The Future of Genomic Medicine II the Neurosciences Institute Auditorium San Diego, California

Total Page:16

File Type:pdf, Size:1020Kb

The Future of Genomic Medicine II the Neurosciences Institute Auditorium San Diego, California SCRIPPS GENOMIC MEDICINE A COLL ABoraTion OF S cripps H ea LT H and T H E S C R I P P S R E S E A RC H I NS T I T U T E TheThe Future Future of of Genomic Genomic MedicineMedicine II II in collaboration with: Friday, February 27 and Saturday, February 28, 2009 The Neurosciences Institute Auditorium San Diego, California Dear Colleague, Scripps Genomic Medicine A collaboration between Scripps Health and The Scripps Research Institute We invite you to a special day and a half program on a Friday, February 27 and Saturday, February 28, 2009 in beautiful La Jolla, California. Once again, Scripps Genomic Medicine, an initiative of Scripps Health in collaboration this year’s program will be held at the Neurosciences Institute Auditorium on The with The Scripps Research Institute, supports basic research and clinical pro- Scripps Research Institute campus. grams focused on defining the genes that underlie susceptibility to disease, As you will see in the enclosed program, we are inviting a dynamic group of and will take these findings into drug discovery programs and ultimately into speakers who will cover a wide range of topics. The Friday afternoon session clinical trials. The program’s work involves genotyping tens of thousands of will focus on Technology Breakthroughs and Challenges whereas the Saturday individuals of diverse ancestry in an attempt to identify and define genes re- session will feature a wide variety of topics along with keynote speakers. Our goal is to continue to examine the salient progress and challenges in the field of sponsible for major disease and the underpinnings of health. The identification genomics with concise, 20-minute presentations, allowing ample time for interac- of these genes will lead to drug discovery and gene-specific clinical trials. The tive panel and participant discussions following each topic series. rich diversity of the San Diego population – the primary patient base of the We look forward to your participation, Scripps program – provides unparalleled opportunities for this research. For more information on Scripps Health, visit www.scripps.org. Eric J. Topol, M.D., and Robert L. Strausberg, Ph.D. For more information on The Scripps Research Institute, visit Course Co-Directors www.scripps.edu. Educational Objectives The J. Craig Venter Institute • Demonstrate the unmet needs of medicine today with respect to more targeted, The J. Craig Venter Institute (JCVI) is a not-for-profit research institute dedicated individualized prevention and treatments. to the advancement of the science of genomics; the understanding of its • Discuss the opportunities of the genome, proteome, metabolome discovery implications for society; and the communication of those results to the scientific to change medical practice as it exists today. community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., • Assess how changes and advances in technology are rapidly ushering in a whole the Institute, through its two divisions—The Institute for Genomic Research array of new pathways for individualized medicine of the future. (TIGR) and The Center for the Advancement of Genomics (TCAG) is home to • Explore specific strategies in cancer, cardiovascular and pharmacogenomic more than 500 scientists and staff with expertise in human and evolutionary futuristic interventions. biology, genetics, bioinformatics/informatics, high-throughput DNA sequenc- ing, information technology, functional genomics, and genomic and environ- Who Should Attend? mental policy research. • Human geneticists For more information on the J. Craig Venter Institute visit, www.venterinstitute.org. • Genomic scientists • Health care professionals of all disciplines interested in the future of medicine, especially with respect to individualized therapies. Faculty COURSE CO-DIREctORS KEYNOTE SPEAKER Hakon Hakonarson, M.D., Ph.D. Bing Ren, Ph.D. Eric J. Topol, M.D. Craig Venter, Ph.D. Director, Center for Applied Genomics Associate Professor, Director, Scripps Translational Chairman and President, Department of Pediatrics & Ludwig Institute for Cancer Research Science Institute (STSI) The J. Craig Venter Institute Division of Genetics Department of Cellular and Chief Academic Officer, Scripps Health Rockville, Maryland The Joseph Stokes Jr. Research Institute Molecular Medicine Senior Consultant, The Children’s Hospital of Philadelphia University of California, San Diego Division of Cardiology, Scripps Clinic University of Pennsylvania La Jolla, California Dean, School of Medicine GUEst FacULTY School of Medicine Scripps Clinic & The Scripps David B. Allison, Ph.D. Stephen W. Scherer, Ph.D., FRSC Philadelphia, Pennsylvania Research Institute Head, Section of Statistical Genetics Senior Scientist, La Jolla, California University of Alabama at Birmingham Eran Halperin, Ph.D. Department of Genetics & Robert L. Strausberg, Ph.D. Birmingham, Alabama Director of Bioinformatics, Genomic Biology Navigenics Incorporated The Hospital for Sick Children Deputy Director, Vineet Bafna, Ph.D. The J. Craig Venter Institute Berkeley, California Professor, Department of Molecular Associate Professor, Computer Science Rockville, Maryland Principal Investigator, Internal and Medical Genetics University of California, San Diego Computer Science Institute The Center for Applied Genomics, La Jolla, California ORGaniZinG COMMittEE Redwood Shores, California Hospital for Sick Children Kelly Frazer, Ph.D. David R. Bentley, Ph.D. University of Toronto, Ontario, Canada Jeffery W. Kelly, Ph.D. Director, Genomic Biology Vice President and Chief Scientist, Richard Simon, Ph.D. Scripps Genomic Medicine Illumina, Inc. Lita Annenberg Hazen Scripps Health and San Diego, California Professor of Chemistry, Chief, Biometric Research Branch The Scripps Research Institute Department of Chemistry & The National Cancer Institute La Jolla, California Joseph R. Ecker, Ph.D. Skaggs Institute of Chemical Biology Rockville, Maryland Professor, Plant Biology Laboratory Dean, Graduate & Postgraduate Studies Samuel Levy, Ph.D. The Salk Institute for Biological Studies The Scripps Research Institute Stephen Turner, Ph.D. Director, Human Genomics Founder and Chief Technology Officer, San Diego, California La Jolla, California The J. Craig Venter Institute Pacific Biosciences Rockville, Maryland Richard A. Gibbs, Ph.D. Patrice M. Milos, Ph.D. Menlo Park, California Wofford Cain Professor, Sarah S. Murray, Ph.D. Vice President and Chief Scientific Officer, Department of Molecular and Helicos BioSciences Corporation John N. Weinstein, M.D., Ph.D. Director, Genetics Professor and Chair, Bioinformatics & Scripps Genomic Medicine Human Genetics Cambridge, Massachusetts Scripps Health and Director, Human Genome Computational Biology The Scripps Research Institute Sequencing Center, Steven G. Potkin, M.D. University of Texas La Jolla, California Baylor College of Medicine Director of Clinical Research and M.D. Anderson Cancer Center Houston, Texas Director of the Brain Imaging Center, Houston, Texas Nicholas J. Schork, Ph.D. Department of Psychiatry and Director of Research, Peter K. Gregersen, M.D. Human Behavior Scripps Genomic Medicine Director, Robert S. Boas Center for Director of Biostatistics and Bioinformatics, University of California, Irvine Genomics and Human Genetics Irvine, California The Scripps Translational Science Institute Feinstein Institute for Medical Research Professor, Molecular and North Shore LIJ Health System Experimental Medicine Scripps Health and Professor of Medicine and Pathology, The Scripps Research Institute NYU School of Medicine La Jolla, California Manhasset, New York Program – Friday, February 27 and Saturday, February 28, 2009 FRidaY, FEBRUARY 27, 2009 SATURDAY, FEBRUARY 28, 2009 – Morning Session 12:00 p.m. Registration, Lunch and View Exhibits 7:30 a.m. Sign In, Breakfast & View Exhibits 12:45 p.m. Welcome and Educational Overview 8:00 a.m. Welcome and Educational Overview Eric J. Topol, M.D. TECHNOLOGY BREAKTHROUGHS AND CHALLENGES Moderators: Robert L. Strausberg, Ph.D. and Kelly Frazer, Ph.D. 8:15 a.m. Keynote: Transforming Genomics to Better Medicine 1:00 p.m. Sequencing 100 or 10,000 Human Genomes Craig Venter, Ph.D. Samuel Levy, Ph.D. Advances IN UnderstandING CHRONIC ILLNESS: 1:25 p.m. Panel Discussion/Q&A WHERE DO WE Stand? What NEXT? 1:30 p.m. Next Generation Sequencing Moderators: Eric J. Topol, M.D. and Brad Patay, M.D. Richard A. Gibbs, Ph.D.; Stephen Turner, Ph.D.; 9:00 a.m. Cardiovascular Diseases Patrice M. Milos, Ph.D.; David R. Bentley, Ph.D. Eric J. Topol, M.D. 2:30 p.m. Panel Discussion/Q&A 9:20 a.m. Cancer 2:50 p.m. Break and View Exhibits Robert L. Strausberg, Ph.D. 3:20 p.m. Bioinformatic Challenges in 9:40 a.m. Immunologic Diseases (Crohn’s, RA, AMD) High Throughput Sequencing Peter K. Gregersen, M.D. Vineet Bafna, Ph.D. 10:00 a.m. Neurodegenerative Diseases 3:45 p.m. Analytic Challenges in Steven G. Potkin, M.D. High Throughput Sequencing 10:20 a.m. Metabolic Diseases (DM, Obesity) Nicholas J. Schork, Ph.D. David B. Allison, Ph.D. 4:10 p.m. Panel Discussion/Q&A 10:40 a.m.. Pediatric Diseases Hakon Hakonarson, M.D., Ph.D. 4:30 – 6:00 p.m. – Adjourn and Shuttle to Welcome Reception 11:00 a.m. Disease Panel Discussion/Q&A Torrey Pines Court – New home of Scripps Genomic Medicine 11:30 a.m. 2nd Annual Scripps Genomic Medicine Award Presentation 11:45 a.m. Lunch and View Exhibits Directions SATURDAY, FEBRUARY 28, 2009 – 3:40 p.m. Companion Therapeutics The Neurosciences Institute Auditorium Afternoon Session John N. Weinstein, M.D., Ph.D. 10640 John Jay Hopkins Dr. HOLES IN OUR KNOWLEDGE BASE 4:00 p.m. Targeted Therapies San Diego, California Moderators: Sarah S. Murray, Ph.D. and Jeffery W. Kelly, Ph.D. 92121 Samuel Levy, Ph.D. 4:20 p.m. Clinical Trials of Individualized 12:30 p.m. • From Interstate 5, exit at Genesee Avenue Genome Wide Association Studies Medicine Sarah S. Murray, Ph.D. and go west for about 0.8 mile to the Richard Simon, Ph.D. second stoplight (not counting any at the 12:50 p.m. Rare Variants 4:40 p.m. I-5 exit). Kelly Frazer, Ph.D. The Next Frontier in Medicine Panel Discussion/Q&A • Turn right (north) onto John Jay Hopkins Drive.
Recommended publications
  • 120421-24Recombschedule FINAL.Xlsx
    Friday 20 April 18:00 20:00 REGISTRATION OPENS in Fira Palace 20:00 21:30 WELCOME RECEPTION in CaixaForum (access map) Saturday 21 April 8:00 8:50 REGISTRATION 8:50 9:00 Opening Remarks (Roderic GUIGÓ and Benny CHOR) Session 1. Chair: Roderic GUIGÓ (CRG, Barcelona ES) 9:00 10:00 Richard DURBIN The Wellcome Trust Sanger Institute, Hinxton UK "Computational analysis of population genome sequencing data" 10:00 10:20 44 Yaw-Ling Lin, Charles Ward and Steven Skiena Synthetic Sequence Design for Signal Location Search 10:20 10:40 62 Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng and Fengzhu Sun Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads 10:40 11:00 178 Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene Robinson and Jian Ma TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq 11:00 11:30 coffee break Session 2. Chair: Bonnie BERGER (MIT, Cambrige US) 11:30 11:50 139 Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner and Max Alekseyev PATH-SETS: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly 11:50 12:10 171 Yan Huang, Yin Hu and Jinze Liu A Robust Method for Transcript Quantification with RNA-seq Data 12:10 12:30 120 Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin and Eleazar Eskin CNVeM: Copy Number Variation detection Using Uncertainty of Read Mapping 12:30 12:50 205 Dmitri Pervouchine Evidence for widespread association of mammalian splicing and conserved long range RNA structures 12:50 13:10 169 Melissa Gymrek, David Golan, Saharon Rosset and Yaniv Erlich lobSTR: A Novel Pipeline for Short Tandem Repeats Profiling in Personal Genomes 13:10 13:30 217 Rory Stark Differential oestrogen receptor binding is associated with clinical outcome in breast cancer 13:30 15:00 lunch break Session 3.
    [Show full text]
  • Albert A. Bowers, Ph.D
    CURRICULUM VITAE Albert A. Bowers, Ph.D. A) PERSONAL INFORMATION Division of Chemical Biology and Medicinal Chemistry Phone: 919-962-4336 Eshelman School of Pharmacy Email : [email protected] 3107 Marsico Hall WeB: http://bowerslab.web.unc.edu 125 Mason Farm Rd. Twitter: @BowersRangers Chapel Hill, NC 27599 B) EDUCATION 2007 Doctor of Philosophy (Ph.D.) in Chemistry The University of Illinois at Chicago, Chicago, IL. 2001 Bachelor of Arts (B.A.) in Art History University of Chicago, Chicago, IL. C) PROFESSIONAL EXPERIENCE 06/2018-present Associate Professor, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 08/2012-05/2018 Assistant Professor, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 08/2011-07/2012 Assistant Professor, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 2011 Visiting scholar, National Institutes of Health, Bethesda, MD Host: Dr. David L. Levens 2005 Visiting scholar, Kyoto University, Kyoto, Japan Host: Prof. Jun-Ichi Yoshida 01/2009-07/2011 Post-doctoral Fellow, Dept. of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA. Advisor: Prof. Christopher T. Walsh 08/2007-12/2008 Post-doctoral Fellow, Dept. of Chemistry, Colorado State University, Fort Collins, CO. Advisor: Prof. RoBert M. Williams D) HONORS AND AWARDS 2018 U. Tokyo/Japan Society for the Promotion of Science Tateshina Young Investigator Award 2016 Boulder Peptide Society Young Investigator Award 2014 Beckman Young Investigator Award 2013 American Association of Colleges of Pharmacy New Investigator Award 2013 Junior Faculty Development Award (UNC) 2008 NIH (NCI) Ruth L Kirschstein Postdoctoral Fellowship (F32) 2006 RoBert M.
    [Show full text]
  • Scripps Florida Funding Corporation Annual Report
    SCRIPPS FLORIDA FUNDING CORPORATION ANNUAL REPORT FOR THE YEAR ENDED SEPTEMBER 30, 2020 Scripps Florida Funding Corporation Annual Report For Year Ended September 30, 2020 INTRODUCTION Florida Statute 288.955 (the “Enabling Statute”) created Scripps Florida Funding Corporation (“SFFC”) to facilitate the establishment and operation of a biomedical research institution for the purposes of enhancing education and research and promoting economic development and diversity. In addition, the Enabling Statute charged SFFC with the obligation to assure the compliance by The Scripps Research Institute (“TSRI”) with the Enabling Statute and the agreement between SFFC and TSRI (the “Operating and Funding Agreement”). The Enabling Statute provides that SFFC shall prepare or obtain certain reports, audits, and evaluations of TSRI’s compliance with the performance expectations and disbursement conditions contained in the Enabling Statute. As such, SFFC is submitting this Annual Report to the Governor, the President of the Senate, and the Speaker of the House, as required by the Enabling Statute to be submitted by December 1 of each year. This SFFC Annual Report addresses the activities and outcomes of SFFC and Scripps Florida (“SF”) for the fiscal year ended September 30, 2020 (“Fiscal 2020”). The Scripps Florida Annual Report addressed the activities and outcomes of Scripps Florida for the year ended June 30, 2020, and the information in the Scripps Florida Annual Report was informally updated for this SFFC Annual Report. The SFFC Annual Report is presented in two parts: first, a summary that highlights the substantial events that have occurred during the year ended September 30, 2020; and second, an itemized report that corresponds with the applicable sections of the Enabling Statute.
    [Show full text]
  • Kalypsys to Provide the Florida Scripps Research Institute with Next- Generation Lead Discovery Technology
    KALYPSYS TO PROVIDE THE FLORIDA SCRIPPS RESEARCH INSTITUTE WITH NEXT- GENERATION LEAD DISCOVERY TECHNOLOGY 6/15/2005 San Diego, June 16, 2005 — Kalypsys, Inc., a privately owned drug discovery and development company and The Scripps Research Institute (TSRI) entered into an agreement in which Scripps will access Kalypsys' proprietary ultra-high throughput screening technologies as a key enablement for the newly created TSRI site in Florida. "We are pleased to be selected for this Florida initiative," stated John P. McKearn, president and CEO of Kalypsys. "Developing a state-of-the-art research center will have a significant impact on Florida's economic development in the area of biotechnology and biomedical research and we are honored our technology has been selected to assist in this endeavor." The Kalypsys technology platform is designed and manufactured to meet the specific needs of each partner. The platform is comprised of a suite of lead discovery solutions, including a highly automated, robotic, ultra-high throughput screening technology capable of screening a variety of biochemical and biologically relevant cellular assays in 1536-well formats. The power and robustness of the Kalypsys technologies make it ideally suited to probe a large number of diverse targets rapidly. With the Kalypsys system, Scripps Florida is developing leading-edge technologies to enable scientists to examine the basic biology of human health and find better treatments for a variety of devastating human diseases. A team of accomplished scientists is implementing research programs addressing diseases such as AIDS, cancer, diabetes, obesity, prion diseases, Parkinson's disease and schizophrenia among others. The research programs focus on genetic disease informatics, cancer biology, infectology, genetics, proteomics, drug metabolism and pharmacokinetics.
    [Show full text]
  • Spontaneous Generation & Origin of Life Concepts from Antiquity to The
    SIMB News News magazine of the Society for Industrial Microbiology and Biotechnology April/May/June 2019 V.69 N.2 • www.simbhq.org Spontaneous Generation & Origin of Life Concepts from Antiquity to the Present :ŽƵƌŶĂůŽĨ/ŶĚƵƐƚƌŝĂůDŝĐƌŽďŝŽůŽŐLJΘŝŽƚĞĐŚŶŽůŽŐLJ Impact Factor 3.103 The Journal of Industrial Microbiology and Biotechnology is an international journal which publishes papers in metabolic engineering & synthetic biology; biocatalysis; fermentation & cell culture; natural products discovery & biosynthesis; bioenergy/biofuels/biochemicals; environmental microbiology; biotechnology methods; applied genomics & systems biotechnology; and food biotechnology & probiotics Editor-in-Chief Ramon Gonzalez, University of South Florida, Tampa FL, USA Editors Special Issue ^LJŶƚŚĞƚŝĐŝŽůŽŐLJ; July 2018 S. Bagley, Michigan Tech, Houghton, MI, USA R. H. Baltz, CognoGen Biotech. Consult., Sarasota, FL, USA Impact Factor 3.500 T. W. Jeffries, University of Wisconsin, Madison, WI, USA 3.000 T. D. Leathers, USDA ARS, Peoria, IL, USA 2.500 M. J. López López, University of Almeria, Almeria, Spain C. D. Maranas, Pennsylvania State Univ., Univ. Park, PA, USA 2.000 2.505 2.439 2.745 2.810 3.103 S. Park, UNIST, Ulsan, Korea 1.500 J. L. Revuelta, University of Salamanca, Salamanca, Spain 1.000 B. Shen, Scripps Research Institute, Jupiter, FL, USA 500 D. K. Solaiman, USDA ARS, Wyndmoor, PA, USA Y. Tang, University of California, Los Angeles, CA, USA E. J. Vandamme, Ghent University, Ghent, Belgium H. Zhao, University of Illinois, Urbana, IL, USA 10 Most Cited Articles Published in 2016 (Data from Web of Science: October 15, 2018) Senior Author(s) Title Citations L. Katz, R. Baltz Natural product discovery: past, present, and future 103 Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and R.
    [Show full text]
  • Extrachromosomal and Other Mechanisms of Oncogene Amplification in Cancer
    Title: Extrachromosomal and other mechanisms of oncogene amplification in cancer Abstract: Increase in the number of copies of tumor promoting (onco-) genes is a hallmark of many cancers, and cancers with copy number amplifications are often associated with poor outcomes. Despite their importance, the mechanisms causing these amplifications are incompletely understood. In this talk, we describe our recent results suggesting that a large faction of amplification is due to formation of extrachromosomal DNA (ecDNA). EcDNA play a critical role in tumor heterogeneity, accelerated cancer evolution, and drug resistance through their unique mechanism of non-chromosomal inheritance. While predominant, ecDNA are not the only mechanism to cause amplification. We also describe recent algorithmic methods required to distinguish ecDNA from other mechanisms including Breakage Fusion Bridge formation, Chromothripsis, and simpler events such as tandem duplications and translocations. The talk is a mix of published and unpublished work, largely in collaboration with Paul Mischel's lab at UCSD. EcDNA was recently recognized as one of the grand challenges of cancer research by Cancer Research UK and the National Cancer Institute. Reading Luebeck, 2020, Verhaak 2019 Biography Vineet Bafna, Ph.D., joined the Computer Science faculty at the University of California, San Diego in 2003, after seven years in the biosciences industry. He received his Ph.D. in computer science from The Pennsylvania State University in 1994 and was an NSF postdoctoral researcher at the Center for Discrete Mathematics and Theoretical Computer Science for two years. From 1996-99, Bafna was a senior investigator at SmithKline Beecham, conducting research on DNA signaling, target discovery and EST assembly.
    [Show full text]
  • Research Organizations and Major Discoveries in Twentieth-Century Science: a Case Study of Excellence in Biomedical Research
    A Service of Leibniz-Informationszentrum econstor Wirtschaft Leibniz Information Centre Make Your Publications Visible. zbw for Economics Hollingsworth, Joseph Rogers Working Paper Research organizations and major discoveries in twentieth-century science: A case study of excellence in biomedical research WZB Discussion Paper, No. P 02-003 Provided in Cooperation with: WZB Berlin Social Science Center Suggested Citation: Hollingsworth, Joseph Rogers (2002) : Research organizations and major discoveries in twentieth-century science: A case study of excellence in biomedical research, WZB Discussion Paper, No. P 02-003, Wissenschaftszentrum Berlin für Sozialforschung (WZB), Berlin This Version is available at: http://hdl.handle.net/10419/50229 Standard-Nutzungsbedingungen: Terms of use: Die Dokumente auf EconStor dürfen zu eigenen wissenschaftlichen Documents in EconStor may be saved and copied for your Zwecken und zum Privatgebrauch gespeichert und kopiert werden. personal and scholarly purposes. Sie dürfen die Dokumente nicht für öffentliche oder kommerzielle You are not to copy documents for public or commercial Zwecke vervielfältigen, öffentlich ausstellen, öffentlich zugänglich purposes, to exhibit the documents publicly, to make them machen, vertreiben oder anderweitig nutzen. publicly available on the internet, or to distribute or otherwise use the documents in public. Sofern die Verfasser die Dokumente unter Open-Content-Lizenzen (insbesondere CC-Lizenzen) zur Verfügung gestellt haben sollten, If the documents have been made available under an Open gelten abweichend von diesen Nutzungsbedingungen die in der dort Content Licence (especially Creative Commons Licences), you genannten Lizenz gewährten Nutzungsrechte. may exercise further usage rights as specified in the indicated licence. www.econstor.eu P 02 – 003 RESEARCH ORGANIZATIONS AND MAJOR DISCOVERIES IN TWENTIETH-CENTURY SCIENCE: A CASE STUDY OF EXCELLENCE IN BIOMEDICAL RESEARCH J.
    [Show full text]
  • UC San Diego Electronic Theses and Dissertations
    UC San Diego UC San Diego Electronic Theses and Dissertations Title Computational methods for genome-wide non-coding RNA discovery and analysis Permalink https://escholarship.org/uc/item/5qc2h8tf Author Zhang, Shaojie Publication Date 2007 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Computational Methods for Genome-Wide Non-Coding RNA Discovery and Analysis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by Shaojie Zhang Committee in charge: Professor Vineet Bafna, Chair Professor Sanjoy Dasgupta Professor Pavel Pevzner Professor Glenn Tesler Professor Steven Wasserman 2007 . Copyright Shaojie Zhang, 2007 All rights reserved. The dissertation of Shaojie Zhang is approved, and it is acceptable in quality and form for publication on micro- ¯lm: Chair University of California, San Diego 2007 iii To my parents. iv TABLE OF CONTENTS Signature Page . iii Dedication . iv Table of Contents . v List of Figures . vii List of Tables . viii Acknowledgements . ix Vita, Publications, and Fields of Study . xi Abstract . xiii 1 Introduction . 1 1.1 Non-coding RNAs . 1 1.2 RNA secondary structure . 4 1.3 The Challenge of ncRNA Discovery and Analysis . 6 1.3.1 RNA Homolog Search . 7 1.3.2 RNA Consensus Folding for ncRNA Discovery . 8 1.4 Dissertation Outline . 9 2 FastR: Fast RNA Search Using Structure-based Filters . 11 2.1 Introduction . 11 2.2 Methods . 14 2.2.1 Strucutre-based Filters . 14 2.2.2 Structure-based Filter Design . 17 2.2.3 Optimal Structure-based Filter Design .
    [Show full text]
  • Chi-Huey Wong
    CHI-HUEY WONG Academia Sinica 128 Academia Road, Section 2, Nankang District Taipei, Taiwan 115 Title of Lecture: “Chemistry and Biology of Glycosylation” Phone: +886-2-2789-9400 Fax: +886-2-2785-3852 Email: [email protected] Education: 1982 Ph.D. Organic Chemistry, Massachusetts Institute of Technology 1977 B.S. & M.S. National Taiwan University Research and Professional Experience 1982–1983 Postdoctoral Fellow, Harvard University 1983–1989 Assistant Professor through Professor, Texas A&M University, 1989–2006 Professor and Ernest W. Hahn Chair, The Scripps Research Institute 1991–1999 Head, Frontier Research Program on Glycotechnology, RIKEN 2000–2004 Board member, The National Research Council on Chemical Sciences & Technology, USA 2000–2008 Scientific Advisor, Max-Planck-Institute, Germany 1993–2010 Editor-in-Chief, Bioorganic & Medicinal Chemistry 2003–2006 Director, The Genomics Research Center Acadmia Sinica 2006-present President, Academia Sinica 2008-2011 Chief Science Advisor, Executive Yuan, Taiwan 2012-present Chief Science Advisor, Ministry of Science, Taiwan Research Interests Chemical Biology, Synthetic Organic Chemistry Awards and Honors 1985 Searle Scholar Award in Biomedical Sciences 1986 Presidential Young Investigator Award in Chemistry 1994 The IUPAC International Carbohydrate Award 1994 Academician, Academia Sinica 1996 Elected Member of The American Academy of Arts and Sciences 1998 The American Chemical Society Harrison Howe Award in Chemistry 1999 The American Chemical Society Claude S. Hudson Award in Carbohydrate Chemistry 1999 The International Enzyme Engineering Award 2000 The Presidential Green Chemistry Challenge Award, USA 2002 Elected Member of the US National Academy of Sciences 2005 The American Chemical Society Award for Creative Work in Synthetic Organic Chemistry 2006 Humboldt Research Award for Senior Scientists, Germany 2007 Elected Member of the World Academy of Sciences (TWAS) 2007 Doctor, Scientiarum Honoris Causa, Technion-Israel Institute of Technology 2008 The F.A.
    [Show full text]
  • The Mystery of Life's Origin
    The Mystery of Life’s Origin The Continuing Controversy CHARLES B. THAXTON, WALTER L. BRADLEY, ROGER L. OLSEN, JAMES TOUR, STEPHEN MEYER, JONATHAN WELLS, GUILLERMO GONZALEZ, BRIAN MILLER, DAVID KLINGHOFFER Seattle Discovery Institute Press Description e origin of life from non-life remains one of the most enduring mysteries of modern science. e Mystery of Life’s Origin: e Continuing Controversy investigates how close scientists are to solving that mystery and explores what we are learning about the origin of life from current research in chemistry, physics, astrobiology, biochemistry, and more. e book includes an updated version of the classic text e Mystery of Life’s Origin by Charles axton, Walter Bradley, and Roger Olsen, and new chapters on the current state of the debate by chemist James Tour, physicist Brian Miller, astronomer Guillermo Gonzalez, biologist Jonathan Wells, and philosopher of science Stephen C. Meyer. Copyright Notice Copyright © 2020 by Discovery Institute, All Rights Reserved. Library Cataloging Data e Mystery of Life’s Origin: e Continuing Controversy by Charles B. axton, Walter L. Bradley, Roger L, Olsen, James Tour, Stephen Meyer, Jonathan Wells, Guillermo Gonzalez, Brian Miller, and David Klinghoffer 486 pages, 6 x 9 x 1.0 inches & 1.4 lb, 229 x 152 x 25 mm. & 0.65 kg Library of Congress Control Number: 9781936599745 ISBN-13: 978-1-936599-74-5 (paperback), 978-1-936599-75-2 (Kindle), 978-1-936599-76-9 (EPUB) BISAC: SCI013040 SCIENCE / Chemistry / Organic BISAC: SCI013030 SCIENCE / Chemistry / Inorganic BISAC: SCI007000 SCIENCE / Life Sciences / Biochemistry BISAC: SCI075000 SCIENCE / Philosophy & Social Aspects Publisher Information Discovery Institute Press, 208 Columbia Street, Seattle, WA 98104 Internet: http://www.discoveryinstitutepress.com/ Published in the United States of America on acid-free paper.
    [Show full text]
  • Call for Papers (Page 1)
    CALL FOR PAPERS IEEE Computational Systems Bioinformatics Conference Stanford, CA • August 8-11, 2005 You are invited to submit papers to the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005). The conference’s goal is to facilitate exchange of ideas and collaborations between computer scientists and biologists by presenting cutting-edge computational biology research findings. Such research has an interdisciplinary character. Computer science and mathematical modeling papers must contain a concise description of the biological problem being solved, and biology papers should show how computation or analysis affects the results. Topics of interest include (but are not limited to): • Microarray Data Analysis • Mathematical and Quantitative Models • MicroRNA and RNAi of Cellular and Multicellular Systems • Pathways, Networks, Systems Biology • Synthetic Biological Systems • Biomedical Applications • Sequence Alignment • Biological Data Visualization • Evolution and Phylogenetics • Protein Structures and Complexes • Functional Genomics • Biological Data Mining • High Performance Bio-computing • Pattern Recognition • Comparative Genomics • Microbial Community Analysis • SNPs and Haplotyping • Promoter Analysis and Discovery Full papers are limited to 12 pages, single-spaced, in 12-point type, including title, abstract (250 words or less), figures, tables, text, and bibliography. The first page should give keywords, authors’ postal and electronic mailing addresses. Papers must not have been previously published and must not be currently under consideration for publication elsewhere. Papers will be submitted electronically in MS Word, postscript or PDF format. This year, the conference will also accept short papers, limited to four pages. These papers should describe new research activity in which a complete set of results may not yet be available. Full and short papers will have 25 and 15 minutes, respectively, of presentation time.
    [Show full text]
  • Winter 2007/2008
    WINTER 2007/08 VOLUME TEN / NUMBER TWO NON-PROFIT U.S. POSTAGE PAID PERMIT 751 SAN DIEGO, CA A PUBLICATION OF THE SCRIPPS RESEARCH INSTITUTE Office of Communications—TPC30 10550 North Torrey Pines Road La Jolla, California 92037 www.scripps.edu PUBLISHER: Keith McKeown EDITOR: Mika Ono Benedyk DESIGN: Octopus Ink COVER ILLUSTRATION: Penelope Dullaghan PORTRAIT PHOTOGRAPHY: Dana Neibert EDITORIAL PHOTOGRAPHY: Kevin Fung Randy Smith PRINTING: Precision Litho Copyright © 2007. Published by TSRI Press™ HEADQUARTERS AND ADVANCED TECHNOLOGIES BUILDING BIOMEDICAL RESEARCH BUILDING First floor Science Education Pavilion, Auditorium, Lakeside Plaza Second floor Atrium, Lounge Second floor Founder’s Suite, Library Research Suites Cancer Biology, Infectology, Cell Biology, Neurobiology Third floor Scripps Florida Headquarters Research Suites Microscopy, IT / Informatics, Genomics, Protein Sciences Renderings courtesy of Zeidler Partnership THE SCRIPPS RESEARCH INSTITUTE ENDEAVOR Founders’ Fund COMMEMorates EarlY Benefactors VOLUME TEN / NUMBER TWO WINTER 2007/08 Scripps Florida is embarking on a drive to raise funds to endow the operation and main- tenance of its striking new campus in Jupiter, Florida. Called the Founders’ Fund, it will commemorate early benefactors for this important new biomedical research institute, sister campus to the renowned Scripps Research Institute in La Jolla, California. 33 If you are interested in having your name, or a loved one’s name commemorated on the new Scripps Florida campus or on the California campus, please go to www.scripps. FEATURES: ALSO: edu/philanthropy/buildings.html for further details (and see a list of naming opportunitites, N A above). For Florida, contact Barbara Suflas Noble at (561) 656-6400 orbsnoble @scripps.edu.
    [Show full text]