. > > -- > Patrick Aloy, ICREA Research Professor > Structural Bioinformatics & Network Biology > Institute for Research in Biomedicine - Barcelona Science Park > c/ Baldiri i Reixac 10-12, 08028 Barcelona, Spain > > Email: patrick.aloy(a)irbbarcelona.org http://sbnb.irbbarcelona.org > Tel : +34 93 4039690 Fax : +34 93 4039954 >

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[Compbio-allhands] Seminar - Dr. Juergen Haas, University of Basel - Friday, Aug. 10, 2012 - 11:00am - 12:00pm - Byers Hall 212
by Hilary Mahon 31 Jul '12

31 Jul '12

Please see attached for information about Dr. Haas's seminar, "New developments in the Continuous Automated Model EvaluatiOn (CAMEO) system". 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] Giovanni Bussi Seminar - July 27
by Hilary Mahon 23 Jul '12

23 Jul '12

Please see information about Dr. Bussi's seminar. Thank you, Hilary --- 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: Rapid Molecular Dynamics Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande
by Andrej Sali 09 Jul '12

09 Jul '12

Begin forwarded message: > From: "Joy P. Ku" <joyku(a)stanford.edu> > Subject: Rapid Molecular Dynamics Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande > Date: July 9, 2012 9:43:06 PM PDT > To: <sali(a)salilab.org> > > Hi Dr. Sali, > > I’m the Director of Simbios, an NIH National Center for Biomedical Computing focused on physics-based simulations of biological structures based at Stanford University. Based on your research activities, I thought you would be interested in our upcoming workshop on rapid prototyping and simulations of molecular dynamics on GPUs that we are hosting with Dr. Vijay Pande. Please see the announcement below for the details. > > We invite you to attend and would appreciate you forwarding the announcement to colleagues and those in your lab that may be interested. > > Thank you. > > Regards, > Joy Ku > On behalf of Vijay Pande and the OpenMM team > --------------------------------------------------------------------------------------------------------- > Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. > OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs) [see benchmarks]. > And with the new application layer in its recent release, OpenMM will allow non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs. > > ***WORKSHOP: RAPID MOLECULAR DYNAMICS PROTOTYPING AND SIMULATIONS ON GPUS *** > > Where: Stanford University > When: September 6-7, 2012 > Description: > > During the workshop, you will gain hands-on experience using OpenMM’s new application layer and application programming interface (API). Learn to: > > * Set up and run an MD simulation on your GPU using both PDB and AMBER files > > * Create a custom force to apply to your simulations > > * Customize the simulation through Python scripting > > You will also have time to work with the OpenMM development team on your own research project. > > This workshop is designed for those interested in accelerating MD simulations on GPUs and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. No programming background is required, thoughprogramming topics will also be covered for those who are interested in them. > Registration: > > Registration is free but required and spaces are limited. To register or for more information, visithttp://simbios.stanford.edu/MDWorkshop.htm. > > OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. > > [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. > [2]Eastman, P. and Pande, V.S., “Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit,” J. Comp. Chem., 2010, 31(6):1268-1272. > > > > > > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at 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: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise
by Tom Ferrin 02 Jul '12

02 Jul '12

-------- Original Message -------- Subject: [Simbiosnews] Job Opening for Software Engineer with Molecular Dynamics Expertise Date: Mon, 2 Jul 2012 13:14:05 -0700 (PDT) From: Joy P. Ku <joyku(a)stanford.edu> To: <dissemination-simbiosnews(a)simtk.org>, <openmm-news(a)simtk.org>, <simbios_postdocs(a)mailman.stanford.edu>, <simbios_all(a)mailman.stanford.edu> Dear Simbios friends: We have an opening for a software engineer with expertise in molecular dynamics simulations and high performance scientific computing. Details about the position are given below. To learn more or to apply, please visit http://bit.ly/ypYq8w. Please forward this to others who may be interested. Thank you, Joy *Software Engineer, Exempt, 4P3, 2 Year Fixed Term * Simbios, the Center for Physics-based Simulation of Biological Structures, is one of eight national centers funded by the National Institutes of Health to build a biomedical-computing infrastructure to speed progress in biomedical research. We are looking for a software engineer with expertise in molecular dynamics simulations and high performance scientific computing to support and extend the functionality of our OpenMM and Folding@Home software projects. OpenMM (http://simtk.org/home/openmm) is an open-source molecular dynamics prototyping and simulation software package that runs accelerated calculations on GPUs. Folding@home (http://folding.stanford.edu) is a distributed computing project that uses the power of hundreds of thousands of CPUs and GPUs around the world to study protein folding. This position is a fixed term position that will be conterminous with our grant funding from NIH. Our NIH grant is scheduled to end on August 31, 2014. Should our funding continue beyond this date, this position would likely be extended. *JOB DETAILS* You will be responsible for the entire software pipeline, including but not limited to: * Develop new algorithms and improve the performance of OpenMM, * Test and validate OpenMM * Migrate OpenMM code into the Folding@home framework * Coordinate the release of new Folding@home GPU cores * Act as liaison to GPU manufacturers NVIDIA and AMD * Actively participate in both the OpenMM and Folding@home support forums * Contribute to user documentation *QUALIFICATIONS* */Minimum Requirements /* * Experience in scientific algorithm development, high performance computing applications, and molecular dynamics simulations * Requires a minimum of five years programming experience * Four year college degree or equivalent years of applicable experience. * Experience and comfort with professional software development practices * Excellent communication skills, both written and oral * Possess an understanding of the underlying biology */Desired Requirements /* * MS or PhD in physics, biochemistry, bioinformatics, computer science, engineering, or life sciences or an equivalent combination of education and experience * Experience programming in C++, Python, and OpenCL * Experience programming graphics processing units (GPUs) * Experience with Windows, Unix, Linux, Mac platform cross-development * Has experience working in an interdisciplinary environment Resume & Cover Letter are mandatory for consideration. *The final candidate will need to successfully pass a background check to be considered for this position.* /Stanford University values diversity and is committed to equal opportunity in employment./ To learn more or to apply, please visit http://bit.ly/ypYq8w / / / / / / /_______________________________________________/ / / /Joy P. Ku, PhD/ /Director, Simbios/ /http://simbios.stanford.edu/ / / /Director of Communications & Training,/ /National Center for Simulation in Rehabilitation Research/ /http://opensim.stanford.edu/ / / /(W) 650.736.8434, (F) 650.723.7461/ /Email: joyku(a)stanford.edu <mailto:joyku@stanford.edu>/

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[Compbio-allhands] Fwd: Post Doctorant positions_BiMoDyM_France
by Andrej Sali 25 Jun '12

25 Jun '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at 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: Luba Tchertanov <luba.tchertanov(a)lbpa.ens-cachan.fr> > Subject: Post Doctorant positions_BiMoDyM_France > Date: June 25, 2012 3:16:39 AM PDT > To: kuriyan(a)berkeley.edu, Mark Sansom <mark.sansom(a)bioch.ox.ac.uk>, jmccammon(a)ucsd.edu, ruthnu(a)helix.nih.gov, roux(a)uchicago.edu, rebecca.wade(a)eml-r.villa-bosch.de, Frank Noe <frank.noe(a)fu-berlin.de>, shoshana.wodak(a)sickkids.ca, "Bahar, Ivet" <bahar(a)pitt.edu>, sali(a)salilab.org, "Ronald M. Levy" <ronlevy(a)lutece.rutgers.edu>, jonuchic(a)ucsd.edu, modesto.orozco(a)irbbarcelona.org, klebe(a)mailer.uni-marburg.de, igor.pivkin(a)usi.ch, mzoppe(a)ifc.cnr.it, Woody.Sherman(a)schrodinger.com, Ruben Abagyan <ruben(a)ucsd.edu>, maculan(a)cos.ufrj.br, okeskin(a)ku.edu.tr, marc_vidal(a)dfci.harvard.edu, "Prof. Haim J. Wolfson" <wolfson(a)tau.ac.il>, pascal.hersen(a)univ-paris-diderot.fr, Fabian Theis <fabian.theis(a)helmholtz-muenchen.de>, jaxelrod(a)stanford.edu, stas(a)princeton.edu, kandt(a)bit.uni-bonn.de, Jaroslaw Polanski <jaroslaw.polanski(a)us.edu.pl>, okamoto(a)phys.nagoya-u.ac.jp, denispt(a)pasteur.fr, yamato(a)phys.nagoya-u.ac.jp, akimura(a)tb.phys.nagoya-u.ac.jp, caflisch(a)bioc.uzh.ch, philippe.derreumaux(a)ibpc.fr, Chantal Prevost <chantal(a)ibpc.fr>, cragnolini(a)ibpc.fr, phuong.nguyen(a)ibpc.fr, francesco.oteri(a)ibpc.fr, charles.robert(a)ibpc.fr, Sophie.Sacquin-Mora(a)ibpc.fr, heidi.koldsoe(a)bioch.ox.ac.uk, michal.linial(a)huji.ac.il, taly(a)ibpc.fr, Viet Duc <frauman05(a)yahoo.de>, Elena.Papaleo(a)bio.ku.dk, Fabian Theis <fabian.theis(a)helmholtz-muenchen.de>, Sara Nichols <sara.nichols(a)gmail.com>, gregor.lichetner(a)fu-berlin.de, "Coulon, Antoine (NIH/NIDDK) [F]" <antoine.coulon(a)nih.gov>, johannes.schoeneberg(a)fu.berlin.de, alexander.ullrich(a)fu-berlin.de, mickael.lelimousin(a)bioch.ox.ac.uk, matthieu.chavent(a)bioch.ox.ac.uk > > Dears Colleagues, > > Two post doctoral research positions are available at the Bioinformatics, Molecular Dynamics and Modeling (BiMoDyM) team (http://tinyurl.com/tchertanov) Molecular Oncology and Pharmacology, LBPA, ENS de Cachan (http://www.ens-cachan.fr/) France. > The required profiles of candidats are descibed in the attached documents. > Thank you very much for larger distribution of this information. > > Sincerely your, > Luba Tchertanov > > ********************* > Dr. Luba Tchertanov > Directeur de Recherche, CNRS > > Membre du Comité de Pilotage du LabEx LERMIT > Coordinateur ENSC-UFRJ > Collége Universitaire Franco-Brésilien Santos Dumont > > Resp. BiMoDyM > LBPA-CNRS, ENS de Cachan, > 61 avenue du Président Wilson > 94235 CACHAN CEDEX, FRANCE > > Tel: +33 (0)1 4740 7662 > Cell: +33 (0)6 6115 9611 > Fax: +33(0)1 4740 7671 > e-mail: Luba.Tchertanov(a)lbpa.ens-cachan.fr > > >

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[Compbio-allhands] Fwd: postdoctoral and PhD positions
by Andrej Sali 25 Jun '12

25 Jun '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at 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: Michael Nilges <michael.nilges(a)pasteur.fr> > Subject: postdoctoral and PhD positions > Date: June 25, 2012 5:03:38 AM PDT > To: Alexandre Bonvin <a.m.j.j.bonvin(a)uu.nl>, Andrej Sali <sali(a)salilab.org>, annick.dejaegere(a)igbmc.fr, Axel Brunger <brunger(a)stanford.edu>, carol.robinson(a)chem.ox.ac.uk, Catherine Etchebest <catherine.etchebest(a)univ-paris-diderot.fr>, Cheryl Arrowsmith <carrow(a)uhnres.utoronto.ca>, Christian Griesinger <cigr(a)nmr.mpibpc.mpg.de>, Christoph Mueller <christoph.mueller(a)embl.de>, "David A. Agard" <agard(a)msg.ucsf.edu>, DavidBaker <dabaker(a)u.washington.edu>, David Perahia <david.perahia(a)ens-cachan.fr>, Dmitri Svergun <svergun(a)embl-hamburg.de>, Edward Egelman <egelman(a)virginia.edu>, Ernest Laue <e.d.laue(a)bioc.cam.ac.uk>, "G. Klebe" <Klebe(a)staff.uni-marburg.de>, Gerald Kneller <gerald.kneller(a)cnrs-orleans.fr>, Gerhard Wagner <gerhard_wagner(a)hms.harvard.edu>, Gilles Labesse <Gilles.Labesse(a)cbs.cnrs.fr>, Helmut Grubmueller <hgrubmu(a)gwdg.de>, Hoch Jeffrey <hoch(a)uchc.edu>, Ivano Bertini <bertini(a)cerm.unifi.it>, Jody Puglisi <puglisi(a)stanford.edu>, Julie Forman-Kay <forman(a)sickkids.ca>, Juri Rappsilber <juri.rappsilber(a)ed.ac.uk>, Konrad Hinsen <research(a)khinsen.fastmail.net>, liliane.mouawad(a)curie.u-psud.fr, Lewis Kay <kay(a)pound.med.utoronto.ca>, Luba Tchertanov <luba.tchertanov(a)lbpa.ens-cachan.fr>, Marc Baaden <baaden(a)smplinux.de>, Marc Baldus <maba(a)mpibpc.mpg.de>, Marius Clore <mariusc(a)intra.niddk.nih.gov>, Martin Beck <martin.beck(a)embl.de>, Michael Levitt <michael.levitt(a)stanford.edu>, Michael Sattler <sattler(a)helmholtz-muenchen.de>, michel kochoyan <michel(a)cbs.cnrs.fr>, Michele Vendruscolo <mv245(a)cam.ac.uk>, Oliver Lange <oliver.lange(a)tum.de>, Roland STOTE <rstote(a)igbmc.fr>, Aebersold Rudolf <aebersold(a)imsb.biol.ethz.ch>, Rebecca Wade <rebecca.wade(a)h-its.org>, ZINN Sophie 140275 <Sophie.ZINN(a)cea.fr>, Tom Simonson <Thomas.Simonson(a)polytechnique.fr>, William.Degrado(a)ucsf.edu, Wolfgang Baumeister <baumeist(a)biochem.mpg.de> > > Dear collegues, > > I would be very grateful indeed if you could transmit the information on the available positions to interested candidates. > > Best regards > > Michael > > Applications are invited for Postdoctoral and PhD positions funded by the ERC project BayCellS, to work on the development of innovative molecular modeling concepts for cellular structural biology. The successful candidates will join the Structural Bioinformatics Unit in the Department of Structural Biology and Chemistry at the Pasteur Institute in Paris, France. > > To characterize 3D structures of the large and often flexible macromolecular complexes that govern cellular processes, high resolution structure determination is the exception, and multiple sources of structural data at multiple resolutions are employed. Integrating these data into one consistent picture poses particular difficulties: data are much more sparse than in high resolution methods; data sets from heterogeneous sources are of highly different and unknown quality and may be mutually inconsistent; data are in general averaged over large ensembles and long measurement times. The project is to develop a consistent framework for this highly complex data integration problem, principally based on Bayesian probability theory. Appropriate models for the major data types used in hybrid approaches (electron microscopy, cross-linking/ mass spectrometry, various spectroscopy techniques, SAXS, ...) will be developed, as well as representations to include structural knowledge for individual components of the complexes. The new methods will be applied to a series of problems with increasing complexity. The ideal candidate has a strong background in mathematics/ statistics, theoretical biophysics or molecular modeling applied to macromolecular structure determination; experience in programming (Python, C); and an interest in Bayesian probability theory. > > Contact: Michael Nilges, Department of Structural Biology and Chemistry, Structural Bioinformatis Unit; michael.nilges(a)pasteur.fr > > > > > > > > ================ > Prof. Michael Nilges > Structural Bioinformatics Unit, Head > Department of Structural Biology and Chemistry, Head > Institut Pasteur, CNRS URA 2185 > 25-28 rue du docteur Roux, F-75015 Paris, France. > Tel: +33 1 45 68 82 30; Fax: +33 1 45 68 87 19 > secrétariat: +33 1 44 38 91 09 > > >

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[Compbio-allhands] FW: Hiring a Computational Biologist
by Jacobson, Matt 22 Jun '12

22 Jun '12

Brian was a BMI graduate student … very good scientist From: brian tuch <brian.tuch(a)gmail.com<mailto:brian.tuch@gmail.com>> Date: Friday, June 22, 2012 1:30 PM To: "btuch(a)onyx.com<mailto:btuch@onyx.com>" <btuch(a)onyx.com<mailto:btuch@onyx.com>> Subject: Hiring a Computational Biologist Hi all, I am looking for the best industry-bound graduate students and postdocs you know to join my new genomics group at Onyx. Onyx is small, but rapidly growing oncology therapeutics company in South San Francisco. My group's goals are to understand why certain patients respond to our existing drugs and to identify new drug targets in patients that do not. A lot of interesting basic and clinical research is involved in these efforts and I expect we will be publishing many of our findings. We will be starting with copious clinical samples and a generous budget, but not much else; our genomics infrastructure must be built from the ground up. This is my group's first hire, so I'm hoping to find an adaptable, star computational scientist, someone you might have thought to hire when you first started your labs. The hire will rapidly gain knowledge of cancer biology and the pharmaceutical process here, so those are not requirements. The most important characteristics are analytical chops and enthusiasm. The job description and specific requirements are attached. Please feel free to circulate this message. Thank you for your assistance. Cheers, Brian

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[Compbio-allhands] Fwd: Open Position for Computer System Administrator
by Andrej Sali 14 Jun '12

14 Jun '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at 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: "Montelione, Gaetano" <guy(a)cabm.rutgers.edu> > Subject: Open Position for Computer System Administrator > Date: June 14, 2012 7:49:06 AM PDT > To: "Tejero, Roberto" <Roberto.Tejero(a)uv.es>, Honig Barry <bh6(a)columbia.edu>, Burkhard Rost <rost(a)columbia.edu>, "Y. Janet Huang" <yphuang(a)cabm.rutgers.edu>, "Ronald M. Levy" <ronlevy(a)lutece.rutgers.edu>, "Gerstein, Mark(a)yale.edu" <Mark.Gerstein(a)yale.edu>, Andrej Sali <sali(a)salilab.org>, "David A. Case" <case(a)biomaps.rutgers.edu> > Cc: John Everett <everett.jk(a)gmail.com> > > Phil Kostenbader, our computer system administrator, has taken a new job and will > be leaving CABM shortly. > > So we are looking for a new full time computer system administrator. Person > should be familiar with Linux system administration, including: > > - experience with Linux cpu clusters > - web server administration / Apache experience > - LDAP authentication > - network and system security /firewall DMZ > > > We will prepare a formal ad soon -- but I will appreciate if you can > circulate this to anyone you know who might be interested. They > can contact me directly > > Guy Montelione

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[Compbio-allhands] Fwd: Postdoc position available -- interactive molecular graphics -- Uppsala, Sweden
by Tom Ferrin 12 Jun '12

12 Jun '12

-------- Original Message -------- Subject: Postdoc position available -- interactive molecular graphics -- Uppsala, Sweden Date: Fri, 8 Jun 2012 12:47:08 -0500 From: Samuel Flores <samuelfloresc(a)gmail.com> To: tef(a)cgl.ucsf.edu Hi Tom, I hope all is well with you. As a longtime user of Chimera, I am familiar with your work. I think you may be able to help me identify a brilliant almost- or recently-graduated PhD for an opening in my lab. I am looking for a rare skill set -- someone who can make a next-generation interactive 3D modeling tool based on my internal coordinate MMB code and a graphics library (Blender, Rasmol, etc). The tool will go far beyond existing viewers, allowing users to assemble macromolecules, flexibilize them where desired, and rearrange domains interactively, as well as performing a number of dynamics tasks supported by MMB. I am attaching the job announcement and hope you can distribute it widely by email and (if possible) on bulletin boards at UCSF. I will be in Palo Alto July 2nd and perhaps 3rd and would love to drop by and chat, so as to receive your advice on this project, if you have the time. Sam

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[Compbio-allhands] Fwd: Referred by Christine Humblet
by Andrej Sali 04 Jun '12

04 Jun '12

Hi Andrej, If you decide to post these positions to your email list please have the students and postdocs contact me at the information below. Jared Jared Kaleck Account Executive Klein Hersh International 215-830-9211 Ext. 116 jkaleck(a)kleinhersh.com www.kleinhersh.com Begin forwarded message: > From: Jared Kaleck <JKaleck(a)kleinhersh.com> > Subject: RE: Referred by Christine Humblet > Date: June 4, 2012 11:26:00 AM PDT > To: Andrej Sali <sali(a)salilab.org> > > > > Eli Lilly – Indianapolis, IN > Principal Research Scientist/Senior Research Scientist > Computational Chemistry > The Discovery Chemistry Research and Technology Division at Eli Lilly Company is looking to further enhance the scientific talent base of the organization by identifying individuals with high potential and emerging track record of delivering drug discovery innovation. > > Ideal Individuals to Compliment Lilly’s Scientific Team > · Talented Ph.D. Computational Chemistry with broad expertise in Computer-Aided Design approaches. > · Creative thinking and problem solving skills – ability to bring new ways of applying or pioneering computational approaches and/or new initiatives to facilitate and enhance drug discovery projects. > · Proven/emerging scientific leadership abilities – must include leadership work with outside partners and/or scientists from academia. > · Ability to influence scientific direction across research sites, discovery functions and teams. A proven desire to make an impact on projects through cross-functional teamwork. > · Strong background in medicinal chemistry and lead generation/lead optimization approaches. > · Organizational development and mentoring skills. > · Excellence in communication and networking skills. > · Demonstrated abilities to multi-task. > · Entrepreneurial and innovative approach to science; good judgment, risk taking and intuition. > · Programming skills (Perl, Python, Pipelining) preferred. > > > > NOVARTIS – Cambridge, MA > Computational Chemical-Biology Research Investigator (Ph.D) > > Job Description: > > A position is available for a highly motivated scientist in the in silico Lead Discovery group of the Center for Proteomic Chemistry platform. This is an exciting opportunity to perform cutting-edge computational research at our Cambridge USA site. The position will be responsible for the development of robust computational hypothesis with a variety of drug discovery project teams for the purposes of lead discovery. You will apply state of the art computational approaches to elucidate the biological profile of small molecules regarding their targets, off-targets and phenotypic outcome via an in-depth understanding of biological networks, systems biology, bioinformatics and cheminformatics > > Minimum requirements: > > The ideal candidates will possess the following qualifications: > > · Ph.D. degree in computational biology, systems biology, bioinformatics, cheminformatics or a related field. > · Experience with 'omics analysis (transcriptomics, proteomics, metabolomics, chemogenomics). > · Ability to computationally navigate molecular pathways and networks and form hypotheses about compounds, targets, phenotype, and disease associations > · Familiarity with compound databases, such as ChEMBL or PubChem, and public bioinformatics databases. > · Understanding of up-to-date biological screening paradigms like reporter assays, mRNA signatures, assays for transcription, translation, stability, and post-translational modifications and high content screens. > · A solid understanding of quantitative data analysis, data mining and pattern recognition methods. > · Ability to work independently and collaborate in multidisciplinary teams locally and globally. > · Strong analytical and problem-solving skills and scientific creativity are essential. > · Excellent oral and written communication skills and organizational skills are required. > · Familiarity with life sciences software (R, Spotfire, Pipeline Pilot, Knime, Cytoscape, GeneGo) is desirable, as is a working knowledge of Relational Databases and SQL. > > > > NOVARTIS – Cambridge, MA > Computational Chemistry or Biology Research Investigator (Ph.D) > > Job Description: A position is available for a highly-motivated scientist to join a dynamic group in the Center for Proteomic Chemistry/Lead Finding Platform. This is an exciting opportunity to perform cutting-edge research at our Cambridge site. > First, you will be responsible for the analysis and development of HTS screening hits to leads. You will apply state of the art chemometric or bioinformatics approaches for the elucidation of the biological profile of small molecules regarding their targets, off-targets and phenotypic outcome. Second, you will provide support, maintenance and further development of key infrastructure related to virtual screening databases and methods, and an internally developed computational services framework. > > Minimum requirements: The ideal candidate will possess the following qualifications: > • Ph.D. degree in computational biology, bioinformatics, cheminformatics or a related field. > • Databases: MySQL, SQL Server and Oracle > • Languages: C, C#, Perl, Python, Web Applications and Tools: HTML, ASP.net, > • Experience with 'omics data and molecular pathway/network analysis to enhance target knowledge. > • Familiarity with compound information databases such as ChEMBL or PubChem. > • Understanding of up-to-date biological screening paradigms like reporter assays, mRNA signatures, assays for transcription, translation, stability, and post-translational modifications and high content screens. > • A solid understanding of basic statistics and quantitative data analysis, data mining and pattern recognition methods. > • Familiarly with PipelipePilot and Knime – a big plus > • Ability to both work independently and collaborate in multidisciplinary teams. > • Strong analytical and problem-solving skills and scientific creativity are essential. > • Excellent oral and written communication skills and organizational skills > > > > > > > > Jared Kaleck > Account Executive > Klein Hersh International > 215-830-9211 Ext. 116 > jkaleck(a)kleinhersh.com > www.kleinhersh.com >

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[Compbio-allhands] Fwd: reminder, seminar by Chia-en Chang
by Jacobson, Matt 01 Jun '12

01 Jun '12

Just a reminder about this seminar, 1pm, BH212 Begin forwarded message: I'm hosting Chia-en Chang on Friday June 1. She will give a seminar at 1 pm in BH212; title and abstract below. Chia-en did her graduate work with Mike Gilson and postdoc with Andy McCammon, and has been at UC Riverside for about 4 years now. The mining minima work she will be discussing is some of the most impressive free energy calculations I've seen. http://chem.ucr.edu/chang If you'd like to meet with her, Lili is helping to coordinate her schedule. Title: Insights from Free Energy Calculations: Protein Conformational Equilibrium, Driving Forces and Ligand Binding Processes Abstract: To accurately calculate ligand-protein binding affinity is still challenging in computational chemistry. In this presentation, we used a free energy calculation method, the mining minima algorithm (M2), to compute the binding affinities of various types of inhibitors to p38α MAP kinase. This end-point approach uses an empirical force field and implicit solvent models to find stable conformations in the free and bound states of a system and then compute the binding free energy of each species. Here we selected 30 different p38α inhibitors that can bind to either DFG-in or DFG-out conformations. Notably, some analogs do not have ligand-p38 co-crystal structures. Our computed absolutely binding free energies yield excellent agreement with experimental data and reveal the driving forces of binding. Our results also show the dynamic equilibrium in the DFG-in and DFG-out states and explain why the conformations can co-exist. In addition, I will introduce a novel method to study ligand binding processes in chemical host-guest system. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences 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 on Friday
by Jacobson, Matt 30 May '12

30 May '12

I'm hosting Chia-en Chang on Friday June 1. She will give a seminar at 1 pm in BH212; title and abstract below. Chia-en did her graduate work with Mike Gilson and postdoc with Andy McCammon, and has been at UC Riverside for about 4 years now. The mining minima work she will be discussing is some of the most impressive free energy calculations I've seen. http://chem.ucr.edu/chang If you'd like to meet with her, Lili is helping to coordinate her schedule. Title: Insights from Free Energy Calculations: Protein Conformational Equilibrium, Driving Forces and Ligand Binding Processes Abstract: To accurately calculate ligand-protein binding affinity is still challenging in computational chemistry. In this presentation, we used a free energy calculation method, the mining minima algorithm (M2), to compute the binding affinities of various types of inhibitors to p38α MAP kinase. This end-point approach uses an empirical force field and implicit solvent models to find stable conformations in the free and bound states of a system and then compute the binding free energy of each species. Here we selected 30 different p38α inhibitors that can bind to either DFG-in or DFG-out conformations. Notably, some analogs do not have ligand-p38 co-crystal structures. Our computed absolutely binding free energies yield excellent agreement with experimental data and reveal the driving forces of binding. Our results also show the dynamic equilibrium in the DFG-in and DFG-out states and explain why the conformations can co-exist. In addition, I will introduce a novel method to study ligand binding processes in chemical host-guest system. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences 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] QBC Journal Club, Tuesday, June 5- 10:45AM, GH Aud
by Nicole Takesono Flowers 30 May '12

30 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, June 5 10:45 am, GH Auditorium Jessica Thomaston, CCB Experimental adaptation of an influenza H5 HA confers respiratoryrndroplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Imai, Masaki et al. Nature. Available online May 2012. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics 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 positions
by Andrej Sali 25 May '12

25 May '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at 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: pettitt <mpettitt(a)utmb.edu> > Subject: Faculty positions > Date: May 25, 2012 12:58:39 PM PDT > To: sali(a)salilab.org > > Dear Andrej, > > To expand our programs in structural biology at the University of Texas Medical Branch in Galveston, we are beginning searches to fill three senior-level faculty positions in the Sealy Center for Structural Biology and Molecular Biophysics. We currently seek individuals whose connection to structural biology is through cryo EM, x-ray or NMR (nominally one position each) and who wish to take advantage of a rich collaborative environment. This is part of a large investment by the university in structural biology and ten related hires are expected over the next 5 years. The first individual(s) hired will have a significant role in selecting the remaining senior and junior individuals hired into the program. > > We have facilities with excellent instrumentation and fully staffed with high quality individuals. Ours is a research resource supported by the University so there are no core charges for Center faculty to use our facilities. That and our location on the outskirts of Houston with proximity to the Texas Medical Center are attractive features. > > If you know of anyone that may have interest, we would be delighted to hear about it. Further information about the position(s) can be found attached. As well, additional information about the Sealy Center for Structural Biology may found on the web at http://www.scsb.utmb.edu/ > Thank you in advance for any help that you can provide in identifying suitable senior-level candidates for these positions. > > Sincerely, > Monte > > B. Montgomery Pettitt > Robert A. Welch Professor of Chemistry > in Pharmacology and Toxicology > Professor of Biochemistry and Molecular Biology > Director, Sealy Center for Structural Biology > and Molecular Biophysics > University of Texas Medical Branch > mpettitt(a)utmb.edu

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[Compbio-allhands] 5/31/12 Seminar with Ira Mellman
by Nicole Takesono Flowers 25 May '12

25 May '12

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 Jim Ferrell Stanford University Dissecting the Mitotic Trigger May 31, 2012 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: Request for assistance - Associate Scientist opportunity with Genentech - Absorption process & PK/PD Formulation
by Jacobson, Matt 23 May '12

23 May '12

-- Matt Sent from my iPhone Begin forwarded message: From: Keith Terry <terry.keith(a)gene.com<mailto:terry.keith@gene.com>> Date: May 23, 2012 11:00:23 AM PDT To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Request for assistance - Associate Scientist opportunity with Genentech - Absorption process & PK/PD Formulation Hi Matthew, My name is Keith Terry and I am an internal recruiter with Genentech in South San Francisco. I am reaching out to you today to ask for your assistance. I am supporting Genentech’s Early Research and Development (gRED) department in the area of formulation development small molecules. We have an outstanding opportunity for a passionate and innovative Ph.D. to join our group. I thought that you might know of a dynamic scientist (either a recent graduate or currently in post doc) that would be interested in the attached job. Potential candidates DO NOT need previous pharmaceutical industry experience. A well published Ph.D. who has recently graduated from a highly regarded program would be perfect. To summarize what we are looking for: • Ph.D. level candidates with strong scientific knowledge in Pharmaceutical Sciences and a proven record of publications. • In-depth knowledge absorption process, PK/PD and application of such knowledge in science-based formulation approaches and drug delivery design. • Good communication and problem-solving skills and be a team player. • Must have a Ph.D in Pharmaceutics, Chemistry, or related fields with minimum of 0-5 years-experience in the Pharmaceutical Industry. Please feel free to pass the attached flier along to individuals that you feel would be qualified and potentially interested. You are welcome to post the flier on your department’s job board. If you have any questions at all regarding this opportunity or would like to learn more about Genentech, please feel to call me directly. Thanks so much for your assistance. Cheers, Keith Keith Terry Talent Acquisition Specialist Genentech, A Member of the Roche Group 650-467-1557<tel:650-467-1557> terry.keith(a)gene.com<mailto:terry.keith@gene.com> Why is Genentech such a great place to work? Check out this video! Our People<http://www.youtube.com/watch?v=DMalKJ0_8-A> (click to view)

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[Compbio-allhands] QBC Journal Club, Tuesday, May 29- 10:45AM, GH Aud
by Nicole Takesono Flowers 23 May '12

23 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 29 10:45 am, GH Auditorium Yu Jack Yue, iPQB Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication. Megan Y. Dennis, et al. Cell 149, 4, 912-922. 2012 Diego Garrido Ruiz, iPQB Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing. Hopf, Thomas A., Colwell, Lucy J.,Sheridan, Robert, Rost, Burkhard, Sander, Chris, Marks, Debora S. Cell, Available online May 2012. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics 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: Genentech postdoc position: request for candidates
by Andrej Sali 22 May '12

22 May '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at 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: "Isidro (Dan) Zarraga" <zarraga.isidro(a)gene.com> > Subject: Genentech postdoc position: request for candidates > Date: May 22, 2012 2:31:30 PM PDT > To: sali(a)salilab.org > Cc: hilary(a)salilab.org > > Dear Prof. Sali, > > Please find attached a description of a Genentech postdoc opportunity. Kindly circulate to those who might be interested. We would like to fill the position soon so those interested are encouraged to send their resumes as soon as possible. Thank you very much. > > Sincerely, > > Dan E. Zarraga, PhD > Late Stage Pharmaceutical Development > Genentech Bldg 56 Rm 2119 > South San Francisco CA 94030 > Tell: 650 2257617

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[Compbio-allhands] 5/24/12 Seminar with Ira Mellman
by Nicole Takesono Flowers 18 May '12

18 May '12

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 Ira Mellman Genentech Next Generation Approaches to Basic Cell Biology & Drug Discovery May 24, 2012 Justin Rettenmeier, 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] QBC Journal Club, Tuesday, May 22- 10:45AM, GH Aud
by Nicole Takesono Flowers 16 May '12

16 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 22 10:45 am, GH Auditorium Andrew Van Benschoten, iPQB Sexual Deprivation Increases Ethanol Intake in Drosophila. Shohat-Ophir et al. Science, 2012 Mar 16; 335 (6074): 1351-5. Naomi Yonis, CCB Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress. Lee, I.H. et al. Science ,336, 225 (2012). bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics 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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