May 2018 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] 5/31/18 Seminar with Andre Levchenko
by Flowers, Nicole 22 May '18

22 May '18

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Livestream: http://tiny.ucsf.edu/yqytD9 [/var/folders/7s/ln22sh2n38z5pq0vj15rm0tm0000gq/T/com.microsoft.Outlook/WebArchiveCopyPasteTempFiles/cidimage001.png(a)01D3C747.62849D60] Co-Sponsored by The Gladstone Center for Cell Circuitry Andre Levchenko Yale Are signaling networks Rube Goldberg machines? Information Processing v. Network Structure May 31, 2018 W. Marshall, 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 Gladstone Center for Cell Circuitry. -- 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

1 0

[Compbio-allhands] two comp bio postdoc positions at A*STAR institute in Singapore
by Andrej Sali 20 May '18

20 May '18

http://www.bii.a-star.edu.sg/career/research/bmad.php -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy 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

1 0

[Compbio-allhands] 5/17/18 Seminar with Tom Rapoport
by Flowers, Nicole 14 May '18

14 May '18

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Livestream: http://tiny.ucsf.edu/yqytD9 Tom Rapoport Harvard Mechanism of ER-associated protein degradation (ERAD) May 17, 2018 A. Frost, Host -- 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

1 0

[Compbio-allhands] Fwd: Hello Tom from Wayne in Chicago
by Tom Ferrin 04 May '18

04 May '18

LanzaTech is recruiting for a Computational Biologist Modeler... -------- Forwarded Message -------- Subject: Hello Tom from Wayne in Chicago Date: Wed, 2 May 2018 14:33:26 +0000 From: Wayne Mitchell <Wayne.Mitchell(a)lanzatech.com> To: tef(a)cgl.ucsf.edu <tef(a)cgl.ucsf.edu> Tom, we are expanding the Computational Biology team, and I thought you might know of strong candidates. We are a modest group of five (3 PhDs, 1 double Masters, 1 BS), doing wide-rangeing computational biology in support of Lanzatech’s microbial technology platform, in particular the synthetic biology, strain development and fermentation teams. Our organism is aenerobic, acetogenic and gas fermenting. The biology is somewhat esoteric but always interesting. We do bacterial evolution and population biology in the context of continuous fermentation, RNAseq, proteomics, and metabolics in pursuit of systems biology insights, extensive annotation and bioinformatics analysis of genomes of interest, software application development, more “hard core” information science stuff (database design and implementation, etc), and genome scale mathematical modeling of metabolism. In addition we have a growing focus on statistical computing (AI and machine learning) Specifically, we are expanding our modelling efforts and are actively recruiting a second fulltime genome scale metabolic modeller. I include the job posting (below), Applications can be lodged at http://www.lanzatech.com/careers/ Feel free to foward this if you think it will be of interest to your network, ( We are also recruiting for a full stack web developer with scientiic visualization experience/ aspirations — just in case you know of one). Thank you If you are going to be at ISMB this summer, lets grab a beer and lunch/ dinner. warmest regards, Wayne Wayne Mitchell, PhD. Director, Computational Biology Lanzatech Computational Biologist Modeler LanzaTech Inc. - Skokie, IL - Full Time _*About LanzaTech*_ LanzaTech is turning our global carbon crisis into a feedstock opportunity with the potential to displace 30% of crude oil use today and reduce global CO2 emissions by 10%. LanzaTech’s carbon recycling technology is like retrofitting a brewery onto an emission source like a steel mill, but instead of using sugars and yeast to make beer, bacteria convert pollution to products! Imagine a day when you can power a plane by recycled carbon emissions, when your yoga pants or sneakers started life as pollution from a steel mill. This future is possible using LanzaTech technology with the first 2 commercial units converting steel mill waste gases to fuels being built; in China with Shougang and in Belgium with the world’s largest steel maker, ArcelorMittal. LanzaTech has an additional 3 commercial projects in the pipeline, in India, South Africa and California. LanzaTech has already produced synthetic jet fuel from recycled carbon emissions and has a partnership with Virgin Atlantic. In 2017, LanzaTech was recognized as the #1 Hottest company in the Advanced Bioeconomy by Biofuels Digest, the world’s most widely-read bioeconomy daily. The company was also inaugurated into the Cleantech100 Hall of Fame, having been listed in the top 100 cleantech companies over the last 7 years. In 2016, the company won the Young Global Leader Award for Circular Economy at the World Economic Forum, LanzaTech was also the top biofuels company in the 2016 CNBC Disruptor 50 Companies list. In 2015, LanzaTech was awarded the U.S. EPA Presidential Green Chemistry Award for Greener Synthetic Pathways. The company’s accomplishments were recognized through a number of prestigious awards in 2014, including the Guardian Sustainable Business Innovation Award for Carbon and Energy Management, Breakthrough Innovation Award at the Platts Global Metals Awards, and the Technical Development Award from the World Petroleum Council. In 2013, the company was named a World Economic Forum Technology Pioneer. _*About the role*_ LanzaTech has developed extensive metabolic modeling capability around our novel gas fermentation platform. This modeling capability is used to guide scientific, engineering and business decisions. You will use your expert knowledge of microbial metabolism to computationally design, develop and refine new microbial strains that specialize in making chemicals from pollution. You will participate in the design-build-test feedback loop with scientists and engineers across the company to refine these strain designs and contribute to the ongoing development and refinement of our models. *Key duties* * Integrate metabolomic, genomic, proteomic and transcriptomic data sets to solve deep biological problems * Contribute to ongoing development and refinement of genome annotations, metabolic knowledgebases and metabolic models * Design in silico experiments for biological discovery, computational strain design, process optimization and the prediction of cellular phenotypes. * Carry out in silico experiments using the latest metabolic modeling technology * Clearly document work and methods by integrating code and narrative text in Jupyter notebooks * Communicate your findings, insights and conclusions to other scientific teams * Present summary of results to group in weekly meetings _*Education & Experience*_ *REQUIRED* * PhD in computational biology, quantitative biology, bioinformatics, computational systems biology or equivalent * Strong knowledge of microbial biochemistry * Significant exposure to prokaryotic biology with emphasis on metabolism, ideally to a gas fermenting acetogen * Deep knowledge of the principles behind genome-scale modeling, flux balance analysis and associated techniques * Expert user of genome-scale modeling tools such as cobrapy, cameo, Escher, OptFlux, COBRA Toolbox * Intermediate Python knowledge or expert in another programming language * Team player balanced with strong individual initiative *NICE TO HAVE* * Industry experience highly desirable * Exposure to microbial fermentation highly desirable * Experience with Gurobi, CPLEX, TOMLAB * Experience with Docker, Kubernetes, Travis CI, Git * Experience designing interactive data visualizations using Bokeh, R Shiny or Tableau * Experience with ME and GEM-Pro genome-scale models, kinetic models and whole-cell models * Experience in synthetic biology /This position is open to candidates authorized to work in the United States on a full-time basis for any employer. LanzaTech is an Equal Employment Opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, gender, sexual orientation, gender identity or expression, national origin, age, genetic information, disability, or veteran status./ *Wayne Mitchell *PhD | *LanzaTech * Director, Computational Biology Wayne.Mitchell(a)lanzatech.com Phone: +1 (847) 324-2508 Mobile: +1 (847) 454-5388 8045 Lamon Ave, Suite 400, Skokie, IL 60077 http://www.lanzatech.com <http://www.lanzatech.com/> /The information in this e-mail and any attachments is confidential to LanzaTech. If you are not the intended recipient, you are not authorized to disclose, copy, distribute or retain this information. / P *Be carbon smart. Please consider the environment before printing this email *

1 0

[Compbio-allhands] Fwd: Advertising a Joint OpenFF-XtalPi Distinguished Postdoctoral Fellowship
by Jacobson, Matt 03 May '18

03 May '18

— Matt Begin forwarded message: From: Michael R Shirts <Michael.Shirts(a)Colorado.EDU<mailto:Michael.Shirts@Colorado.EDU>> Subject: Advertising a Joint OpenFF-XtalPi Distinguished Postdoctoral Fellowship Date: May 3, 2018 at 11:36:31 AM PDT Cc: David Mobley <dmobley(a)uci.edu<mailto:dmobley@uci.edu>>, Lee-Ping Wang <leeping(a)ucdavis.edu<mailto:leeping@ucdavis.edu>>, "John Chodera" <john.chodera(a)choderalab.org<mailto:john.chodera@choderalab.org>>, "Gilson, Michael" <mgilson(a)ucsd.edu<mailto:mgilson@ucsd.edu>> Hello, colleagues- The Open Force Field Consortium (OpenFF, openforcefield.org<http://openforcefield.org>) and XtalPi, Inc. (xtalpi.com<http://xtalpi.com>) are seeking a postdoctoral fellow to perform cutting-edge research in a unique academic-industrial joint effort. The postdoctoral fellow will work with OpenFF and XtalPi to improve the accuracy of molecular mechanics force fields for predicting crystal structures and binding free energies. Please pass this opportunity on to any of your recent students or postdocs that might be interested. See the full ad here: http://www.ccl.net/cca/jobs/joblist/mess0044564.shtml This particular postdoctoral position has some interesting advantages such as 1) the opportunity to transition into an industrial position doing computational chemistry right afterwards, 2) the chance to work in a highly collaborative team setting, and 3) flexibility to be located at any of the participating academic institutions. OpenFF is an academic collaboration (based at UC Irvine / UC Davis / UC San Diego / Univ. Colorado Boulder / Sloan Kettering Institute in New York) that seeks to develop next-generation molecular mechanics force fields and associated parameterization software and data infrastructure. XtalPi is a pharmaceutical technology company founded in 2014 that is introducing revolutionary advances in drug research and development, and has established strategic partnerships with several major pharmaceutical companies and recently completed a Series B funding round with Sequoia, Tencent, and Google. Best, ~~~~~~~~~~~~~~~~ Michael Shirts Associate Professor michael.shirts(a)colorado.edu<mailto:michael.shirts@colorado.edu> http://www.colorado.edu/lab/shirtsgroup/ Phone: (303) 735-7860 Office: JSCBB C123 Department of Chemical and Biological Engineering University of Colorado Boulder

1 0

[Compbio-allhands] 5/10/18 Seminar with Forest White
by Flowers, Nicole 02 May '18

02 May '18

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Livestream: http://tiny.ucsf.edu/yqytD9 Forest White MIT Mechanisms of therapeutic resistance revealed by quantitative functional proteomics May 10, 2018 N. Jura, Host -- 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

1 0