Angela N. Koehler
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Using Web-Based Annotation Tools for Bioinformatic Analyses of Proteomics Data
Using web-based annotation tools for bioinformatic analyses of proteomics data Kasper Lage, PhD Massachusetts General Hospital Harvard Medical School the Broad Institute Overview of this session 1) Biological networks 2) Annotating genetic and proteomic data using biological networks 3) Tissue-specific networks with disease resolution 4) Emerging resources at the Broad Institute What is a biological network? Jeong et al., Nature 2001 1) Gene expression correlations 2) Protein-protein interactions 3) Co-mentioning in text D 4) Synthetic lethality 5) TF binding 6) Pathway database mining 7) Epigenetic data 8) All of the above Building a human protein-protein interaction network - InWeb Email [email protected] if you want to use the data. Lage, Karlberg et al., Nat. Biotech., 2007 Lage, Hansen et al. PNAS, 2008 Lage et al., Mol Syst Biol, 2010 Rossin et al., PLoS Genetics, 2011 Lage et al., PNAS, 2012 Social human networks D are a good model for understanding biological networks Social networks People are represented by “nodes”, work related interactions by “edges” daily weekly monthly Social networks People that work together are close to each other in the network daily weekly monthly Social networks People that work together are close to each other in the network daily weekly monthly Social networks People that work together are close to each other in the network daily weekly monthly Lone< wolf Social networks People that work together are close to each other in the network Do loci connect more than a random expectation? Quantify -
Senior Counsel's Office
Senior Counsel’s Office In its fifth year, fiscal year 2004, the Senior Counsel’s Office is MIT’s central in‐house counsel’s office, providing comprehensive legal services and counseling on MIT matters in all areas of concern to the academy and the administration (except intellectual property law). The office represents MIT’s president, provost, executive vice president, and chancellor, as well as the deans, vice presidents, the departments, laboratories, and research centers, and administrative offices. We also arrange for and manage outside legal services when needed and oversee all litigation. Our office includes MIT’s senior counsel Jamie Lewis Keith, contracts counsel Margaret Brill, and litigation and risk management counsel Mark DiVincenzo, as well as a law clerk, Kathryn Johnson. (In FY2004 our office also included a part‐time environmental counsel. In FY2005 the office will include an associate counsel.) We are problem solvers and strategic‐thinking partners for our clients. We strive to be enablers, helping MIT’s senior officers, faculty, and staff to accomplish their mission‐critical objectives and to make informed decisions. Our office also brings the lessons learned from litigation, other disputes, and major transactions back to the MIT community through counseling and education. These lessons support management and faculty initiatives to minimize and avoid those reputational, financial, operational, and legal risks that can be appropriately managed, while still achieving MIT’s core mission. The Senior Counsel’s Office advises -
HBS Annual Report 2008
2 0 0 8 h a r v a r d u n i v harvard university e r s i t y f i financial report n a n c i a l r e p o r t fiscal year 2008 001215 We want all students who might dream of a Harvard “ education to know that it is a realistic and affordable option . Education is fundamental to the future of individuals and the nation, and we are determined to do our part to restore its place as an engine of opportunity, rather than a source An upperclass student in Kirkland House sketches during her free time. of financial stress…This is a huge investment for Harvard, but there is no more important commitment we could make. Excellence and opportunity must go hand in hand. ” —President Drew Gilpin Faust announcing the Middle Income Financial Aid Initiative, December 10, 2007 2 message from the president 3 financial highlights s t 8 annual report of the harvard n e t management company n o 15 report of independent auditors c f financial statements o 16 e l b 20 notes to financial statements a t Message from the President I am pleased to present Harvard University’s financial report for fiscal 2008. Under very challenging market conditions, we achieved endowment returns of 8.6%, raising the endowment to $36.9 billion. Income from the endowment contributed approximately one-third of the University’s operating budget, while also supporting substantial capital outlays. In addition, our alumni and friends contributed $690.1 million during fiscal 2008, the second highest level of fundraising receipts in the University’s history. -
CURRICULUM VITAE – June 13, 2017
Chris Cotsapas PhD CURRICULUM VITAE – June 13, 2017 Education ARCS Imperial College, London UK (Biochemistry) 2000 BSc Imperial College, London UK (Biochemistry) 2000 PhD University of New South Wales, Sydney, Australia (Biochemistry & Molecular Genetics) 2007 Career/Academic Appointments: 2005-2007 Research Associate, Center for Human Genetics Research, MGH (Boston, MA) 2007-2010 Research Fellow, Center for Human Genetics Research, MGH (Boston, MA) 2005-present Research Affiliate, Broad Institute of MIT and Harvard (Cambridge, MA) 2010-present Visiting Faculty, Analytical/Translational Genetics Unit, MGH (Boston, MA) 2010-2016 Assistant Professor, Dept. of Neurology, Yale School of Medicine (New Haven, CT) 2011-2016 Assistant Professor, Dept. of Genetics, Yale School of Medicine (New Haven, CT) 2011-present Research Affiliate, Stanley Center for Psychiatric Research (Boston, MA) 2016-present Associate Professor, Dept. of Neurology, Yale School of Medicine (New Haven, CT) 2016-present Associate Professor, Dept. of Genetics, Yale School of Medicine (New Haven, CT) Funding Record Current Grants Agency: NIH/NIAID I.D.# R01 AI122220 Title: “Genomics of NFkB-mediated gene regulation in multiple sclerosis” P.I.: Chris Cotsapas PhD Percent effort: 12% Total costs for project period: $1,827,500 Project period: 09/01/2015 – 08/31/2020 Agency: European Commission (Horizon 2020 program) I.D.#: 733161 Title: “MultipleMS: Multiple manifestations of genetic and non-genetic factors in multiple sclerosis disentangled with a multi-omics approach to accelerate -
CV Than, NA Rosenberg
Noah A. Rosenberg Department of Biology Stanford University Stanford, CA 94305-5020 USA (650) 721-2599 (phone) (650) 724-5114 (fax) [email protected] http://rosenberglab.stanford.edu/ August 9, 2017 Academic appointments 2014- Stanford Professor of Population Genetics and Society, Stanford University School of Humanities and Sciences 2014- Professor, Stanford University Department of Biology 2011-2014 Associate Professor, Stanford University Department of Biology 2009-2011 Associate Professor, University of Michigan Depts. of Human Genetics, Ecology & Evolutionary Biology, and Biostatistics Research Associate Professor, University of Michigan Life Sciences Institute and Center for Computational Medicine & Bioinformatics 2005-2009 Assistant Professor, University of Michigan Depts. of Human Genetics, Ecology & Evolutionary Biology (2006-2009), and Biostatistics Research Assistant Professor, University of Michigan Life Sciences Institute and Center for Computational Medicine & Bioinformatics Education 2001-2005 Postdoc, University of Southern California, Molecular and Computational Biology 1998-2001 PhD, Stanford University, Biological Sciences 1997-1999 MS, Stanford University, Mathematics 1993-1997 BA, Rice University, Mathematics and Russian Studies, summa cum laude Awards Fellowships 2007 Faculty Research Grant, University of Michigan Rackham Graduate School 2006 Faculty Fellowship Enhancement Award, University of Michigan Rackham Graduate School 2006-2010 Alfred P. Sloan Research Fellowship in Computational and Evolutionary Molecular -
September 29 & 30, 2020
SALTIEL LIFE SCIENCES SYMPOSIUM BROADENING THE BIOSCIENCES: EXPLORING DIVERSE APPROACHES TO BIOLOGICAL AND BIOMEDICAL RESEARCH SEPTEMBER 29 & 30, 2020 NINETEENTH ANNUAL LSI SYMPOSIUM ZOOM WEBINAR #LSIsymposium2020 SCHEDULE TUESDAY, SEPTEMBER 29 2:00 P.M. TALK SESSION 2: SOCIAL BIOMIMICRY Welcome Roger D. Cone, Ph.D. 3:10 P.M. Vice Provost and Director, Biosciences Initiative; Towards living robots: Using biology to make better Mary Sue Coleman Director, Life Sciences Institute; machines Professor of Molecular and Integrative Physiology, Medical School; Professor of Molecular, Cellular, and Barry A. Trimmer, Ph.D. Developmental Biology, College of Literature, Science, Henry Bromfield Pearson Professor of Natural Sciences; and the Arts, University of Michigan Director, Neuromechanics and Biomimetic Devices Laboratory, School of Arts and Sciences, Tufts University Marschall S. Runge, M.D., Ph.D. Dean, Medical School, University of Michigan; Executive 4:05 P.M. Vice President, Medical Affairs, CEO, Michigan Medicine How the physics of slithering can teach multilegged robots to walk TALK SESSION 1: HUMAN ADAPTATION Shai Revzen, Ph.D. AND EVOLUTION Associate Professor of Electrical Engineering and Computer Science, College of Engineering, University of Michigan 2:10 P.M. Introduction of the Mary Sue and Kenneth Coleman Life 4:25 P.M. Sciences Lecturer What wasps can teach us about the evolution of Alan R. Saltiel, Ph.D. animal minds Professor and Director, Institute for Diabetes and Elizabeth Tibbetts, Ph.D. Metabolic Health, University of California San Diego Professor of Ecology and Evolutionary Biology, College School of Medicine; Director, Life Sciences Institute of Literature, Science, and the Arts, University of Michigan (2002–2015) 5:20 P.M. -
Boston Tech Hub Faculty Working Group Annual Report: 2019-2020
BOSTON TECH HUB FACULTY WORKING GROUP Annual Report 2019–2020 Technology and Public Purpose Project Belfer Center for Science and International Affairs Harvard Kennedy School 79 JFK Street Cambridge, MA 02138 www.belfercenter.org/TAPP Harvard John A. Paulson School of Engineering and Applied Sciences 29 Oxford St., Cambridge, MA 02138 www.seas.harvard.edu Statements and views expressed in this report are solely those of the authors and do not imply endorsement by Harvard University, Harvard Kennedy School, Harvard Paulson School, or the Belfer Center for Science and International Affairs. Design and Layout by Andrew Facini Copyright 2020, President and Fellows of Harvard College Printed in the United States of America BOSTON TECH HUB FACULTY WORKING GROUP Annual Report 2019-2020 Table of Contents Foreword ........................................................................................................................1 FWG Members and Guests .........................................................................................5 Introduction ................................................................................................................ 13 Summary ..................................................................................................................... 14 FWG Session Briefs: Fall 2019 ................................................................................19 FWG Session Briefs: Spring 2020 ..........................................................................31 Carol Rose, Executive Director -
BIOGRAPHICAL SKETCH NAME: Arlene H. Sharpe Era COMMONS
OMB No. 0925-0001 and 0925-0002 (Rev. 12/2020 Approved Through 02/28/2023) BIOGRAPHICAL SKETCH Provide the following information for the Senior/key personnel and other significant contributors. Follow this format for each person. DO NOT EXCEED FIVE PAGES. NAME: Arlene H. Sharpe eRA COMMONS USER NAME (credential, e.g., agency login): asharpe POSITION TITLE: George Fabyan Professor of Comparative Pathology EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable. Add/delete rows as necessary.) DEGREE Completion (if Date FIELD OF STUDY INSTITUTION AND LOCATION applicable) MM/YYYY Radcliffe College, Cambridge, MA AB 05/1975 Biochemistry Harvard University, Cambridge, MA PhD 05/1981 Microbiology Harvard Medical School, Boston, MA MD 05/1982 Medicine A. Personal Statement My laboratory investigates T cell costimulation and its immunoregulatory functions. My laboratory focUses on the roles of T cell costimUlatory and coinhibitory pathways in regUlating immUne responses needed for the indUction and maintenance of T cell tolerance and effective antimicrobial and antitumor immunity. My laboratory has been at the forefront of this field for two decades. We have discovered T cell costimulatory pathways, and elucidated their functions, inclUding the functions of B7-1 and B7-2, CTLA-4, ICOS, PD-1 and PD-1 ligands. We are also involved in stUdies aimed at translating fUndamental Understanding of T cell costimUlation into new therapies for autoimmune diseases, viral infections, and cancer. Understanding how costimulatory pathways regulate tissUe inflammation, tolerance and anti-tumor immUnity is an important aspect of my cUrrent research. -
Hypr-Seq: Single-Cell Quantification of Chosen Rnas Via Hybridization and Sequencing of DNA Probes
HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes Jamie L. Marshalla,1, Benjamin R. Doughtya,1, Vidya Subramaniana, Philine Guckelbergera,b, Qingbo Wanga,c,d, Linlin M. Chena, Samuel G. Rodriquesa,e,f,2, Kaite Zhanga, Charles P. Fulcoa,3, Joseph Nassera, Elizabeth J. Grinkevicha, Teia Noela, Sarah Mangiamelia, Drew T. Bergmana, Anna Grekaa,g, Eric S. Landera,h,i,4,5, Fei Chena,4,5, and Jesse M. Engreitza,j,k,4,5 aBroad Institute of MIT and Harvard, Cambridge, MA 02142; bDepartment of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; cAnalytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114; dProgram in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115; eDepartment of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139; fMIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139; gDepartment of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115; hDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115; iDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; jDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305; and kBasic Science and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford University School of Medicine, Stanford, CA 94305 Contributed by Eric S. Lander, November 9, 2020 (sent for review May 29, 2020; reviewed by Alexander Meissner, Kathrin Plath, and Chun J. Ye) Single-cell quantification of RNAs is important for understanding and quantify specific transcripts in single cells, for example using cellular heterogeneity and gene regulation, yet current approaches target-specific reverse transcription of RNA during library prep- suffer from low sensitivity for individual transcripts, limiting their aration (13–15) or hybrid selection, PCR, or linear amplification utility for many applications. -
Human Molecular Genetics and Genomics — Important Advances and Exciting Possibilities Francis S
The NEW ENGLAND JOURNAL of MEDICINE Perspective January 7, 2021 A Half-Century of Progress in Health: The National Academy of Medicine at 50 Human Molecular Genetics and Genomics — Important Advances and Exciting Possibilities Francis S. Collins, M.D., Ph.D., Jennifer A. Doudna, Ph.D., Eric S. Lander, Ph.D., and Charles N. Rotimi, Ph.D. Human Molecular Genetics and Genomic he breathtaking progress in molecular genet- ing to understand the fundamen- ics that has occurred over the past five decades tals of the human genetic code to examining the ways in which Tand the transition to genomic medicine would this code varies among people, have been difficult to imagine in 1970, when the and then applying this knowl- edge to interventions that are Institute of Medicine (IOM), now quence the human genome seemed tailored to target, with precision, the National Academy of Medicine radical. the underlying causes of disease. (NAM), was formed. The term In 1987, the New York Times Mag- The development of genomic “genomics” hadn’t yet been coined, azine characterized the Human tools and data sets has trans- the tools and technologies that are Genome Project as the “biggest, formed the nature of medical the foundation of modern biotech- costliest, most provocative bio- discovery, enabling scientists to nology were in their infancy, and medical research project in his- undertake comprehensive and methods for sequencing even a few tory.”2 But in the years between powerful explorations rather than nucleotides were barely workable.1 the project’s launch in 1990 and being confined to testing hypoth- The IOM’s early years coincided its completion in 2003, genomic eses focused on candidate path- with paradigm-shifting discover- technology advanced dramatically. -
The Broad Institute, Inc. Report on Federal Awards in Accordance with the Uniform Guidance for the Year Ended June 30, 2019 EIN # 26-3428781
The Broad Institute, Inc. Report on Federal Awards in Accordance with the Uniform Guidance For the Year Ended June 30, 2019 EIN # 26-3428781 The Broad Institute, Inc. Index Year Ended June 30, 2019 Page(s) Part I - Consolidated Financial Statements and Schedule of Expenditures of Federal Awards Report of Independent Auditors ............................................................................................................... 1–2 Consolidated Financial Statements and Footnotes ............................................................................... 3–22 Schedule of Expenditures of Federal Awards ...................................................................................... 23–29 Note to Schedule of Expenditures of Federal Awards ............................................................................... 30 Part II - Reports on Internal Control and Compliance Report of Independent Auditors on Internal Control Over Financial Reporting and on Compliance and Other Matters Based on an Audit of Financial Statements Performed in Accordance With Government Auditing Standards ........................................................ 31–32 Report of Independent Auditors on Compliance With Requirements That Could Have a Direct and Material Effect on Each Major Program and on Internal Control Over Compliance in Accordance With the Uniform Guidance ...................................................................... 33–34 Part III - Findings and Questioned Costs Schedule of Findings and Questioned Costs ............................................................................................ -
Brevia Pursues a $3-Billion Capital Campaign
Journal-Front_final 2/7/07 5:41 PM Page 69 Engineering Emerges ulation by about 15 percent, raising class Concluding work begun last spring, the size from 1,300 to 1,500; a committee is Faculty of Arts and Sciences on Decem- studying the idea this semester, as Yale ber 12 approved the renaming of the Divi- Brevia pursues a $3-billion capital campaign. sion of Engineering and Applied Sci- Among smaller research universities, ences, recognizing it as a separate School Rice is scaling up enrollment about 30 of Engineering and Applied percent, and the University Sciences (see “Quantum of Rochester is planning Leap for Engineering,” July- a one-quarter increase, August 2006, page 63). The according to Inside Higher school, with greater visibil- Education. ity, expects to be better able to recruit faculty and at- Genetic Gains tract students. It will ad- The Broad Institute of Har- minister and finance itself, vard and MIT (see “Bigger while still conducting ad- Biology,” January-February, missions through the Col- page 72) has received a lege and the Graduate $200-million grant from the School of Arts and Sciences. National Human Genome The Corporation and Board Research Institute to exam- of Overseers approved the ine links between cancer change in early February. and genetics; other grants were made to Washington Sudan Stockholdings University School of Med- In April 2005, responding to icine and Baylor College concerns about support for of Medicine. Separately, the government of Sudan Strong professor of infec- during the war in Darfur, tious disease Dyann F. the Corporation instructed Harvard AN EYE ON IMMIGRATION.