- 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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