January 2015 - compbio-allhands@cgl.ucsf.edu

[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 January 2015