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

[Compbio-allhands] Fwd: Michael Chimenti Referral
by Jacobson, Matt 25 Nov '15

25 Nov '15

- Matt Begin forwarded message: From: Kate Nelson <knelson(a)payettegroup.com<mailto:knelson@payettegroup.com>> Subject: Michael Chimenti Referral Date: November 25, 2015 at 2:26:22 PM PST To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, Michael Chimenti passed along your information. I’m hiring a Principal Bioinformatician in the Bay Area and Michael said that you often circulate job postings via a listserv. It’s a long shot, but I thought I’d pass along the JD in case you wanted to share with your network. JD --> https://goo.gl/o9g5r7 Job description Principal Bioinformatician It was only a matter of time before the big data explosion impacted the food we eat, buy, and sell. We’re the team that wants to make sure that what we think is in our food products, is actually in it. Our analytics platform transforms quality control, analytics, and safety in the global food industry. Built on the foundation of a robust big data engine, our proprietary platform translates quantifiable molecular tests into actionable food data insights. We’re using the same tools and technologies used by clinical genomicists to perform fast and accurate affordable genomic analysis at scale. As our Principal Bioinformatician, you will work directly with the VP of Engineering and be responsible for the development statistical algorithms, methods, and programs for analysis of genomics data. You'll have unparalleled food quality data and domain experts within the company to grow and develop both personally and professionally. With our recent funding, it’s a great time to join us! Food fraud is bigger than ever and this is your chance to solve a real world problem – there is nothing else like this in the world and you could have the opportunity to work on it. Responsibilities • Develop and maintain robust software tools to improve the speed, accuracy, and automation of our analysis pipeline in the cloud • Evaluate third-party tools and libraries we may wish to leverage in our pipeline • Develop novel data analysis and data-mining methods to optimize the performance and accuracy of our platform • Work closely with our science and product team to help define product requirements, spec technical requirements, develop project plans and generate test cases Key responsibilities Requirements • B.S. in Math, Computer Science, Physics, Engineering or equivalent • Minimum 2 years of experience in bioinformatics in industry setting, with strong experience in developing algorithms processing next-generation sequencing data • Familiar with cloud computing and working in cloud environment • Proficiency with SQL and UNIX shells • Proven development experience with an object-oriented language • Strong communication skills both written and verbal with engineers and product marketers • Ability to work independently in a fast paced and high performing environment Preferred Skills • Proven ability to develop algorithms dealing with large-scale data • Extensive experience in biostatistics, advanced mathematics and system modeling • Expertise in Python Thanks in advance and if you have any questions, feel free to reach out! Cheers- Kate Nelson Sr. Technical Recruiter Payette Group 650-326-0760 ext. 104 LinkedIn<https://goo.gl/avPNOa> Twitter<https://goo.gl/GO1Uuw>

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[Compbio-allhands] faculty positions at Shanghaitech, Shanghai
by Andrej Sali 23 Nov '15

23 Nov '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 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] SAVE THE DATE- PETER KOLLMAN LECTURESHIP- JANUARY 21, 2016
by Flowers, Nicole 19 Nov '15

19 Nov '15

SAVE THE DATE- THURSDAY, January 21, 2016 AT 12:00 PM Michael Gilson UC San Diego PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS S-161 Reception in Byers Hall 3rd Floor Lounge at 3:30 pm. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Reminder: Janet Iwasa Seminar TODAY 2-3 PM
by Jacobson, Matt 16 Nov '15

16 Nov '15

Not sure if this got sent out to this list - Matt Begin forwarded message: From: "Brewer, Melanie" <Melanie.Brewer(a)ucsf.edu<mailto:Melanie.Brewer@ucsf.edu>> Subject: Reminder: Janet Iwasa Seminar TODAY 2-3 PM Date: November 16, 2015 at 9:15:28 AM PST To: Melanie Bennett Brewer <melaniebbrewer(a)gmail.com<mailto:melaniebbrewer@gmail.com>> Janet Iwasa of the University of Utah will give a HARC-sponsored seminar “Animating Molecules” TODAY Nov. 16, 2-3 PM in Genentech Hall Room N114. Janet is an award-winning animator and TED speaker who uses 3D animation to provide new insights into macromolecular and cellular systems. Come hear about Janet’s work and learn how we might collaborate with her to animate some of the pathways studied in HARC. ------------------------------------------------------- Melanie Bennett Brewer, Ph.D. Program Manager, The HARC Center University of California, San Francisco Genentech Hall S572, MC 2280 600 16th Street San Francisco, CA 94158-2517 HARC Website: harc.ucsf.edu<http://harc.ucsf.edu/> View my publications at Google Scholar<http://scholar.google.com/citations?hl=en&user=HhJKtigAAAAJ&view_op=list_wo…> Connect on: Linked In<https://www.linkedin.com/profile/view?id=35890499&trk=nav_responsive_tab_pr…>

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[Compbio-allhands] faculty jobs at iHuman, ShaghaiTech
by Andrej Sali 11 Nov '15

11 Nov '15

Computational Biology Faculty Positions at the iHuman Institute, ShanghaiTech University The iHuman Institute at ShanghaiTech University was established to understand human cell signaling at a level beyond what is achievable today. The institute encourages interdisciplinary research combining chemistry, biology, imaging, and structural biology of the cellular components involved in signal transduction. Academic basic science and applied industry research is integrated, providing researchers with unique opportunities. The Institute is recruiting 2 regular tenured and/or tenure-track faculty in 2015 in the areas of computer-aided drug design (CADD) and whole cell modeling. Junior level position applicants should have a Ph.D. degree in computational biology/chemistry, as well as 3+ years postdoctoral or industrial experience. Senior position applicants are expected be leading scientists in their research area. The successful applicant will be expected to establish an independent, internationally recognized research program and to hire and supervise postgraduate, graduate and undergraduate students. Each group is encouraged to recruit up to 10 members and be highly collaborative with other laboratories in different disciplines. A strong core infrastructure has been established within the institute to serve the faculty needs. All financial support is provided by the institute. Importantly, grant writing is not required, particularly for junior faculty members so they can focus on creative research and mentoring of their first students. Initial Research Support Package: The Institute will provide internationally competitive start-up funds plus support of Research Associates and Post-Doctoral Fellows up to 10 full time lab members. Research laboratory and office space will be provided to match the research needs. Faculty have access to some of the world’s best research facilities and resources of the Chinese Academy of Science including the National Protein Center, Shanghai Synchrotron, and Chinese National Compound Library. Compensation and Benefits: Starting salary will be competitive at the international level and commensurate with qualifications and experience. We offer a comprehensive benefits package including health benefits as well as subsidized campus housing. The iHuman Institute will also sponsor applications of national and local Talent Programs based on individuals’ qualification and experience. The iHuman Institute is located in Shanghai, China, which is an exciting and rapidly growing global center of excellence for scientific research. Application Procedure: Submit a cover letter, a 2-3 page statement of research interests, a CV and the names and addresses of three individuals who can serve as references to the mail addresses given below: The iHuman Institute ShanghaiTech University, Building 8, 319 Yueyang Road, Shanghai 200031, China Email: iHuman(a)shanghaitech.edu.cn <mailto:iHuman@shanghaitech.edu.cn> Review of applications will start immediately and will continue until positions are filled. For more information, please visit our website: ihuman.shanghaitech.edu.cn -- 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 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Job openings at Veracyte, South San Francisco
by Seung Joong Kim 10 Nov '15

10 Nov '15

Hi all, Veracyte (South San Francisco) has two job openings in a senior level. 1. DAT: Senior Scientist/Associate Director, Machine Learning 2. R&D Lab: Principal Scientist/Associate Director, Discovery R&D Please see the attached word files for job description. Thanks a lot! About Veracyte Veracyte is pioneering molecular cytology; we are dedicated to helping people avoid unnecessary invasive procedures just to get a diagnosis and to reducing healthcare costs at the same time. We use rigorous science to unlock genomic answers from tiny numbers of cells obtained through minimally invasive methods before surgery is needed. We launched our first product the Afirma® Thyroid FNA Analysis, with a genomic test at its core in record time and have already helped save thousands of patients from unnecessary surgery due to ambiguous thyroid nodule biopsy results. Our genomic test is offered by hundreds of physicians around the country, is covered by Medicare and private payers, and is clinically validated, including in a multicenter study published in the New England Journal of Medicine. Earlier this year, we entered the pulmonology space with the launch of Percepta. The Percepta test uses advanced genomic technology to help patients avoid unnecessary invasive, risky procedures on suspicious lung nodules or lesions that were initially found on computed tomography (CT) scans. Percepta is clinically validated, with its key studies recently published in the New England Journal of Medicine. Looking to our pulmonology pipeline, we are also developing a product to target idiopathic pulmonary fibrosis. The Wall Street Journal named us to its list of top-50 venture capital-funded companies in 2011, BayBio honored us with its Fast Start award in 2012, and In Vivo: The Business and Medicine Report featured us recently as a model for how to build a molecular cytology company. In 2014 and 2015 our employees voted us a Bay Area News Group Top Workplace. Veracyte affords equal employment opportunities to all qualified persons, regardless of race, color, religion, national origin, age, sex, disability, sexual orientation, gender expression, veteran or marital status. Veracyte participates in E-Verify in the United States. - Seung Joong Kim -- Seung Joong Kim, Ph.D. Postdoctoral Scholar, Andrej Sali group Department of Bioengineering and Therapeutic Sciences University of California at San Francisco (UCSF) 1-217-649-2147 http://salilab.org/~sjkim

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[Compbio-allhands] Fwd: DBDS Faculty Search
by Patricia C. Babbitt 09 Nov '15

09 Nov '15

-------- Forwarded Message -------- Subject: DBDS Faculty Search Date: Mon, 9 Nov 2015 17:39:40 +0000 From: Laura Dunkin-Hubby <lhubby(a)stanford.edu> To: babbitt(a)cgl.ucsf.edu <babbitt(a)cgl.ucsf.edu> Dear Dr. Babbitt, I am writing on behalf of Dr. Carlos Bustamante to ask your help in identifying candidates for an Assistant, Associate or Full Professor position in the new Department of Biomedical Data Science (DBDS) at the Stanford University School of Medicine. This appointment will be in the University Tenure Line (UTL). The predominant criterion for appointment in the University Tenure Line is a major commitment to research and teaching. We define biomedical data science as the study of biomedical data and information, of how such data and information may be structured, and of how analysis and processing of biomedical data and information will lead to new discoveries and to advances in health and healthcare. We are particularly interested in candidates dedicated to the development of novel computational and statistical methods for acquiring, representing, storing, analyzing, and applying biological and clinical data at all scales, who can apply their expertise in biomedical informatics and/or biostatistics to meet departmental goals. Further information on the Department of Biomedical Data Science can be found at[dbds.stanford.edu]dbds.stanford.edu. Applicants should have demonstrated strong ability and interest in conducting both methodological and collaborative research, and in teaching. We expect the successful candidate to conduct a vigorous, independent research program, to advise students, and to assist in program administration. Formal teaching in the classroom will be encouraged. An MD, MD/PhD, or PhD in biostatistics, statistics, biomedical informatics, computer science, biomedical engineering or a related area is required. Faculty rank will be determined by the qualifications and experiences of the successful candidate. Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty. It welcomes nominations of and applications from women, members of minority groups, protected veterans and individuals with disabilities, as well as from others who would bring additional dimensions to the university's research, teaching and clinical missions. I would appreciate your forwarding this announcement to individuals whom you feel would be particularly suited for this position. Interested candidates should send a copy of their curriculum vitae, a brief letter outlining their research and teaching interests, and arrange for three letters of reference to be submitted to: Euan Ashley, MD, PhD and Daniel Rubin, MD, MS Search Committee Co-Chairs Department of Biomedical Data Science Stanford University School of Medicine DBDSjobs_SOM(a)stanford.edu<mailto:DBDSjobs_SOM@stanford.edu> Applications will continue to be accepted and considered until the opening is filled. Sincerely yours, Carlos D. Bustamante, PhD Chair, Department of Biomedical Data Science Stanford University School of Medicine - Laura Dunkin-Hubby Administrative Assistant to Dr. Carlos Bustamante Stanford Center for Computational, Evolutionary and Human Genomics T 650.725.5067<file://localhost/tel/+1-650-723-2643> * cehg.stanford.edu -- 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 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Josel Tongson, +1 415-514-1214, 415-514-4861 GraciaJoselina.Tongson(a)ucsf.edu

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[Compbio-allhands] 11/12/15 Seminar with Xuewu Zhang
by Flowers, Nicole 06 Nov '15

06 Nov '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 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Xuewu Zhang UT Southwestern Regulation mechanisms of the neuronal axon guidance receptor plexin November 12, 2015 N. Jura, 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 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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