UCSF Diversity, Equity and Inclusion Annual Report 2018-2019
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Collins Challenged Over NCI-Funded Research Linking Tea Party
Vol. 39 No. 10 March 8, 2013 © Copyright 2013 The Cancer Letter Inc. All rights reserved. Price $405 Per Year. To subscribe, call 800-513-7042 or visit www.cancerletter.com. PO Box 9905 Washington DC 20016 Telephone 202-362-1809 Capitol Hill Collins Challenged Over NCI-Funded Research Capitol Hill Linking Tea Party With Tobacco Companies Collins: "I am quite By Paul Goldberg troubled by this NIH Director Francis Collins told a House subcommittee that he was “troubled” by a paper in which a prominent tobacco control expert, who particular circumstance." is funded by NCI, claims to have found a relationship between tobacco . Page 4 companies and the Tea Party conservative movement. The paper in question appeared in Tobacco Control, a peer-reviewed journal published by British Medical Journal Group. Drawing on documents Sequestration dating back to the 1980s and obtained from tobacco companies, the authors NCI Director Harold point to several instances in which the Tea Party and its predecessor Varmus Seeks to Protect organizations appear to act as proxies for tobacco interests. The paper cites Competitive Awards an NCI grant that supports analysis of tobacco industry documents. Page 5 The paper’s senior author is Stanton Glantz, professor in the Department of Medicine at the University of California San Francisco, a member of the Varmus' Address to Helen Diller Family Comprehensive Cancer Center, and director of the Center for Tobacco Control Research and Education. The NCI Board of (Continued to page 2) Scientific Advisors Sequestration . Page 7 Federal Budget Cuts Enacted March 1; HHS Agencies Grapple with Consequences BSA Approves RFA By Matthew Bin Han Ong Reissuance for the The across-the-board 5.1 percent budget cuts that went into effect March Pediatric Brain 1 slash the NIH budget by $1.553 billion and the NCI budget by $219 million for the remaining fiscal year, officials say. -
Amy Elizabeth Herr
Amy E. Herr, Ph.D. John D. & Catherine T. MacArthur Professor Bioengineering, University of California, Berkeley UNIVERSITY OF CALIFORNIA, Berkeley, CA 94720 BERKELEY [email protected] | herrlab.berkeley.edu EDUCATION 01/98 – 09/02 STANFORD UNIVERSITY Stanford, CA Doctor of Philosophy, Mechanical Engineering National Science Foundation Graduate Research Fellow “Isoelectric Focusing for Multi-Dimensional Separations in Microfluidic Devices” Advisors: Profs. Thomas W. Kenny & Juan G. Santiago 09/97 – 01/99 STANFORD UNIVERSITY Stanford, CA Master of Science, Mechanical Engineering National Science Foundation Graduate Research Fellow 09/93 – 06/97 CALIFORNIA INSTITUTE OF TECHNOLOGY (CALTECH) Pasadena, CA Bachelor of Science, Engineering & Applied Science with Honors APPOINTMENTS 07/19 – now JOHN D. & CATHERINE T. MACARTHUR PROFESSOR, UNIVERSITY OF CALIFORNIA, BERKELEY 07/14 – 07/19 LESTER JOHN & LYNNE DEWAR LLOYD DISTINGUISHED PROFESSOR (5-year appointment), UC BERKELEY 07/12 – 07/15 ASSOCIATE PROFESSOR, BIOENGINEERING, UNIVERSITY OF CALIFORNIA, BERKELEY 07/07 – 07/12 ASSISTANT PROFESSOR, BIOENGINEERING, UNIVERSITY OF CALIFORNIA, BERKELEY UC BERKELEY/UCSF GRADUATE GROUP IN BIOENGINEERING Directing a research group focused on design and study of microanalytical tools and methods that exploit scale-dependent physics & chemistry to address questions in the biosciences and biomedicine. Chan Zuckerberg Biohub Investigator (2017-21), National Advisory Council for Biomedical Imaging and Bioengineering (2020-23), Faculty Director of Bakar Faculty Fellows Program (2016-now), Co-Convener of Chancellor’s Advisory Committee on Life Sciences (2019-22), BioE Vice-chair for Engagement (2016- now), Director’s Council for Jacobs Institute of Design Innovation, Board Member of Chemical & Biological Microsystems Society (2013-19; Awards Chair 2016-18), Director of Bioengineering Immersion Experience (2012-22; NIH R25). -
Software for Microscopy Workshop Whitepaper
Software for Microscopy Workshop White Paper Raghav Chhetri1, Stephan Preibisch1,2, Nico Stuurman3 1 HHMI Janelia Research Campus, Ashburn, VA, USA 2 Berlin Institute for Molecular Systems Biology, MDC, Berlin, Germany 3 Dept. of Cellular and Molecular Pharmacology, University of San Francisco and HHMI/UCSF, USA Workshop Participants: Nenad Amodaj, Luminous Point Hazen Babcock, Harvard University David Bennett, Janelia Research Campus/HHMI Andreas Boden, KTH Royal Institute of Technology, Stockholm Ulrike Boehm, Janelia Research Campus/HHMI Peter Brown, Arizona State University Ahmet Can Solak, Chan Zuckerberg Biohub Yannan Chen, Columbia University Raghav Chhetri, Janelia Research Campus/HHMI Kevin Dean, UT Southwestern Medical Center Michael DeSantis, Janelia Research Campus/HHMI Brian English, Janelia Research Campus/HHMI Paul French, Imperial College London Adam Glaser, University of Washington John Heddleston, Janelia Research Campus/HHMI Elizabeth Hillman, Columbia University Georg Jaindl, Vidrio Technologies Justine Larsen, Chan Zuckerberg Initiative Jeffrey Kuhn, Massachusetts Institute of Technology Sunil Kumar, Imperial College London Xuesong Li, National Institutes of Health/NIBIB Brian Long, Allen Institute Rusty Nicovich, Allen Institute Henry Pinkard, University of California, Berkeley Stephan Preibisch, Janelia Research Campus/HHMI Blair Rossetti, Janelia Research Campus/HHMI Loic Royer, Chan Zuckerberg Biohub Doug Shepherd, Arizona State University Nicholas Sofroniew, Chan Zuckerberg Initiative Elliot Steel, University -
Improved COVID-19 Serology Test Performance by Integrating Multiple Lateral Flow Assays Using Machine Learning
medRxiv preprint doi: https://doi.org/10.1101/2020.07.15.20154773; this version posted July 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Improved COVID-19 Serology Test Performance by Integrating Multiple Lateral Flow Assays using Machine Learning Cody T. Mowery1-6, Alexander Marson3-11, Yun S. Song10,12-13,*, and Chun Jimmie Ye9-11,14-16,* 1Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA 2Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA 3Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA 4J. David Gladstone Institutes, San Francisco, CA 94158, USA 5Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA 6Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA 7Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA 8Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA 9Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA 10Chan Zuckerberg Biohub, San Francisco, CA, USA 11Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA 12Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA 13Department of Statistics, University of California, Berkeley, CA 94720, USA 14Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA 15Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA 16Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA *Correspondence should be addressed to Y.S.S. -
Patrick J. H. Bradley
(415) 734-2745 Patrick J. H. Bradley Gladstone Institutes, GIDB [email protected] 1650 Owens Street Pronouns: he/him/his Bioinformatics Fellow San Francisco, CA 94158 Current Position ······················································································· 2013— J. David Gladstone Institutes at UCSF Bioinformatics Fellow, Prof. Katherine S. Pollard Lab Academic History ····················································································· 2012—13 Lewis-Sigler Institute for Integrative Genomics, Princeton University Postdoctoral Fellow, Prof. Olga G. Troyanskaya Lab 2005—12 Dept. of Molecular Biology, Princeton University Ph.D. in Molecular Biology, Specialization in Quantitative and Computational Biology Thesis: Inferring Metabolic Regulation from High-Throughput Data Advisors: Prof. Joshua D. Rabinowitz, Prof. Olga G. Troyanskaya Committee: Prof. Ned S. Wingreen, Prof. David Botstein 2005 Dept. of Biology, Harvard College A.B. in Biology Peer-Reviewed Publications ·········································································· 1. Patrick H. Bradley, Katherine S. Pollard. “phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.” Bioinformatics, 2019; btz722.∗;z 2. Patrick H. Bradley, Patrick A. Gibney, David Botstein, Olga G. Troyanskaya, Joshua D. Rabinowitz. “Minor isozymes tailor yeast metabolism to carbon availability.” mSystems, 2019; 4:e00170-18.∗;y 3. Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard. “Phylogeny-corrected identification -
Research Grants
RESEARCH GRANTS 1 HDF RESEARCH GRANTS We like the philosophy of the Hereditary Disease Foundation that monies raised go directly to support research and that scientists from around the world “are encouraged to collaborate and share their work. “ We’ve devoted ourselves to being supporters and research partners, and we have not been disappointed. The research is vibrant with possibilities. Sandy Fox Member, Board of Directors Hereditary Disease Foundation 1 HDF RESEARCH GRANTS Osama Al-Dalahmah, MD, DPhil Anna Pluciennik, PhD Columbia University, New York, NY Thomas Jefferson University, Philadelphia, PA Cheryl Arrowsmith, PhD Paul Ranum, PhD University of Toronto, Canada Children’s Hospital of Philadelphia, PA Anne Ast, PhD Piere Rodriguez-Aliaga, PhD Max Delbrück Center for Molecular Medicine Stanford University, Palo Alto, CA Berlin, Germany Jennie C. L. Roy, PhD Kristina Becanovic, PhD Massachusetts General Hospital Karolinska Institutet, Stockholm, Sweden Harvard Medical School, Boston, MA Abdellatif Benraiss, PhD David M. Sabatini, MD, PhD University of Rochester, Rochester, NY Whitehead Institute for Biomedical Research Massachusetts Institute of Technology, Cambridge, MA Veronica Ines Brito, PhD University of Barcelona Charlene Smith-Geater, PhD Instituto de Neurosciencias, Spain University of California, Irvine, CA Lauren Byrne, PhD Joan Steffan, PhD University College London (UCL), England University of California, Irvine, CA Amit Laxmikant Deshmukh, PhD Xiao Sun, PhD The Hospital for Sick Children, Toronto, Canada Southwestern Medical Center, Dallas, TX Steven Finkbeiner, MD, PhD Leslie Thompson, PhD Gladstone Institutes University of California, Irvine, CA University of California, San Francisco, CA Nicholas Todd, PhD Brent Fitzwalter, PhD Brigham and Women’s Hospital Broad Institute of MIT and Harvard, Cambridge, MA Harvard Medical School, Boston, MA Ali Khoshnan, PhD Ray Truant, PhD California Institute of Technology, Pasadena, CA McMaster University, Ontario, Canada Ryan Lim, PhD Jean Paul G. -
A SARS-Cov-2 Variant That Occurs Worldwide and Has Spread In
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.25.265074; this version posted August 26, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Article Summary Line: A SARS-CoV-2 variant that occurs worldwide and has spread in 2 California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to 3 employ multiple viral targets for detection. 4 Running Title: N gene variant reduces SARS-CoV-2 test sensitivity 5 Keywords: SARS-CoV-2, COVID-19, diagnosis, phylogeny, PCR, nucleocapsid 6 Title: Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts 7 detection by a widely-used RT-PCR assay. 8 Authors: Manu Vanaerschot, Sabrina A. Mann, James T. Webber, Jack Kamm, Sidney M. Bell, 9 John Bell, Si Noon Hong, Minh Phuong Nguyen, Lienna Y. Chan, Karan D. Bhatt, Michelle 10 Tan, Angela M. Detweiler, Alex Espinosa, Wesley Wu, Joshua Batson, David Dynerman, 11 CLIAHUB Consortium, Debra A. Wadford, Andreas S. Puschnik, Norma Neff, Vida Ahyong, 12 Steve Miller, Patrick Ayscue, Cristina M. Tato, Simon Paul, Amy Kistler, Joseph L. DeRisi, 13 Emily D. Crawford 14 Affiliations: 15 Chan Zuckerberg Biohub, San Francisco, California, USA (Manu Vanaerschot, Sabrina A. 16 Mann, James T. Webber, Jack Kamm, Lienna Y Chan, Karan D. Bhatt, Michelle Tan, Angela M. 17 Detweiler, Wesley Wu, Josh Batson, David Dynerman, Andreas S. Puschnik, Vida Ahyong, 18 Norma Neff, Patrick Ayscue, Cristina M. Tato, Amy Kistler, Joseph L. -
Preexposure Prophylaxis for HIV Infection Integrated with Municipal- and Community-Based Sexual Health Services
Research Original Investigation Preexposure Prophylaxis for HIV Infection Integrated With Municipal- and Community-Based Sexual Health Services Albert Y. Liu, MD, MPH; Stephanie E. Cohen, MD, MPH; Eric Vittinghoff, PhD; Peter L. Anderson, PharmD; Susanne Doblecki-Lewis, MD; Oliver Bacon, MD, MPH; Wairimu Chege, MD, MPH; Brian S. Postle, BS; Tim Matheson, PhD; K. Rivet Amico, PhD; Teri Liegler, PhD; M. Keith Rawlings, MD; Nikole Trainor, MPH; Robert Wilder Blue, MSW; Yannine Estrada, PhD; Megan E. Coleman, FNP; Gabriel Cardenas, MPH; Daniel J. Feaster, PhD; Robert Grant, MD, MPH; Susan S. Philip, MD, MPH; Richard Elion, MD; Susan Buchbinder, MD; Michael A. Kolber, PhD, MD Invited Commentary page 85 IMPORTANCE Several randomized clinical trials have demonstrated the efficacy of Supplemental content at preexposure prophylaxis (PrEP) in preventing human immunodeficiency virus (HIV) jamainternalmedicine.com acquisition. Little is known about adherence to the regimen, sexual practices, and overall effectiveness when PrEP is implemented in clinics that treat sexually transmitted infections (STIs) and community-based clinics serving men who have sex with men (MSM). OBJECTIVE To assess PrEP adherence, sexual behaviors, and the incidence of STIs and HIV infection in a cohort of MSM and transgender women initiating PrEP in the United States. DESIGN, SETTING, AND PARTICIPANTS Demonstration project conducted from October 1, 2012, through February 10, 2015 (last date of follow-up), among 557 MSM and transgender women in 2 STI clinics in San Francisco, California, and Miami, Florida, and a community health center in Washington, DC. Data were analyzed from December 18, 2014, through August 8, 2015. INTERVENTIONS A combination of daily, oral tenofovir disoproxil fumarate and emtricitabine was provided free of charge for 48 weeks. -
A Chimeric Nuclease Substitutes a Phage CRISPR-Cas System
RESEARCH ARTICLE A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence- specific immunity against subviral parasites Zachary K Barth1†, Maria HT Nguyen1, Kimberley D Seed1,2* 1Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States; 2Chan Zuckerberg Biohub, San Francisco, United States Abstract Mobile genetic elements, elements that can move horizontally between genomes, have profound effects on their host’s fitness. The phage-inducible chromosomal island-like element (PLE) is a mobile element that integrates into the chromosome of Vibrio cholerae and parasitizes the bacteriophage ICP1 to move between cells. This parasitism by PLE is such that it abolishes the production of ICP1 progeny and provides a defensive boon to the host cell population. In response to the severe parasitism imposed by PLE, ICP1 has acquired an adaptive CRISPR-Cas system that targets the PLE genome during infection. However, ICP1 isolates that naturally lack CRISPR-Cas are still able to overcome certain PLE variants, and the mechanism of this immunity against PLE has thus far remained unknown. Here, we show that ICP1 isolates that lack CRISPR-Cas encode an endonuclease in the same locus, and that the endonuclease provides ICP1 with immunity to a subset of PLEs. Further analysis shows that this endonuclease is of chimeric origin, incorporating a DNA-binding domain that is highly similar to some PLE replication origin-binding proteins. This similarity allows the endonuclease to bind and cleave PLE origins of replication. The endonuclease appears to exert considerable selective pressure on PLEs and may drive PLE replication module *For correspondence: [email protected] swapping and origin restructuring as mechanisms of escape. -
Comparative Host-Coronavirus Protein Interaction Networks Reveal Pan-Viral Disease Mechanisms
RESEARCH ARTICLES Cite as: D. E. Gordon et al., Science 10.1126/science.abe9403 (2020). Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms David E. Gordon1,2,3,4*, Joseph Hiatt1,4,5,6,7*, Mehdi Bouhaddou1,2,3,4*, Veronica V. Rezelj8*, Svenja Ulferts9*, Hannes Braberg1,2,3,4*, Alexander S. Jureka10*, Kirsten Obernier1,2,3,4*, Jeffrey Z. Guo1,2,3,4*, Jyoti Batra1,2,3,4*, Robyn M. Kaake1,2,3,4*, Andrew R. Weckstein11*, Tristan W. Owens12*, Meghna Gupta12*, Sergei Pourmal12*, Erron W. Titus12*, Merve Cakir1,2,3,4*, Margaret Soucheray1,2,3,4, Michael McGregor1,2,3,4, Zeynep Cakir1,2,3,4, Gwendolyn Jang1,2,3,4, Matthew J. O’Meara13, Tia A. Tummino1,2,14, Ziyang Zhang1,2,3,15, Helene Foussard1,2,3,4, Ajda Rojc1,2,3,4, Yuan Zhou1,2,3,4, Dmitry Kuchenov1,2,3,4, Ruth Hüttenhain1,2,3,4, Jiewei Xu1,2,3,4, Manon Eckhardt1,2,3,4, Danielle L. Swaney1,2,3,4, Jacqueline M. Fabius1,2, Manisha Ummadi1,2,3,4, Beril Tutuncuoglu1,2,3,4, Ujjwal Rathore1,2,3,4, Maya Modak1,2,3,4, Paige Haas1,2,3,4, Kelsey M. Haas1,2,3,4, Zun Zar Chi Naing1,2,3,4, Ernst H. Pulido1,2,3,4, Ying Shi1,2,3,15, Inigo Barrio-Hernandez16, Danish Memon16, Eirini Petsalaki16, Alistair Dunham16, Downloaded from Miguel Correa Marrero16, David Burke16, Cassandra Koh8, Thomas Vallet8, Jesus A. Silvas10, Caleigh M. Azumaya12, Christian Billesbølle12, Axel F. Brilot12, Melody G. Campbell12,17, Amy Diallo12, Miles Sasha Dickinson12, Devan Diwanji12, Nadia Herrera12, Nick Hoppe12, Huong T. -
Clinical Efficacy and Increased Donor Strain Engraftment After Antibiotic
medRxiv preprint doi: https://doi.org/10.1101/2021.08.07.21261556; this version posted August 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . Clinical efficacy and increased donor strain engraftment after antibiotic pretreatment in a randomized trial of ulcerative colitis patients receiving fecal microbiota transplant Byron J. Smith A,B (ORCID: 0000-0002-0182-404X) Yvette Piceno C (ORCID: 0000-0002-7915-4699) Martin Zydek D Bing Zhang D (ORCID: 0000-0002-3377-0963) Lara Aboud Syriani E Jonathan P. Terdiman D Zain Kassam F Averil Ma G (ORCID: 0000-0003-4817-1258) Susan V. Lynch D,H (ORCID: 0000-0001-5695-7336) Katherine S. Pollard A,B,I,* (ORCID: 0000-0002-9870-6196) Najwa El-Nachef D,* A The Gladstone Institute of Datascience and Biotechnology, San Francisco, CA B Department of Epidemiology and Biostatistics, University of California, San Francisco, CA C Symbiome, Inc., San Francisco, CA D Division of Gastroenterology, University of California, San Francisco, CA E College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA F Finch Therapeutics, Somerville, MA G Department of Medicine, University of California, San Francisco, CA H Benioff Center for Microbiome Medicine, University of California, San Francisco, CA I Chan-Zuckerberg Biohub, San Francisco, CA * Corresponding authors: [email protected] [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. -
Non-Confidential Report.Pdf
2009 Annual Report I. Table of Contents Pages Cover 1 Table of Contents 2 Overview of the Activities of the Taube-Koret Center for HD Research 3–5 Oversight of the Taube-Koret Center for HD Research Biographies of our Advisors 6 Report from Dr. Pagno Paganetti 7–10 Report from Dr. Norbert Bischofberger 11–13 Publications and Presentations of the Taube-Koret Center for HD Research Bibliography of Publications 14 HD-related Academic Seminars 15 HD-related Industry Consultations and Seminars 16 Taube-Koret Center for HD Research and the Community Press releases 17–22 News stories 23–33 The Taube-Koret Center for HD Research and 34 HD Families Appendix of Publications 35–113 2 II. Overview of the Activities of the Taube-Koret Center for Huntington’s Disease Research for 2009 We are pleased to provide this annual report describing the activities of the Taube-Koret Center for Huntington’s Disease Research during 2009. The Center was established in 2009 with a joint gift from Taube Philanthropies and the Koret Foundation. It has been a very exciting year. I am delighted to say that we exceeded all five of the scientific and financial goals we set for the first year of operation. Our progress in each area is described in detail below. Goal 1. Establish the Taube-Koret Center for Huntington’s Disease Our initial goal was to establish a Center focused on developing therapeutics for Huntington’s disease (HD). We proposed to develop an infrastructure that would be capable of identifying and validating drug targets for HD and of discovering compounds that modify HD and have the potential to become drugs.