October 2020 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] 11/5/20 BBC Seminar with Pardis Sabeti, PhD
by Flowers, Nicole 23 Oct '20

23 Oct '20

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/aJBL3J Pardis Sabeti, Ph.D. Harvard Outbreak Response in the Genomic Age November 5, 2020 W. Saylor, 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.proofpoint.com/v2/url?u=https-3A__calendar.google.com_ca… > Use this address to access this calendar from other applications.<https://urldefense.proofpoint.com/v2/url?u=https-3A__calendar.google.com_ca… > 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 recordings from Fall 2020, please go to this link: https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.box.com_v_2020BBC… -- Nicole Takesono Flowers she/her/hers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94143 P: 415.502.6518

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[Compbio-allhands] 10/22/20 BBC Seminar with Mikhail Shapiro, PhD
by Flowers, Nicole 16 Oct '20

16 Oct '20

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/miFF7x Mikhail Shapiro, Ph.D. CalTech Biomolecular Ultrasound for Non-Invasive Imaging and Control of Cellular Function October 22, 2020 J. Witte, 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.proofpoint.com/v2/url?u=https-3A__calendar.google.com_ca… > Use this address to access this calendar from other applications.<https://urldefense.proofpoint.com/v2/url?u=https-3A__calendar.google.com_ca… > 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 recordings from Fall 2020, please go to this link: https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.box.com_v_2020BBC… -- Nicole Takesono Flowers she/her/hers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94143 P: 415.502.6518

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[Compbio-allhands] Fwd: Jnana Therapeutics
by Jacobson, Matt 15 Oct '20

15 Oct '20

Two more job postings for comp chemists, via UCSF alum https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jnanatx.com_job-2D… https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jnanatx.com_job-2D… — Matt Begin forwarded message: From: Justin Rettenmaier <jrettenmaier(a)jnanatx.com<mailto:jrettenmaier@jnanatx.com>> Subject: Jnana Therapeutics Date: October 13, 2020 at 2:12:57 PM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, It’s been quite some time since I’ve seen you! I hope you are well and staying safe during these crazy times. One of our last interactions I remember was taking your CADD mini-course. We just had a candidate interview a few weeks ago who was surprised that a “biologist” would have ever heard of free energy perturbations :) After leaving Jim Wells' lab at UCSF, I ended up taking a postdoc position with Sue Lindquist at the Whitehead Institute up until she tragically passed away in late 2016. I was planning to continue my postdoc with Stuart Schreiber, but once I found out about a new company he was forming, I decided to jump in as employee #6. Jnana is focused on identifying small-molecule therapeutics targeting the SLC family of metabolite transporters for a range of therapeutic indications, including inborn errors of metabolism, autoimmune disease, and neurological disease. I co-invented a novel ligand discovery technology here at Jnana that we call RAPID, which was inspired by Ben Cravatt’s work with covalent fragment screening in live cells as well as my experiences with Tethering in Jim’s lab. It would be really fun to tell you a bit about it at some point if you were interested. I am writing to let you know that we have two job openings - one in cheminformatics and another in computational modeling (postings here<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jnanatx.com_join-2…>). I’ve tried and failed miserably in the past to recruit my old friends from the Bay Area to come out to the East Coast! I wonder if you could recommend any brave souls that might want to make the journey. All the best, Justin

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[Compbio-allhands] Fwd: post-doc offer front edge academic/industrial setting
by Andrej Sali 10 Oct '20

10 Oct '20

-- 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 > Begin forwarded message: > > From: dp devos <damienpdevos(a)gmail.com> > Subject: post-doc offer front edge academic/industrial setting > Date: October 10, 2020 at 3:19:46 AM PDT > To: Francisco Melo <fmelo(a)bio.puc.cl>, Maya Topf <m.topf(a)cryst.bbk.ac.uk>, Christian Jogler <Christian(a)jogler.de>, Ida van der Klei <i.j.van.der.klei(a)rug.nl>, Laura van Niftrik <l.vanniftrik(a)science.ru.nl>, Lucas Nicolás Alberca (vía Google Drive) <lucasalberca(a)gmail.com>, Luciano Marcon <lmarcon(a)upo.es>, Xavier De Bolle <xavier.debolle(a)unamur.be>, Cedric Govaerts <cgovaert(a)ulb.ac.be>, Lista IPs y asociados del CABD <cabd_associates(a)upo.es>, Simonetta Gribaldo <simo(a)pasteur.fr>, celine brochier <celine.brochier-armanet(a)univ-lyon1.fr>, Ricardo Rodriguez de la Vega <ricardo.rodriguezdelavega(a)gmail.com>, lazaro centanin <lazaro.centanin(a)cos.uni-heidelberg.de>, Maximiliano Gutierrez <max.g(a)crick.ac.uk>, Claudia Chica <ensentis(a)gmail.com>, "Mark C. Field" <mfield(a)mac.com>, Emmanuel Reynaud <emmanuel.reynaud(a)ucd.ie>, Marco Carraro <refract(a)ngp-net.bio.unipd.it>, Edu Andrés León <eduardo.andres.leon(a)gmail.com>, Andrey Kajava <andrey.kajava(a)crbm.cnrs.fr>, Silvio C E Tosatto <silvio.tosatto(a)unipd.it>, IDPfun - Diana Battistella <idpfun(a)ngp-net.bio.unipd.it>, Luis Sanchez-Pulido <sanchezpulido(a)gmail.com>, "Andrade, Dr. Miguel" <andrade(a)uni-mainz.de>, "Antonio J. Perez" <ajperez(a)upo.es>, Bruno Contreras Moreira <bcontreras(a)eead.csic.es>, Andrej Sali <sali(a)salilab.org>, "Michael P. Rout" <rout(a)mail.rockefeller.edu>, "Korkin, Dmitry" <dkorkin(a)wpi.edu> > > Dear colleague, > Please spread around this opportunity for realizing a post-doc between my lab and the industry in Seville. > Thanks in advance > d > > > > > Looking forward to applying your academic knowledge in an industrial setting? Here is a great opportunity to work at the front edge of collaboration between university research and commercial application. > > The CABD in collaboration with CITRE, a Bristol-Myers Squibb Company is offering a postdoctoral position on the groundbreaking topic of targeted protein degradation, in the context of an academic-industrial research collaboration. The project involves studying and understanding fundamental aspects of targeted protein degradation, involving molecular glue and heterobifunctional degraders (aka PROTACs) of enormous therapeutic potential. We are looking for a talented scientist with: > • PhD in a relevant discipline, such as structural biology, computational biology, bioinformatics or related fields, accompanied by original research publications. > • Experience in understanding protein structures and sequences from a computational perspective, combined with a strong interest in evolution and fundamental principles. > • Strong expertise in scripting and programming (e.g. R, Python, C++ or others), machine/deep learning and methods development experience is a plus. > • Attention to detail and capacity to communicate technical/scientific concepts clearly and > concisely to audiences of varied backgrounds. > • Verbal and written English language fluency. > > The position will be shared between the CABD and CITRE in Seville, Spain. Please send a short motivation letter, CV and 2 contacts for references to Alejandro Panjkovich and Damien Devos at damienpdevos at gmail.com <http://gmail.com/> and Alejandro.Panjkovich at bms.com <http://bms.com/>. > --- > Damien P. Devos, Cientifico Titular CSIC > Andalusian Center for Developmental Biology (CABD) > Pablo de Olavide University (UPO) > Spanish Science Council (CSIC) > > Latest publication: Origin and evolution of polycyclic triterpene synthesis. Santana-Molina et al., MBE. 2020 > https://doi.org/10.1093/molbev/msaa054 <https://doi.org/10.1093/molbev/msaa054> > > Research highlight: > https://www.csic.es/es/actualidad-del-csic/las-bacterias-podrian-ser-el-ori… <https://www.csic.es/es/actualidad-del-csic/las-bacterias-podrian-ser-el-ori…> > > Direction: > CABD/UPO, > Carretera de Utrera km1, > 41013 Sevilla, Spain > Tel: +34 (0) 954977930 > Fax: +34 954349376 > http://cellcollectives.com/dt_doctors/microbiologys-platypus/ <http://cellcollectives.com/dt_doctors/microbiologys-platypus/> > http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summa… <http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summa…> > > ORCID: orcid.org/0000-0002-9453-4753 <http://orcid.org/0000-0002-9453-4753> > Scopus author ID: 7004062844 > https://www.scopus.com/authid/detail.uri?authorId=7004062844 <https://www.scopus.com/authid/detail.uri?authorId=7004062844> > Twitter: @pvcbacteria > > PVC bacteria: > http://www.pvcbacteria.org <http://www.pvcbacteria.org/> > > Next conference: > PVC meeting, Bergen, NO 2021 > > "Education is the most powerful weapon which you can use to change the world." > Nelson R. Mandela (1918-2013) >

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[Compbio-allhands] 10/8/20 BBC Seminar with Cole Trapnell, PhD
by Flowers, Nicole 08 Oct '20

08 Oct '20

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/XsDVET Cole Trapnell, Ph.D. University of Washington Embryo scale single-cell spatial transcriptomics October 8, 2020 S. Bandyopadhyay, 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.proofpoint.com/v2/url?u=https-3A__calendar.google.com_ca… > Use this address to access this calendar from other applications.<https://urldefense.proofpoint.com/v2/url?u=https-3A__calendar.google.com_ca… > Use this URL to view the calendar in iCal.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> -- Nicole Takesono Flowers she/her/hers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94143 P: 415.502.6518

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[Compbio-allhands] 10/15/20 Seminar with Nicholas Ball, PhD, Noon
by Flowers, Nicole 07 Oct '20

07 Oct '20

Seminar with Nicholas D. Ball, PhD Pomona College Synthetic strategies toward fluorosulfurylation of organic molecules & sulfer-fluoride exhange (SUFEX) Thursday, October 15, 2020 Noon Danica Galonic Fujimori, Host 415.514.0147 danica.fujimori(a)ucsf.edu<mailto:danica.fujimori@ucsf.edu> https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.zoom.us_j_9995012… <https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.zoom.us_j_9995012… > Meeting ID: 999 5012 2338 Password: 590025 -- Nicole Takesono Flowers she/her/hers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94143 P: 415.502.6518

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[Compbio-allhands] Fwd: Invitation | Sir Ernst Chain Lecture 2020 | 4 November 2020: Enzymes, evolution and disease: 50 years of Bioinformatics Prof Dame Janet Thornton
by Andrej Sali 07 Oct '20

07 Oct '20

> Begin forwarded message: > > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: FW: Invitation | Sir Ernst Chain Lecture 2020 | 4 November 2020: Enzymes, evolution and disease: 50 years of Bioinformatics Prof Dame Janet Thornton > Date: October 7, 2020 at 9:48:31 AM PDT > > > Dear Colleague > > You may wish to attend and/or advertise to your colleagues this virtual talk. > > Best > > Mike > --------------------------------------- > > > > > The honour of your company is requested at the Sir Ernst Chain Lecture 2020: > > Enzymes, Evolution and Disease: 50 years of bioinformatics > Professor Dame Janet Thornton, FRS, FMedSci, EMBL-EBI > > Date: Wednesday 4 November 2020 > Time: 17:00 – 18:30 GMT > Venue: Microsoft Teams Live Event > > The lecture is free to attend and open to all, but registration is required in advance. > Register to attend on Eventbrite <https://www.eventbrite.co.uk/e/sir-ernst-chain-lecture-2020-enzymes-evoluti…> > The link to join the event will be circulated in the joining instructions > > Abstract > The last 50 years have seen bioinformatics evolve from a relatively minor pursuit into one of the major areas of biological research today. This has been driven by the DNA sequencing revolution and the rise of structural biology, which was only just beginning 50 years ago. Some of the first protein structures were of enzymes and were determined in Oxford – a prelude to understanding how they functioned as catalysts and performed their biological function. Today we have garnered data on almost 1000 enzymes, whose structures and functions are known, to improve our understanding of biocatalysis. One surprising finding has been that most enzymes have evolved from other ‘older’ enzymes, by slight modification of the binding sites or occasionally the catalytic mechanism. Another is that many diseases occur because of single amino acids variants which affect enzyme function. Even ageing can be modulated by single variants. These variants are gradually being identified and understood in terms of their effects on health, diseases and ageing. > > Despite all these data, biology remains in a ‘discovery phase’, where there are many many basic facts we still do not know or do not understand about how living organisms work. However, in parallel we now see an increasing push to exploit this flood of data to improve the world we live in. Bioinformatics provides the glue and the analytical approaches to develop quantitative models of life, which in the clinic can potentially help in diagnosis, prognosis and even sometimes identify a therapy. It is clear that the next 50 years will see the emergence of robust mathematical models to characterize living processes and make predictions. The relatively recent emergence of machine learning and synthetic biology have further fuelled the possibilities to harness all this molecular data for the benefit of society – addressing some of our major societal issues like infectious diseases, antimicrobial resistance and designing green waste disposal. > > The lecture will highlight the contributions of bioinformatics over the last 50 years and provide a glimpse of future opportunities. > > Biography > Janet Thornton is a Senior Scientist at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) on the Wellcome Genome Campus at Hinxton, near Cambridge, UK. She was Director of the Institute from 2001-2015. > > She studied for her PhD at the National Institute for Medical Research at Mill Hill after graduating as a physicist. After a post-doc in Oxford, Janet moved to London (Birkbeck and later UCL) before becoming Director at EMBL-EBI. Janet’s research is focused on proteins, especially their structure, function and evolution. She is a computational biologist, working at the interface of biology with physics, chemistry, and computing. This includes a detailed analysis of enzyme biocatalysts, their mechanisms and the evolution of new functions. Her group is also investigating the molecular basis of ageing. She has published more than 500 scientific papers, was elected to the Royal Society in 1999 and is a Foreign Associate of US National Academy of Sciences. In 2012 she became a Dame Commander of the Order of the British Empire for services to bioinformatics. > > Please note that Imperial College London processes your personal data in line with the Advancement Privacy Notice. <http://www.imperial.ac.uk/advancement/about-us/advancement-policies/privacy…> If you have any questions or concerns about this, please contact events(a)imperial.ac.uk <mailto:events@imperial.ac.uk>

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compbio-allhands October 2020