Mathematical Association of America Ohio Section
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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 -
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 -
Prizes and Awards
MathFest 2010 Prizes and Awards Pittsburgh, Pennsylvania August 6, 2010 Program Opening and Closing Remarks David Bressoud, President Mathematical Association of America Carl B. Allendoerfer Awards ..................................... 1 Trevor Evans Awards ............................................... 7 Lester R. Ford Awards ............................................ 12 George Pólya Awards ............................................. 25 Annie and John Selden Prize ................................. 29 Henry L. Alder Awards ........................................... 31 Carl B. Allendoerfer Awards The Carl B. Allendoerfer Awards, established in 1976, are made to authors of expository articles published in Mathematics Magazine. The Awards are named for Carl B. Allendoerfer, a distinguished mathematician at the University of Washington and President of the Mathematical Association of America, 1959-60. Ezra Brown and Keith Mellinger “Kirkman‟s Schoolgirls Wearing Hats and Walking Through Fields of Numbers,” Mathematics Magazine, 82:1 (2009), p. 3-15. The historical basis for this interesting article is a problem in recreational mathematics posed by T. P. Kirkman in 1850. Kirkman‘s problem states: ―Fifteen young ladies of a school walk out three abreast for seven days in succession: it is required to arrange them daily so that no two shall walk abreast more than once.‖ Using this problem as a springboard, the authors treat the reader to a captivating exploration of the theory and applications of block designs. In the process, solutions to the schoolgirls problem are uncovered in such seemingly unrelated areas as the subfield structure of algebraic number fields and the configuration of ―spreads‖ and ―packings‖ in finite projective geometry. Additional connections to the schoolgirls problem are revealed by the authors‘ extension of Todd Ebert‘s ―Three Hats‖ problem to an analogous problem involving fifteen hats. -
Angela N. Koehler
Angela N. Koehler Broad Institute of MIT and Harvard Office: 617-714-7364 Chemical Biology Program Fax: 617-714-8943 7 Cambridge Center Email: [email protected] Cambridge, MA 02142 Website: www.broadinstitute.org/node/2445 Education Ph.D. Chemistry, Harvard University, 2003 B.A. Biochemistry and Molecular Biology, Reed College, 1997 Research Experience Investigator, Chemical Biology Program, Broad Institute 2009-present Project & Center Manager, Broad NCI Cancer Target Discovery and Development (CTD2) Center 2010-2012 Institute Fellow, Chemical Biology Program, Broad Institute 2003-2009 Director, Ligand Discovery, NCI Initiative for Chemical Genetics (ICG) at Harvard 2003-2009 Graduate Student, Department of Chemistry and Chemical Biology, Harvard University 1998-2003 Laboratory of Professor Stuart L. Schreiber Thesis: Small molecule microarrays: A high-throughput tool for discovering protein-small molecule interactions Researcher, Department of Chemistry, California Institute of Technology 1997-1998 Laboratory of Professor Barbara Imperiali Project: Biochemical reconstitution of the oligosaccharyltransferase (OST) complex Undergraduate Researcher, Department of Chemistry, Reed College 1995-1997 Laboratory of Professor Arthur Glasfeld Co-mentored by Professor Richard G. Brennan at Oregon Health Sciences University Thesis: Biochemical and structural characterization of the tRNA-modifying enzyme QueA from Escherichia coli Teaching Experience Research Advisor to postdoctoral fellows, undergraduates, high school students, and staff scientists 2003-present Broad Institute of MIT and Harvard Instructor, Biochemical Sciences Research (BS91r) 2004-2006, 2010-2011 Harvard University Associated Instructor, Experimental Research in the Life Sciences (LS100r) 2009 Harvard University Associated Instructor, Experimental Molecular and Cellular Biology (MCB100) 2004-2006 Harvard University Teaching Fellow, Chemical Biology (Chem 170) 1999, 2000 Harvard University, Professor David R. -
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. -
Prize Is Awarded Every Three Years at the Joint Mathematics Meetings
AMERICAN MATHEMATICAL SOCIETY LEVI L. CONANT PRIZE This prize was established in 2000 in honor of Levi L. Conant to recognize the best expository paper published in either the Notices of the AMS or the Bulletin of the AMS in the preceding fi ve years. Levi L. Conant (1857–1916) was a math- ematician who taught at Dakota School of Mines for three years and at Worcester Polytechnic Institute for twenty-fi ve years. His will included a bequest to the AMS effective upon his wife’s death, which occurred sixty years after his own demise. Citation Persi Diaconis The Levi L. Conant Prize for 2012 is awarded to Persi Diaconis for his article, “The Markov chain Monte Carlo revolution” (Bulletin Amer. Math. Soc. 46 (2009), no. 2, 179–205). This wonderful article is a lively and engaging overview of modern methods in probability and statistics, and their applications. It opens with a fascinating real- life example: a prison psychologist turns up at Stanford University with encoded messages written by prisoners, and Marc Coram uses the Metropolis algorithm to decrypt them. From there, the article gets even more compelling! After a highly accessible description of Markov chains from fi rst principles, Diaconis colorfully illustrates many of the applications and venues of these ideas. Along the way, he points to some very interesting mathematics and some fascinating open questions, especially about the running time in concrete situ- ations of the Metropolis algorithm, which is a specifi c Monte Carlo method for constructing Markov chains. The article also highlights the use of spectral methods to deduce estimates for the length of the chain needed to achieve mixing. -
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 ............................................................................................