Ambros, Baulcombe, and Ruvkun Share $500,000 Gruber Genetics
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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]. -
USA Education Ph.D., Biology, Massachusetts Institute of Tech
Victor R. Ambros, Ph.D. Silverman Professor of Natural Sciences Program in Molecular Medicine University of Massachusetts Medical School373 Plantation Street, Suite 306 Worcester, MA 01605 (508) 856-6380 [email protected] Personal Born: Hanover, NH, USA on December 1, 1953 Citizenship: USA Education Ph.D., Biology, Massachusetts Institute of Technology, Cambridge, MA 1976-1979 Thesis Title: The protein covalently linked to the 5' end of poliovirus RNA Advisor: Dr. David Baltimore B.S., Biology, Massachusetts Institute of Technology, Cambridge, MA 1971-1975 Professional Appointments Silverman Professor of Natural Sciences 2009-present Co-Director, RNA Therapeutics Institute 2009-2016 Professor, Program in Molecular Medicine 2008-present University of Massachusetts Medical School, Worcester, MA Professor of Genetics, Dartmouth Medical School 2001-2007 Professor, Biological Sciences, Dartmouth Medical School 1996-2001 Associate Professor, Biological Sciences, Dartmouth Medical School 1992-1996 Associate Professor, Department of Cellular and Development Biology, 1988-1992 Harvard University, Cambridge, MA Assistant Professor, Department of Cellular and Development Biology, 1985-1988 Harvard University, Cambridge, MA Postdoctoral Research 1979-1985 Supervisor: Dr. H. Robert Horvitz Massachusetts Institute of Technology, Cambridge, MA Graduate Research 1976-1979 Supervisor: Dr. David Baltimore Massachusetts Institute of Technology, Cambridge, MA Research Assistant 1975-1976 Supervisor: Dr. David Baltimore Center for Cancer Research, -
ERC Advanced Grant 2008 Project Acronym Title Principal Investigator Host Institution Host Country 226037 NSYS Nonlinear System
ERC Advanced Grant 2008 Project Acronym Title Principal Investigator Host Institution Host Country Nonlinear System Identification and Analysis in the Time, Prof. Stephen Alec 226037 NSYS THE UNIVERSITY OF SHEFFIELD UK Frequency, and Spatio-Temporal Domains Billings HOWTOCONT Search for mechanisms to control massless electrons in 226043 ROLGRAPHE Prof. Carlo Beenakker UNIVERSITEIT LEIDEN. NL graphene NE THE HEBREW UNIVERSITY OF 226135 EXPANDERS Expander Graphs in Pure and Applied Mathematics Prof. Alexander Lubotzky IL JERUSALEM. 226136 VISCHEM Visualizing Molecular Change Prof. Villy Sundström LUNDS UNIVERSITET SE Consistent computation of the chemistry-cloud THE CYPRUS RESEARCH AND 226144 C8 Prof. Johannes Lelieveld CY continuum and climate change in Cyprus EDUCATIONAL FOUNDATION Modern Approaches to Temperature Reconstructions in 226172 MATRICS Dr. Hubertus Fischer UNIVERSITAET BERN CH polar Ice Cores FUndamental studies and innovative appROaches of Prof. Roland Martin 226180 FURORE UNIVERSITAET HAMBURG DE REsearch on magnetism Wiesendanger EBERHARD KARLS 226187 SOCATHES Solid State/Cold Atom Hybrid Quantum Devices Prof. Reinhold Kleiner DE UNIVERSITAET TUEBINGEN KUNGLIGA TEKNISKA 226203 APPROXNP Approximation of NP-hard optimization problems Prof. Johan Håstad SE HOEGSKOLAN Patchy colloidal particles: a powerful arsenal for the PATCHYCOLL fabrication of tomorrow new super-molecules . A UNIVERSITA DEGLI STUDI DI 226207 Prof. Francesco Sciortino IT OIDS theoretical and numerical study of their assembly ROMA LA SAPIENZA processes. ERC Advanced Grant 2008 Analytic Techniques for Geometric and Functional UNIVERSITA DEGLI STUDI DI 226234 ANTEGEFI Prof. Nicola Fusco IT Inequalities NAPOLI FEDERICO II. Multiscale Models for Catalytic-Reaction-Coupled 226238 MMFCS Prof. Bengt Sundén LUNDS UNIVERSITET SE Transport Phenomena in Fuel Cells WEIZMANN INSTITUTE OF 226246 NANOSQUID Scanning Nano-SQUID on a Tip Prof. -
Nature Medicine Essay
COMMENTARY LASKER BASIC MEDICAL RESEARCH AWARD Of maize and men, or peas and people: case histories to justify plants and other model systems David Baulcombe One of the byproducts of molecular biology cork is altogether filled with air, and that air is has been support for the ‘model system’ con- perfectly enclosed in little boxes or cells distinct cept. All living organisms are based on the same from one another.”)2 (Fig. 1). Two hundred fifty genetic code, they have similar subcellular years later, Beijerinck discovered a contagium structures and they use homologous metabolic vivum fluidum in extracts of diseased tobacco pathways. So, mechanisms can be investigated plants that he later referred to as a virus3. using organisms other than those in which In contemporary science, a green alga— the knowledge will be exploited for practical Chlamydomonas reinhardtii—is a useful model benefit. Model systems are particularly use- in the analysis of kidney disease4. However, ful in the early discovery phase of a scientific in this article, I refer to the contribution of endeavor, and recent progress in biomedical plant biology to a family of mechanisms that I science has fully vindicated their use. Jacques refer to as RNA silencing. This topic has been Monod, for example, famously justified his reviewed comprehensively elsewhere5,6, so here work on a bacterial model system by stating I focus on personal experience and my view of that “what is true for Escherichia coli is also future potential from this work. true for elephants.” My fellow laureates, Victor Ambros and Gary Ruvkun, can defend the use The early history of RNA silencing in of the worm Caenorhabditis elegans as a good plants model system and so I will focus on plants. -
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 -
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. -
3718 Issue63july2010 1.Pdf
Issue 63.qxd:Genetic Society News 1/10/10 14:41 Page 1 JULYJULLYY 2010 | ISSUEISSUE 63 GENETICSGENNETICSS SOCIETYSOCIEETY NENEWSEWS In this issue The Genetics Society NewsNewws is edited by U Genetics Society PresidentPresident Honoured Honoured ProfProf David Hosken and items ittems for future future issues can be sent to thee editor,editor, preferably preferably U Mouse Genetics Meeting by email to [email protected],D.J.Hosken@@exeter.ac.uk, or U SponsoredSponsored Meetings Meetings hardhard copy to Chair in Evolutionary Evoolutionary Biology, Biology, UniversityUniversity of Exeter,Exeter, Cornwall Cornnwall Campus, U The JBS Haldane LectureLecture Tremough,Tremough, Penryn, TR10 0 9EZ UK.UK. The U Schools Evolutionn ConferenceConference Newsletter is published twicet a year,year, with copy dates of 1st June andand 26th November.November. U TaxiTaxi Drivers The British YeastYeaste Group Group descend on Oxford Oxford for their 2010 meeting: m see the reportreport on page 35. 3 Image © Georgina McLoughlin Issue 63.qxd:Genetic Society News 1/10/10 14:41 Page 2 A WORD FROM THE EDITOR A word from the editor Welcome to issue 63. In this issue we announce a UK is recognised with the award of a CBE in the new Genetics Society Prize to Queen’s Birthday Honours, tells us about one of Welcome to my last issue as join the medals and lectures we her favourite papers by Susan Lindquist, the 2010 editor of the Genetics Society award. The JBS Haldane Mendel Lecturer. Somewhat unusually we have a News, after 3 years in the hot Lecture will be awarded couple of Taxi Drivers in this issue – Brian and seat and a total of 8 years on annually to recognise Deborah Charlesworth are not so happy about the committee it is time to excellence in communicating the way that the print media deals with some move on before I really outstay aspects of genetics research to scientific issues and Chris Ponting bemoans the my welcome! It has been a the public. -
Fire Departments of Pathology and Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Room L235, Stanford, CA 94305-5324, USA
GENE SILENCING BY DOUBLE STRANDED RNA Nobel Lecture, December 8, 2006 by Andrew Z. Fire Departments of Pathology and Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Room L235, Stanford, CA 94305-5324, USA. I would like to thank the Nobel Assembly of the Karolinska Institutet for the opportunity to describe some recent work on RNA-triggered gene silencing. First a few disclaimers, however. Telling the full story of gene silencing would be a mammoth enterprise that would take me many years to write and would take you well into the night to read. So we’ll need to abbreviate the story more than a little. Second (and as you will see) we are only in the dawn of our knowledge; so consider the following to be primer... the best we could do as of December 8th, 2006. And third, please understand that the story that I am telling represents the work of several generations of biologists, chemists, and many shades in between. I’m pleased and proud that work from my labo- ratory has contributed to the field, and that this has led to my being chosen as one of the messengers to relay the story in this forum. At the same time, I hope that there will be no confusion of equating our modest contributions with those of the much grander RNAi enterprise. DOUBLE STRANDED RNA AS A BIOLOGICAL ALARM SIGNAL These disclaimers in hand, the story can now start with a biography of the first main character. Double stranded RNA is probably as old (or almost as old) as life on earth. -
Unfolding Plant Disease Resistance : the Involvement of HSP90 and Its Co- Chaperone PP5 in I-2-Mediated Signalling De La Fuente Van Bentem, S
UvA-DARE (Digital Academic Repository) Unfolding plant disease resistance : the involvement of HSP90 and its co- chaperone PP5 in I-2-mediated signalling de la Fuente van Bentem, S. Publication date 2005 Document Version Final published version Link to publication Citation for published version (APA): de la Fuente van Bentem, S. (2005). Unfolding plant disease resistance : the involvement of HSP90 and its co-chaperone PP5 in I-2-mediated signalling. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:05 Oct 2021 Unfolding plant disease resistance the involvement of HSP90 and its co-chaperone PP5 in I-2-mediated signalling ACADEMISCH PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Universiteit van Amsterdam, op gezag van de Rector Magnificus prof. -
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.