February 2013 - compbio-allhands@cgl.ucsf.edu

[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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