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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]. -
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 -
From the President's Desk
JAN/FEB 2006 From the President’s desk: 2006, the 75th anniversary of the Genetics Society of America, will be marked by a number of initiatives to reinvigorate the Society’s mission of promoting research and education in genetics. A highlight was the recently held GSA sponsored conference, “Genetic Analysis: From Model Organisms to Human Biology” in San Diego from January 5-7. This conference emphasized the importance of model organism research by illustrating the crucial contributions to human biology resulting from discoveries in these organisms. The National Institutes of Health (NIH) supported this conference both financially and by participation of key NIH administrators, including Jeremy M. Berg, director of the National Institute of General Medical Sciences. In addition to the superb science talks by international leaders the MOHB conference showcased other important and new GSA initiatives including education, public policy advocacy, graduate student support and recognition of outstanding model organism geneticists. Robin Wright, Education Committee chair, led a round table discussion on undergraduate education and the Joint Steering Committee for Public Policy and the Congressional Liaison Committee sponsored a session on science advocacy and public policy. There was a mentor lunch to support graduate students and postdocs in the next steps of their careers, and the three GSA medals were presented during the banquet, with Victor Ambros receiving the GSA Medal, Fred Sherman the Beadle Award, and Masatoshi Nei the Morgan Award. (For research highlights at the meeting, see pages 6 and 7 of this issue.) The 75th anniversary will also usher in changes to our society’s journal, GENETICS. -
Fred Sherman: a Pioneer in Genetics
CLASS NOTES TRIBUTE Fred Sherman: A Pioneer in Genetics Fred Sherman, a pioneer in genetics and long hours of laboratory work, large doses mance of Indian dance (dance was a major molecular biology, was a member of the of Fred’s zany humor, and after-hours interest and activity of Fred’s), his thoughts Rochester faculty for 52 years, from 1961 sampling of the local night-life. It provided and conversation quickly returned to yeast. until his death last September. The breadth an introduction to yeast for many scientists His encyclopedic memory of 50 years of of his scientific contributions over the span who went on to become leaders in modern yeast genetics included much information of years that saw the development of that was never published and is now, modern molecular biology is simply sadly, lost. Fortunately, his engagement breathtaking. Fred’s early scientific with science was tempered by humor studies focused on the gene encoding that found expression both in a staple the protein cytochrome c in baker’s of often-repeated jokes for every occa- yeast, establishing this as a power- sion and in carefully crafted comedic ful system that allowed him to make remarks that he proffered in the guise fundamental contributions to the initial of questions and comments at scientific deciphering of the genetic code. His seminars. He semi-seriously referred to determination of the DNA sequence himself as the world’s expert in yeast of the gene encoding cytochrome c, genetic nomenclature, and once tried one of the first eukaryotic genes to be to win a dispute with an editor about sequenced, served as the basis for the the naming of a particular yeast gene first cloning of a gene from a eukary- by announcing that he had tattooed otic organism. -
Molecular and Cellular Biology
MOLECULAR AND CELLULAR BIOLOGY VOLUME 3 * NUMBER 1 o JANUARY 1983 Aaron J. Shatkin, Editor-in-Chief (1985) Roche Instituite of Molecular Biology Nutlex, N.J. Harvey F. Lodish, Editor (1986) Louis Siminovitch, Editor (1985) Massachuisetts Institute of Technology Hospital for Sick Children Cambridge Toronto, Canadal David J. L. Luck, Editor (1987) Paul S. Sypherd, Editor (1985) Rockefeller Unis'ersity University of California Ness York, N.Y. Irvine EDITORIAL BOARD Renato Baserga (1985) Ira Herskowitz (1984) Daniel B. Rifkin (1985) Alan Bernstein (1984) Larry Kedes (1985) Robert G. Roeder (1985) J. Michael Bishop (1984) Marilyn Kozak (1985) James E. Rothman (1984) Joan Brugge (1985) Elias Lazarides (1985) David Sabatini (1985) Breck Byers (1985) John B. Little (1985) Phillip A. Sharp (1985) John A. Carbon (1984) William F. Loomis, Jr. (1985) Fred Sherman (1985) Lawrence A. Chasin (1985) Paul T. Magee (1985) Pamela Stanley (1985) Nam-Hai Chua (1985) Robert L. Metzenberg (1985) Joan A. Steitz (1985) Terrance G. Cooper (1984) Robert K. Mortimer (1985) James L. Van Etten (1985) James E. Darnell, Jr. (1985) Harvey L. Ozer (1985) Jonathan R. Warner (1984) Gary Felsenfeld (1985) Mary Lou Pardue (1985) Robert A. Weinberg (1984) Norton B. Gilula (1985) Mark Pearson (1985) I. Bernard Weinstein (1985) James E. Haber (1984) Jeremy Pickett-Heaps (1985) Harold Weintraub (1985) Benjamin Hall (1985) Robert E. Pollack (1985) Reed B. Wickner (1985) Ari Helenius (1984) Keith R. Porter (1985) Leslie Wilson (1985) Susan A. Henry (1985) John R. Pringle (1985) Edward Ziff (1985) Helen R. Whiteley, Chairman, Publications Board Walter G. Peter III, Director, Puiblications Linda M. -
Profile of Gary Ruvkun
PROFILE Profile of Gary Ruvkun wash in the faint glow of a fluo- Brush with Molecular Biology rescent lamp, a pair of serpentine The story of Ruvkun’s metamorphosis Anematode worms lie on a Petri from a keen undergraduate into a leading plate, their see-through bodies light in his field of study begins at Har- magnified 100-fold by one of several vard University, where he enrolled in microscopes arrayed in a darkened bay in a Ph.D. program in 1976 upon returning National Academy of Sciences member to the United States. Like many other Gary Ruvkun’s laboratory at Massachu- scientific institutions across the world in setts General Hospital. While one of the the mid-1970s, Harvard was astir with the worms wiggles its way around the plate, promise of recombinant DNA technol- the other shows no signs of life, ogy, and Ruvkun wasted no time em- its midsection ruptured and its innards bracing its tools. “My undergraduate strewn asunder. A filter slides into place, education had not prepared me at all for and the worms are bathed in a dull recombinant DNA, but I immersed my- green haze. The wiggling worm has a bea- self into its culture at Harvard, much of con of nerve cells in its head, the ganglia which was James Watson’s creation from lit up by a genetic trick that has rescued a decade earlier,” Ruvkun says. Propelled the worm from death; its neighbor wears Gary Ruvkun. by a desire to be a part of the culture of no such beacon. The worms were deprived basic molecular biology, all while per- of a tiny RNA molecule, called a micro- forming science with the potential to im- RNA, which helps shepherd them through not 5-year-old children. -
Fred Sherman an Introduction to the Genetics and Molecular
Fred Sherman An Introduction to the Genetics and Molecular Biology of the Yeast Saccharomyces cerevisiae. (2001) http://dbb.urmc.rochester.edu/labs/sherman_f/yeast/index.html Table of Contents • 1 Yeast as a Model Eukaryote • 11 Manipulating the Genome In • 2 Information on Yeast Vitro with Plasmids • 3 Yeast Strains 11.1 Cloning by Complementation • 4 Growth and Life Cycles 11.2 Mutagenesis In Vitro • 5 The Yeast Genome 11.3 Two-step Gene Replacement • 6 Genetic Nomenclature 11.4 Gene Disruption and One-step 6.1 Chromosomal Genes Gene Replacement 6.2 Mitochondrial Gene 11.5 Plasmid Shuffle 6.3 Non-Mendelian Determinants 11.6 Recovering mutant alleles • 7 Genetic Analyses • 12 Interactions of Genes 7.1 Overviews with Examples 12.1 Heterozygosity and Dominant- 7.2 Tetrad Analysis negative Mutations 7.3 Non-Mendelian Inheritance 12.2 Intragenic Complementation • 8 Transformation 12.3 Nonallelic Non- 8.1 Yeast Vector and DNA complementation Fragments 12.4 Suppressors 8.2 Synthetic Oligonucleotides 12.5 Synthetic Enhancement and 8.3 Mitochondrial Transformation Epistatic Relationships • 9 Yeast Vectors • 13 Genomic Analysis 9.1 YIp Vectors • 14 Analyses with Yeast Systems 9.2 YEp Vectors 14.1 Two-hybrid Systems 9.3 YCp Vectors 14.2 Yeast Artificial Chromosomes • 10 Genes Important for Genetic (YACs) Studies 14.3 Expression of Heterologous 10.1 URA3 and LYS2 Protein in Yeast 10.2 ADE1 and ADE2 • Key Words 10.3 GAL1 Promoter • Bibliography 10.4 lacZ and Other Reporters 1 1 Yeast is a Model Eukaryote mutations can be conveniently isolated and manifested in haploid strains, and This chapter deals only with the yeast S. -
2008 Harvard / Paul F
The 2008 Harvard / Paul F. Glenn Symposium on Aging June 23, 2008 Paul F. Glenn Laboratories for the Biological Mechanisms of Aging Welcome to the 3rd Annual Harvard/Paul F. Glenn Symposium on Aging. Each year, the Paul F. Glenn Laboratories host the Harvard Symposium on Aging with a mission to educate the wider research community about advancements in this fast-paced field and to stimulate collaborative research in this area. We have been fortunate to have many of the leaders in the aging field speak at these symposia. As a result, attendees come not only from the Harvard research community but from across the nation and from overseas for this one day event. We are glad you could join us here today. The reasons for accelerating research molecular biology of aging are clear. First and foremost, the number of aged individuals in developed countries is growing rapidly, which is going to place an unprecedented burden on the families and the economies of those nations. Because chronic illness in the elderly is a major medical cost, enormous savings would be achieved if mortality and morbidity could be compressed within a shorter duration of time at the end of life. A study by the RAND Corporation in 2006 concluded that advances in medicine arising from aging research would be 10-100 times more cost-effective than any other medical breakthrough. Advances in aging research have shown that it is possible to extend the healthy lifespan of laboratory animals through genetic and pharmacological means. Many leaders in the aging field predict that significant strides will be made in understanding how human health and lifespan are regulated, leading to novel medicines to forestall and treat diseases of aging such as diabetes, cancer, Alzheimer’s and heart disease. -
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. -
Differential Regulation of the Duplicated Isocytochrome C Genes in Yeast (Yeast Regulation/Heme Deficiency/Glucose Repression/Cytochrome C Regulation) THOMAS M
Proc. NatI. Acad. Sci. USA Vol. 81, pp. 4475-4479, July 1984 Genetics Differential regulation of the duplicated isocytochrome c genes in yeast (yeast regulation/heme deficiency/glucose repression/cytochrome c regulation) THOMAS M. LAZ, DENNIS F. PIETRAS, AND FRED SHERMAN Departments of Biochemistry and of Radiation Biology and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642 Communicated by Herschel L. Roman, March 26, 1984 ABSTRACT The two unlinked genes CYCI and CYC7 en- acid (ALA) synthetase (10, 12); since ALA is an intermedi- code iso-l-cytochrome c and iso-2-cytochrome c, respectively, ate in the biosynthesis of heme, hemi mutants are deficient in the yeast Saccharomyces cerevisiae. An examination of the in heme and all heme-containing proteins, including the iso- steady-state level of CYCI and CYC7 mRNAs in normal and cytochromes c. In contrast, the CYC2 and CYC3 genes ap- mutant strains grown under different conditions, along with pear to affect only the isocytochromes c. These mutants may previous results of apoprotein levels, demonstrate that CYCI be involved in some aspect of the enzymatic attachment of a and CYC7 have similar and different modes of regulation. heme to the apoisocytochromes c or the transport of the apo- Both CYCI and CYC7 mRNAs are diminished after anaerobic cytochromes c into the mitochondria (9). Whereas hemi and growth. In contrast, CYCI mRNA but not CYC7 mRNA is de- cyc3 mutations can completely block the isocytochrome c creased by heme deficiency in hem) mutants. Although both production, the cyc2 mutation can block at most only 90% of CYCI and CYC7 mRNAs are substantially lowered after the isocytochromes c. -
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.