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

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

26 Apr '13

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

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

26 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus HSW 303 Laura Kiessling University of Wisconsin-Madison Probing and Perturbing the Cell's Glycan Coat May 2, 2013 K. Shokat, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: postdoc ad
by Tom Ferrin 23 Apr '13

23 Apr '13

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

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

23 Apr '13

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Dan Hostetter <dan(a)cytomx.com> > Subject: Bioinformatics Summer Intern Posting_Ltr(2).docx > Date: April 22, 2013 4:29:09 PM PDT > To: Dave Barkan <davebarkan(a)gmail.com>, "sali(a)salilab.org" <sali(a)salilab.org> > Cc: Luc Desnoyers <luc(a)cytomx.com> > > Hi Dave and Andrej, > > Hope you are both doing really well! > > I’ve been having a great time applying my protease knowledge at CytomX . We have started our very first summer internship program and need bioinformatics expertise. I thought both of you would be a great resource for recommendations. > > CytomX has applied the pro-drug concept to antibody therapeutics to address toxicities that occur when antibodies bind to target in healthy tissue. We call our protease activated antibodies “Probodies”. Our technology leverages protease activity that is present in tumor tissue and not healthy tissue to activate our Probodies. We would love to mine RNA expression databases for targets that fit certain criteria such as (1) extracellular and therefore accessible to an antibody therapeutic and (2) a protease that can cleave our Probody is also expressed. The ideal candidate would be comfortable working with RNA expression databases and able to create filters based on the needs of our Probody platform. I’ve attached a description of the intern position to this email as a Word document. > > I’m copying Luc Desnoyers on this email. Luc is the head of our cell biology group and is a great mentor. The student intern would be working with Luc and someone in the cell biology group. I can vouch that everyone in Luc’s group is nice and all of them are patient teachers. > > If you have anyone in mind that would be a good fit, please let us know. I’m confident they would have a great experience at CytomX. > > Thanks guys! > > Best, > Dan

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

19 Apr '13

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

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

19 Apr '13

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

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

16 Apr '13

Begin forwarded message: From: "Groban, Eli" <EGroban(a)intrexon.com<mailto:EGroban@intrexon.com>> Subject: FW: Computational biologist position at Monsanto Date: April 16, 2013 11:33:58 AM PDT To: "matt(a)cgl.ucsf.edu<mailto:matt@cgl.ucsf.edu>" <matt(a)cgl.ucsf.edu<mailto:matt@cgl.ucsf.edu>> FYI. Thank you, Eli Groban, PhD Director, Metabolic Engineering and Systems Biology Industrial Products Division Intrexon Corporation 201 Industrial, Suite 450, San Carlos, CA 94070 p: 650.597.4026 | m: 415.971.7517 | egroban(a)intrexon.com<mailto:name@intrexon.com> www.dna.com<http://www.dna.com/> From: Kevin Costa <kcosta(a)berkeley.edu<mailto:kcosta@berkeley.edu>> Date: Tuesday, April 16, 2013 11:19 AM To: "all(a)synberc.org<mailto:all@synberc.org>" <all(a)synberc.org<mailto:all@synberc.org>> Subject: Computational biologist position at Monsanto Monsanto seeks a creative, mathematically-minded Computational Biologist to help us transform big data into higher yielding crops. In this role you role will support research across Monsanto Technology by integrating, modeling, and interpreting unprecedented genomic, transcriptomic, metabolic, phenotypic, population genetic, and geospatial data, all with the goal of driving interpretation into practical use. We aim to help feed the mid-21st century world using less water, less fertilizer, and less pesticide. https://monsanto.taleo.net/careersection/2/jobdetail.ftl?job=262740&lang=en… -- [cid:part2.03050501.00000805@berkeley.edu]<http://synberc.org/> Kevin Costa Administrative Director SynBERC - Synthetic Biology Engineering Research Center University of California, Berkeley 5885 Hollis Street, Room 4214, Mailcode 3224 Emeryville, CA 94608-2015 510-486-7568 510-432-7568 (cell) 510-486-4252 (fax) kcosta(a)berkeley.edu<mailto:kcosta@berkeley.edu> www.synberc.org<http://www.synberc.org/> ________________________________ CONFIDENTIAL TRANSMISSION - This message, including any attachments, is confidential and may be privileged. If you are not the intended recipient, please delete it without further distribution and reply to the sender that you have received the message in error. [cid:part2.03050501.00000805@berkeley.edu] Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] 4/18/13 Seminar with Garry Nolan
by Nicole Takesono Flowers 12 Apr '13

12 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Garry Nolan Stanford A structure for cancer and immunity at the single cell level by mass cytometry April 18, 2013 J. Rettenmaier, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 4/11/13 Seminar with Brenda Schulman
by Nicole Takesono Flowers 04 Apr '13

04 Apr '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Brenda Schulman St. Jude Children's Research Hospital Twists and Turns in Ubiquitin Conjugation Cascades April 11, 2013 J. Gross, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: A summer intern position opening in computational chemistry at GlaxoSmithKline
by Jacobson, Matt 02 Apr '13

02 Apr '13

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

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

01 Apr '13

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

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[Compbio-allhands] 3/14/13 Seminar with Celeste Nelson
by Nicole Takesono Flowers 07 Mar '13

07 Mar '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Celeste Nelson Princeton Physical control of tissue morphogenesis March 14, 2013 Z. Gartner, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 3/7/13 Seminar with Michael Laub
by Nicole Takesono Flowers 04 Mar '13

04 Mar '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Michael Laub MIT Specificity and evolution of bacterial signaling pathways March 7, 2013 A. Shiver, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: University of Calgary, Canada Research Chair-II Chair in Computational NanoBioMedicine
by Andrej Sali 28 Feb '13

28 Feb '13

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Peter Tieleman <tieleman(a)ucalgary.ca> > Subject: University of Calgary, Canada Research Chair-II Chair in Computational NanoBioMedicine > Date: February 28, 2013 6:07:27 PM PST > To: "Prof. J. Andrew McCammon" <jmccammon(a)mail.ucsd.edu>, Ken Dill <dill(a)laufercenter.org>, "\"\"\"\"jonuchic\"@rice. edu"@guitar.compbio.ucsf.edu, "'Hue Sun Chan'" <chan(a)arrhenius.med.utoronto.ca>, Régis Pomès <pomes(a)sickkids.ca>, "'Gilles H. Peslherbe'\"" <Gilles.Peslherbe\"@Concordia.ca>, mgilson(a)ucsd.edu, mlklein(a)temple.edu, hgrubmu@��gwdg.de, Bert de Groot <bgroot(a)gwdg.de>, Erik Lindahl <lindahl(a)cbr.su.se>, Qiang Cui <cui(a)chem.wisc.edu>, Arun Yethiraj <yethiraj(a)chem.wisc.edu>, Marc Baaden <baaden(a)smplinux.de>, David Spoel <spoel(a)xray.bmc.uu.se>, Benoit Roux <roux(a)uchicago.edu>, g.gompper(a)fz-juelich.de, Sandeep Patel <spatel(a)mail.chem.udel.edu>, Edward Lyman <elyman(a)udel.edu>, sali(a)salilab.org, Mark Sansom <mark.sansom(a)bioch.ox.ac.uk>, Michael Feig <feig(a)msu.edu>, "Baker,"Nathan <Nathan.Baker"@pnnl.gov>, David Sept <dsept(a)umich.edu>, David Shaw <David.Shaw(a)DEShawResearch.com>, Simon Bernèche <simon.berneche(a)unibas.ch>, bb8(a)columbia.edu, amackere(a)rx.umaryland.edu, Thomas Cheatham III <tec3(a)utah.edu>, Ross Walker <ross(a)rosswalker.co.uk>, Bernard.Brooks2(a)nih.hhs.gov, Wilfred F. van Gunsteren <wfvgn(a)igc.phys.chem.ethz.ch>, Siewert Jan Marrink <S.J.Marrink(a)rug.nl>, hummer(a)helix.nih.gov, Christine Peter <peter(a)mpip-mainz.mpg.de>, "> > > Dear colleagues, > > Please bring the attached ad to the attention of potential candidates. We think this is a great opportunity for excellent younger scholars. > > With best regards, > > Peter > > -- > Dr. D. Peter Tieleman, Professor, AIHS Scientist > AITF Strategic Chair in (Bio)Molecular Simulation > Department of Biological Sciences, University of Calgary

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

28 Feb '13

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

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

22 Feb '13

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 David Liu Harvard Small-molecule and macromolecule discovery driven by evolution February 28, 2013 Z. Gartner, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: bioinformatics/programmer opening for BindingDB project
by John Irwin 21 Feb '13

21 Feb '13

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

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[Compbio-allhands] Fwd: recruitment letter...
by Andrej Sali 21 Feb '13

21 Feb '13

Begin forwarded message: > From: Ram Samudrala <ram(a)compbio.washington.edu> > Subject: recruitment letter... > Date: February 21, 2013 4:31:36 PM PST > To: sali(a)salilab.org > Reply-To: ram(a)compbio.washington.edu > > Hi Andrej, I hope you are well. I am wondering if you could forward > this email around to your local CompBio groups? Thanks. > > --Ram > > > Postdoctoral opportunity in Translational Research Project at the Samudrala > Group in University of Washington, Seattle > > -- > > The Samudrala group at the University of Washington in Seattle is > seeking to recruit 2-3 postdoctoral fellows to work on the > Computational Analysis of Noval Drug Opportunities (CANDO) drug > discovery project funded by a 2012 NIH Director's Pioneer Award > (http://cando.compbio.washington.edu) The project goals are to screen > all human ingestible compounds against all proteins (primarily solved > protein structures) computationally to identify new uses for existing > drug compounds. Computational hits/leads are verified in vitro quickly > followed by clinical studies (since all compounds studied initially > are FDA approved drugs) for more than 30 indications with the aid of > numerous collaborations. > > The project has just begin its 3rd year, and an initial version of the > compound-protein matrix covering several thousand drugs (mostly FDA > approved drugs) vs. ~40,000 protein structures has been > completed. Bench studies are underway for two of the initial > indications we are going after (beta thalessemia major and multi-drug > resistant tuberculosis) and numerous other bench studies are soon to > follow. This is based on the multitargeting idea of how one compound > (or more) interacts with multiple proteins (all structures and > homologues) in a given system to produce a desired outcome (which is > how it happens in nature). More importantly, anything we find can be > directly evaluated by quick clinical study to demonstrate efficacy > since everything we'll initially focus on would've made it clinical > trials or through phase 2 testing at least. > > We are looking for individuals with the passion and skill set to help > us complete and deploy the pipeline for maximal benefit. Particularly > we are interested in a pipeline developer who would ideally be an > expert on machine learning techniques that will help integrate the > chem- and bioinformatic data with docking simulations, i.e., create a > more robust and automated pipeline that is adaptable to individual > indications and genotypes. We are also interested in a docking code > developer that will help implement the third version of the > fragment-based docking with dynamics protocol we have developed and > integrate the pipeline and docking methodology as a systems-based drug > discovery product. Another role which is part of the developer job > description is to work on a web application that can handle > personalisation and integrate it with our in-house cando database > API. This will finally give one-stop-shop-software to find putative > drugs for a particular indication of interest done using all the > proteins of the related organisms. So the final output of our > methodology is a drug-disease network which is linked back to > protein-compounds network, i.e. an atomistic description of all > existing and new drug prediction we are making. > > Gaurav Chopra, one of my postdocs and the overall project manager of > CANDO, will be attending CASP10 and is the person who you'd closely > work with should you accept this position. So please talk to him and > if you're interested in this position, and if you feel the project is > a good fit for you, send us both your CV and a brief statement of > interest to gaurav(a)compbio.washington.edu and > ram(a)compbio.washington.edu > > -- > > -- > > --- > You received this message because you are subscribed to the Google Groups "samudrala-compbio" group. > To unsubscribe from this group and stop receiving emails from it, send an email to samudrala-compbio+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > > > > --20cf306f722a5dcabe04d6442e13 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Hi = > George,<div> =3D"arial,helvetica,sans-serif"> </div><div> olor=3D"#000000">Here is th= > e email we sent out for CASP when I met people there. Please change as need= > ed and spread the word for recruiting two postdocs!</d= > iv> > > <div> "> </div><div> ace=3D"arial,helvetica,sans-serif">Thanks,</div><div><= > font color=3D"#000000">Gaur= > av</div> > > <div> "> </div><div> =3D"arial, helvetica, sans-serif">--</div><div> style-span" face=3D"arial, helvetica, sans-serif"> e-span" style=3D"border-collapse:collapse;color:rgb(34,34,34);font-family:a= > rial,sans-serif;font-size:13px"> > > Postdoctoral opportunity in Translational Research Project at the Samudrala= > Group in University of Washington, Seattle -- The Samudrala = > group at the University of Washington in Seattle is seeking to recruit 2= > -3 postdoctoral fellows to work on the > > Computational Analysis of Noval Drug Opportunities (CANDO) drug discover= > y project funded by a 2012 NIH Director's Pioneer Award (<a href=3D"= > http://cando.compbio.washington.edu/" target=3D"_blank" style=3D"color:rgb(= > 17,85,204)">http://cando.compbio.washington.edu</a>). The project goals are= > to screen > > all human ingestible compounds against all proteins (primarily solved pr= > otein structures) computationally to identify new uses for existing drug= > compounds. Computational hits/leads are verified in vitro quickly > followed by clinical studies (since all compounds studied initially > are FDA approved drugs) for more than 30 indications with the aid of num= > erous collaborations. The project has just begin its 3rd year, and a= > n initial version of the compound-protein matrix covering several thousa= > nd drugs (mostly FDA > > approved drugs) vs. ~40,000 protein structures has been completed. Bench= > studies are underway for two of the initial indications we are going af= > ter (beta thalessemia major and multi-drug resistant tuberculosis) and n= > umerous other bench studies are soon to > > follow. =A0This is based on the multitargeting idea of how one compound = > (or more) interacts with multiple proteins (all structures and homologue= > s) in a given system to produce a desired outcome (which is how it happe= > ns in nature). More importantly, anything we find can be > > directly evaluated by quick clinical study to demonstrate efficacy since= > everything we'll initially focus on would've made it clinical t= > rials or through phase 2 testing at least. We are looking for indivi= > duals with the passion and skill set to help > > us complete and deploy the pipeline for maximal benefit. Particularly we= > are interested in a pipeline developer who would ideally be an expert o= > n machine learning techniques that will help integrate the chem- and bio= > informatic data with docking simulations, i.e., create a > > more robust and automated pipeline that is adaptable to individual indic= > ations and genotypes. We are also interested in a docking code developer= > that will help implement the third version of the fragment-based dockin= > g with dynamics protocol we have developed and > > integrate the pipeline and docking methodology as a systems-based drug d= > iscovery product. Another role which is part of the developer job descri= > ption is to work on a web application that can handle personalisation an= > d integrate it with our in-house cando database > > API. This will finally give one-stop-shop-software to find putative drug= > s for a particular indication of interest done using all the proteins of= > the related organisms. So the final output of our methodology is a drug= > -disease network which is linked back to > > protein-compounds network, i.e. an atomistic description of all existing= > and new drug prediction we are making. Gaurav Chopra, one of my pos= > tdocs and the overall project manager of CANDO, will be attending CASP10= > and is the person who you'd closely > > work with should you accept this position. So please talk to him and if = > you're interested in this position, and if you feel the project is a= > good fit for you, send us both your CV and a brief statement of interes= > t to=A0<a href=3D"mailto:gaurav@compbio.washington.edu" style=3D"color:rgb(= > 17,85,204)">gaurav(a)compbio.washington.edu</a>=A0and > > <a href=3D"mailto:ram@compbio.washington.edu" style=3D"color:rgb(17,85,204)= > ">ram(a)compbio.washington.edu</a></div><div></div><div> lass=3D"Apple-style-span" color=3D"#222222" face=3D"arial, sans-serif"><spa= > n class=3D"Apple-style-span" style=3D"border-collapse:collapse"> > > </div><div> lvetica, sans-serif">--</div> > > > > -- >   > --- > You received this message because you are subscribed to the Google Groups &= > quot;samudrala-compbio" group. > To unsubscribe from this group and stop receiving emails from it, send an e= > mail to samudrala-compbio+unsubscribe(a)googlegroups.com. > For more options, visit <a href=3D"https://groups.google.com/groups/opt_out= > ">https://groups.google.com/groups/opt_out</a>. >   >   > > --20cf306f722a5dcabe04d6442e13-- -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] 2/21/13 Seminar with Bridget Carragher
by Nicole Takesono Flowers 15 Feb '13

15 Feb '13

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

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

15 Feb '13

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

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

14 Feb '13

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

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

14 Feb '13

Begin forwarded message: > From: Gene Myers <myers(a)mpi-cbg.de> > Subject: Open Positions: ELBE Postdoc Program in Dresden > Date: February 14, 2013 7:48:29 AM PST > To: undisclosed-recipients:; > > Dear colleague, > > The Max-Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG) and the MPI for the Physics of Complex Systems (MPI-PKS) in Dresden have formed a new Systems Biology Center that is particularly focused on combining genomics, image-based, and bio-physical approaches. > We are beginning the next cycle of a fully-funded postdoctoral program and are seeking applicants. > > We kindly ask you to bring the attached one-page announcement to the attention of your students. > > Best regards, > Gene Myers > Founding Director, The Systems Biology Center at Dresden > > > Dr. Gene Myers, Director > Tschira Chair of Systems Biology > Max-Planck Institute of > Molecular Cell Biology & Genetics > Pfotenhauerstr. 108 > 01307 Dresden > > Tel: +49 351 210-1220 > Fax: +49 351 210-1209 > -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: Job Openings with the RCSB PDB in San Diego
by Andrej Sali 09 Feb '13

09 Feb '13

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

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

08 Feb '13

Peter A. Kollman Lectureship Michael Levitt, Ph.D. Stanford Combinatorial Methods Solve a Difficult Structural Problem to Reveal How Chaperonins Work in Eukaryotes Thursday, February 14, 2013 12:00 PM J. Gross, Host Genentech Hall Byers Auditorium UCSF Mission Bay Campus Simulcast to Parnassus. Room S161 Reception in Byers Hall 5th Floor Lounge at 3:30 Sponsor: The Peter Kollman Fund Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Post-doctoral positions available
by Andrej Sali 07 Feb '13

07 Feb '13

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: "Alan E. Mark" <a.e.mark(a)uq.edu.au> > Subject: Re: Post-doctoral positions available > Date: February 7, 2013 5:29:40 PM PST > To: Robert Best <robertbe(a)helix.nih.gov> > Cc: mlklein(a)temple.edu, dietmar.paschek(a)uni-rostock.de, marrink(a)chem.rug.nl, Ron Elber <ron(a)ices.utexas.edu>, jernigan(a)iastate.edu, dmz(a)ccbb.pitt.edu, Richard Lavery <richard.lavery(a)ibcp.fr>, kremer(a)mpip-mainz.mpg.de, Cecilia Clementi <cecilia(a)rice.edu>, Juan J de Pablo <depablo(a)engr.wisc.edu>, ftama(a)u.arizona.edu, Bruce Berne <bb8(a)columbia.edu>, David Coker <coker(a)chem.bu.edu>, Peter Rossky <rossky(a)mail.utexas.edu>, Dmitry Matyushov <dmitrym(a)asu.edu>, Kenneth Jordan <ken(a)visual1.chem.pitt.edu>, Doug Tobias <dtobias(a)uci.edu>, "Richard A. Friesner" <rich(a)chem.columbia.edu>, Bernhardt Trout <trout(a)mit.edu>, Karl Freed <k-freed(a)uchicago.edu>, Ken Dill <dill(a)maxwell.compbio.ucsf.edu>, David Reichman <reichman(a)chem.columbia.edu>, Jonathan Essex <J.W.Essex(a)soton.ac.uk>, bbagchi(a)sscu.iisc.ernet.in, gardes(a)rpi.edu, Jay Ponder <ponder(a)dasher.wustl.edu>, skolnick(a)gatech.edu, Andrei Tokmakoff <tokmakof(a)mit.edu>, Mark E Tuckerman <mark.tuckerman(a)nyu.edu>, pdebene(a)Princeton.EDU, william.jorgensen(a)yale.edu, lpratt(a)tulane.edu, aluzar(a)vcu.edu, bertil.halle(a)bpc.lu.se, Berend Smit <Berend-Smit(a)Berkeley.edu>, truskett(a)che.utexas.edu, Alexander Grosberg <ayg1(a)nyu.edu>, Barry Honig <bh6(a)columbia.edu>, Christopher Jarzynski <cjarzyns(a)umd.edu>, Eric Vanden-Eijnden <eve2(a)cims.nyu.edu>, Eugene Stanley <hes(a)bu.edu>, Felix Ritort <ritort(a)ffn.ub.es>, George Oster <goster(a)nature.berkeley.edu>, Hank Ashbaugh <hanka(a)tulane.edu>, Leonid Mirny <leonid(a)mit.edu>, Massimo Marchi <marchi(a)dsi.unimi.it>, Michael Shirts <michael.shirts(a)virginia.edu>, Michelle Parrinello <parrinello(a)phys.chem.ethz.ch>, Nicolae-Viorel Buchete <buchete(a)ucd.ie>, PieterRein tenWolde <tenwolde(a)amolf.nl>, Terry Hwa <hwa(a)ucsd.edu>, Thomas Miller <tfm(a)caltech.edu>, William Swope <swope(a)almaden.ibm.com>, "Wilfred F. van Gunsteren" <wfvgn(a)igc.phys.chem.ethz.ch>, "Alexandre M.J.J. Bonvin" <a.m.j.j.bonvin(a)uu.nl>, Xavier Daura <Xavier.Daura(a)uab.cat>, Helmut Grubmüller <hgrubmu(a)gwdg.de>, Daan Geerke <d.p.geerke(a)vu.nl>, David Smith <dsmith(a)irb.hr>, Christine Peter <peter(a)mpip-mainz.mpg.de>, Peter Tieleman <tieleman(a)ucalgary.ca>, "Megan O'Mara" <m.omara(a)uq.edu.au>, Alan Mark <a.e.mark(a)uq.edu.au>, David Fairlie <d.fairlie(a)imb.uq.edu.au>, Jennifer Martin <j.martin(a)imb.uq.edu.au>, Ricardo Mancera <R.Mancera(a)curtin.edu.au>, Durba Sengupta <d.sengupta(a)ncl.res.in>, Julian Gale <julian(a)ivec.org>, Irene Yarovsky <irene.yarovsky(a)rmit.edu.au>, jill.gready(a)anu.edu.au, Shin-Ho Chung <shin-ho.chung(a)anu.edu.au>, pande(a)stanford.edu, Ken Merz <merz(a)qtp.ufl.edu>, sali(a)salilab.org, Nilges Michael <nilges(a)pasteur.fr>, giorgio colombo <g.colombo(a)icrm.cnr.it>, lucy.forrest(a)biophys.mpg.de, ben.corry(a)anu.edu.au, Toby Allen <e88304(a)ems.rmit.edu.au>, dominik.marx(a)theochem.ruhr-uni-bochum.de, brookscl(a)umich.edu, roux(a)uchicago.edu, Rebecca Wade <rebecca.wade(a)h-its.org>, "michael.shirts(a)virginia.edu" <michael.shirts(a)virginia.edu>, Chandra Verma <chandra(a)bii.a-star.edu.sg>, "Dr M. Vendruscolo" <mv245(a)cus.cam.ac.uk>, Emanuele Paci <e.paci(a)leeds.ac.uk>, Chris Oostenbrink <chris.oostenbrink(a)boku.ac.at>, Bojan Zagrovic <bojan.zagrovic(a)univie.ac.at> > > Dear All, > > I would greatly appreciate it if you could pass the attached advertisement onto suitable post-doctoral candidates. I currently have two post-doctoral positions available funded by the Australian Health and Medical Research council (NHMRC) in my group at the University of Queensland, Australia. > > The specific projects focus on the use of molecular dynamics simulations to investigate the mechanism of action of ABC transporters and cytokine receptors as well as the interaction of small molecules and antimicrobial peptides with lipid bilayers. Applicants should hold or have recently submitted a PhD in computational chemistry or biophysics, or a related discipline. Experience in molecular dynamics simulations or related computational techniques, strong computational and programming skills are essential. Prior experience in free energy simulation techniques, simulations of membrane protein systems, or forcefield parameterisation will be an advantage. The University of Queensland (UQ) is located in sub tropical Brisbane on the east coast of Australia. UQ is one of the top research Universities in the Country and is consistently ranked within the top 50 Universities world wide. UQ was also one one of only two Institutions to receive a top ranking on Computational Chemistry in the most recent national research assessment. > > Interested applicants must apply online according to the instructions given in the attached file or see http://uqjobs.uq.edu.au/jobDetails.asp?sJobIDs=494312. > > If applicants have specific questions they can also contact me <a.e.mark(a)uq.edu.au> or Megan O'Mara <m.omara(a)uq.edu.au> directly. >> > Best wishes, > > Alan Mark > -- > -------------------------------------------------------------------- > This message was composed using voice recognition software. Please forgive any strange words I fail to correct. > ____________________________________________________________________ > Prof. Alan E. Mark > > BRISBANE > Molecular Dynamics Group > School of Chemistry and Molecular Biosciences (SCMB) > University of Queensland > Brisbane, QLD 4072, > Australia > > http://scmb.uq.edu.au/staff/alan-mark > http://compbio.biosci.uq.edu.au > > Physical address: > Rm 331 Level 3, Molecular Biosciences Building (#76) > > Email a.e.mark(a)uq.edu.au > Secretary: md.secretary(a)uq.edu.au > Phone: +61-7-3365 4180 > FAX: +61-7-3365 3872 > Secr: +61-7-3365 3821 > > Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland

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