February 2022 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] 3/17/22 BBC Seminar with Squire Booker, PhD, Noon
by Flowers, Nicole 24 Feb '22

24 Feb '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF Squire Booker, PhD Pennsylvania State University Moving beyond methionine synthase: New insight into cobalamin-dependent methylation reactions Marh 17, 2022 D. Fujimori, 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. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Fwd: Job at EMBL Hamburg - Senior Scientific Software Engineer: New Methods for Structural Modeling
by Andrej Sali 22 Feb '22

22 Feb '22

> Begin forwarded message: > > From: Jan Kosinski <jan.kosinski(a)embl.de> > Subject: Job at EMBL Hamburg - Senior Scientific Software Engineer: New Methods for Structural Modeling > Date: February 22, 2022 at 6:39:11 AM PST > To: Andrej Sali <sali(a)salilab.org> > > Dear Andrej, > > We are having the below job opening, and I would be grateful if you could forward it to anyone who might be interested: > > We are seeking to recruit a Senior Scientific Software Engineer: New Methods for Structural Modeling, to develop and apply computational methods for modeling based on electron microscopy and other data, with the particular focus on using recent Artificial Intelligence-based modeling tools like AlphaFold and RoseTTAfold. Three years contract with possibility of extension. > > More information and application form: https://www.embl.org/jobs/position/HH00209 <https://www.embl.org/jobs/position/HH00209> > Closing date: 27 March 2022 > > Please check more about our lab <https://www.embl.org/groups/kosinski/> and our publications <https://www.embl.org/groups/kosinski/publications/>. > > We offer access to superb computational infrastructure, experimental data from electron microscopy and other techniques, competitive salaries, and excellent working conditions. > > Best, > Jan > > -- > Group leader at European Molecular Biology Laboratory (EMBL) Hamburg > Joint appointment Structural and Computational Biology Unit EMBL Heidelberg > Group leader at Centre for Structural Systems Biology (CSSB) > > c/o DESY, Building 15 (CSSB), Room 02.247 > Notkestraße 85 > 22607 Hamburg, Germany > Phone: +49(0)40 8998-87573 > https://www.embl.org/kosinski/ <https://www.embl.org/kosinski/> > https://www.cssb-hamburg.de/research/research_groups/kosinski_group/index_e… <https://www.cssb-hamburg.de/research/research_groups/kosinski_group/index_e…> > > Twitter: @jankosinski >

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[Compbio-allhands] Fwd: in silico modeling expert
by Brian Shoichet 16 Feb '22

16 Feb '22

FYI ---------- Forwarded message --------- From: Joseph Wu <joewu(a)stanford.edu> Date: Tue, Feb 15, 2022 at 9:39 PM Subject: RE: in silico modeling expert To: Brian Shoichet <bshoichet(a)gmail.com> Dear Brian, I hope all is well. I recently started a startup company using clinical genomics, AI/ML, and patient-specific iPSCs to accelerate drug discovery. I wonder if you know of any graduates in your program or department who may be interested in joining our company. The expertise would be as follow: 1.) Computational ligand screening (e.g. docking) for hit identification 2.) Hit-to-lead optimization for establishing quantitative structure-activity-relationship (QSAR) 3.) Computational protein modeling, e.g. homology modeling. If yes, please feel free to introduce me to him/her and I’ll be happy to set up a zoom call. Thank you in advance. Best wishes, Joe Joseph C. Wu, MD, PhD Director, Stanford Cardiovascular Institute Simon H. Stertzer, MD, Professor of Medicine & Radiology Stanford University School of Medicine 265 Campus Drive, Rm G1120B Stanford, CA 94305-5454 Ph: 650-736-2246; Fax: 650-736-0234 Email: joewu(a)stanford.edu Lab: http://wulab.stanford.edu Stanford CVI: http://med.stanford.edu/cvi <http://med.stanford.edu/cvi.html> [image: cid:image001.jpg@01D58538.54058B90] <http://med.stanford.edu/cvi.html> [image: cid:ff7027d6-b10c-47d4-9a0c-6aac03848d78] <https://twitter.com/Joseph_C_Wu> *From:* Brian Shoichet <bshoichet(a)gmail.com> *Sent:* Wednesday, November 3, 2021 11:19 AM *To:* Hao Zhang <zhanghao(a)stanford.edu> *Cc:* Stefan Gahbauer <steffgahbauer(a)gmail.com>; Joseph Wu < joewu(a)stanford.edu> *Subject:* Re: Mentor team for my career development grant (in collaboration with Stefan) Hi Hao, Yes, I'd be willing to do it. Brian On Wed, Nov 3, 2021 at 8:06 AM Hao Zhang <zhanghao(a)stanford.edu> wrote: Dear Brian, I hope you are doing well. In the past few months, Stefan and I have been working together to design novel compounds aiming to eliminate neurological off-target effects in CGS15943, a non-selective adenosine antagonist for antifibrotic therapy. Stefan and I had many discussions, in which he taught me the strategy for in-silico drug development, including ligand-receptor docking, protein homology prediction, and polarized side-chain design. The new design compound is being synthesized, and we will test the effects soon. I am writing a career development grant for the American Heart Association. As "in-silico based drug development" takes a major part of my proposal. I wonder if you would like to join my mentor team, responsible for the drug design. Our chemistry department or CRO is responsible for the chemical synthesis with your supervision. I can draft the mentor letter with your approval. Thanks for your consideration. Best wishes, Hao -- Brian Shoichet, Professor, UCSF latest science from the lab: *http://www.bkslab.org/ <http://www.bkslab.org/contact.php>* -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] Fwd: Searching for Postdoc Candidate in AI/ML and mathematical methods for Biology @ IBM Almaden
by Andrej Sali 15 Feb '22

15 Feb '22

> Begin forwarded message: > > From: Sara CAPPONI <Sara.CAPPONI(a)ibm.com> > Subject: Searching for Postdoc Candidate in AI/ML and mathematical methods for Biology @ IBM Almaden > Date: February 12, 2022 at 4:24:23 PM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Andrej, > > I hope that this email finds you well! > > I am reaching out because I was awarded as IBM PI of the NSF Center for Cellular Construction grant and I am looking for a postdoctoral researcher willing to work using advanced AI/ML methods for Biology. I am wondering if you are aware of someone looking for such position, e. g. a student in the final year of Ph.D. training or a postdoc at the end of the contract. If so, maybe you can point this person to me (sara.capponi(a)ibm.com <mailto:sara.capponi@ibm.com>). > > Also, I would appreciate if you could forward this email to anyone who might be interested in applying to this position. The postdoc ad is at the bottom of the email. > > Thanks for your time! > > Best, > Sara > > --------------- > > Postdoctoral Research Scientist in Cellular Engineering at IBM Almaden Research Center > > The Cellular Engineering laboratory at IBM Almaden Research Center is looking for a postdoctoral research scientist. The position is slated to begin immediately. The candidate is expected to apply advanced AI/ML methods in cellular engineering and synthetic biology to understand biological systems and cellular dynamics. > > The Cellular Engineering laboratory integrates multidisciplinary methods to understand the basic principles underlying cell functions in order to modify and build cells with designed activity. For this purpose, we have access to several IBM supercomputers, which are among the fastest in the world. The laboratory is part of the NSF Center for Cellular Construction in partnership with UC San Francisco, UC Berkeley, Stanford University, SF State University, and the SF Exploratorium. The overall goal of the Center is to develop an engineering discipline to design cells. The candidate will work in close collaboration with world known scientists. > > Our focus is to leverage AI/ML methods for harnessing the power of cells and develop powerful predictive models of cellular structure and function. The candidate is expected to integrate and develop novel AI/ML algorithms to understand the basic principles underlying cell functions in order to modify and build cells with designed activity. The ideal candidate should have strong background in computational biology and modeling, biophysics, AI/ML methods for biological system analysis and cellular dynamics. Relevant areas of expertise might include direct application of machine learning methods to cellular systems. > > Interested candidates should contact Sara Capponi, PhD, (sara.capponi(a)ibm.com <mailto:sara.capponi@ibm.com>) with a brief statement of research interest/cover letter, a CV, and contact information of 2-3 references. Students in their final year of Ph.D. training are encouraged to apply. > > > Qualifications: > > • PhD in Computational Biology, Computational Biophysics, Physics, Bioengineering or related field. > • Experience in chemistry, physics, engineering, computer science, computational biology, or related fields. > • Experience in computational modeling methods. > • Experience in machine learning, deep learning packages. > • Proven experience with python programming. > • Excellent English (oral and written) and good communication skills are necessary.

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[Compbio-allhands] Fwd: New position in computational chemistry, Pfizer Cambridge, MA
by John Irwin 15 Feb '22

15 Feb '22

Computational chemistry job at Pfizer in Cambridge. John Irwin UCSF Pharmaceutical Chemistry http://irwinlab.compbio.ucsf.edu ---------- Forwarded message --------- From: Mathiowetz, Alan M <alan.m.mathiowetz(a)pfizer.com> Date: Tue, Feb 15, 2022 at 10:53 AM Subject: New position in computational chemistry, Pfizer Cambridge, MA To: John Irwin <jir322(a)gmail.com> Hi, John- I wanted to let you know that we have a new opening for a computational chemist in my group at Pfizer, located in Cambridge, MA. The work primarily involves small molecule drug discovery in the therapeutic areas of Inflammation, Immunology, and Rare Diseases. If you know of a current or recent Ph.D. student or postdoc who is looking for such a position, please share the following link with them: Senior Scientist, Computational Chemistry Thank you and best regards, Alan

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[Compbio-allhands] Check Out the Winter Line Up for the Gladstone Data Science Training Program
by Zainab Yusufsada 12 Feb '22

12 Feb '22

The Gladstone Data Science Training Program <https://gladstone.org/events?series=data-science-training-program> provides you with learning opportunities and hands-on workshops to improve your skills in bioinformatics and computational analysis. Join one of these upcoming workshops to gain new skills and get support with your data. Winter 2022 Series All workshops are virtual this winter! Unix Command Line February 14, 2022 Register <https://gladstone.org/events/unix-command-line> Introduction to Statistics and Experimental Design February 22, 2022 Register <https://gladstone.org/events/introduction-statistics-and-experimental-desig…> Introduction to RNA-Seq, Sessions 1- 2 March 10–11, 2022 Register <https://gladstone.org/events/introduction-rna-seq-analysis-2> Intermediate RNA Seq Analysis Using R March 21, 2022 Register <https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-0> Cordially, *Zainab Yusuf Sada* | Administrative Specialist Gladstone Institute of Data Science & Biotechnology 1700 Owens Street, San Francisco, CA 94518 T 415.734.4827|zainab.yusufsada(a)gladstone.ucsf.edu

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[Compbio-allhands] 2/17/22 BBC Seminar with David Baker, PhD, Noon
by Flowers, Nicole 11 Feb '22

11 Feb '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF David Baker, PhD University of Washington Protein design using deep learning February 17, 2022 C. Bracken & P. Burroughs, 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 Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] 2/10/22 BBC Seminar, HARC Lecture with Greg Towers, PhD, Noon, IN PERSON
by Flowers, Nicole 10 Feb '22

10 Feb '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursday, Noon Genentech Hall Byers Auditorium- IN PERSON Livestream: http://tiny.ucsf.edu/Y5D1RO HARC Speaker Greg Towers, Ph.D. University College London What's so special about pandemic viruses? HIV and SARS-CoV-2 vs. Innate Immunity February 10, 2022 N. Krogan, 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. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Check Out the Winter Line Up for the Gladstone Data Science Training Program
by Zainab Yusufsada 01 Feb '22

01 Feb '22

The Gladstone Data Science Training Program <https://gladstone.org/events?series=data-science-training-program> provides you with learning opportunities and hands-on workshops to improve your skills in bioinformatics and computational analysis. Join one of these upcoming workshops to gain new skills and get support with your data. Winter 2022 Series All workshops are virtual this winter! Introduction to R for Data Analysis February 4, 2022 Register <https://gladstone.org/events/introduction-r-data-analysis-2> Intermediate Cytoscape: Networks and Omics Data Visualization February 7, 2022 Register <https://gladstone.org/events/intermediate-cytoscape-networks-and-omics-data…> Unix Command Line February 14, 2022 Register <https://gladstone.org/events/unix-command-line> Introduction to Statistics and Experimental Design February 22, 2022 Register <https://gladstone.org/events/introduction-statistics-and-experimental-desig…> Introduction to RNA-Seq, Sessions 1- 2 March 10–11, 2022 Register <https://gladstone.org/events/introduction-rna-seq-analysis-2> Intermediate RNA Seq Analysis Using R March 21, 2022 Register <https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-0> Cordially, *Zainab Yusuf Sada* | Administrative Specialist Gladstone Institute of Data Science & Biotechnology 1700 Owens Street, San Francisco, CA 94518 T 415.734.4827|zainab.yusufsada(a)gladstone.ucsf.edu

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