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

[Compbio-allhands] 4/6/17 Seminar with George Peng Wang
by Flowers, Nicole 30 Mar '17

30 Mar '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Livestream: https://lecture.ucsf.edu/ets/Catalog/Full/6cc7b194adc54d1eb01b99ca12d91ec221 George Peng Wang Georgia State University Chemical biology concepts and experiments for everyone April 6, 2017 L. Wang, 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

1 0

[Compbio-allhands] 3/30/17 Seminar with
by Flowers, Nicole 24 Mar '17

24 Mar '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Patrick Griffin The Scripps Research Institute, Florida Differential HDX to Probe Ligand-Mediated Receptor Signaling March 30, 2017 B. DeGrado & A. Sali, Hosts 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

1 0

[Compbio-allhands] RESCHEDULED: Jure Leskovec Seminar
by Rizk-Jackson, Angela 22 Mar '17

22 Mar '17

I am pleased to inform you that the ICHS Seminar featuring Jure Leskovec has been rescheduled. See below for info and mark your calendars! Reminders will be sent out as the date approaches. "Scaled computation & inferential methods in biomedicine: Machine learning for biomedical applications” Jure Leskovec, PhD Associate Professor of Computer Science, Stanford University Chief Scientist, Pinterest Wednesday, May 17, 2017 @ 10am Lecture: 10-11am Reception: 11-11:30pm (light refreshments will be served) Mission Bay Campus: Mission Hall 1400, 550 16th St About the Speaker: Jure’s research focuses on mining and modeling large social and information networks, their evolution, and diffusion of information and influence over them; and at Pinterest he works on machine learning problems. Contact: Angela.Rizk-jackson(a)ucsf.edu<mailto:Angela.Rizk-jackson@ucsf.edu>

1 0

[Compbio-allhands] Fwd: Recuitment_computational biology by iHuman Institute ShanghaiTech University
by Jacobson, Matt 16 Mar '17

16 Mar '17

- Matt Dear Professors: This is a letter from iHuman Institute of ShanghaiTech University, Shanghai, China. Now we are seeking candidates for our Faculty and Postdoc Positions, who focus on computational biology, especially Whole Cell Modeling. It's an honor for us if you can recommend highly motivated and outstanding international candidates. You can get more details from the attached file. About iHuman: iHuman Institute is a new international effort established as a research institute located on the campus of ShanghaiTech University. The institute is a gateway to the world of Shanghai life science research. What makes iHuman Institute special is that it is focused exclusively on the basic and applied science of human cell signaling, integrating multiple tools for scientific discovery, and bringing together leading researchers throughout the world. Cell surface receptors and their related intracellular proteins are responsible for human cellular communications with each other and their environment, and are involved in a wide range of physiological activities. Such a central role in human biology makes cell signaling the target for intervention for tuning physiological responses and fighting numerous conditions and diseases. These proteins are central to understanding the evolution of mankind and human cognition at a molecular level. Please let us know if you have any questions, also you can contact us by replying the E-mail directly. Thank you for your time. iHuman HR Team http://ihuman.shanghaitech.edu.cn/ [cid:07755f86-88bf-4a6f-a3ca-c06c93f99b63] [cid:07AE44DF-E495-4781-B290-5DD2A125D5A3]

1 0

[Compbio-allhands] informal seminar announcement
by Tom Ferrin 16 Mar '17

16 Mar '17

Please let students and other researchers in your lab know about the following informal seminar. Tristan has created a nice plug-in tool for our ChimeraX software that he'll talk about. * Tristan Croll * * PhD Student *Cambridge University * * *Friday, March 24* *2 - 3pm* *Genentech Hall S-203* *Title:* ISOLDE: a next-generation model-building environment for challenging molecular structures *Abstract:* Given an experimental dataset of sufficiently high resolution, modern model-building and refinement software can often build high-quality, near-complete models almost entirely automatically. However, as resolution degrades to the point where individual atoms are no longer resolved, the task becomes substantially more challenging and dependent upon user intervention. Current standards at these resolutions remain quite poor, with structures regularly deposited to the Protein Data Bank with outlier rates 1-2 orders of magnitude higher than expected of high resolution structures. ISOLDE is a set of tools which applies interactive molecular dynamics to significantly improve the ease and fidelity of model-building into such data, in essence by making the task feel similar to interacting with a real, physical molecule. In this seminar I will give a preview of the ISOLDE package and workflow, with examples from both EM and crystallographic structures.

1 1

[Compbio-allhands] 3/16/17 Seminar with Emily Balskus
by Flowers, Nicole 15 Mar '17

15 Mar '17

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Livestream URL available upon request Emily Balskus Harvard Chemical Discovery in the Human Microbiota March 16, 2017 F. Ugur, 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

1 1

[Compbio-allhands] Fwd: Postdoc in Protein 3D Modelling Imperial College
by Andrej Sali 15 Mar '17

15 Mar '17

-- 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 > Begin forwarded message: > > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: FW: Postdoc in Protein 3D Modelling Imperial College > Date: March 15, 2017 at 5:56:23 AM MDT > > > Research Associate in Bioinformatics – Protein 3D Modelling > > Imperial College, Department of Life Sciences > > Salary £36,070 - £43,350 per annum > > Applications are invited for a Research Associate position to join the Structural Bioinformatics Group, within the Department of Life Sciences based at the South Kensington Campus. The post is part of a joint UK (funded by the BBSRC) and USA (funded by the NSF) grant. Our colleagues in the USA are the group of Prof Vakser (university of Kansas) who will be using our predicted structures as the basis to predict structures for protein complexes. > > The post holder will work as a member of a small team that is developing methods for enhance protein structure prediction, using these methods to predict protein structures and mapping genetic variants to these structures. > > You must have, or have submitted, a research orientated PhD (or equivalent) involving the development and application of software to a scientific problem, ideally applied to protein structure. You will have proven programming experience that results in the development of a substantive algorithm tackling a problem modelling protein structure. You will have experience in developing high-level code to a professional standard of robustness and clarity. You will have extensive knowledge and experience in code development in C (or variants) or Python, or Perl (or very close equivalent). Experience/knowledge developing scientific software to a standard suitable for public distribution is also essential. Experience of working with protein data bank files and a successful track record in academic publication where you made a substantial contribution to the project via computational work are desirable. Experience of developing web sites for use by the scientific community, ideally in bioscience or biomedicine and experience of database development, ideally in bioscience or biomedicine, are also desirable. > > Any candidate who has not been awarded their PhD, will be appointed as a Research Assistant within the salary range £31,740 - £33,370 per annum. > > This is a full time position, funded by the BBSRC available for up to 30 months. > Closing Date 5 April 2017 (Midnight GMT) > > For initial enquiries contact Prof Mike Sternberg m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > > For full details and application procedure see: > > > https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf… <https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf…>..

1 0

[Compbio-allhands] Fwd: Postdoc position in the SIBYLS group
by Andrej Sali 14 Mar '17

14 Mar '17

-- 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 > Begin forwarded message: > > From: Michal Hammel <mhammel(a)lbl.gov> > Subject: Postdoc position in the SIBYLS group > Date: March 14, 2017 at 5:04:26 PM MDT > To: Michal Hammel <mhammel(a)lbl.gov> > Cc: Jane Tanamachi <JTanamachi(a)lbl.gov> > > Dear Colleagues, > > I would like to draw your attention to a postdoc position in the SIBYLS group i at the Lawrence Berkeley National Laboratory in Berkeley. Please, spread this advertisement to students that could be interested in this position. > Thanks and best regards > > Michal Hammel > > > > __________________ > Michal Hammel PhD > Scientist at Advanced Light Source > Lawrence Berkeley National Laboratory > > 1 Cyclotron Road MS 6R2100 > Berkeley, CA 94720 > (phone) 510-495-8179 > (cell) 510-457-6317 > > mhammel(a)lbl.gov > ____________________ > >

1 0

[Compbio-allhands] ICHS Seminar Series: Udi Manber, 4/19 @ 4pm
by Rizk-Jackson, Angela 13 Mar '17

13 Mar '17

We hope you will join us for the following talk in our ICHS Seminar Series (flyer attached): "Healthcare as an information business” Udi Manber, PhD Professor and Director of Digital Transformation, Department of Medicine, UCSF Technical Advisor, Institute for Computational Health Sciences, UCSF Former head of Google Search (2009-2014) Wednesday, April 19, 2017 @ 4pm Lecture: 4-5pm Reception: 5-6pm (refreshments will be served) Mission Bay Campus: 1550 4th St, Genentech Hall, Byers Auditorium (Simulcast in Toland Hall at Parnassus Campus) RSVPs Appreciated: click here<https://ucsf.co1.qualtrics.com/SE/?SID=SV_eVB5Fapad8DCcZf> Hosted by Robert Wachter, MD, Chair of the Department of Medicine Contact: Angela.Rizk-jackson(a)ucsf.edu<mailto:Angela.Rizk-jackson@ucsf.edu>

1 0

[Compbio-allhands] Fwd: Atomwise Job Openings
by Brian Shoichet 09 Mar '17

09 Mar '17

---------- Forwarded message ---------- From: Michael Mysinger <michael(a)atomwise.com> Date: Thu, Mar 9, 2017 at 5:26 PM Subject: Atomwise Job Openings To: Brian Shoichet <shoichet(a)cgl.ucsf.edu>, John Irwin <jji(a)cgl.ucsf.edu>, Michael Keiser <keiser(a)keiserlab.org> Hello Brian, John, and Mike, Atomwise is hiring for 3 different positions, including a computational chemist, a data engineer, and an infrastructure engineer. The relevant link is: http://www.atomwise.com/careers/ It would be great if you can get the word out for those that may be interested. Cheers, Michael -- Michael Mysinger Principal Scientist Atomwise San Francisco, CA -- 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

1 0