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Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
Springer A++ Viewer
PublisherInfo PublisherName : BioMed Central PublisherLocation : London PublisherImprintName : BioMed Central Ira Herskowitz dies ArticleInfo ArticleID : 4766 ArticleDOI : 10.1186/gb-spotlight-20030506-01 ArticleCitationID : spotlight-20030506-01 ArticleSequenceNumber : 118 ArticleCategory : Research news ArticleFirstPage : 1 ArticleLastPage : 4 RegistrationDate : 2003–5–6 ArticleHistory : OnlineDate : 2003–5–6 ArticleCopyright : BioMed Central Ltd2003 ArticleGrants : ArticleContext : 130594411 Brendan Maher Email: [email protected] Ira Herskowitz, professor of genetics at the University of California, San Francisco (UCSF), died at home on April 28 of pancreatic cancer. He was 56. Remembered for clarity of mind, exceptional science, enthusiastic teaching, and a love of music, his death sent a shock throughout the yeast community this week, where Herskowitz made many great contributions and friends. "It's a great loss to us all," said Paul Nurse, Nobel Laureate and new president of The Rockefeller University. "Ira Herskowitz had a huge influence on the yeast field and on me personally." Laureate Leland Hartwell, president of Fred Hutchinson Cancer Research Center told us in an e-mail, "I'll bet there are few scientists in genetics, molecular and cell biology who were not personally affected by him." Born in Brooklyn, NY, Herskowitz moved with his family about the country as father Irwin, a Drosophilageneticist, took various academic positions. Herskowitz received a bachelor's degree in science from the California Institute of Technology in 1967 and a PhD in microbiology from the Massachusetts Institute of Technology (MIT) in 1971. After a short postdoctoral stint there, he assumed an assistant professor position at the University of Oregon. Moving in 1982 to UCSF, he immediately revamped the genetics program there, chaired the department of biochemistry and biophysics from 1990 to 1995, and co-directed the program in human genetics from 1997. -
Masthead (PDF)
Proceedings of the National Academy ofPNAS Sciences of the United States of America www.pnas.org PRESIDENT OF Robert G. Roeder Geophysics John J. Mekalanos THE ACADEMY Michael Rosbash Michael L. Bender Peter Palese Ralph J. Cicerone David D. Sabatini Thomas E. Shenk Gertrud M. Schupbach Human Environmental Thomas J. Silhavy SENIOR EDITOR Robert Tjian Sciences Peter K. Vogt Solomon H. Snyder Susan Hanson Cellular and Molecular Physics ASSOCIATE EDITORS Neuroscience Immunology Anthony Leggett William C. Clark Pietro V. De Camilli Peter Cresswell Paul C. Martin Alan Fersht Richard L. Huganir Douglas T. Fearon Jack Halpern L. L. Iversen Richard A. Flavell Physiology and Jeremy Nathans Charles F. Stevens Dan R. Littman Pharmacology Thomas C. Su¨dhof Tak Wah Mak Susan G. Amara Joseph S. Takahashi William E. Paul David Julius EDITORIAL BOARD Hans Thoenen Michael Sela Ramon Latorre Ralph M. Steinman Masashi Yanagisawa Animal, Nutritional, and Chemistry Applied Microbial Sciences Stephen J. Benkovic Mathematics Plant Biology David L. Denlinger Bruce J. Berne Richard V. Kadison Maarten J. Chrispeels R. Michael Roberts Harry B. Gray Robion C. Kirby Enrico Coen Robert Haselkorn Linda J. Saif Mark A. Ratner George H. Lorimer Ryuzo Yanagimachi Barry M. Trost Medical Genetics, Hematology, and Nicholas J. Turro Anthropology Oncology Plant, Soil, and Charles T. Esmon Microbial Sciences Jeremy A. Sabloff Computer and Joseph L. Goldstein Roger N. Beachy Information Sciences Mark T. Groudine Steven E. Lindow Applied Mathematical Sciences Shafrira Goldwasser David O. Siegmund Tony Hunter M. S. Swaminathan Philip W. Majerus Susan R. Wessler Economic Sciences Newton E. Morton Applied Physical Sciences Ronald W. -
CURRICULUM VITAE George M. Weinstock, Ph.D
CURRICULUM VITAE George M. Weinstock, Ph.D. DATE September 26, 2014 BIRTHDATE February 6, 1949 CITIZENSHIP USA ADDRESS The Jackson Laboratory for Genomic Medicine 10 Discovery Drive Farmington, CT 06032 [email protected] phone: 860-837-2420 PRESENT POSITION Associate Director for Microbial Genomics Professor Jackson Laboratory for Genomic Medicine UNDERGRADUATE 1966-1967 Washington University EDUCATION 1967-1970 University of Michigan 1970 B.S. (with distinction) Biophysics, Univ. Mich. GRADUATE 1970-1977 PHS Predoctoral Trainee, Dept. Biology, EDUCATION Mass. Institute of Technology, Cambridge, MA 1977 Ph.D., Advisor: David Botstein Thesis title: Genetic and physical studies of bacteriophage P22 genomes containing translocatable drug resistance elements. POSTDOCTORAL 1977-1980 Postdoctoral Fellow, Department of Biochemistry TRAINING Stanford University Medical School, Stanford, CA. Advisor: Dr. I. Robert Lehman. ACADEMIC POSITIONS/EMPLOYMENT/EXPERIENCE 1980-1981 Staff Scientist, Molec. Gen. Section, NCI-Frederick Cancer Research Facility, Frederick, MD 1981-1983 Staff Scientist, Laboratory of Genetics and Recombinant DNA, NCI-Frederick Cancer Research Facility, Frederick, MD 1981-1984 Adjunct Associate Professor, Department of Biological Sciences, University of Maryland, Baltimore County, Catonsville, MD 1983-1984 Senior Scientist and Head, DNA Metabolism Section, Lab. Genetics and Recombinant DNA, NCI-Frederick Cancer Research Facility, Frederick, MD 1984-1990 Associate Professor with tenure (1985) Department of Biochemistry -
Curriculum Vitae Jasper Rine Address: Work Home Department of Molecular and Cellular Biology 400 Western Drive Division of Genet
Curriculum Vitae Jasper Rine Address: Work Home Department of Molecular and Cellular Biology 400 Western Drive Division of Genetics Richmond, California 94801 California Institute for Quantitative Biosciences 374A Stanley Hall 510-232-4293 University of California Birth Date: October 16, 1953 Berkeley, CA 94720-3202 Tel: 510-642-7047 Fax: 510-666-2768 Higher Education Post-doctoral Fellow 1980-1982 Stanford University School of Medicine Advisor: Ronald W. Davis University of Oregon, Ph.D. 1975-1979 Molecular Genetics Advisor: Ira Herskowitz State University of New York at Albany 1971-1975 B.S. Biological Sciences, Magna Cum Laude Professional Experience Professor of Genetics Division of Genetics, Genomics and Development Department of Molecular and Cell Biology University of California, Berkeley 1990-Present Director, Human Genome Center Lawrence Berkeley Labs Berkeley, California 1991-1994 Associate Professor of Genetics Division of Genetics Department of Molecular and Cell Biology University of California, Berkeley 1989-1990 Assistant Professor of Biochemistry Department of Biochemistry University of California, Berkeley 1982-1988 Honors/Awards N.I.H. Postdoctoral Fellowship 1980-1982 The Camille and Henry Dreyfus Teacher Scholar Award 1986 Miller Research Professor, UC Berkeley 1993 Philips Distinguished Lecturer, Haverford College 1993 American Academy of Microbiology – Fellow Election 1993 Streisinger Lecturer, University of Oregon 1993 UCB Distinguished Teaching Award 1997 Richard & Rhoda Goldman Distinguished Professor of Biology -
2009 NIH Director's Transformative Research Award Reviewers
2009 NIH Director’s Transformative Research Award Reviewers Editorial Board Members Chairs David Botstein Keith Robert Yamamoto Princeton University University of California, San Francisco Members John T. Cacioppo Myron P. Gutmann University of Chicago Inter-University Consortium for Political and Social Research Aravinda Chakravarti Johns Hopkins School of Medicine Nola M. Hylton-Watson University of California, San Francisco Garret A. Fitzgerald Cecil B. Pickett University of Pennsylvania Biogen Idec Alfred G. Gilman Susan S. Taylor University of Texas Southwestern Medical University of California at San Diego Center Michael J. Welsh University of Iowa Mail Reviewers Craig Kendall Abbey Margaret Ashcroft University of California, Santa Barbara Division of Medicine Samuel Achilefu Richard Herbert Aster School of Medicine Blood Research Institute Manuel Ares Arleen D. Auerbach University of California Rockefeller University Bruce A. Armitage J. Thomas August Carnegie Mellon University Johns Hopkins University Mark A. Arnold Kevin A. Ault University of Iowa Emory University School of Medicine David C. Aron Jennifer Bates Averill Case Western Reserve University University of New Mexico 1 Mary Helen Barcellos-Hoff Leslie A. Bruggeman New York University School of Medicine Case Western Reserve University David P. Bartel Peter Burkhard New Cambrige Center University of Connecticut Ralf Bartenschlager Alma L. Burlingame University of Heidelberg University of California, San Francisco Rashid Bashir Frederic D. Bushman University of Illinois at Urbana – Champaign University of Pennsylvania Carl A. Batt Robert William Caldwell Cornell University Medical College of Georgia Mark T. Bedford Phil Gordon Campbell Research Division Carnegie Mellon University Kevin D. Belfield Joseph Nicholas Cappella University of Central Florida University of Pennsylvania Andrew Steven Belmont William A. -
Molecular and Cellular Biology Volume 8 May 1988 Number 5
MOLECULAR AND CELLULAR BIOLOGY VOLUME 8 MAY 1988 NUMBER 5 Aaron J. Shatkin, Editor in Chief(1990) Randy W. Schekman, Editor Joan A. Steitz, Editor (1990) Center for Advanced (1992) Yale University Biotechnology and Medicine University of California New Haven, Conn. Piscataway, N.J. Berkeley Robert Tjian, Editor (1991) David J. L. Luck, Editor (1992) Louis Siminovitch, Editor (1990) University of California Rockefeller University Mount Sinai Hospital Berkeley New York, N.Y. Toronto, Canada Harold E. Varmus, Editor (1989) Steven L. McKnight, Editor (1992) University of California Carnegie Institution of Washington San Francisco Baltimore, Md. EDITORIAL BOARD Frederick W. Alt (1990) Michael Green (1988) Douglas Lowy (1990) Matthew P. Scott (1989) Susan Berget (1990) Jack F. Greenblatt (1988) Paul T. Magee (1988) Fred Sherman (1988) Arnold J. Berk (1988) Leonard P. Guarente (1988) James Manley (1989) Arthur Skoultchi (1988) Alan Bernstein (1990) Christine Guthrie (1989) Janet E. Mertz (1990) Barbara Sollner-Webb (1989) Barbara K. Birshtein (1990) James E. Haber (1990) Robert L. Metzenberg (1988) Frank Solomon (1988) J. Michael Bishop (1990) Hidesaburo Hanafusa (1989) Robert K. Mortimer (1988) Karen Sprague (1989) Michael R. Botchan (1990) Leland D. Hartwell (1990) Bernardo Nadal-Ginard (1990) Pamela Stanley (1988) David Botstein (1990) Ari Helenius (1990) Paul Neiman (1989) Nat Sternberg (1989) Bruce P. Brandhorst (1990) Ira Herskowitz (1990) Joseph R. Nevins (1990) Bruce Stiliman (1988) James R. Broach (1988) James B. Hicks (1989) Carol Newlon (1988) Kevin Struhl (1989) Joan Brugge (1988) Alan Hinnebusch (1988) Mary Ann Osley (1990) Bill Sugden (1988) Mario R. Capecchi (1990) Michael J. Holland (1990) Brad Ozanne (1989) Lawrence H. -
From Controlling Elements to Transposons: Barbara Mcclintock and the Nobel Prize Nathaniel C
454 Forum TRENDS in Biochemical Sciences Vol.26 No.7 July 2001 Historical Perspective From controlling elements to transposons: Barbara McClintock and the Nobel Prize Nathaniel C. Comfort Why did it take so long for Barbara correspondence. From these and other to prevent her controlling elements from McClintock (Fig. 1) to win the Nobel Prize? materials, we can reconstruct the events moving because their effects were difficult In the mid-1940s, McClintock discovered leading up to the 1983 prize*. to study when they jumped around. She genetic transposition in maize. She What today are known as transposable never had any inclination to pursue the published her results over several years elements, McClintock called ‘controlling biochemistry of transposition. and, in 1951, gave a famous presentation elements’. During the years 1945–1946, at Current understanding of how gene at the Cold Spring Harbor Symposium, the Carnegie Dept of Genetics, Cold activity is regulated, of course, springs yet it took until 1983 for her to win a Nobel Spring Harbor, McClintock discovered a from the operon, François Jacob and Prize. The delay is widely attributed to a pair of genetic loci in maize that seemed to Jacques Monod’s 1960 model of a block of combination of gender bias and gendered trigger spontaneous and reversible structural genes under the control of an science. McClintock’s results were not mutations in what had been ordinary, adjacent set of regulatory genes (Fig. 2). accepted, the story goes, because women stable alleles. In the term of the day, they Though subsequent studies revealed in science are marginalized, because the made stable alleles into ‘mutable’ ones. -
2020 Online Session Descriptions
Thursday, April 16 2:00 pm - 6:00 pm Mammalian Trainee Symposium Session Chairs: Fernando Pardo-Manuel de Villena, UNC Chapel Hill Linda Siracusa, Hackensack Meridian School of Medicine at Seton Hall University 538A 2:00 pm No more paywalls: cost-benefit analysis across scRNA-seq platforms reveals biological insight is reproducible at low sequencing depths. Kathryn McClelland, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK/NIH) 882C 2:15 pm Control of target gene specificity in Wnt signaling by transcription factor interactions. Aravindabharathi Ramakrishnan, University of Michigan, Ann Arbor 2217C 2:30 pm Evolutionary genomics of centromeric satellites in House Mice (Mus). Uma Arora, The Jackson Laboratory 2:45 pm Reference quality mouse genomes reveal complete strain-specific haplotypes and novel functional loci. Mohab Helmy, EMBL-EBI 887B 3:00 pm Divergence in KRAB zinc finger proteins is associated with pluripotency spectrum in mouse embryonic stem cells. Candice Byers Jackson Laboratory 531C 3:15 pm Replicability and reproducibility of genetic analysis between different studies using identical Collaborative Cross inbred mice. UNC CHAPEL HILL 3:30 pm Proteomics reveals the role of translational regulation in ES cells. Selcan Aydin, The Jackson Laboratory for Mouse Genetics 563B 3:45 pm Super-Mendelian inheritance mediated by CRISPR–Cas9 in the female mouse germline. Hannah Grunwald, University of California San Diego 2103C 4:00 pm Gene Editing ELANE in Human Hematopoietic Stem and Progenitor Cells Reveals Variant Pathogenicity and Therapeutic Strategies for Severe Congenital Neutropenia. Shuquan Rao, Boston Childrens Hospital 4:15 pm Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression. -
David Botstein 2015 Book.Pdf
Princeton University HONORS FACULTY MEMBERS RECEIVING EMERITUS STATUS May 2015 The biographical sketches were written by colleagues in the departments of those honored. Copyright © 2015 by The Trustees of Princeton University 550275 Contents Faculty Members Receiving Emeritus Status 2015 Steven L. Bernasek .......................3 David Botstein...........................6 Erhan Çinlar ............................8 Caryl Emerson.......................... 11 Christodoulos A. Floudas ................. 15 James L. Gould ......................... 17 Edward John Groth III ...................20 Philip John Holmes ......................23 Paul R. Krugman .......................27 Bede Liu .............................. 31 Alan Eugene Mann ......................33 Joyce Carol Oates .......................36 Clarence Ernest Schutt ...................39 Lee Merrill Silver .......................41 Thomas James Trussell ...................43 Sigurd Wagner .........................46 { 1 } { 2 } David Botstein avid Botstein was educated at Harvard (A.B. 1963) and the D University of Michigan (Ph.D. 1967). He joined the faculty of the Massachusetts Institute of Technology, rising through the ranks from instructor to professor of genetics. In 1987, he moved to Genentech, Inc. as vice president–science, and, in 1990, he joined Stanford University’s School of Medicine, where he was chairman of the Department of Genetics. In July, 2003 he became director of the Lewis-Sigler Institute for Integrative Genomics and the Anthony B. Evnin ’62 Professor of Genomics at Princeton University. David’s research has centered on genetics, especially the use of genetic methods to understand biological functions. His early work in bacterial genetics contributed to the discovery of transposable elements in bacteria and an understanding of their physical structures and genetic properties. In the early 1970s, he turned to budding yeast (Saccharomyces cerevisiae) and devised novel genetic methods to study the functions of the actin and tubulin cytoskeletons. -
Celebrating Years of 60Science Welcome to the 60Th Anni- Versary Symposium of the Miller Institute
Celebrating Years of 60Science Welcome to the 60th Anni- versary Symposium of the Miller Institute. In an age of ever increasing special- ization, the Miller Institute stands apart as one of the very few enterprises to embrace all of Science as its purview. For 60 years the Miller Institute has provided generous sup- port to some of the lead- ing postdoctoral fellows in all fields of science, has supported extended visits from famous scientists from around the world, and has provided critical adminis- trative and teaching relief for Berkeley faculty at par- ticularly important points in their career. This grand tradition lives on, even in the face of ever-greater challenges, with a refresh- ing emphasis on clarity in cross-discipline communi- cation. We have assembled a panel of eight luminaries drawn from past and pres- ent members of the Miller Institute each of whom leads their field with cre- ative research at the fron- tiers of human knowledge. So relax, enjoy, and be sure to ask that question that you always wanted to have answered. Jasper Rine, Professor of Genetics and Developmental Biology Chair, Miller Institute 60th 60th Anniversary Agenda Friday, January 15 – Sunday, January 17, 2016 Friday evening - Alumni House 5:00 - 7:00 Reception Saturday – Stanley Hall 8:00 - 8:45 Registration 8:45 - 9:00 Welcome 9:00 - 11:45 Maha Mahadevan: “On growth and form: geometry, physics and biology” Alice Guionnet: “About Universal Laws” Roger Bilham: “Earthquakes and Money: Frail Buildings, Philanthropic Engineers and a Few Corrupt Bad Guys -
Annual Rpt 2004 For
I N S T I T U T E for A D V A N C E D S T U D Y ________________________ R E P O R T F O R T H E A C A D E M I C Y E A R 2 0 0 3 – 2 0 0 4 EINSTEIN DRIVE PRINCETON · NEW JERSEY · 08540-0631 609-734-8000 609-924-8399 (Fax) www.ias.edu Extract from the letter addressed by the Institute’s Founders, Louis Bamberger and Mrs. Felix Fuld, to the Board of Trustees, dated June 4, 1930. Newark, New Jersey. It is fundamental in our purpose, and our express desire, that in the appointments to the staff and faculty, as well as in the admission of workers and students, no account shall be taken, directly or indirectly, of race, religion, or sex. We feel strongly that the spirit characteristic of America at its noblest, above all the pursuit of higher learning, cannot admit of any conditions as to personnel other than those designed to promote the objects for which this institution is established, and particularly with no regard whatever to accidents of race, creed, or sex. TABLE OF CONTENTS 4·BACKGROUND AND PURPOSE 7·FOUNDERS, TRUSTEES AND OFFICERS OF THE BOARD AND OF THE CORPORATION 10 · ADMINISTRATION 12 · PRESENT AND PAST DIRECTORS AND FACULTY 15 · REPORT OF THE CHAIRMAN 20 · REPORT OF THE DIRECTOR 24 · OFFICE OF THE DIRECTOR - RECORD OF EVENTS 31 · ACKNOWLEDGMENTS 43 · REPORT OF THE SCHOOL OF HISTORICAL STUDIES 61 · REPORT OF THE SCHOOL OF MATHEMATICS 81 · REPORT OF THE SCHOOL OF NATURAL SCIENCES 107 · REPORT OF THE SCHOOL OF SOCIAL SCIENCE 119 · REPORT OF THE SPECIAL PROGRAMS 139 · REPORT OF THE INSTITUTE LIBRARIES 143 · INDEPENDENT AUDITORS’ REPORT 3 INSTITUTE FOR ADVANCED STUDY BACKGROUND AND PURPOSE The Institute for Advanced Study was founded in 1930 with a major gift from New Jer- sey businessman and philanthropist Louis Bamberger and his sister, Mrs.