January 2017 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] Claus Seidel seminar, Feb 8
by Andrej Sali 08 Feb '17

08 Feb '17

“Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems in vitro and in live cells” 11am, Feb 8, BH 212 -- 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 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: Summer Internship openings at Genentech in the computational chemistry group
by Brian Shoichet 31 Jan '17

31 Jan '17

FYI. ---------- Forwarded message ---------- From: Daniel Ortwine <ortwine.daniel(a)gene.com> Date: Tue, Jan 31, 2017 at 12:05 PM Subject: Summer Internship openings at Genentech in the computational chemistry group To: Brian Shoichet <shoichet(a)cgl.ucsf.edu> Hello Brian! I am contacting you to ask if you know of any candidate that might be suitable for internship positions that we have open for this coming summer in the computational chemistry group at Genentech. Short descriptions of each position and the position requirements can be found below. These internships can start at different times during the summer. We are recruiting for these positions now! It would be great if you could suggest candidates that fit the profiles and/or circulate the job descriptions among your students. Any student that would like to apply for a position should send a cover letter and their CV to Genentech via the the link provided below: https://www.gene.com/careers/detail/00450980/Intern-Discovery-Chemistry- Computational-Chemistry Here is some information on the logistics of the internship: - Internships are scheduled for the duration of 12 weeks - There will be 3-4 intern start dates in June 2017. - Interns are paid an hourly rate based on their degree level. - Recent (within 2 years) graduates of BS/BA or MS/MA programs are eligible. They are paid based on their most recent degree completed. - Travel assistance is given to all intern candidates - Interns are eligible to use the Genentech bus system at no cost, which connects the Genentech campus to several locations in the San Francisco bay area for morning and evening commutes. - All interns must clear a background check. - Interns do not receive medical/dental benefits and do not accrue vacation - We do not currently offer formal housing assistance for interns. However, we do provide networking assistance so interns can contact each other to make living arrangements. I am also happy to answer any questions you or any candidates might have. With best regards, Dan Project 1: The intern will work with Alberto Gobbi to implement and evaluate a method for computing strain energies of drug molecules in their bound conformation. The strain energy is a component of the binding energy and significantly contributes to the strength of a small molecule protein interaction. A drug that binds its protein target without increasing its strain energy may be given at a lower dose, thereby reducing the risk of toxicity. Part of the work includes evaluating open source and commercial software for computing molecular energies at a quantum mechanical level. The other part will be the development of an automated workflow to perform the calculation on an in-house computer cluster at Genentech. The candidate will learn about small molecule energetics, binding conformations, and ligand protein interactions. This work may also lead to a publication of a manuscript and or open source software. Candidates must be full-time undergraduate or graduate students, with a working knowledge of chemistry, familiarity with the Unix operating system and programming experience (preferably in Java or Python). A familiarity with computational chemistry software is a plus. Project 2: The intern will work with Paul Gibbons to improve our ability to use existing software to aid the design of small organic molecules. The work will include evaluating virtual libraries, improving them, evaluating current workflows for virtual molecule modification and proposing/ implementing improved workflows. The intern should have knowledge of basic UNIX commands and some scripting. In addition, the candidate must be a full-time undergraduate or graduate student who has completed a full year of undergraduate organic chemistry. Formal coursework in computer science would be advantageous but is not essential. -- Daniel Ortwine Computational Drug Discovery Genentech, Inc. 1 DNA Way, ms 18b South San Francisco, CA 94080 Office 650-225-2749 <(650)%20225-2749> Cell 925-323-0504 <(925)%20323-0504> email ortwine.daniel(a)gene.com -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

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[Compbio-allhands] 2/2/17 Seminar with Eric Alm
by Flowers, Nicole 27 Jan '17

27 Jan '17

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 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Eric Alm MIT The ecology of the human microbiome in health and disease February 2, 2017 L. Morinishi, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Open position for a Postdoc in 3DGenomics in Barcelona (CNAG-CRG)
by Andrej Sali 25 Jan '17

25 Jan '17

Sent from my iPhone Begin forwarded message: > From: Marc Marti Renom <martirenom(a)cnag.crg.eu> > Date: January 25, 2017 at 9:33:59 AM GMT > To: Marc Marti Renom <martirenom(a)cnag.crg.eu> > Subject: Open position for a Postdoc in 3DGenomics in Barcelona (CNAG-CRG) > > Dear colleagues and friends, > > Could you please forward this email to anybody in your research institutions who could be interested in a computational biology postdoc in 3DGenomics? > > Detailed information can be found in the attached PDF or in this link: https://recruitment.crg.eu/content/jobs/position/postdoctoral-position-stru… > > Many thanks in advance! > Marc > ... > OPEN PostDoc POSITION IN THE LAB! https://recruitment.crg.eu/content/jobs/position/postdoctoral-position-stru… > > Marc A. Marti-Renom, ICREA Research Professor > Structural Genomics Group Leader > Centre Nacional d’Anàlisi Genòmica - Centre de Regulació Genòmica (CNAG-CRG) > Parc Científic de Barcelona – Torre I (10th floor) > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email: martirenom(a)cnag.crg.eu > Web: http://marciuslab.org · http://cnag.crg.eu · http://crg.cat > > CRG PhD positions available at “la Caixa” INPhINIT Doctoral fellowships programme http://www.inphinitlacaixa.org > Application deadline: February 2, 2017 > “This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklowdowska- Curie grant agreement No. 713673” > > *** Consider the environment. Print responsibly. *** > > > > > > >

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[Compbio-allhands] 1/26/17 Seminar with Gerhard Wagner
by Flowers, Nicole 20 Jan '17

20 Jan '17

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 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Gerhard Wagner Harvard Engineering nanodiscs for membrane protein studies January 26, 2017 D. Asarnow, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 1/19/17 Seminar with Joachim Frank
by Flowers, Nicole 13 Jan '17

13 Jan '17

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 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Joachim Frank Columbia Time-resolved cryo-EM: first biological results with the mixing/spraying microfluidic chip January 19, 2017 R. Woldeyes, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: job opening at Novartis Emeryville
by Andrej Sali 09 Jan '17

09 Jan '17

> Begin forwarded message: > > From: Dave Barkan <davebarkan(a)gmail.com> > Subject: job opening at Novartis Emeryville > Date: January 9, 2017 at 3:49:18 PM PST > To: Andrej Sali <sali(a)salilab.org> > > Hey Andrej! > > Hope things are going well in Mission Bay! > > We have another job opening here in Emeryville for an entry-level Investigator position in our Infectious Diseases Bioinformatics group. Talented post-docs and recent PhD graduates from bioinformatics-focused labs at UCSF would be good candidates. Could you please circulate the following link? > > https://sjobs.brassring.com/tgwebhost/jobdetails.aspx?jobId=2444628&Partner… <https://sjobs.brassring.com/tgwebhost/jobdetails.aspx?jobId=2444628&Partner…> > > Thanks! > Dave

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[Compbio-allhands] 1/12/17 Seminar with Kimberly Reynolds
by Flowers, Nicole 06 Jan '17

06 Jan '17

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 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Kimberly Reynolds University of Texas, Southwestern A conserved evolutionary unit in central metabolism January 12, 2017 Y. Birman, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Job for a Masters or PhD Bioinformatician - Scientific Software Developer
by Andrej Sali 06 Jan '17

06 Jan '17

> Begin forwarded message: > > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: FW: Job for a Masters or PhD Bioinformatician - Scientific Software Developer > Date: January 6, 2017 at 8:18:25 AM PST > > > Dear colleague – I’d be grateful if you would advertise. We are looking for strong web development skills and a Masters or PhD is the ideal qualification. > Thanks > > Mike > ******************************************** > m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > > > From: Sternberg, Michael J E > Sent: 06 January 2017 16:15 > To: Sternberg, Michael J E > Subject: Job for a Masters or PhD Bioinformatician - Scientific Software Developer > > Scientific Software Developer > Imperial College London – Structural Bioinformatics Group - Department of Life Sciences > Location: > London > Salary: > £35,140 to £43,350 per annum > Hours: > Full Time > Contract Type: > Contract / Temporary > Closes: > 5th February 2017 > Job Ref: > NS 2017 001 PB > Applications are invited for a Scientific Software Developer to join the Structural Bioinformatics Group of Prof Mike Sternberg, within the Department of Life Sciences based at the South Kensington Campus. The post holder will work as a member of a small team developing the PhyreRisk dynamic web portal which will provide the bioscience and biomedical communities with a resource relating human genetic variation, disease, protein structure and biological pathways. > > The post will focus on the development of a dynamic web site to map genetic variants onto experimental and predicted structures of proteins. You must have at least a Master’s postgraduate degree (or equivalent), and ideally a PhD (or equivalent) from a course that involved substantial computational work such as computer science, physics, chemistry, mathematics or computational-biology/bioinformatics or a comparable vocational qualification together with comparable experience in a relevant role. You must have demonstrable strong programming experience required to develop a substantive dynamic web site to a professional standard using HTML/JavaScript/Django and server side languages (Java, Perl-CGI), ideally applied to a scientific problem. You must also have demonstrable strong programming experience for data processing and/or algorithm development in a high level language such as C, C++ or Python (or a close equivalent), ideally applied to a scientific problem. > > This is a full time position, funded by the Wellcome Trust until 30 November 2019. > > For initial enquiries please contact Professor Michael Sternberg by email: m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > The preferred method of application is online via our websitehttp://www3.imperial.ac.uk/employment <http://www3.imperial.ac.uk/employment> (please select “Job Search” then enter the job title or vacancy reference number including spaces – NS 2017 001 PB. Please complete and upload an application form as directed and attach a full CV. > > ******************************************** > Professor Michael J E Sternberg > Director Centre for Integrative Systems Biology and Bioinfomatics (CISBIO) > Room 306 - Sir Ernst Chain Building > Department of Life Sciences > Imperial College London, London SW7 2AZ,UK > m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > http://www3.imperial.ac.uk/cisbio <http://www3.imperial.ac.uk/cisbio> (CISBIO) > www.sbg.bio.imperial.ac.uk <http://www.sbg.bio.imperial.ac.uk/> (Group's research) > > Tel +44 (0)20 7594 5212 > ****************************************************************************

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[Compbio-allhands] Fwd: Postdoc position in computational biology
by Andrej Sali 05 Jan '17

05 Jan '17

> Begin forwarded message: > > From: pau bernado <pau.bernado(a)cbs.cnrs.fr> > Subject: Postdoc position in computational biology > Date: January 5, 2017 at 1:03:02 AM PST > To: Alessandro Barducci <barducci(a)cbs.cnrs.fr> > > Dear Colleagues, > > I would like to draw your attention to a postdoc position in computational biology in the group of Alessandro Barducci at the Centre de Biochimie Structurale in Montpellier. Please, spread this advertisement to students that could be interested in this position. > Thanks and best regards > > Pau Bernado

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compbio-allhands January 2017