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

[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

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[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 *

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[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

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[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

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[Compbio-allhands] Fwd: Recruiting Info Sessions in Bay Area - Please Share with Students & Alumni Interested in Academia
by Tom Ferrin 27 Apr '18

27 Apr '18

-------- Forwarded Message -------- Subject: Recruiting Info Sessions in Bay Area - Please Share with Students & Alumni Interested in Academia Date: Fri, 27 Apr 2018 02:53:17 -0400 From: North America Chinese Association of Science, Technology, and Commerce <nacastc(a)gmail.com> Dear Professor, I am reaching out on behalf ofJinan University (JNU) <http://english.jnu.edu.cn/>from Guangzhou, China, to request your help with sharing our recruiting info session events in Los Angeles and San Francisco to your students and network. The deans and HR directors from JNU are hosting a series of info sessions in California, where the closest to UCSF would be at UC Berkeley and Stanford University. We welcome UCSF students and alumni to RSVP and attend any of them. Please see details of the events and recruiting information at the end of the email. Because the university is hiring in a variety of disciplines in Medicine and Health Sciences, offering competitive salary and benefits, we believe it would be a great opportunity for your students and alumni who would like to seek employment overseas. Thank you very much for your kind consideration and our apologies for the extended email. We look forward to hearing from you. Best Regards, Chun Qiu Event Coordinator Email:nacastc@gmail.com <mailto:nacastc@gmail.com> --------------------Event Descriptions Below------------------------- One of the oldest and most ethnically diverse universities established in mainland China, Jinan University (JNU) is recruiting members or candidates of the “High-level Overseas Young Talents Program” as well as researchers and postdoctoral students from home and abroad. The disciplines we are hiring include the following: ** *Medicine and Health Sciences: *Pharmaceutical Science, Science of Chinese pharmacology, Basic Medical Science, Clinical Medicine, Chinese Medicine, Integrative Medicine, Stomatology, Public Health and Preventive Medicine, Sports Science, Nursing. *Engineering: *Materials Science and Engineering, Mechanics, Civil engineering, Architecture, Optical Engineering, Electrical Engineering, Electronic Science and Technology *Information Technology: *Computer Science and Technology, Information and Communication engineering, Cyberspace Security, Software engineering *Other (Biology, Physics, Chemistry, Math, Earth) Sciences: *Mathematics, Biology, Biomedical Engineering, Ecology, Environmental Science and Engineering, Chemistry, Physics, Food Science and Engineering. *Social Sciences and Arts:*Philosophy, Journalism, Chinese Language and Literature, China History, World History, Foreign Language and Literature, Theoretical Economics, Applied Economics, Business Management, Management Science, Public Administration, Psychology, Law, Politics, Marxist Theory, Art, and so on. *Meet the deans and HR directorfromJinan University to discuss more on working at JNU! * * Date & Time University Event Location 5/3/2018, 6:00-8:00 pm University of California, Los Angeles Sunset, 17-256 CHS Address: School of Public Health, 650 Charles E. Young Drive South, Los Angeles, CA 90095-1772 5/4/2018, 6:00-8:00 pm University of Southern California Trojan Presentation Room (STU) B3 *Address: 3601 Trousdale Parkway, Student Union B3, Los Angeles, CA 90089* 5/5/2018, 12:00-2:00 pm California Institute of Technology Spalding 113 1200 E California Blvd, Pasadena, CA 91125 5/6/2018, 5:30-7:30 pm Stanford University Tresidder Memorial Union, Cypress North Address: 459 Lagunita Drive, Stanford, CA 94305-2072 5/7/2018, 6:00-8:00 pm University of California, Berkeley Alumni House Sibley Room Address: 1 Alumni House, Berkeley, CA 94720 * */NOTE: Food and travel reimbursement for graduate students will be provided at the event. /* *Please RSVP Via: https://goo.gl/forms/25AkURZnG2qJALDr2 <https://goo.gl/forms/25AkURZnG2qJALDr2>* Jinan University offers work authorizations in China and a very competitive salary and benefits package to qualified talents. For more information, please take a look at the detailed *job descriptions and employer introduction*here: https://goo.gl/LqMNaA Our English website: english.jnu.edu.cn <http://english.jnu.edu.cn/> Prior to the event, attendees may send CV and sample of papers to otalents(a)jnu.edu.cn <mailto:otalents@jnu.edu.cn>. If you have any questions regarding the events, please do not hesitate to contact us by email at nacastc(a)gmail.com <mailto:nacastc@gmail.com>.

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[Compbio-allhands] 5/3/18 Seminar with Christopher Burge
by Flowers, Nicole 26 Apr '18

26 Apr '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 Christopher Burge MIT Protein-RNA Interactions and RNA Processing May 3, 2018 H. Madhani, 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

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[Compbio-allhands] Fwd: Open positions in gene therapy
by Andrej Sali 21 Apr '18

21 Apr '18

Sent from my iPhone Begin forwarded message: > From: Christina Chaivorapol <cchaivorapol(a)audentestx.com> > Date: April 21, 2018 at 5:57:38 AM GMT+2 > To: "sali(a)salilab.org" <sali(a)salilab.org> > Subject: Open positions in gene therapy > > Hi Andrej, > > I currently have two open positions in my group at Audentes Therapeutics. One is a bioinformatics scientist position to analyze NGS data from research all the way through clinical trials, and the other is a wet bench scientist position to work on developing a wide range of NGS-based assays and methods. Both positions are in the gene therapy space. If you know of any enthusiastic, independent scientists that would like to work on cutting edge science that will have direct impact on patients, please have them apply to the appropriate positions below: > > https://audentestx.snaphire.com/jobdetails/ajid/2SGH7/Scientist-I-Bioinform… > https://audentestx.snaphire.com/jobdetails/ajid/ewWH7/Scientist-I-II-NGS,11… > > Thanks in advance for your help, > Christina > > -- > Christina Chaivorapol, Ph.D. > Director, Bioinformatics > > Audentes Therapeutics, Inc. > 600 California Street > 17th Floor > San Francisco, CA 94108 > mobile: +1-628-220-9588 > office: +1-650-834-9704 > email: cchaivorapol(a)audentestx.com

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[Compbio-allhands] 4/26/18 Seminar with Klaus Hahn
by Flowers, Nicole 18 Apr '18

18 Apr '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 Klaus Hahn UNC Chapel Hill Building proteins to peek and poke at GTPase circuits in vivo April 26, 2018 X. Shu, 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

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[Compbio-allhands] Fwd: Senior Computational Chemist (CADD) at Atomwise
by Andrej Sali 17 Apr '18

17 Apr '18

Sent from my iPhone Begin forwarded message: > From: Adrian Stecula <adrian(a)atomwise.com> > Date: April 17, 2018 at 2:28:39 PM PDT > To: sali(a)salilab.org > Subject: Senior Computational Chemist (CADD) at Atomwise > > Hi Andrej. > I hope this email finds you well. A senior computational chemist position has opened up at Atomwise and I was wondering if you could pass on the information internally at UCSF. Candidates can apply directly on our website. > Thank you so much. > > _adrian > > Adrian Stecula, Ph.D. > Scientist > Atomwise | Better Medicines Faster > > > Senior Computational Chemist (CADD), Atomwise Inc, San-Francisco > We are looking for a senior computational chemist (CADD) to join our > production team. The production team is in charge of identifying > customer needs, implementing the most suitable solution, executing > projects using Atomwise technologies, and communicating results. > > Our customers are scientists; you should be, too. Results should be > considered guilty until proven innocent: sanity checking, skepticism, > problem-solving, analysis, and investigation are our constant companions. > You should be comfortable discussing and reasoning about projects with > the precision necessary to deliver what the customer needs, and possess > enough clear articulable pragmatism to get things done even in the face > of inevitable and unavoidable ambiguity. > > You will: > --------- > * Interact with customers to understand their project requirements > * Generate and analyze predictive results, and deliver these to our clients > * Communicate our results and capabilities through scientific publications > * Analyze, curate, and automate the processing of our biochemical databases > * Help to develop our modeling software > > Required Qualifications: > ------------------------ > * Ph.D. in chemistry, biology, bioinformatics, physics, or a related field > * +3 years of experience in Molecular Modeling: computational chemistry/biology > * Experience in Computer-Aided Drug Design: structure/ligand-based drug > design, docking, virtual screening, QSAR, pharmacophore modeling > * Comfortable on the Linux command-line > * Undergraduate knowledge of statistics > > Preferred Qualifications: > ------------------------- > * Good knowledge of Python, Perl, Bash, or related scripting languages > * Statistical modeling > * Knowledge of medicinal chemistry > * Experience with cloud computing environments (AWS/Azure/GCE) > > Compensation & benefits: > ------------------------ > * Competitive salary, commensurate with experience > * Stock compensation plan -- you will be an Atomwise co-owner > * Platinum health, dental, and vision benefits as well as an FSA > * 401k with 4% match > * Flexible work schedule > > *** Currently, we are not offering visa sponsorships for these positions, please only apply if eligible to work in the U.S ***. > > http://www.atomwise.com/careers/ > > > ᐧ

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[Compbio-allhands] 4/19/18 Seminar with Matt Simon
by Flowers, Nicole 13 Apr '18

13 Apr '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 Matt Simon Yale Chemistry to study the dynamics of cellular RNA populations April 19, 2018 K. Shokat, 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

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