January 2014 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] 2/13/14 Seminar with Benjamin Cravatt
by Nicole Takesono Flowers 31 Jan '14

31 Jan '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Benjamin Cravatt Scripps Activity-based proteomics- applications for enzyme and inhibitor discovery. February 13, 2014 C. Fitzsimmons & R. Levin, 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 CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Astex Postdoctoral Training Program
by Brian Shoichet 29 Jan '14

29 Jan '14

FYI ---------- Forwarded message ---------- From: Marcel Verdonk <Marcel.Verdonk(a)astx.com> Date: Wed, Jan 29, 2014 at 10:48 AM Subject: Astex Postdoctoral Training Program To: "bshoichet(a)gmail.com" <bshoichet(a)gmail.com> Dear Brian, I hope you are well! I wanted to bring to your attention that Astex is starting a Postdoctoral Training Program this year. This will involve a number of postdocs each year, working in and across a range of disciplines, doing cutting edge science. These are fully industrial postdocs, based at the Astex site in Cambridge, UK, with supervision provided by Astex scientists. Assuming we can get a candidate of high enough calibre, one of these postdocs will be working with me in the Astex Computational Chemistry group. We have posted an advert on the CCL web site describing the Postdoctoral Training Program, and a little bit about a possible project in computational structure-based design: http://www.ccl.net/cca/jobs/joblist/mess0028548.shtml We are looking for outstanding young scientists with a background in computational chemistry, preferably with an expertise in structure-based methods. Given your outstanding work in Computational Chemistry I wondered if you were aware of a potential candidate in your group or department who might be suitable, and to whom you could pass on this message? Best wishes, Marcel _______________________________ *Marcel Verdonk, PhD* Director, Computational Chemistry & Informatics Astex Pharmaceuticals 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 226206 Fax: +44(0)1223 226201 marcel.verdonk(a)astx.com <m.verdonk(a)astex-therapeutics.com> www.astx.com <http://www.astex-therapeutics.com> _______________________________ This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. -- Brian Shoichet, Professor http://www.uoft.bkslab.org/ University of Toronto, Leslie Dan Faculty of Pharmacy Donnelly Centre Room 604 (416) 978-7224 University of California, San Francisco Dept. of Pharmaceutical Chemistry

1 0

[Compbio-allhands] Fwd: Group leader search FMI
by Jacobson, Matt 28 Jan '14

28 Jan '14

Begin forwarded message: From: "Gasser, Susan" <susan.gasser(a)fmi.ch<mailto:susan.gasser@fmi.ch>> Subject: Group leader search FMI Date: January 28, 2014 6:28:00 AM PST To: "'matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>'" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Cc: _DS directors office <directors.office(a)fmi.ch<mailto:directors.office@fmi.ch>> Dear Matthew, I am writing to ask your help in identifying promising candidates for tenure-track group leader positions at the Friedrich Miescher Institute in Basel, Switzerland. As you know, the FMI pursues biomedical research of a basic nature, being particularly strong in the study of neuronal circuits, epigenetics (both chromatin and small RNAs) and in mechanisms that signal and determine cell fate. With the impending retirements of two senior scientists, we have decided to expand into a new area – that of quantitative cell biology. This means we are looking for individuals trained in either physics, math or computational sciences, who address basic biological questions both computationally and experimentally. Of course, we also accept applications from biologists, but we are particularly interested in attracting persons who will probe cell physiology quantitatively, such that they can propose and test models of complex cell and/or organismal function. The research environment at the FMI is outstanding. Young group leaders are given up to 6 years before tenure evaluation, and they have a large range of efficient core facilities at their disposal. They will have sufficient funding to run a group of 4-5 scientists without raising external support. The language of the institute is English and Basel has a lively biomedical research community. The exact research topic is less critical than the energy and enthusiasm with which the candidates address their question, and their willingness to interact with other FMI research teams. The deadline for application is April 15, 2014. Applications should be submitted online at www.fmi.ch/gl_search<http://www.fmi.ch/gl_search> and enquiries can be sent to Dirk Schuebeler (dirk(a)fmi.ch<mailto:dirk@fmi.ch>) or to me. We would be grateful if you could distribute the attached flyer in your institute and among promising scientists in your field. Best wishes, Susan Professor S. M. Gasser Director of the Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 CH-4058 Basel Switzerland tel +41 61 697 7255 (assistant) tel +41 61 697 5025 (direct) fax +41 61 697 3976 susan.gasser(a)fmi.ch<mailto:susan.gasser@fmi.ch> http://www.fmi.ch/<http://www.fmi.ch%3chttp:/www.fmi.ch/> Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

1 0

[Compbio-allhands] 1/30/14 Seminar with Kate Carroll
by Nicole Takesono Flowers 24 Jan '14

24 Jan '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursday, 1 pm CVRI 159 **PLEASE NOTE THE TIME AND ROOM CHANGE** Kate Carroll Scripps Painting the Cysteine Chapel: New Tools to Probe Oxidation Biology January 30, 2014 B. DeGrado, Host **PLEASE NOTE THE TIME AND ROOM CHANGE** This seminar is sponsored by Novartis. BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

1 0

[Compbio-allhands] Fwd: Grabe lab post-doc candidate
by Jacobson, Matt 22 Jan '14

22 Jan '14

-- Matt Sent from my iPhone Begin forwarded message: From: "Grabe, Michael" <Michael.Grabe(a)ucsf.edu<mailto:Michael.Grabe@ucsf.edu>> Date: January 22, 2014, 4:02:52 PM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: Grabe lab post-doc candidate Hi Matt, I have a post-doc candidate, David Argudo, interviewing this Friday from Penn. His background is in the mechanical behavior of DNA under force. Please feel free to share the information on his talk with your group - they are more than welcome to attemd if the topic is of any interest. Cheers, Michael Speaker: David Argudo, University of Pennsylvania, Department of Mechanical Engineering (post-doc candidate in Grabe Lab) Presentation Title : "The Mechanical Response of DNA: Twisting the Molecule" Time: 10:30 am Friday January 24th, 2014 Room: 342 Smith Building (3rd floor) Abstract: Since the structure of double stranded DNA was discovered about six decades ago, there have been great developments in the fields of biology, genetic engineering, molecular biology, biophysics and numerous others. It is the objective of our work to carry on with these developments by providing new insights and understanding of DNA behavior/function using mechanics as our primary tool. To achieve this goal we focus on building analytical models for DNA molecules using rod theory and statistical mechanics. We model a key experiment in which a tensile force is applied on the DNA while simultaneously twisting it using optical or magnetic tweezers. In these experiments, DNA has been seen to form helical structures (supercoils), collapse into tightly condensed structures (toroids) and undergo structural changes (phase transitions). Our work focuses on studying all these phenomena by accounting for DNA elasticity, entropic effects due to thermal fluctuations and electrostatics. ------------------------------------------------------------------- Michael Grabe Associate Professor University of California, San Francisco Cardiovascular Research Institute Department of Pharmaceutical Chemistry 555 Mission Bay Blvd South, Room 452T, MC 3122 San Francisco, California 94158-9001

1 0

[Compbio-allhands] Fwd: 5 year post-doctoral fellowship in Medical Image Analysis
by Tom Ferrin 21 Jan '14

21 Jan '14

-------- Original Message -------- Subject: 5 year post-doctoral fellowship in Medical Image Analysis Date: Tue, 21 Jan 2014 23:58:17 +0000 From: Bob Fisher <rbf(a)inf.ed.ac.uk> To: tef(a)cgl.ucsf.edu 5 year post-doctoral fellowship in Medical Image Analysis The University of Edinburgh is advertising a number of 5 year fellowships that are expected to evolve into open ended tenured positions. Of particular interest to this email are applicants in Medical Image Analysis However, the School of Informatics is also looking for applicants in Algorithms for Big Data and distributed Systems, Cryptography, Automated reasoning, Cyber-security, Robotic hardware control, Geo-location and modelling of natural systems, Data-intensive biomedicine, Analysis of gene regulation data and data-driven modelling of gene networks controlling neural development, Design with data, Data-intensive social systems The advertisement is below. Closing date 7 February 2014 (5pm). Candidates likely to be considered for interview will already have a PhD and several publications in quality journals or top conferences. Best wishes, Bob ================================================================ Chancellor's Fellowships: Informatics University of Edinburgh - School of Informatics 37,756 - 45,053 GBP College of Science and Engineering The University of Edinburgh, a global top 20 University located in one of the world`s finest cities, continues to invest in the future of its academic staff with the appointment of a cohort of 50 tenure-track Chancellor's Fellowships across all disciplines. These 5-year Fellowships are intended to support candidates at the start of their independent academic careers. Subject to satisfactory review at the end of year 3, the Fellow will then move to a standard University academic open-ended contract. It is anticipated that most appointees will be successful in obtaining an open ended contract. Our people have been making their mark on the world for more than four centuries. They've explored space, revolutionised surgery, won Nobel Prizes, published era-defining books, paved the way for life-saving medical breakthroughs and laid the foundations for solving the mysteries of the universe. We are looking for highly talented academics who will contribute to our continued achievement of excellence in research. Colleagues addressing data intensive research are encouraged. You will already be working in an independent research capacity and will be developing your reputation for high quality research. Chancellor's Fellows also make an important contribution to enriching student learning experiences through their research, teaching and personal tutoring. You will concentrate on research initially, but will be trained in teaching skills and progressively take up this core academic activity. As we are a global University, we are interested in candidates from any location and we can offer relocation support. The culture of the University is open and diverse and we strive to replicate that in our appointments. Whilst we are proud of our rich heritage, we are a University that looks to the future. We are a global University with world leading interdisciplinary research capability, ideal for collaborative work as required. By joining our research-led community of international academics you will enjoy excellent career opportunities and support. Appointment will normally be made on the Grade 8 Academic scale (37,756-45,053 GBP), dependent on experience. In exceptional circumstances a more senior appointment may be made. This is an excellent opportunity to be part of one of the world's top Universities where you will develop your career in a stimulating, friendly and diverse environment that nurtures talent and rewards success. We welcome applications from everyone irrespective of gender or ethnic group. As women and members of ethnic minorities are currently under-represented in posts at this level we particularly encourage applications from members of these groups. For more information visit our website https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.disp… Closing date: 7 February 2014 (5pm). Committed to Equality and Diversity The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

1 0

[Compbio-allhands] Fwd: Novartis Symposium on Novel Approaches to Therapeutics and Targets - January 30th
by Jacobson, Matt 21 Jan '14

21 Jan '14

-- Matt Sent from my iPhone Begin forwarded message: From: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Date: January 21, 2014, 11:55:41 AM PST To: <BBCFACULTY(a)LISTSRV.UCSF.EDU<mailto:BBCFACULTY@LISTSRV.UCSF.EDU>> Subject: Novartis Symposium on Novel Approaches to Therapeutics and Targets - January 30th Reply-To: "Molla, Julia" <Julia.Molla(a)UCSF.EDU<mailto:Julia.Molla@UCSF.EDU>> Please join us for the Novartis Symposium on Novel Approaches to Therapeutics and Targets. Speakers include Eric Martin and Cindy Shafer of Novartis and Kate Carroll from the Scripps Research Institute. See the attached flyer for more details. Thursday, January 30th 9:00 am - 2:00 pm Smith Cardiovascular Research Building Room 159 **Please note, Kate Carroll’s BBC Seminar Series talk will be from 1-2pm in CVRI Rm 159 and NOT in Byers Auditorium at 12pm. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ About the invited speakers: Eric Martin is Director of Computational Chemistry at Novartis. He is credited with having started the field of combinatorial library design in the early 90s. Over the past 25 years he has worked in computational chemistry, analytical instrument development, environmental-fate modeling, drug design and herbicide design. His recent research includes the development of three novel kinase virtual screening methods, which he has combined with experimental IC50 and structural data to screen 4 million compounds across the entire kinome achieving unprecedented speed and accuracy. Cindy Shafer is a Project Leader in the Global Discovery Chemistry Group at Novartis. While at Novartis, she has worked on oncology, diabetes and anti-viral programs from the hit-to-lead stage through lead optimization. Several of these programs have progressed to the clinic including TKI258/dovitinib (Ph III), HSP990 and the mutant-b-Raf inhibitors RAF265 and LGX818 (Ph III). In addition, she has led several early stage programs to develop tool compounds to further elucidate the biological relevance in oncology settings. Kate Carroll is an Associate Professor of Chemistry at The Scripps Research Institute, Florida Campus. Her research focuses on the role of oxidative thiol modifications in the dynamic regulation of signaling pathways and physiological processes. Her work includes the development of chemical probes and proteomic technologies for the dissection of redox signaling pathways. Recently she has applied these tools to the global analysis of sulfenic acid modified proteins for the identification of signaling networks regulated by cysteine oxidation. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We thank Novartis, CVRI and UCSF BBC Graduate Groups for their participation and generous financial support. Julia Molla UC San Francisco Program Coordinator, Biological& Medical Informatics and Chemistry& Chemical Biology 600-16th St. MC2280 San Francisco, CA 94158-2517 415-476-1914 phone ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BBCFACULTY&A=1> from this mailing list.

1 0

[Compbio-allhands] Fwd: Post-doc with Rhoades and Miranker
by Andrej Sali 20 Jan '14

20 Jan '14

-- 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 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Andrew Miranker <Andrew.Miranker(a)YALE.EDU> > Subject: Post-doc with Rhoades and Miranker > Date: January 20, 2014 at 8:37:04 AM PST > To: Andrej Sali <sali(a)salilab.org> > > Dear Andrej, > > I am looking to recruit a post-doc in the near future for a position joint between myself and the lab of > Prof Liz Rhoades. I've attached a job-ad below. > Please encourage your graduating students to send me an application and/or come find Prof Rhoades > or myself at the Biophysical Society Meeting next month. > > Sincerely, > > Andrew > > > Andrew Miranker > Professor | Office: (203) 432-8954 > Dept of Molecular Biophysics & Biochemistry | Lab: (203) 432-5563 > Yale University | Assistant: (203) 432-5708 > 266 Whitney Avenue / Bass 318 | Fax: (203) 432-8492 > PO Box 208114 | Email: andrew.miranker(a)yale.edu > New Haven, CT 06520-8114 | Web: www.yale.edu/miranker/ > > **Please note. This is my professional email address and as such is read and > managed by my assistant, Lisa Adams (lisa.adams(a)yale.edu) >

1 0

[Compbio-allhands] postdoc jobs ad in Singapore
by Andrej Sali 17 Jan '14

17 Jan '14

-- 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 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

1 0

[Compbio-allhands] Fwd: Reminder for TDT competition
by Jacobson, Matt 12 Jan '14

12 Jan '14

-- Matt Sent from my iPhone Begin forwarded message: From: Hanneke Jansen <hanneke(a)tdti.org<mailto:hanneke@tdti.org>> Date: January 12, 2014, 3:10:08 PM PST To: "'Jacobson, Matt'" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: Reminder for TDT competition Dear Matt, A quick reminder that the deadline for the second round of the TDT competition is coming up! There are four exciting challenges that focus on developing and disseminating computational workflows for drug discovery of neglected diseases with a premium on reproducibility (use freely available software tools!). Note that one of these challenges is an open innovation challenge which is a great place to submit truly novel workflows that can be exemplified on any publicly available dataset. The other three challenges are structured around specific questions with held-out test data to compare across the various submissions. Three cash prizes - plus partial reimbursement of travel - will be awarded! Winners are required to present their work at the TDT Award symposium during the Fall 2014 ACS National Meeting in San Francisco, California. Detailed information about the 2014 Competition can be found here: http://www.TDTproject.org/2014-competition.html Submissions deadline is February 3, 2014. Please remind people in your group and let me know if there are any questions. Ciao, Hanneke ++++++++++++++++++++++++++ Hanneke Jansen Hanneke(a)TDTi.org<mailto:Hanneke@TDTi.org> 415.336.3036 (cell)

1 0