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

[Compbio-allhands] Fwd: open position in Gilead's modeling group
by Jacobson, Matt 21 Nov '20

21 Nov '20

— Matt Begin forwarded message: From: Vickie Tsui <Vickie.Tsui(a)gilead.com<mailto:Vickie.Tsui@gilead.com>> Subject: open position in Gilead's modeling group Date: November 17, 2020 at 1:03:43 PM PST To: "Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, It has been a long time since we talked, and I hope you and your family are doing well in spite of the crazy time. I wanted to let you know that our Modeling Group at Gilead has an opening currently. We are a group of 7 modelers (one just left last week – hence the open position), and we work closely with the other two groups (crystallography and informatics) in the Department of Structural Chemistry. We are parallel with the Medicinal Chemistry and Biology departments, and work closely with them on project teams. Modelers are involved from the target conception stage all the way to delivering a development candidate, and also have opportunities to be Core Team members or even to lead a project. Please feel free to pass this information on to your group, or to recommend specific people in your lab. My email isVickie.tsui(a)gilead.com<mailto:Vickie.tsui@gilead.com>, and my number is 650-534-8426. Thank you very much - I hope you take care and stay healthy. Best Regards, Vickie Vickie Tsui, Ph.D. Senior Director, Structural Chemistry Gilead Sciences, Inc. (650)653-9447

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[Compbio-allhands] FW: Reminder: Gustavo Silva seminar at noon today
by Flowers, Nicole 19 Nov '20

19 Nov '20

From: "Floor, Stephen" <Stephen.Floor(a)ucsf.edu> Date: Thursday, November 19, 2020 at 6:17 AM Subject: Reminder: Gustavo Silva seminar at noon today Hi everyone, Quick reminder there's a special seminar from Gustavo Silva from Duke at noon today. His talk is titled "K63 ubiquitin and translation control during oxidative stress”. His CV and the flyer are attached. The talk zoom is at http://tiny.ucsf.edu/SilvaSeminar. Hope you can make it! Best regards, Stephen

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[Compbio-allhands] Fwd: help with recrutiment
by Andrej Sali 16 Nov '20

16 Nov '20

> Dear Andrej > Please find the ad below and many thanks for helping out: > > The A*STAR Bioinformatics Institute in Singapore is a leading esearch institute connecting clinical, biological and cellular omics > data to biomolecular mechanisms through big data analysis and computational method development. We advance science and > develop innovative technology to further economic growth and improve lives. > > We are recruiting internationally recognized new group leaders with experience in biomolecular mechanism discovery through > computational data analysis of clinical, biological or cellular omics data. These could be genomics, transcriptomics, proteomics or > other omics data ideally intersecting with clinical data sets. > > Research areas include metabolic, infectious and neurological diseases including early childhood development. Experience in > applying AI and Machine learning is a plus. > > The applicant is expected to: > > 1. have solid background in Computer Science and Bioinformatics > 2. have shown abilities to combine and integrate data from multiple data sources linking data to molecular mechanisms > 3. be very versatile in understanding concepts in diverse biological fields and have the ability to use domain knowledge > effectively in the design and execution of analyses > 4. have good communication skills and fit in well in teams of very diverse background > 5. have strong publication background and academic track record > > Please contact chandra verma (chandra(a)bii.a-star.edu.sg <mailto:chandra@bii.a-star.edu.sg>) with your CV and have 3-4 letters of reference sent > > chandra >

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[Compbio-allhands] Fwd: Hiring a postdoc in my group
by Jacobson, Matt 15 Nov '20

15 Nov '20

— Matt Begin forwarded message: From: Chia-en Chang <chiaenc(a)ucr.edu<mailto:chiaenc@ucr.edu>> Subject: Hiring a postdoc in my group Date: November 12, 2020 at 1:41:26 PM PST To: Chia-En Angelina Chang <chia-en.chang(a)ucr.edu<mailto:chia-en.chang@ucr.edu>> Cc: chiaenc(a)ucr.edu<mailto:chiaenc@ucr.edu> Dear friends, I'm looking for a postdoc to work in the area of ligand and protein binding kinetics and free energy. The position is available immediately and will focus on developing and applying our newly developed Binding Kinetics (BKiT) package to compute unbinding free energy profile to problems in pharmaceutical drug discovery. Ideal candidates are someone with programming experience and expertise with MD and/or other molecular mechanics simulation techniques. Please pass along this link to anyone suitable you might be aware of: https://urldefense.proofpoint.com/v2/url?u=http-3A__chemcha-2Dgpu0.ucr.edu_… <https://urldefense.proofpoint.com/v2/url?u=http-3A__chemcha-2Dgpu0.ucr.edu_…> Hope all is well and stay safe! Thank you very much, Chia-en -- Chia-en A. Chang, Ph.D. Professor and Vice Chair of Chemistry Cooperating Faculty Member in the Department of Chemical Eng ETOX Program, GGB Program and Biochemistry program UC, Riverside Riverside, CA 92521 Ph:951-827-7263 https://urldefense.proofpoint.com/v2/url?u=http-3A__chemcha-2Dgpu0.ucr.edu_… <https://urldefense.proofpoint.com/v2/url?u=http-3A__chemcha-2Dgpu0.ucr.edu_…> https://urldefense.proofpoint.com/v2/url?u=https-3A__profiles.ucr.edu_app_h… <https://urldefense.proofpoint.com/v2/url?u=https-3A__profiles.ucr.edu_app_h…>

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[Compbio-allhands] 11/19/20 Seminar with Gustavo Silva
by Flowers, Nicole 05 Nov '20

05 Nov '20

Seminar with Dr. Gustavo Silva Duke University K63 upbiquitin and translation control during oxidative stress Stephen Floor, Host November 19, 2020 Noon http://tiny.ucsf.edu/silvaseminar Flyer attached -- 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: computational biology positions in the Pritykin lab at Princeton
by Andrej Sali 04 Nov '20

04 Nov '20

> Begin forwarded message: > > From: Matvei Khoroshkin <khorms21(a)gmail.com> > Subject: Fwd: computational biology positions in the Pritykin lab at Princeton > Date: November 4, 2020 at 6:27:26 PM PST > To: Andrej Sali <sali(a)salilab.org> > > Hi Andrej, > A friend of mine has just started as an Assistant Professor at Princeton and he is looking for people. Is there a chance you could spread the word through Compbio-allhands listserv? > Thank you! > > Best, > Matvei > > ---------- Forwarded message --------- > From: Yury Pritykin <pritykin(a)princeton.edu <mailto:pritykin@princeton.edu>> > Date: Wed, Nov 4, 2020 at 6:13 PM > Subject: computational biology positions in the Pritykin lab at Princeton > To: Matvei Khoroshkin <khorms21(a)gmail.com <mailto:khorms21@gmail.com>> > > > Computational biology positions at multiple levels are available in the Pritykin lab in the Lewis-Sigler Institute for Integrative Genomics and the Computer Science Department at Princeton University. > > The lab is broadly interested in developing computational methods for design and analysis of high-throughput functional genomic assays and perturbations, with a focus on multi-modal single-cell technologies, and applying these methods to study regulatory genomics of cell function and cell-cell interactions in vivo in close collaboration with experimental biologists, with a focus on immunology and cancer. More information is available at https://pritykin.github.io/ <https://pritykin.github.io/> > > Postdoctoral, staff scientist, internship positions are available for highly motivated individuals with strong background in computational biology and other quantitative and computational fields. (Prospective PhD students interested in working in the lab are encouraged to apply for QCB (https://lsi.princeton.edu/qcbgraduate <https://lsi.princeton.edu/qcbgraduate>) and/or COS (https://www.cs.princeton.edu/grad <https://www.cs.princeton.edu/grad>) programs at Princeton.) > > For any questions and additional details about the positions, please contact Yuri Pritykin at pritykin(a)princeton.edu <mailto:pritykin@princeton.edu> > >

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[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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