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

[Compbio-allhands] 4/2/15 Seminar with Jennifer Doudna
by Flowers, Nicole 26 Mar '15

26 Mar '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Jennifer Doudna UC Berkeley Signaling pathways in cancer April 2, 2015 B. DeGrado, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant 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: Company looking for a bioinformaticist (or two)
by Tom Ferrin 16 Mar '15

16 Mar '15

-------- Forwarded Message -------- Subject: Company looking for a bioinformaticist (or two) Date: Mon, 16 Mar 2015 14:02:47 +0000 From: Jose Haresco <JHaresco(a)jmpsecurities.com> To: 'tef(a)cgl.ucsf.edu' <tef(a)cgl.ucsf.edu> Hi Tom, It has been quite a while, so I hope this reaches you well. One of the companies I am working with is looking for a bioinformaticist or two. I thought I would pass the job description along in case any of the students or post-docs graduating this year are looking around. Have them contact me if they are interested. Best regards, J ------------------------- Asuragen is seeking an exceptional computational biologist to join its rapidly growing Bioinformatics group. The Sr. Scientist, Computational Biologist will function in a highly interdisciplinary environment, interacting with other Bioinformatics scientists as well as wet bench scientists and the R&D leadership to push the boundaries of diagnostic assay development and overcome computational challenges in data analysis, interpretation and visualization. Specific areas of research and development focus include: ·Application of innovative approaches to identify biomarkers predictive of disease, prognosis, and response to therapy with an emphasis on applications in oncology ·Design of new machine learning and combinatorial optimization algorithms to improve in-silico assay design processes, particularly in the areas of next-generation sequencing and digital PCR ·Development of next-generation sequencing analysis pipelines to take advantage of novel library types and capable of integrating across multiple modalities such as RNA, DNA, and epigenetic modifications. *J.T. Haresco III, Ph.D.* *Managing Director and Senior Equity Analyst*** *Medical Devices / Life Science Tools & Diagnostics* *JMP Securities, LLC* 600 Montgomery Street, Suite 1100 San Francisco, CA 94111 Direct: 415.869.4477 Cell: 415.350.7574 IMPORTANT NOTICE: This message is intended only for the addressee. If you are not the intended recipient, please notify the sender by e-mail reply and delete this message from your computer. You may not copy, disclose, distribute or otherwise make use of this message or its contents for yourself or for any other person, as that action may be unlawful. ORDERS AND INSTRUCTIONS: JMP Securities LLC does not accept action-oriented, time-sensitive instructions or transaction orders via e-mail. JMP Securities LLC will not be responsible for carrying out such instructions or orders, including orders to purchase or sell securities. IMPORTANT DISCLOSURE REGARDING Reg FD AND MATERIAL NON-PUBLIC INFORMATION: JMP Securities LLC maintains strict policies and adherence to all regulatory guidelines and rules pertaining to Reg FD and "material non-public information." Institutional and corporate clients are expected to abide by all similar rules, laws and regulations as they conduct meetings sponsored by JMP Securities LLC. CONFIDENTIALITY AND PRIVACY: JMP Group LLC. reserves the right to monitor and review the content of all e-mail communications sent and/or received by its employees.

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[Compbio-allhands] 3/12/15 BBC Seminar CANCELLED
by Flowers, Nicole 06 Mar '15

06 Mar '15

Please note: There is no BBC Seminar for 3/12/15. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant 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: Postdoc Positions
by Andrej Sali 04 Mar '15

04 Mar '15

> Begin forwarded message: > > From: "Gregory A. Voth" <gavoth(a)uchicago.edu> > To: "Gregory A. Voth" <gavoth(a)uchicago.edu>, "Voth-Group-Mailing(a)vothgroup.uchicago.edu" <Voth-Group-Mailing(a)vothgroup.uchicago.edu> > Subject: Postdoc Positions > Date: March 4, 2015 at 6:46:41 PM PST > Reply-To: gavoth(a)uchicago.edu > > > Dear Colleague, > > There is the possibility of one or more postdoc position in my group, subject to the qualifications and experience of the applicant as well as > the final availability of funding. For information on my group and our research interests please see my group web page listed below. Interested parties should contact me by email. > > Best wishes, > Greg Voth > > PS-I apologize if you get this email more than once > > __________________________________________________________________ > > Gregory A. Voth, Ph.D. > Haig P. Papazian Distinguished Service Professor > Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, > and Computation Institute > > Department of Chemistry > The University of Chicago > 5735 S. Ellis Avenue > Chicago, Illinois 60637 > Phone: 773-702-9092 > Fax: 773-795-9106 > Administrative Assistant: 773-702-9096 > Email: gavoth(a)uchicago.edu <mailto:gavoth@uchicago.edu> > Group Web Site: vothgroup.uchicago.edu <http://vothgroup.uchicago.edu/> > Office: 231 Searle > Admin Office: 233 Searle > ___________________________________________________________________ > > > _______________________________________________ > Voth-group-mailing mailing list > Voth-group-mailing(a)vothgroup.uchicago.edu > https://vothgroup.uchicago.edu/cgi-bin/mailman/listinfo/voth-group-mailing

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[Compbio-allhands] 3/5/15 Seminar with Ruth Nussinov
by Flowers, Nicole 27 Feb '15

27 Feb '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Ruth Nussinov NIH Signaling pathways in cancer March 5, 2015 D. Garrido Ruiz, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant 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] 2/26/15 Seminar with Samie Jaffrey
by Flowers, Nicole 20 Feb '15

20 Feb '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Samie Jaffrey Cornell Imaging RNA and RNA biology using RNA mimics of green fluorescent protein February 26, 2015 D. Weinberg, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant 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: Open PhD and Postdoc positions in Bioinformatics in Austria
by Scooter Morris 18 Feb '15

18 Feb '15

-------- Forwarded Message -------- Subject: Open PhD and Postdoc positions in Bioinformatics Date: Wed, 18 Feb 2015 23:11:33 +0100 From: Mario Albrecht <mario.albrecht(a)tugraz.at> To: mario.albrecht(a)tugraz.at Dear colleagues, Please forward these bioinformatics job offers for PhD students and Postdocs to others, thank you much! Kind regards, Mario Albrecht ================================================ Open PhD and Postdoc positions in Bioinformatics ================================================ Deadline: 28 February 2015 Contact: Prof. Dr. Mario Albrecht, Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria, info(a)mario-albrecht.at Further information at http://www.medbioinf.at and below! Note: Please send your application both to info(a)mario-albrecht.at and informatik(a)tugraz.at citing the reference number 7090/15/001. Open full-time paid bioinformatics PhD student position for molecular network research until 28 February 2015, for details see http://wwww.medbioinf.at and as follows: Molecular networks and proteins are involved in many biological processes. Therefore, we aim at the development and application of computational network methods for the analysis and prediction of molecular interactions and their structural and functional changes due to sequence mutations. The mutations might occur in disease genes or bacterial and viral genomes. Based on the analysis results, we also want to develop innovative bioinformatics approaches for modeling pathways and their changes as well as for the design and prioritization of follow-up experiments. Open full-time paid bioinformatics postdoc position for integrative omics research until 28 February 2015, for details see http://bioinf.tugraz.at/images/Postdoc.pdf and as follows: Cancer is the leading cause of death and involves altered lipid metabolism. The rate-limiting enzyme in triacylglyceride degradation, the adipose triglyceride lipase (ATGL), might not participate only in lipid mobilization and degradation, but also in signaling pathways by generating lipid signaling molecules. Therefore, we aim at the large-scale elucidation of the functional role of ATGL in cancer progression using different omics strategies combined with computational approaches. Novel bioinformatics methods are developed for analyzing the data of molecular proteomics and metabolomics networks related to lipolysis in cancer. ________________________________________________________ Prof. Dr. Mario Albrecht http://www.medbioinf.at Institute for Knowledge Discovery Head of Bioinformatics Graz University of Technology Inffeldgasse 13/IV, 8010 Graz, Austria ________________________________________________________

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[Compbio-allhands] 2/19/15 Seminar with Anne-Claude Gingras
by Flowers, Nicole 13 Feb '15

13 Feb '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Anne-Claude Gingras Lunenfeld Kinase-phosphatase interactomes: a tale of Hippos and mulberries February 19, 2015 R. Levin, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant 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: MATLAB Seminars Coming to UCSF – Feb 25, 2015]
by Patricia Babbitt 06 Feb '15

06 Feb '15

-- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics 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] 2/12/15 Seminar with Judith Klinman
by Flowers, Nicole 06 Feb '15

06 Feb '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Judith Klinman UC Berkeley Moving through Barriers: Unlocking the Mysteries of How Enzymes Really Work February 12, 2015 S. Miller, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant 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: Open PostDoc position at the Structural Genomics Group (CNAG-CRG, Barcelona)
by Andrej Sali 05 Feb '15

05 Feb '15

Sent from my iPhone Begin forwarded message: > From: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Date: February 5, 2015 at 3:29:51 AM PST > To: "Marc A. Marti-Renom" <mmarti(a)pcb.ub.cat> > Subject: Open PostDoc position at the Structural Genomics Group (CNAG-CRG, Barcelona) > > Dear friends and colleagues, > > Apologies for the mass posting... > > I would appreciate if you could forward this add to whom may be interested. > > 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 (10th floor) > 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] AZ
by Jacobson, Matt 29 Jan '15

29 Jan '15

From: Dry, Jonathan R Sent: Thursday, January 29, 2015 3:45 PM Cc: Hudson, Kevin Subject: New vacancy in Oncology Bioinformatics - AstraZeneca Cambridge UK Hello Informatics colleagues http://jobs.astrazeneca.com/jobs/details/l1rRD1247-senior-bioinformatics-sc… We have an exciting opportunity for a talented, motivated bioinformatics scientist to join the Oncology Bioinformatics team at AstraZeneca and help with our analyses of clinical NGS data. The career level will be relevant to individuals emerging from a strong PhD, a first post-doctoral role, or equivalent (e.g. a Masters with some experience). I was hoping I might rely on you to reach out to your internal/external informatics network, especially in Cambridge UK and Europe, and highlight this post to relevant individuals. Closing date for applications is 1st March 2015 Many thanks in advance. Jonathan Jonathan R. Dry Bioinformatics discipline lead, Oncology iMED AstraZeneca Boston, Waltham, MA +1 781 839 4845

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[Compbio-allhands] 2/5/15 Seminar with Robert Keenan
by Flowers, Nicole 29 Jan '15

29 Jan '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Robert Keenan University of Chicago Tail-anchored membrane proteins biogenesis February 5, 2015 B. DeGrado, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant 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: Open position_structure guided protein design
by Andrej Sali 29 Jan '15

29 Jan '15

-- 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 > > > From: HGRQ (Hanne Grøn) [mailto:hgrq@novonordisk.com <mailto:hgrq@novonordisk.com>] > Sent: Tuesday, January 20, 2015 1:50 PM > To: Boris Turk > Subject: Open position_structure guided protein design > > Dear Boris, > > Happy New Year – I hope you are doing well. > > I am writing to you, because we have an open position in my Department for a scientist interested in structure-guided protein design. Unfortunately, Ole Olsen, our very experienced and creative molecular modeler, had decided to retire. Therefore, we are looking to fill his position. The candidate profile is listed in the Job Ad where you can also find a description of our Department (as we see it J). > > I would very much appreciate, if you would please share the link with your network of former students, colleagues, and friends. You can link directly to LinkedIn and other media from the ad: > > http://www.novonordisk.com/careers/job_section/jp.asp?jobid=26462BR&joblng=… <http://www.novonordisk.com/careers/job_section/jp.asp?jobid=26462BR&joblng=…> > > It will be hard to replace Ole, but now the search has started. Please let me know, if I can further elaborate on the Department or the profile of the ideal candidate. > > Kind regards, > Hanne > > Molecular Modelling - Experienced Scientist > Research & Development > > Denmark - Måløv > > The Department of Haemophilia Biochemistry is seeking an experienced scientist for structure-guided protein optimization and design > > About the Department > Haemophilia Biochemistry is an integral part of the Novo Nordisk haemophilia research area in Global Research located in Måløv. We are a diverse department with 22 enthusiastic scientists, research assistants, and students who all support the haemophilia research portfolio through innovation and structure-guided design and development of novel protein-based therapies. The department has a solid base of expertise in haemostasis biology, mode of action studies, protein chemistry, enzyme assays, protein-ligand interaction studies, and molecular modelling. > > The Job > This is a dynamic and challenging position in an innovative discovery department with many cross-functional activities in project teams and focus groups. Ambitious scientific goals will require collaboration with highly specialized colleagues. Your main focus will be structure-guided design and development of novel protein therapeutic candidates as well as proteins with improved biological, formulation, and pharmacological properties. Your responsibilities will include generation of protein homology models, advanced data mining and analysis, and molecular dynamics calculations in interpretation of experimental data (structure and biology). You will have the opportunity to influence your own development and grow into a key role in an exciting and diverse discovery department. > > Qualifications > As a key member of a discovery research team, the ideal candidate has extensive experience in in silico structure-guided design and optimization of protein based therapies, and can combine structural and computational research with experimental data. The candidate holds a PhD and at least three years of documented post-doctoral experience in structural biology or molecular modelling. Experience could include one or more of the following: simulation and visualizing packages, homology modelling, protein-structure prediction, calculation of protein-protein energetics, and/or docking software. Research experience in large-scale data mining and analysis, bioinformatics, and using computational and/or statistical approaches is a plus. The candidate must be fluent in English, have excellent communication skills, a collaborative mind-set, and a passion for innovation. > > Contact > For further information about this position, please contact Hanne Grøn at (+45) 3079 0765 > > Deadline > 15-Feb-2014 > > > ______________________________________ > > Hanne Grøn, Ph.D. > Director of Haemophilia Biochemistry > Biopharmaceutical Research Unit > > Novo Nordisk A/S > Novo Nordisk Park > Room F5.2.11 > DK-2760 Måløv > Denmark > +45 4444 8888 (phone) > +45 3079 0765 (mobile) > hgrq(a)novonordisk.com <mailto:hgrq@novonordisk.com> > > Changing possibilities in haemophilia > Novo Nordisk is focused on the quality of life of people living with haemophilia; for this reason our pipeline continues to evolve, it is why we continue to strengthen our existing formula. Learn more <http://www.novonordisk.com/about_us/improving_haemophilia/ChangingPossibili…> > > This e-mail (including any attachments) is intended for the addressee(s) stated above only and may contain confidential information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information contained herein is strictly prohibited and may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete it immediately hereafter. Thank you. >

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[Compbio-allhands] Tomorrow! ChEMBL: The Organization of Drug Discovery Data - 1:30pm in Byers Hall 212
by Hilary Mahon 29 Jan '15

29 Jan '15

For more information, please see attached. --- 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] 1/22/15 Seminar with Barak Cohen
by Flowers, Nicole 16 Jan '15

16 Jan '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Barak Cohen Washington University in St. Louis Why don’t transcription factors get lost? January 22, 2015 N. Ahituv, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant 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: Biophysics Myth-buster Wanted for TV Documentary
by Jacobson, Matt 15 Jan '15

15 Jan '15

definitely one of the more amusing phone calls i've received lately feel free to pass along! Begin forwarded message: From: Poppy Riddle <poppy(a)offthefence.com<mailto:poppy@offthefence.com>> Subject: Biophysics Myth-buster Wanted for TV Documentary Date: January 15, 2015 12:25:55 PM PST To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, I would be incredibly grateful if you could circulate this email amongst your post-grads. I do hope that it pique's someones interest! All the best, Poppy Dear UCSF Students, I am emailing from a TV company based in the United Kingdom called Off the Fence<http://www.offthefence.com/>. We will be flying to California next month to begin filming on a new documentary series looking at extraordinary people with remarkable skills. One of these people is a man called Kanzawa Sensei <https://www.youtube.com/watch?v=vlR15Gnj8wc> - a chi expert from Japan, who claims he has the ability to heal people, and even put animals to sleep by directing 'chi'. The essence of this 'chi' seems to be an "energy" property that he is able to harness and direct at his subjects... We are looking for a post-grad to act as a myth-buster for us for 1 day in February, and perhaps run some basic tests to find out if biophysics can explain what's happening, or if it really is just an elaborate hoax! This programme will be going out internationally and will hopefully prove a fun (possibly enlightening?) experience, so if you think you could handle being on camera and be able to find the time and join us on location, we would love to have you! All the best, Poppy -- Poppy Riddle Researcher and Coordinator Direct: +44 (0)117 909 7561 Off the Fence Productions | 20 Elmdale Road | Tyndalls Park | BS81SG Bristol Tel: +44 (0)117 909 7560 [http://i.imgbox.com/p8RxD9eN.png]<https://twitter.com/PoppyRiddle> [http://i.imgbox.com/Hog3oA2p.png] <https://www.linkedin.com/pub/poppy-riddle/37/49a/4b4> [http://i.imgbox.com/2Nx08TDr.png] <https://plus.google.com/+PoppyRiddle> www.offthefence.com<http://offthefence.com/> [http://i62.tinypic.com/14l3ul4.jpg] Good planets are hard to find - please think of the environment before you print this email.The information in this email including any attachments is confidential and may be legally privileged. If you are not the intended recipient, please advise the sender immediately by return email and then delete this email and any attachment from your system. The unauthorised use, distribution, copying or alteration of this email and any attachments is strictly forbidden. No employee or agent is authorized to conclude any binding agreement on behalf of Off the Fence B.V. with another party by email without a binding written agreement between your company and Off the Fence B.V. Prior to the execution of such agreement, Off the Fence B.V. shall have no obligations with respect to any deal terms discussed and/or agreed to in principle. Any costs/expenses or other activities are incurred at your own cost and risk until full execution of the relevant agreement. 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: Please forward to interest parties – Postdoc position available
by Andrej Sali 14 Jan '15

14 Jan '15

-- 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: > > Date: January 14, 2015 at 11:24:59 AM PST > Subject: Fwd: Please forward to interest parties – Postdoc position available > From: Ben Sellers <sellers.benjamin(a)gene.com> > To: Andrej Sali <sali(a)salilab.org> > > > > Hi Andrej > > It was nice speaking with you yesterday. Here is the Stanford/Genentech postdoc position I mentioned. I would appreciate your forwarding it to whomever you see fit. > > Thanks > -Ben > > > > > Stanford‐Genentech > Postdoctoral Research Fellow (Computational) > > We invite interested candidates to apply for this truly unique joint Stanford/Genentech postdoctoral position, co-mentored by Prof. Vijay Pande, PhD (Chemistry, Structural Biology, and Computer Science at Stanford) and Ben Sellers, PhD (Computational Drug Discovery at Genentech). > > The position > We are seeking a highly motivated postdoctoral research fellow to investigate basic function and small molecule modulation of protein receptors using large scale molecular dynamics simulations. Theprimaryaimoftheproposedresearchistopredictmetastablestatesinprotein receptors to identify alternative drug-able conformations. Membrane-bound receptors are of particular interest. > > Who you are > We are looking for a candidate with a PhD in biophysics, theoretical chemistry or related field with a strong background in computational modeling of proteins and small molecules. Expertise in molecular mechanics forcefields, molecular dynamics simulation, and statistics is required. A productive track record and at least one first-author publication in a reputable journal are also required. Programming experience and an ability to analyze massive data sets are also desirable. Most importantly, we seek a driven individual who will lead his/her research independently and communicate frequently and clearly to the field. > > To apply > Please apply to Job# 00436268 on the http://www.gene.com <http://www.gene.com/> website as a preliminary step. Direct Link: http://www.gene.com/careers/detail/00436268 <http://www.gene.com/careers/detail/00436268>/GenentechStanfordPostdoctoralResearchFell owComputationalChemistry > > For more information > > http://pande.stanford.edu/ <http://pande.stanford.edu/> > > http://www.gene.com/careers <http://www.gene.com/careers>/academicprograms/postdocs > > > > > > -- > > Ben Sellers, PhD > Discovery Chemistry > Genentech, Inc. > sellers.benjamin(a)gene.com <mailto:sellers.benjamin@gene.com> > 650-467-3995

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[Compbio-allhands] Reminder -- Tom Blundell Seminar -- Thursday, Jan. 15, 10:30am -- Genentech Hall Auditorium
by Hilary Mahon 13 Jan '15

13 Jan '15

For more information, please see attached. --- 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] Fwd: Happy 2015!
by Brian Shoichet 12 Jan '15

12 Jan '15

Anyone interested in a wet-lab position on discovering the MoA of active compounds, and in assay development, this might be a good opportunity. Brian ---------- Forwarded message ---------- From: <federica.morandi(a)emdserono.com> Date: Fri, Jan 9, 2015 at 1:20 PM Subject: Happy 2015! To: bshoichet(a)gmail.com Hi Brian, I wanted to tell you that I have an open position for a PhD Scientist in my team. If there is somebody in your group who is looking for a job in industry I would be happy to consider him/her. It is a lab based position; we develop and run all the biochemical assays for enzyme targets in within the US based therapeutic areas (Immunology and immune oncology). The new hire will also be responsible for studying the MoA of lead compounds and a core member of some of the project teams. I am trying to go through the hiring process as fast as possible because you never know when things will change and the position frozen. Thanks and talk to you soon, Federica This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

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[Compbio-allhands] 1/15/15 Seminar with Edward Marcotte
by Flowers, Nicole 09 Jan '15

09 Jan '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Edward Marcotte University of Texas at Austin Evolution, the proteome, and disease January 15, 2015 J. Webber, 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 Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, & 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: postdoc opening
by Jacobson, Matt 08 Jan '15

08 Jan '15

Begin forwarded message: From: "Jansen, Johanna" <johanna.jansen(a)novartis.com<mailto:johanna.jansen@novartis.com>> Subject: postdoc opening Date: January 8, 2015 4:55:49 PM PST To: "'Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>'" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, "shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>" <shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>> Dear Matt & Brian, It was good seeing you at the event today. Below is the summary of the postdoc position that is opening in our group. I will be the mentor and Heinz Moser will be co-mentor. I would appreciate it if you could advertise this at UCSF and I’ll be happy to speak with any interested graduate students to provide further information. Thanks ! Hanneke New in silico descriptors for correlations with biological endpoints and drug design principles: The Computer-Aided Drug Discovery (CADD) group has a strong focus on utilizing the vast Novartis knowledgebase to extract relationships between properties of molecules and their biological activity, and on developing approaches to make predictions based on those relationships using properties calculated from chemical structure (in silico descriptors). We work closely with experimentalists to design the compound sets for measurements of biological and physical properties in an effort to drive drug discovery and determine which molecular properties we can calculate that are predictive of the experimental properties. Two molecular properties that are not well described by the in silico descriptors commonly used in drug discovery are conformational flexibility and hydrogen-bonding strength. These properties play an important role in many biological activities, including various aspects of permeability (entry into mammalian cells, entry into gram-negative pathogens, blood-brain-barrier penetration, and passage across epithelial barriers). In order to better guide chemistry designs in drug discovery, we need better in silico descriptors to capture flexibility and hydrogen bonding strength. Our platform brings together computational, medicinal, and analytical chemistry, with the scientists that measure the relevant physicochemical and biological properties. This environment of experts, software, instruments, and data is particularly suited to develop new approaches for predicting these properties, including creating experimental datasets, and developing and evaluating new in silico descriptors. Applications of such descriptors include selection efforts (archive enhancement, library design, screening set design) as well as prospective chemistry designs during optimization. Qualifications: PhD degree holders, and PhD students within one year of completing of their degrees are eligible to apply. For more information, contact Hanneke Jansen at Johanna.Jansen(a)novartis.com<mailto:Johanna.Jansen@novartis.com>. To download the cover letter template and apply, please visit http://postdoc.nibr.com/ 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] Murcko talk at noon
by Jacobson, Matt 08 Jan '15

08 Jan '15

A reminder that Mark Murcko is giving the Kollman lecture today at noon, on free energy calculations in drug discovery. Hope to see a good turnout -- Matt Sent from my iPhone

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[Compbio-allhands] Fwd: Bioinformatics/biostats positions at Roche Sequencing
by Andrej Sali 05 Jan '15

05 Jan '15

-- 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: "Chaivorapol, Christina" <christina.chaivorapol(a)roche.com> > Date: January 5, 2015 at 10:59:48 AM PST > Subject: Bioinformatics/biostats positions at Roche Sequencing > To: Andrej Sali <sali(a)salilab.org> > > Hi Andrej, > > Happy new year! I hope things are well with you. I'm not sure if you heard, but I moved to Roche Sequencing to build a bioinformatics group that will focus on developing diagnostics based on NGS technology. I am currently looking to fill a few positions in my group and hope you will be able to forward this to people in your lab and/or at UCSF who might be interested in these jobs. > > Attached are the job postings for the positions in my group. If anyone is interested, please have them apply to the position of interest at the following links: > > Principal Scientist <http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-3017264312&locale=…> > Senior Biostatistican <http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-3017264212&locale=…> > > Thanks, > Christina > -- > Christina Chaivorapol, Ph.D. > Research Leader, Bioinformatics > > Roche Sequencing > Bioinformatics > 4300 Hacienda Dr. > Pleasanton, CA 94588 > Email: christina.chaivorapol(a)roche.com <mailto:christina.chaivorapol@roche.com> > Phone: +1 925-474-7343 > Fax: +1 925-730-8988 > > Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. >

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[Compbio-allhands] CheMBL: The Organization of Drug Discovery Data Workshop, January 30, 2015, 1:30pm, Byers Hall 212
by Hilary Mahon 18 Dec '14

18 Dec '14

For more information, please see attached. --- 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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