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

[Compbio-allhands] Fwd: Happy New Year and hiring at new company
by Jacobson, Matt 09 Jan '14

09 Jan '14

Job opportunity ... Begin forwarded message: I’ve recently moved from Amazon because this is a compelling opportunity. IO is the global leader in software-defined data centers, and has pioneered the next-generation of data center infrastructure technology and Intelligent Control. We are a mature startup with over 600 clients, including for example Goldman Sachs. The Applied Intelligence team in San Francisco uses predictive modeling, analytics and simulation to impact both design and intelligent control. Are there any great people that spring to mind? I will attach the two job descriptions and may I ask you to let people know about the opportunity? Thank you and I’d love to catch up soon, Jim James Arnold, Ph.D. | Director Applied Intelligence Software M +1.415.216.5655 E jarnold(a)io.com<mailto:jarnold@io.com> | www.io.com<http://www.io.com> The communication contained in this e-mail is confidential and is intended only for the named recipient(s) and may contain information that is privileged, proprietary, attorney work product or exempt from disclosure under applicable law. If you have received this message in error, or are not the named recipient(s), please note that any form of distribution, copying or use of this communication or the information in it is strictly prohibited and may be unlawful. Please immediately notify the sender of the error, and delete this communication including any attached files from your system. Thank you for your cooperation. 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>

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[Compbio-allhands] Fwd: Lunenfeld Tanenbaum Research Institute PI Search
by Andrej Sali 08 Jan '14

08 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: Donna Doherty <doherty(a)lunenfeld.ca> > Subject: Lunenfeld Tanenbaum Research Institute PI Search > Date: January 8, 2014 at 11:30:30 AM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Professor Sali, > > Please find enclosed information related to recruitment of scientists at the Lunenfeld Tanenbaum Research Institute at Mt. Sinai Hospital. Please feel free to forward this information to your colleagues. > > Sincerely, > > > Donna Doherty on behalf of Professors Jim Woodgett, Dan Durocher, and Daniel Drucker >

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[Compbio-allhands] 1/9/14 Seminar with Wah Chiu
by Nicole Takesono Flowers 06 Jan '14

06 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 Wah Chiu Baylor College of Medicine Structures of Viruses Inside and Outside the Host Cells January 9, 2014 Y. Cheng, Host 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

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[Compbio-allhands] Mini-course: Information Theory and Biology
by David Sivak 03 Jan '14

03 Jan '14

Hi. You ever noticed how people around here use the word "Information" like it's going out of style? You ever wondered what's the big deal? We (David Sivak, Raj Bhatnagar, Michael Chevalier) plan on getting to the heart of all that in a mini-course at Mission Bay this spring on "Information Theory and Biology." If you have any interest in possibly taking this mini-course, please help us get a sense of numbers and backgrounds by sharing a little information [sorry] about yourself at: https://docs.google.com/forms/d/1HtENxOKiXyZXyzq9-4zoK0qWpTklQHLPpZC-UKqQYA… Feel free to pass along to other interested parties. Apologies for any mailing list duplication... Thanks, David -- David Sivak Systems Biology Fellow University of California, San Francisco david.sivak(a)gmail.com davidsivak.com 510-541-9006

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[Compbio-allhands] SAVE THE DATE- PETER A. KOLLMAN LECTURESHIP - April 3, 2014
by Nicole Takesono Flowers 20 Dec '13

20 Dec '13

SAVE THE DATE- THURSDAY, APRIL 3, 2014 AT 12:00 PM PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS LIBRARY 221 Reception in Byers Hall 5th Floor Lounge at 3:30 Please see attached flyer. 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

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[Compbio-allhands] Peter Kolb Seminar - Thursday, Dec. 12 - 10am - Byers Hall 212
by Hilary Mahon 10 Dec '13

10 Dec '13

Please see attached. Thank you. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

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[Compbio-allhands] BBC Seminar Speaker David Allis Talk CANCELLED
by Nicole Takesono Flowers 05 Dec '13

05 Dec '13

Please note that Dr. Allis had to cancel his previously scheduled talk (1/16/14) for the BBC Seminar Series. Thank you, Nicole 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

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[Compbio-allhands] Janet Thornton Seminar: Thurs., Dec. 5
by Patsy Babbitt 01 Dec '13

01 Dec '13

Please add to your calendars a special seminar by Janet Thornton: "The Evolution of Enzyme Mechanisms and Functional Diversity" Thursday, December 5th, 2013 3:00 – 4:00 PM Genentech Hall Auditorium Professor Dame Janet Thornton is the Director of the European Molecular Biology Laboratory — European Bioinformatics Institute (EMBL-EBI). She has been a leader in computational biology and bioinformatics throughout her career and has be awarded many honors, among them her election as a Fellow of the Royal Society and as a foreign associate of the National Academy of Sciences. >From her biography on Wikipedia, she is rightfully described as "one of the world’s leading researchers in structural bioinformatics, using computational methods to understand protein structure and function." Don't miss it! (Hosted by Patsy Babbitt) -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94158-2330, USA (CA 94158 for direct delivery by courier) Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Joslyn Polzien, +1 415-514-1214, 415-514-4861 Joslyn.Polzien(a)ucsf.edu

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[Compbio-allhands] Fwd: Faculty positions in computational biology at the University of Rochester
by Jacobson, Matt 23 Nov '13

23 Nov '13

-- Matt Sent from my iPad Begin forwarded message: From: Sina Ghaemmaghami <sghaemma(a)bio.rochester.edu<mailto:sghaemma@bio.rochester.edu>> Date: November 22, 2013 9:18:43 AM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Subject: Faculty positions in computational biology at the University of Rochester Dear Matt, I hope everything is going well with you. At the University of Rochester, we have undertaken a Data Science initiative. As part of that initiative, we are having tenure track job searches this year for individuals using computational approaches to investigate cross-disciplinary topics. One of the identified target areas is Computational Biology and Computational Bioengineering, e.g. functional and evolutionary genomics, proteomics and protein folding, systems biology, multi-scale modeling in bioengineering, or multimodal bio-imaging informatics. I am contacting you to see if you know of candidates on the job market (e.g. promising postdocs or already established researchers) who you could recommend, or let them know about this job search. An emphasis here would be on individuals for whom computational approaches are a key part of their research. Attached is the job description with information on how to apply, and please feel free to circulate this among your colleagues. Further information on the Data Science initiative and instructions for this search can be found at: http://www.rochester.edu/rocdata/recruit/interdisciplinary.html. The search is open to senior level candidates. So, if you know of someone who may be interested, please let me know. Sincerely, Sina Ghaemmaghami Department of Biology, University of Rochester 326 Hutchison Hall Rochester NY 14627 Tel (office): 585-275-4829 Tel (cell): 415-992-2594

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[Compbio-allhands] from Hanneke Jansen
by Jacobson, Matt 20 Nov '13

20 Nov '13

Forwarding ... ------------ Teach-Discover-Treat (TDT) is excited to announce our 2014 Competition. We have four exciting challenges that focus on developing and disseminating computational workflows for drug discovery of neglected diseases with a premium on reproducibility. 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. Create and submit computational workflows that inspire drug discovery activities using freely available software tools. Detailed information about the 2014 Competition can be found here: http://www.TDTproject.org/2014-competition.html Submissions deadline is February 3, 2014. The TDT Steering Committee Hanneke Jansen, Rommie Amaro, Jane Tseng, Wendy Cornell, Patrick Walters and Emilio Xavier Esposito www.TDTproject.org<http://www.tdtproject.org/> twitter.com/TeachDiscoTreat<http://twitter.com/TeachDiscoTreat>

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[Compbio-allhands] Fwd: FINAL CALL: Faculty positions in Bioinformatics/Computational Biology in the Crick at LRI
by Andrej Sali 17 Nov '13

17 Nov '13

-- 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: Nicholas Luscombe <nick(a)valleyofpigs.org> > Subject: FINAL CALL: Faculty positions in Bioinformatics/Computational Biology in the Crick at LRI > Date: November 15, 2013 at 2:40:52 AM PST > To: Paul Nurse <paul.nurse(a)royalsociety.org> > Cc: Richard Treisman <richard.treisman(a)cancer.org.uk>, Jim Smith <director(a)nimr.mrc.ac.uk>, Paul Nurse <paul.nurse(a)royalsociety.org> > > Dear Colleagues, > > Thank you for your help in circulating information about the Bioinformatics/Computational Biology position at the Crick@LRI. We’ve had a lot of interest and we’re hoping that many will result in applications! > > I would like to remind you that the deadline is 22 November 2013; I should be grateful if you would continue to spread the word. > > With many thanks for your support, > > Nick Luscombe > > > Website: http://tinyurl.com/ohgnxw8 > Application deadline: 22 November 2013 > Informal enquiries may be made by e-mail to nicholas.luscombe(a)cancer.org.uk > > --- > > Faculty positions for Bioinformatics and Computational Biology > Francis Crick Institute group leaders at the CRUK London Research Institute > > An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis. > > The Francis Crick Institute http://www.crick.ac.uk > The Francis Crick Institute will open at St Pancras in central London in 2015. Its research will use interdisciplinary approaches to investigate the biology of human health and disease, supported by core funding from CRUK, the MRC, and the Wellcome Trust, and by grants from UK and international funding agencies. > > The Crick is expanding Computational Biology research as a key component of its scientific strategy. The institute will offer an outstanding environment for computational research, with excellent opportunities for wet/dry collaborations across the range of biomedical and clinical research disciplines, supported by a strategic alliance with the Wellcome Trust Sanger Institute. The new Crick laboratories will feature excellent computational facilities including a state-of-the-art data centre. > > The London Research Institute http://www.london-research-institute.org.uk > The London Research Institute (LRI) is the largest Cancer Research UK research institute, with 40 research groups focusing on fundamental cancer biology. The Institute is based in well-equipped laboratories at Lincoln's Inn Fields in central London, and at Clare Hall in Hertfordshire. > > Computational Biology in Cancer http://tinyurl.com/ohgnxw8 > An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis. The LRI recruitment process for 2013 will carried out jointly with the Crick Institute. We shall appoint outstanding scientists seeking to establish independent and innovative research programmes focussed on: > > Newly appointed group leaders will receive core funding for research personnel, travel and consumables, and access to the Institute's comprehensive computational core facilities, backed by competitive employment terms. The new group leaders will move to the Crick laboratories in 2015. > > Website: http://tinyurl.com/ohgnxw8 > Application deadline: 22 November 2013 > Informal enquiries may be made by e-mail to nicholas.luscombe(a)cancer.org.uk > > > --- > Check out our new website: www.luscombelab.org > > Nicholas M LUSCOMBE, Professor of Computational Biology > > University College London (joint appointment) > UCL Genetics Institute, Dept of Genetics, Evolution & Environment, > University College London, Gower Street, London WC1E 6BT, UK > > Cancer Research UK London Research Institute (joint appointment) > 44 Lincoln's Inn Fields, London WC2A 3LY, UK > > Okinawa Institute of Science & Technology (adjunct faculty) > 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan > > > > > >

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[Compbio-allhands] 11/21/13 Seminar with Dana Pe'er
by Nicole Takesono Flowers 15 Nov '13

15 Nov '13

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 Dana Pe'er Columbia What can you do with 40 dimensions in single cells, mapping development, signal processing and disease? November 21, 2013 W. Lim, Host 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

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[Compbio-allhands] Fwd: Computational and Systems Biology Positions at the Genome Institute of Singapore
by Tom Ferrin 14 Nov '13

14 Nov '13

-------- Original Message -------- Subject: Computational and Systems Biology Positions at the Genome Institute of Singapore Date: Thu, 14 Nov 2013 19:15:30 +0800 From: Tara Leah HUBER (GIS) <hubertl(a)gis.a-star.edu.sg> CC: Shyam PRABHAKAR (GIS) <prabhakars(a)gis.a-star.edu.sg>, Niranjan NAGARAJAN (GIS) <nagarajann(a)gis.a-star.edu.sg> Dear Colleague, We have some immediate Faculty openings in Computational and Systems biology at the Genome Institute of Singapore. Applicants with computational expertise in all areas and at all levels are welcome; areas of particular interest include: Regulatory Genomics and Epigenomics, Microbial Evolution and Metagenomics, Systems Biology and Cancer Genomics. Applicants should submit a CV, a statement of research interests and the names of three references by email (with job code "CSB-I" in the subject line) to: gisrecruit(a)gis.a-star.edu.sg <mailto:gisrecruit@gis.a-star.edu.sg> We are seeking outstanding researchers with the potential to establish impactful, independent and creative research programs at the GIS. Candidates are expected to have significant experience in the analysis of genome-wide/cell-wide biological datasets and to have demonstrated exceptional originality and excellence in their work. We would appreciate if you would share this information with your colleagues and bring it to the attention of any qualified candidate for these positions. With best regards, Niranjan and Shyam Niranjan Nagarajan Group Leader Associate Director, Computational and Systems Biology Shyam Prabhakar Group Leader Associate Director, Integrative Genomics Genome Institute of Singapore 60 Biopolis Street, #02-01 Genome, Singapore 138672 Tel: +65 6808 8071 (Niranjan Nagarajan) +65 6808 8046 (Shyam Prabhakar) http://www.gis.a-star.edu.sg ------------------------------- This e-mail and any attachments are only for the use of the intended recipient and may be confidential and/or privileged. If you are not the recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person as it may be an offence under the Official Secrets Act. -------------------------------

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[Compbio-allhands] Fwd: Institute for Genomic Biology Fellowship
by Andrej Sali 13 Nov '13

13 Nov '13

Begin forwarded message: > From: Taekjip Ha <TaekjipHa(a)mx.uillinois.edu> > Subject: Institute for Genomic Biology Fellowship > Date: November 13, 2013 at 10:03:13 AM PST > > > Dear colleagues, > > I wanted to bring to your attention an exciting postdoctoral fellows program at the University of Illinois at Urbana-Champaign. The Institute of Genomic Biology (IGB) opened its $70 M building in 2007 and is research home to dozens of world-class scientists. The IGB Fellows program appoints several new fellows each year through theme-based competition. For the Cellular Decision Making in Cancer Theme that I am involved with, the first two fellows became professors in Princeton and UIUC, both winning the NIH new innovators awards, just to give you some examples of the excellence of the program. This year’s application deadline is December 1st and I am attaching an ad that ran on Science magazine. The link below points to the application site which also shows a nice video about the virtue of living in Champaign-Urbana among other things. Please share this exciting opportunity with your young colleagues. > > http://www.igb.illinois.edu/education/igb-fellows > > Best wishes, > Taekjip Ha

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[Compbio-allhands] Fwd: Two junior group leader positions at the CRG (Barcelona)
by Andrej Sali 09 Nov '13

09 Nov '13

Sent from my iPhone Begin forwarded message: > From: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Date: November 9, 2013 at 8:11:26 AM PST > To: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Cc: Juan Valcarcel Juarez <juan.valcarcel(a)crg.eu> > Subject: Two junior group leader positions at the CRG (Barcelona) > > Dear friends, > > I would appreciate if you could forward this e-mail to whom you may think could be interested in a Junior Group Leader position at CRG in Barcelona. > > Additional information in the attached PDF. > > Many thanks in advance, > Marc > > > > ... > Marc A. Marti-Renom, ICREA Research Professor > Genome Biology Group Leader - CNAG - Centre Nacional d’Anàlisi Genòmica > Structural Genomics Group Leader - CRG - Centre de Regulació Genòmica > Parc Científic de Barcelona – Torre I > Baldiri Reixac, 4 > 08028 Barcelona > Tel +34 9340 33743 > Email mmarti(a)pcb.ub.cat > Web http://marciuslab.org - http://cnag.cat - http://crg.cat > > *** Consider the environment. Print responsibly. *** >

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[Compbio-allhands] Fwd: Postdoctoral opportunities at Princeton
by Andrej Sali 07 Nov '13

07 Nov '13

Sent from my iPhone Begin forwarded message: > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Date: November 7, 2013 at 1:47:15 PM PST > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Subject: Postdoctoral opportunities at Princeton > > Dear Colleagues, > > In an effort to attract the strongest possible candidates, we are extending our annual search for young theorists interested in problems at the interface of physics and biology, broadly interpreted. Princeton offers a very interactive community, with a nearly unique combination of theoretical mentors and friendly experimental collaborators. We have been fortunate so far in attracting a steady stream of wonderful postdoctoral scholars. We would like to continue this pattern, and ask for your further help in pointing a few more excellent new candidates in our direction. Thank you in advance for your willingness to contribute to this effort. > > We have extended the deadline for applications and letters another week, to November 15th. > > For more details, please see http://www.princeton.edu/physics/about/employment/biophysics/index.xml > > Best wishes, > > William Bialek > Chase Broedersz > Curtis Callan > Benjamin Machta > Ned Wingreen > > > Lee Morgan > 257 Carl Icahn Laboratory > Lewis-Sigler Institute of Integrative Genomics > Princeton University > Princeton, NJ 08544 > 609-258-0859 >

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[Compbio-allhands] Fwd: POSTDOCTORAL POSITION IN COMPUTATIONAL NEUROSCIENCE AT ENS, PARIS
by Andrej Sali 07 Nov '13

07 Nov '13

Sent from my iPhone Begin forwarded message: > From: "Rava A. da Silveira" <rava(a)ens.fr> > Date: November 6, 2013 at 9:27:17 PM CST > To: "Rava A. da Silveira (Me)" <rava(a)ens.fr> > Subject: POSTDOCTORAL POSITION IN COMPUTATIONAL NEUROSCIENCE AT ENS, PARIS > > Dear colleague, > > Would you be so kind as to forward the postdoc ad pasted below to > potential candidates? > > Many thanks, and best regards, > > Rava > (Apologies for multiple postings.) > > ********* > > POSTDOCTORAL POSITION available in the group of RAVA AZEREDO DA > SILVEIRA at the ECOLE NORMALE SUPERIEURE, Paris > > This position will be devoted, in part, to the analysis and modeling > of exciting retina data sets from the labs of Botond Roska (FMI) and > Andreas Hierlemann (ETH). Experience with data analysis and > proficiency with numerical methods and programming, in addition to > familiarity with neuroscience topics and mathematical and statistical > methods, are desirable. In addition, research may be pursued on > problems of single-cell and network dynamics, neural coding, or > cognitive and behavioral modeling (inference, sensory integration, > decision making, etc), with more or less connection with data > depending upon the specific problem. Thus, a spirit of intellectual > adventure and eagerness is at least as desirable. > > The ENS, together with a number of neighboring institutions (College > de France, Institut Curie, ESPCI, Universités Paris 5, 6, and 7, and > Institut Pasteur), offers a rich scientific and intellectual > environment, with a strong representation in computational > neuroscience and related fields. Furthermore, as far as cities go, > Paris is not bad. > > The postdoctoral salary will be supplemented by travel and equipment funds. > > To apply, please send a letter of motivation and statement of > research, a curriculum vitae, a list of publication, and arrange for > three letters of recommendations to be sent, to rava(a)ens.fr. Reviewing > of the applications with start on 25 November 2013.

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[Compbio-allhands] Fwd: opening at Principia Biopharma
by Jacobson, Matt 05 Nov '13

05 Nov '13

Begin forwarded message: From: Ken Brameld <ken.brameld(a)principiabio.com<mailto:ken.brameld@principiabio.com>> Subject: opening at Principia Biopharma Date: November 5, 2013 10:31:24 AM PST To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, We met briefly at the Frontiers in Medicinal Chemistry meeting this past June. Things continue to go will at Principia and we are expanding. I have an opening for a recent PhD or postdoc in comp chem/chem informatics. The ideal candidate will be an enthusiastic and self-motivated individual who is seeking a position with the potential to broadly influence the efficiency and outcome of discovery research at Principia. The job description is attached. Would you mind circulating this to your group or to anyone you feel may be interested and qualified? Kind regards, -Ken Ken Brameld, Ph.D. Executive Dir., Research Technologies Principia Biopharma 650-416-7714 ken.brameld(a)principiabio.com<mailto:ken.brameld@principiabio.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 contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto. 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>

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[Compbio-allhands] Dr. James Petersson Talk, 11/5/13 10:00 am
by Flowers, Nicole 04 Nov '13

04 Nov '13

Dr. James Petersson, University of Pennsylvania, Department of Chemistry Tuesday, November 5 – 10 AM, RH-102, Pottruck Auditorium Thioamides: Minimalist chromophores for monitoring protein folding and stability Abstract: Our laboratory is developing new tools to understand protein folding, conformational changes, and proteolysis. We have recently shown that the thioamide - a single-atom substitution of the peptide backbone - can be used as a probe to monitor structural changes in proteins by quenching fluorophores, including the natural amino acids tryptophan and tyrosine, and several unnatural amino acids. We have developed methods for incorporating the thioamides into full-sized proteins by chemically synthesizing peptides containing the thioamides, and ligating them to proteins expressed in E. coli cells. Donor fluorophores can be incorporated into the cellularly-expressed fragment using unnatural amino acid mutagenesis or post-expression labeling, so that double-labeled proteins can be generated with a minimum of unnecessary peptide synthesis. Development of these methods allows us to begin study of the role of protein motion in processes such as cell signaling and amyloid diseases. We have alsoadapted our fluorophore/thioamide pairs to make probes of proteolysis, using the minimally-perturbing nature of the thioamide to investigate cleavage at specific sequences. We have used these tools in vitro, and we are working to extend them to use in lysates and living cells. 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

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[Compbio-allhands] FREE Laser Toner Cartridges
by babbitt 28 Oct '13

28 Oct '13

The Babbitt lab is giving away four unused toner cartridges: HP-96A (part #C4096A). These cartridges fit HP LaserJet Series 2100/2200* (really old) printers. Please contact Joslyn Polzien atjoslyn.polzien(a)ucsf.edu<mailto:%20joslyn.polzien@ucsf.edu> if you are interested in some or all of them. *2100, 2100EP, 2100M, 2100SE, 2100TN, 2100XI, 2200, 2200D, 2200DN, 2200DT, 2200DSE, 2200DTN -- Patricia Babbitt, Professor Dept. of Bioengineering & Therapeutic Sciences 1700 4th Street, MC2550 University of California San Francisco, CA 94158 Phone: 1-415-476-3784 Email: babbitt(a)cgl.ucsf.edu Assistant: Ms. Joslyn Polzien Email: Joslyn.Polzien(a)ucsf.edu 8 AM – 12 PM: (415) 514-1214 1 PM – 5 PM: (415) 514-4861

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[Compbio-allhands] Fwd: ignite Bay Area (protein) Dynamics - November 5th
by Flowers, Nicole 28 Oct '13

28 Oct '13

Want to get together and talk science with other Bay Area researchers interested in the ways macromolecules move? Come to ignite Bay Area Dynamics (iBAD) on November 5th. Absolutely everyone is invited, from student to professor and academia to industry. Hear the latest work on dynamics in a fast, pithy form: Ignite talks are only five minutes apiece, with auto-advancing slides! Refreshments are provided and there will be plenty of time to chat with colleagues and speakers. Speakers: Susan Marqusee (Berkeley) Vijay Pande (Stanford) Jacob Corn (Genentech) Gira Bhabha (UCSF) November 5th, 2013 - 7 PM UCSF - Mission Bay Campus Byers Hall 212 More info: http://www.fraserlab.com/ibad or email Jaime Fraser (james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu>) or Jacob Corn (corn.jacob(a)gene.com<mailto:corn.jacob@gene.com>) Sponsored by the Protein Society (Society membership not required to attend). James Fraser, PhD Assistant Professor Department of Bioengineering and Therapeutic Sciences Office: N212C Genentech Hall, Lab: N216 Genentech Hall james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu> // jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com> (415) 493-8421 http://www.fraserlab.com 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

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[Compbio-allhands] Fwd: Protein Society Sponsored Dynamics Meeting - Tuesday November 5th 7PM at UCSF
by Jacobson, Matt 27 Oct '13

27 Oct '13

-- Matt Sent from my iPad Begin forwarded message: From: James Fraser <jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com>> Date: October 27, 2013 12:58:39 PM PDT To: Mark Kelly <mark.kelly(a)ucsf.edu<mailto:mark.kelly@ucsf.edu>>, Tanja Kortemme <kortemme(a)cgl.ucsf.edu<mailto:kortemme@cgl.ucsf.edu>>, Agard Dave <agard(a)msg.ucsf.edu<mailto:agard@msg.ucsf.edu>>, Robert Stroud <stroud(a)msg.ucsf.edu<mailto:stroud@msg.ucsf.edu>>, Fletterick Robert <flett(a)msg.ucsf.edu<mailto:flett@msg.ucsf.edu>>, Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>>, Jim Wells <Jim.Wells(a)ucsf.edu<mailto:Jim.Wells@ucsf.edu>>, Jack Taunton <taunton(a)cmp.ucsf.edu<mailto:taunton@cmp.ucsf.edu>>, Patsy Babbitt <babbitt(a)cgl.ucsf.edu<mailto:babbitt@cgl.ucsf.edu>>, Charles Craik <Charles.Craik(a)ucsf.edu<mailto:Charles.Craik@ucsf.edu>>, "Danica Fujimori" <fujimori(a)cmp.ucsf.edu<mailto:fujimori@cmp.ucsf.edu>>, Natalia Jura <natalia.jura(a)ucsf.edu<mailto:natalia.jura@ucsf.edu>>, "Degrado, William" <Bill.DegRado(a)ucsf.edu<mailto:Bill.DegRado@ucsf.edu>>, "England, Pamela" <Pamela.England(a)ucsf.edu<mailto:Pamela.England@ucsf.edu>>, John Gross <jdgross(a)cgl.ucsf.edu<mailto:jdgross@cgl.ucsf.edu>>, Bo Huang <bo.huang(a)ucsf.edu<mailto:bo.huang@ucsf.edu>>, Xiaokun Shu <xiaokun.shu(a)ucsf.edu<mailto:xiaokun.shu@ucsf.edu>>, Susan Miller <smiller(a)cgl.ucsf.edu<mailto:smiller@cgl.ucsf.edu>>, "Gestwicki, Jason" <Jason.Gestwicki(a)ucsf.edu<mailto:Jason.Gestwicki@ucsf.edu>>, "Cheng, Yifan" <YCheng(a)ucsf.edu<mailto:YCheng@ucsf.edu>>, Alan Frankel <frankel(a)cgl.ucsf.edu<mailto:frankel@cgl.ucsf.edu>>, "Narlikar, Geeta" <geeta.narlikar(a)ucsf.edu<mailto:geeta.narlikar@ucsf.edu>>, "Lim, Wendell" <Wendell.Lim(a)ucsf.edu<mailto:Wendell.Lim@ucsf.edu>>, <Shawn.Douglas(a)ucsf.edu<mailto:Shawn.Douglas@ucsf.edu>>, Chris Waddling <waddling(a)msg.ucsf.edu<mailto:waddling@msg.ucsf.edu>>, Ajay Jain <ajain(a)jainlab.org<mailto:ajain@jainlab.org>>, Adam Abate <arabate(a)gmail.com<mailto:arabate@gmail.com>>, Michael Fischbach <fischbach(a)fischbachgroup.org<mailto:fischbach@fischbachgroup.org>>, "John Kuriyan" <kuriyan(a)berkeley.edu<mailto:kuriyan@berkeley.edu>>, Jamie Cate <jcate(a)lbl.gov<mailto:jcate@lbl.gov>>, <doudna(a)berkeley.edu<mailto:doudna@berkeley.edu>>, Bryan Krantz <bakrantz(a)berkeley.edu<mailto:bakrantz@berkeley.edu>>, David Wemmer <DEWemmer(a)lbl.gov<mailto:DEWemmer@lbl.gov>>, Andreas Martin <a.martin(a)berkeley.edu<mailto:a.martin@berkeley.edu>>, Judith Klinman <klinman(a)berkeley.edu<mailto:klinman@berkeley.edu>>, <jfkirsch(a)berkeley.edu<mailto:jfkirsch@berkeley.edu>>, Ron Vale <vale(a)cmp.ucsf.edu<mailto:vale@cmp.ucsf.edu>>, James Partridge <partridge.james(a)gmail.com<mailto:partridge.james@gmail.com>>, David Sivak <david.sivak(a)gmail.com<mailto:david.sivak@gmail.com>> Cc: Jacob Corn <corn.jacob(a)gene.com<mailto:corn.jacob@gene.com>> Subject: Protein Society Sponsored Dynamics Meeting - Tuesday November 5th 7PM at UCSF Want to get together and talk science with other Bay Area researchers interested in the ways macromolecules move? Come to ignite Bay Area Dynamics (iBAD) on November 5th. Absolutely everyone is invited, from student to professor and academia to industry. Hear the latest work on dynamics in a fast, pithy form: Ignite talks are only five minutes apiece, with auto-advancing slides! Refreshments are provided and there will be plenty of time to chat with colleagues and speakers. Speakers: Susan Marqusee (Berkeley) Vijay Pande (Stanford) Jacob Corn (Genentech) Gira Bhabha (UCSF) November 5th, 2013 - 7 PM UCSF - Mission Bay Campus Byers Hall 212 More info: http://www.fraserlab.com/ibad or email Jaime Fraser (james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu>) or Jacob Corn (corn.jacob(a)gene.com<mailto:corn.jacob@gene.com>) Sponsored by the Protein Society (Society membership not required to attend). -- -- James Fraser, PhD Assistant Professor Department of Bioengineering and Therapeutic Sciences Office: N212C Genentech Hall, Lab: N216 Genentech Hall james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu> // jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com> (415) 493-8421 http://www.fraserlab.com

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[Compbio-allhands] Fwd: Postdoctoral Fellow Position - The Rockefeller University
by Jacobson, Matt 25 Oct '13

25 Oct '13

-- Matt Sent from my iPad Begin forwarded message: From: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Date: October 25, 2013 11:17:43 AM PDT To: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Subject: Postdoctoral Fellow Position - The Rockefeller University We would greatly appreciate sharing the attached position within your graduate students and postdocs. Best regards, Melanie J. Lee Administrative Assistant Center for Studies in Physics and Biology The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: 212-327-8636 Fax: 212-327-8544 http://www.rockefeller.edu/research/intercenter/cenphysics

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[Compbio-allhands] 10/31/13 Seminar with Erin Carlson
by Nicole Takesono Flowers 24 Oct '13

24 Oct '13

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 Erin Carlson Indiana Chemical Probes to Explore and Inhibit Bacterial Pathogenesis October 31, 2013 D. Fujimori, Host 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

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[Compbio-allhands] 10/24/13 Seminar with David Bartel
by Nicole Takesono Flowers 18 Oct '13

18 Oct '13

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 David Bartel MIT MicroRNAs and a developmental switch in the nature of translational control. October 24, 2013 H. Madhani, Host 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

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