May 2016 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] Christos Ouzounis seminar Friday, June 3, 2 pm, BH212
by Patricia Babbitt 31 May '16

31 May '16

Hi all, Christos Ouzounis is giving an informal seminar this Friday, detailed in the subject line of this email. He has been a major contributor to many aspects of the field and was a founding officer of the International Society for Computational Biology. One of his early efforts was the development of clustering algorithms for biological networks, including creation of TRIBE-MCL, an approach used for rapid and accurate clustering of protein sequences into families. The method relies on the Markov cluster (MCL) algorithm for the assignment of proteins into families based on precomputed sequence similarity information (PMID: 11917018). The title of Friday's talk is "Comparative Genomics 2.0: From reading to writing" -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Sydney Russell Leed, +1 415-514-1214, 415-514-9816 Sydney.RussellLeed(a)ucsf.edu <mailto:Sydney.RussellLeed@ucsf.edu>

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[Compbio-allhands] Christos Ouzounis seminar Friday, June 3, 2 pm, BH212
by Patricia Babbitt 31 May '16

31 May '16

Hi all, Christos Ouzounis is giving an informal seminar this Friday, detailed in the attached flyer. He has been a major contributor to many aspects of the field and was a founding officer of the International Society for Computational Biology. One of his early efforts was the development of clustering algorithms for biological networks, including creation of TRIBE-MCL, an approach used for rapid and accurate clustering of protein sequences into families. The method relies on the Markov cluster (MCL) algorithm for the assignment of proteins into families based on precomputed sequence similarity information (PMID: 11917018). The title of Friday's talk is "Comparative Genomics 2.0: From reading to writing" -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Sydney Russell Leed, +1 415-514-1214, 415-514-9816 Sydney.RussellLeed(a)ucsf.edu <mailto:Sydney.RussellLeed@ucsf.edu>

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[Compbio-allhands] a computational / structural biology job at Biodesy, South San Francisco
by Andrej Sali 24 May '16

24 May '16

-- 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: A New Job Posting for 'Computational Protein Engineering' at Amgen Thousand Oaks
by Jacobson, Matt 19 May '16

19 May '16

- Matt From: <Alba>, Ben <balbaphd(a)amgen.com<mailto:balbaphd@amgen.com>> Date: Thursday, May 19, 2016 at 10:01 AM To: Charles Craik <charles.craik(a)ucsf.edu<mailto:charles.craik@ucsf.edu>> Subject: A New Job Posting for 'Computational Protein Engineering' at Amgen Thousand Oaks Hi Charly, I hope you are well!! Thousand Oaks is looking for a talented ‘Computational Protein Engineer’ (e.g. PhD. in computational biophysics or related fields). Do you have any candidates who might fit this bill? Best, Ben http://careers.amgen.com/job-en/6072153/scientist-computational-protein-eng… Scientist – Computational Protein Engineering and Design Category: Scientific Job ID: R-14827 Location: Thousand Oaks, CA Posted Date:May 13, 2016 Amgen is seeking a scientist with expertise in computational protein engineering and design to join the Therapeutic Discovery Department at our campus in Thousand Oaks, CA. The candidate will be part of multidisciplinary teams that seek to advance our biologics drug discovery programs, spanning multiple modalities including therapeutic proteins, antibodies, and bispecific molecules. The work involves protein structure analysis and modeling, biophysical property prediction, protein-protein interaction analysis, as well as novel molecular design. Basic Qualifications: Doctorate degree OR Master’s degree & 4 years of scientific experience OR Bachelor’s degree & 6 years of scientific experience Preferred Qualifications: PhD. in computational biophysics or related fields Strong track record of research accomplishment with three or more scientific publications or conference presentations in the area of computational protein modeling and design Strong communication and interpersonal skills and the ability to work flexibly in a cross-functional team environment Experience in antibody modeling and engineering Experience with one or more protein modeling software packages (MOE, Discovery Studio, Schrodinger, etc.). Experience working on a biologics project in a biopharmaceutical setting. Amgen is an Equal Opportunity employer and will consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability status. Benjamin Alba, Ph.D. Senior Scientist Biologics Amgen, Inc. 1120 Veterans Blvd Drop Zone ASF5/234 South San Francisco, CA 94080 650-228-4943 (cell); 650-244-3119 (desk) "This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message."

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[Compbio-allhands] Fwd: Recommendations for job positions @ GSK
by Brian Shoichet 19 May '16

19 May '16

FYI. ---------- Forwarded message ---------- From: Brian Shoichet <shoichet(a)cgl.ucsf.edu> Date: Thu, May 19, 2016 at 9:38 AM Subject: Re: Recommendations for job positions @ GSK To: Eric Manas <eric.s.manas(a)gsk.com> Cc: Constantine Kreatsoulas <constantine.x.kreatsoulas(a)gsk.com>, Kris Brown <Kristin.K.Brown(a)gsk.com> Hi Guys, I'll keep my eyes open, and pass this around. No one in my lab is quite ready yet, but there are certainly other talented folks in the comp. chem. groups here at UCSF. brian On Thu, May 19, 2016 at 9:14 AM, Eric Manas <eric.s.manas(a)gsk.com> wrote: > Hi Brian, > > Just to chime in...some of the skill sets we are looking for are around > protein modeling, physics of equilibrium binding and kinetics, structure > based design...etc. As Kris suggested we'd be happy to chat more at any > time. > > Eric > > Sent from my iPhone > > On May 19, 2016, at 5:02 PM, Kris Brown <Kristin.K.Brown(a)gsk.com> wrote: > > Dear Brian: > > > > I wanted to reach out to let you know that we are currently recruiting for > several open positions in the computational molecular design group at GSK. > The job descriptions are given as links below. If you know of anyone who > might be interested please feel free to pass along the job descriptions and > my contact information. I’d be happy to schedule a phone call if you’d like > to hear more detail about what these positions entail. > > > > Best Regards, > > Kris Brown > > > > > > Grade 7 Cheminformatics: WD64811 - http://tinyURL.gsk.com/91fd3f > <http://tinyurl.gsk.com/91fd3f> > > Grade 6/7 Data Science: WD59234 - http://tinyURL.gsk.com/2e27fa > <http://tinyurl.gsk.com/2e27fa> > > Grade 7 Investigator: WD58496 - http://tinyURL.gsk.com/55ac18 > <http://tinyurl.gsk.com/55ac18> > > > > > > *Kristin Brown* > > *Director**, Molecular Design US* > > Computational & Modeling Sciences > > RD Platform Technology & Science > > > > *GlaxoSmithKline* > > 709 Swedeland Road UW2412, King of Prussia, PA 19406 > > *Email *Kristin.K.Brown(a)gsk.com > > *Tel *610-270-4638 > > > > -- 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 -- 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] 5/19/16 Seminar with Xiaowei Zhuang
by Flowers, Nicole 13 May '16

13 May '16

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.) Xiaowei Zhuang Harvard Illuminating Biology at the Nanoscale with Single-molecule and Super-resolution Imaging May 19, 2016 B. Huang, 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 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] computational postdoc @ ucsf
by Michael Keiser 10 May '16

10 May '16

FYI. Recommendations & help getting the word out much appreciated! -- We're looking for highly motivated postdoctoral candidates with a background in machine learning, systems pharmacology, computational chemistry, bioinformatics, or a related field. The candidate would work to integrate deep learning with pharmacology. The project involves the design of deep neural networks for the prediction of small molecule binding activities and their role in phenotypic screens. Desired, albeit not strictly required, skills include experience with theano, lasagne/keras, TensorFlow, pandas, and sklearn. Expertise with CUDA and/or massive dataset analysis (e.g., NoSQL, AWS, Google Cloud) is a plus. A productive track record with at least one first-author publication is required. We seek a driven individual who will lead his/her research independently and communicate frequently and clearly to the field. Just north of Silicon Valley, the Keiser lab’s location at UCSF Mission Bay directly adjoins SoMa district and the heart of SF’s tech and artificial intelligence startup scene. Interested candidates should submit a CV and arrange that three letters of reference be sent directly to apply(a)keiserlab.org. Please reference “postdoc-dnn”. -- Michael J Keiser, PhD Assistant Professor, UCSF Dept Pharmaceutical Chemistry Dept Bioengineering & Therapeutic Sciences Institute for Neurodegenerative Diseases p/1-415-886-7651 keiserlab.org <http://www.keiserlab.org> calendly.com/mjke

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[Compbio-allhands] Fwd: Comp Chem position at MD Anderson Cancer Center
by Jacobson, Matt 10 May '16

10 May '16

-- Matt Sent from my iPhone Begin forwarded message: From: "Cross,Jason B" <JBCross(a)mdanderson.org<mailto:JBCross@mdanderson.org>> Date: May 10, 2016 at 9:32:58 AM PDT To: "'matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>'" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Comp Chem position at MD Anderson Cancer Center Dear Dr. Jacobson, I’m contacting you to let you know that I currently have a junior position available, appropriate for a newly minted PhD or someone completing their post-doctoral training. The position is in the Institute for Applied Cancer Science (IACS) at the University of Texas MD Anderson Cancer Center in Houston, providing computational chemistry support for ongoing drug discovery projects. IACS is part of the cancer moonshots program and has essentially been built as a “biotech” within the cancer center, populated mostly by ex-pharma drug discovery scientists, and is a great environment for junior scientists to learn and contribute to exciting projects. If you have current or former students, or know of others within your network, that would be interested, I would appreciate if you could forward this information. Links to the position description and the MD Anderson IACS website are listed below. Interested applicants will need to apply through the career website, but can also forward their CVs directly to me. Job posting<https://mdanderson.referrals.selectminds.com/jobs/institute-rsch-investigat…> Institute for Applied Cancer Science<http://www.cancermoonshots.org/platforms/institute-for-applied-cancer-scien…> Thank you for your time and consideration. Best regards, Jason Jason Cross, Ph.D. Institute Senior Research Scientist Institute for Applied Cancer Science University of Texas – MD Anderson Cancer Center South Campus Research Bldg 3 (3SCR3.3438) Houston, TX 77054 Office: 713-745-7499 Email: jbcross(a)mdanderson.org<mailto:jbcross@mdanderson.org> The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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[Compbio-allhands] Fwd: job opportunity in disease modeling
by Jacobson, Matt 09 May '16

09 May '16

- Matt Begin forwarded message: From: Jaline Gerardin <jgerardin(a)idmod.org<mailto:jgerardin@idmod.org>> Subject: job opportunity in disease modeling Date: May 9, 2016 at 11:37:29 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, My team at the Institute for Disease Modeling<http://www.idmod.org/> is looking to hire a few research scientists. Could you circulate our job posting below to the compbio listserv? This is a great opportunity for anyone with a quantitative background who wants to continue doing research but not necessarily in an academic environment. Previous knowledge of malaria or epidemiology is not required. Thanks, Jaline TITLE: Research Scientist – Malaria LOCATION: Bellevue, WA, USA The Institute for Disease Modeling (IDM) team is composed of research scientists and software professionals who focus on creating powerful and innovative disease modeling and data analysis tools to help researchers and policy makers understand diseases, their causes, the way they spread, and the best types of interventions to use for the particular situation faced. IDM partners with selected universities, NGOs, government ministries, and other research and public health institutions focused on researching new ways to understand and combat diseases both locally and globally. We seek a full-time Research Scientist to work as part of the IDM malaria team and collaborate on the development, refinement, and utilization of sophisticated infectious disease models for epidemiological research and eradication-campaign planning. The IDM team architects advanced models of disease transmission, develops computational tools to inform global disease eradication policy, conducts innovative analysis of epidemiologically- and policy-relevant data (programmatic data, financial data, clinical trials data, and cluster surveys data), and identifies epidemiologically critical knowledge gaps. As part of our work, we routinely collaborate with groups at the World Health Organization, the Center for Disease Control, PATH, the Bill and Melinda Gates Foundation, ministries of health in the developing world, as well as universities and research institutes. As part of this group, the researcher will design and build new modules for the existing malaria disease model. The researcher will configure, calibrate, and exercise disease models to answer questions aimed at refining the malaria research agenda, improving understanding of disease dynamics, informing effective public health campaigns, and guiding rational development of new public-health interventions. The research, models, and results will be presented to key stakeholders, displayed at conferences, and published in academic journals. Joining our group provides unique opportunities to interact with global-health policymakers, to collaborate with world-class research laboratories and non-profit organizations, and to contribute to global and national disease-eradication strategies. Responsibilities: · Reviews scientific literature and determines which aspects of biology, demography, geography, and climate are relevant to the model. · Builds new modules for existing disease models; builds and develops new disease models. · Works closely with the modelers, programmers, and statisticians on the team to refine the models and use them to conduct sensitivity analyses, explore tradeoffs among possible interventions, and optimize eradication plans for time, cost, or other factors. · Finds sources for the necessary input data to the models and helps to organize the necessary data for input to the models. · Writes software code (in C/C++) to implement model features. · Collects, analyzes, and presents data on model results and performance. · Assists in the preparation of research articles and conference presentations communicating the project and its results to the scientific community. Key Qualifications and Required Skills: · Ph.D. in a quantitative field (e.g. Applied Mathematics, Statistics, Epidemiology, Quantitative Biology) · Numerical analysis, dynamical systems, stochastic processes, and biostatistics. · Read and write research articles in biology and applied mathematics. · Principles, techniques, and tools of computational epidemiology. · Work extended hours to meet a deadline; demonstrated ability to work productively as part of a small team. · At least 2 years’ experience in C/C++ software development. · Proficiency in at least one data-analysis or scripting language (e.g. MATLAB, python, R) · Multiple published articles in peer-reviewed scientific journals (to be submitted with application). · Knowledge of developing-world public health issues and the malaria disease system preferred. Jaline Gerardin Senior Research Scientist jgerardin(a)idmod.org<mailto:jgerardin@idmod.org> T - 425.691.3343 [cid:image001.png@01D1A9E7.29107920] This message may contain confidential information which may also be legally privileged information. If you are not an intended recipient of the message, please delete it and notify the sender via reply email. Any unauthorized dissemination, distribution or copying of the material in this message, and any attachments to the message, is strictly forbidden.

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[Compbio-allhands] 5/12/16 Seminar with Chris Voigt
by Flowers, Nicole 06 May '16

06 May '16

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.) Chris Voigt MIT Cello: A programming language for living cells May 12, 2016 W. Lim, 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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