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

[Compbio-allhands] Check Out the Spring Line Up for the Gladstone Data Science Training Program
by Zainab Yusufsada 28 Mar '22

28 Mar '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. Spring 2022 Series All workshops are virtual! Single Cell RNA-Seq Analysis April 15-19, 2022 Register <https://gladstone.org/events/single-cell-rna-seq-analysis-2> Statistics of Enrichment Analysis April 22, 2022 Register <https://gladstone.org/events/statistics-enrichment-analysis-0> Introductory Machine Learning for Biologists May 3, 2022 Register <https://gladstone.org/events/introductory-machine-learning-biologists-2> Advanced Cytoscape Automation May 10, 2022 Register <https://gladstone.org/events/advanced-cytoscape-automation-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] Fwd: Opportunities at Schrödinger - Protein Structure Prediction/Optimization Scientist (Dynamics Simulations/Enhanced Sampling)
by Brian Shoichet 24 Mar '22

24 Mar '22

FYI ---------- Forwarded message --------- From: Annabel Cook <annabel.cook(a)schrodinger.com> Date: Wed, Mar 23, 2022 at 10:09 AM Subject: Opportunities at Schrödinger - Protein Structure Prediction/Optimization Scientist (Dynamics Simulations/Enhanced Sampling) To: <bshoichet(a)gmail.com> Dear Prof Shoichet, My name is Annabel Cook and I work in the Strategic Growth team at Schrödinger, Inc. Following our recent acquisition of XTAL BioStructures in Natick, MA, we are significantly expanding our structural biology capabilities, and are seeking scientists with expertise in structural biology, and protein structure prediction, optimization, and refinement. One of several roles we are looking to fill is a Protein Structure Prediction/Optimization Scientist (Dynamics Simulations/Enhanced Sampling) position, and I thought you may have some current or former group members who would be interested in hearing about the role. If so, please feel free to forward my contact information. I have included the specifics of the role below and applicants may apply directly here <https://grnh.se/a34dade13us>. Thank you in advance for your help. Do not hesitate to contact me if you have any questions! Kind regards, Annabel Protein Structure Prediction/Optimization Scientist (Dynamics Simulations/Enhanced Sampling) We’re seeking a Protein Structure Prediction/Optimization Scientist to join us in our mission to improve human health and quality of life through the development, distribution, and application of advanced computational methods! As a member of our Desmond (Molecular Dynamics) team, you’ll facilitate the refinement and optimization of predicted structures (homology models or AlphaFold V2) and validate these models in predictive free energy calculations for lead optimization. By advancing our methodology and immediately applying it to both our and our customers’ drug-discovery platforms, you’ll help tackle diseases that have been recalcitrant to structure-based drug design in the past. Schrödinger’s recent acquisition of XTAL BioStructures puts us in a unique position to advance the state of the art in protein structure prediction and refinement with experimental validation and support. We have other openings in this area that require slightly different skill sets. Please see our posts for Protein Structure Prediction/Optimization Scientist (Machine Learning) <https://grnh.se/e759b1a83us> and Protein Structure Prediction/Optimization Scientist (Core Homology) <https://grnh.se/aa293f6b3us>. Who will love this job: - A computational chemist with experience in biomolecular simulation, enhanced sampling, and free energy calculations - A passionate scientist who loves to push the boundaries of existing technology and creatively comes up with new ideas to address important problems - A methods developer who can implement a prototype using modern coding practices What you’ll do: - Identify problems in predicted structures from homology models or AlphaFold and develop strategies for refinement - Collaborate with scientists in other teams, including Machine Learning and Prime (Protein Structure Prediction), to exploit new developments and iteratively refine our strategy to improve the quality of predicted structures - Work with our drug discovery group to deploy new technologies in active projects and realize real-world impact What you should have: - PhD in computational chemistry, biochemistry, biophysics, or a related field, with a robust track record of publications in biomolecular simulations or enhanced sampling techniques - Proficiency in building complex workflows with Python - Experience with pharmaceutically relevant proteins, such as kinases, GPCRs, proteases, transferases, and/or ion channels is a plus Pay and perks: Schrödinger understands it’s people that make a company great. Because of this, we’re prepared to offer a competitive salary, stock options, and a wide range of benefits that include healthcare (with dental and vision), a 401k, pre-tax commuter benefits, a flexible work schedule, and a parental leave program. We have catered meals in the office every day, a company culture that is relaxed but engaged, and over a month of paid vacation time. Our Administrative and Human Resources departments also plan a myriad of fun company-wide events. New York is home to our largest office, but we have teams all over the world. Schrödinger is honored to have been selected as one of Crain's New York Best Places to Work for the past three years running. -- *Annabel Cook, PhD* | Principal Associate, Strategic Growth [image: Schrödinger, Inc.] <https://schrodinger.com> Schrödinger is hiring! Check out our careers page <https://www.schrodinger.com/careers> Our transparency document according to article 13 and 14 GDPR is available here <https://schrodinger.com/transparencydocinc>. -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] 3/31/22 BBC Seminar with Joanna Wysocka
by Flowers, Nicole 24 Mar '22

24 Mar '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Genentech Hall Auditorium Livestream: http://tiny.ucsf.edu/Y5D1RO Co-sponsored by the [cid:705c2812-9d04-4873-93a4-a6d52e62f537] Joanna Wysocka, PhD Stanford University Transcriptional regulation and emergence of form and function during development and evolution Marh 31, 2022 L. Weinberger, 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] Spring 2022 BBC Seminar Schedule
by Flowers, Nicole 18 Mar '22

18 Mar '22

Attached, please find the schedule of speakers for BBC Seminar Series spring quarter. Thank you! Nicole Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94158-2517 Phone: (415) 502-6518

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[Compbio-allhands] Canceled: 3/17/22 BBC Seminar with Squire Booker, PhD, Noon
by Flowers, Nicole 14 Mar '22

14 Mar '22

Unfortunately, Dr. Booker has a family emergency and will not be able to deliver his lecture. This seminar has been cancelled.

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[Compbio-allhands] Fwd: data science job posting at Novartis Emeryville
by Andrej Sali 10 Mar '22

10 Mar '22

Sent from my iPhone Begin forwarded message: > From: Dave Barkan <davebarkan(a)gmail.com> > Date: March 10, 2022 at 10:42:27 AM PST > To: Andrej Sali <sali(a)salilab.org> > Subject: data science job posting at Novartis Emeryville > > > Hi Andrej, > > Hope everything is going well. We have a new Structural Bioinformatician position opening in our Data Science group in Emeryville and I was wondering if you could circulate this link across relevant labs and graduate programs. This is a great opportunity for new PhDs and post-docs to get into the biotech industry while still working in an environment that emphasizes scientific curiosity. > > https://www.novartis.us/careers/career-search/job-details/339342BR > > Thanks, > Dave Barkan

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[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 15 Feb '22

15 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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