1993 Human Genome Program Report
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Plant Pangenome: Impacts on Phenotypes and Evolution Christine Tranchant-Dubreuil, Mathieu Rouard, Francois Sabot
Plant Pangenome: Impacts On Phenotypes And Evolution Christine Tranchant-Dubreuil, Mathieu Rouard, Francois Sabot To cite this version: Christine Tranchant-Dubreuil, Mathieu Rouard, Francois Sabot. Plant Pangenome: Im- pacts On Phenotypes And Evolution. Annual Plant Reviews, Wiley Online Library 2019, 10.1002/9781119312994.apr0664. hal-02053647 HAL Id: hal-02053647 https://hal.archives-ouvertes.fr/hal-02053647 Submitted on 1 Mar 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright Plant Pangenome: Impacts On Phenotypes And Evolution Christine Tranchant-Dubreuil1,3, Mathieu Rouard2,3, and Francois Sabot1,3 1DIADE University of Montpellier, IRD, 911 Avenue Agropolis, 34934 Montpellier Cedex 5, France 2Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France 3South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, Montpellier, France With the emergence of low-cost high-throughput sequencing all the genes from a given species are not obtained using a technologies, numerous studies have shown that a single genome single genome (10–12). In plants, evidence first from maize is not enough to identify all the genes present in a species. Re- (13, 14) showed that only half of the genomic structure is cently, the pangenome concept has become widely used to in- conserved between two individuals. -
Algorithms for Computational Biology 8Th International Conference, Alcob 2021 Missoula, MT, USA, June 7–11, 2021 Proceedings
Lecture Notes in Bioinformatics 12715 Subseries of Lecture Notes in Computer Science Series Editors Sorin Istrail Brown University, Providence, RI, USA Pavel Pevzner University of California, San Diego, CA, USA Michael Waterman University of Southern California, Los Angeles, CA, USA Editorial Board Members Søren Brunak Technical University of Denmark, Kongens Lyngby, Denmark Mikhail S. Gelfand IITP, Research and Training Center on Bioinformatics, Moscow, Russia Thomas Lengauer Max Planck Institute for Informatics, Saarbrücken, Germany Satoru Miyano University of Tokyo, Tokyo, Japan Eugene Myers Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Marie-France Sagot Université Lyon 1, Villeurbanne, France David Sankoff University of Ottawa, Ottawa, Canada Ron Shamir Tel Aviv University, Ramat Aviv, Tel Aviv, Israel Terry Speed Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia Martin Vingron Max Planck Institute for Molecular Genetics, Berlin, Germany W. Eric Wong University of Texas at Dallas, Richardson, TX, USA More information about this subseries at http://www.springer.com/series/5381 Carlos Martín-Vide • Miguel A. Vega-Rodríguez • Travis Wheeler (Eds.) Algorithms for Computational Biology 8th International Conference, AlCoB 2021 Missoula, MT, USA, June 7–11, 2021 Proceedings 123 Editors Carlos Martín-Vide Miguel A. Vega-Rodríguez Rovira i Virgili University University of Extremadura Tarragona, Spain Cáceres, Spain Travis Wheeler University of Montana Missoula, MT, USA ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notes in Bioinformatics ISBN 978-3-030-74431-1 ISBN 978-3-030-74432-8 (eBook) https://doi.org/10.1007/978-3-030-74432-8 LNCS Sublibrary: SL8 – Bioinformatics © Springer Nature Switzerland AG 2021 This work is subject to copyright. -
Michael S. Waterman: Breathing Mathematics Into Genes >>>
ISSUE 13 Newsletter of Institute for Mathematical Sciences, NUS 2008 Michael S. Waterman: Breathing Mathematics into Genes >>> setting up of the Center for Computational and Experimental Genomics in 2001, Waterman and his collaborators and students continue to provide a road map for the solution of post-genomic computational problems. For his scientific contributions he was elected fellow or member of prestigious learned bodies like the American Academy of Arts and Sciences, National Academy of Sciences, American Association for the Advancement of Science, Institute of Mathematical Statistics, Celera Genomics and French Acadèmie des Sciences. He was awarded a Gairdner Foundation International Award and the Senior Scientist Accomplishment Award of the International Society of Computational Biology. He currently holds an Endowed Chair at USC and has held numerous visiting positions in major universities. In addition to research, he is actively involved in the academic and social activities of students as faculty master Michael Waterman of USC’s International Residential College at Parkside. Interview of Michael S. Waterman by Y.K. Leong Waterman has served as advisor to NUS on genomic research and was a member of the organizational committee Michael Waterman is world acclaimed for pioneering and of the Institute’s thematic program Post-Genome Knowledge 16 fundamental work in probability and algorithms that has Discovery (Jan – June 2002). On one of his advisory tremendous impact on molecular biology, genomics and visits to NUS, Imprints took the opportunity to interview bioinformatics. He was a founding member of the Santa him on 7 February 2007. The following is an edited and Cruz group that launched the Human Genome Project in enhanced version of the interview in which he describes the 1990, and his work was instrumental in bringing the public excitement of participating in one of the greatest modern and private efforts of mapping the human genome to their scientific adventures and of unlocking the mystery behind completion in 2003, two years ahead of schedule. -
Taxonomic Classifiers IMPRS Lecture – Maxime Borry
Taxonomic classifiers IMPRS Lecture – Maxime Borry 1 Why do I care ? DNA Endogenous Other To extract information from the 90% ”other”, you need a taxonomic classifier to answer the question: Who is there ? 10% 90% Maxime Borry 2 What is a taxonomic classifier ? Fastq preprocessing Taxonomic classifier List of DB matches LCA if ambiguity List of taxon in Fastq Maxime Borry 3 Why not species classifier ? • Species level assignation is not always possible. P R • Possibility of hits in different species E C • Ambiguities solved by LCA (Lowest E S Common Ancestor) algorithm. I O N Maxime Borry 4 LCA example Hit Identity Pan paniscus 97% Pan troglodytes 96% Homo sapiens 92% LCA 95% Pan Gorilla gorilla 87% LCA 90% Hominini LCA 85% Homininae Maxime Borry 5 Taxonomic classifiers overview Reference Strategy Query Strategy Single Locus Alignment free Algorithm Multi Locus Alignment based Whole Genome DNA to DNA Data type DNA to Protein Maxime Borry 6 Reference strategy: single locus PCR WGS (Also known as Amplicon metataxonomics, Phylotyping, Metabarcoding) Targeted amplification and deep sequencing of clade-universal gene • Amplification of locus by PCR with primers targeting conserved regions or directly from WGS Hypevariable region • (Deep) Sequencing of amplicons • Comparison to reference marker database Conserved region Maxime Borry 7 Side note: vocabulary matters ! (to some) Metataxonomics vs Metagenomics Maxime Borry 8 Single locus marker genes for bacteria: 16s 50s 30s 16s rRNA - Part of the 30s prokaryotic ribosome subunit - Stems are more stable -> conserved - Loops are mutating faster -> variable Yang, B., Wang, Y., & Qian, P. Y. (2016). Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. -
Celebrating 40 Years of Rita Allen Foundation Scholars 1 PEOPLE Rita Allen Foundation Scholars: 1976–2016
TABLE OF CONTENTS ORIGINS From the President . 4 Exploration and Discovery: 40 Years of the Rita Allen Foundation Scholars Program . .5 Unexpected Connections: A Conversation with Arnold Levine . .6 SCIENTIFIC ADVISORY COMMITTEE Pioneering Pain Researcher Invests in Next Generation of Scholars: A Conversation with Kathleen Foley (1978) . .10 Douglas Fearon: Attacking Disease with Insights . .12 Jeffrey Macklis (1991): Making and Mending the Brain’s Machinery . .15 Gregory Hannon (2000): Tools for Tough Questions . .18 Joan Steitz, Carl Nathan (1984) and Charles Gilbert (1986) . 21 KEYNOTE SPEAKERS Robert Weinberg (1976): The Genesis of Cancer Genetics . .26 Thomas Jessell (1984): Linking Molecules to Perception and Motion . 29 Titia de Lange (1995): The Complex Puzzle of Chromosome Ends . .32 Andrew Fire (1989): The Resonance of Gene Silencing . 35 Yigong Shi (1999): Illuminating the Cell’s Critical Systems . .37 SCHOLAR PROFILES Tom Maniatis (1978): Mastering Methods and Exploring Molecular Mechanisms . 40 Bruce Stillman (1983): The Foundations of DNA Replication . .43 Luis Villarreal (1983): A Life in Viruses . .46 Gilbert Chu (1988): DNA Dreamer . .49 Jon Levine (1988): A Passion for Deciphering Pain . 52 Susan Dymecki (1999): Serotonin Circuit Master . 55 Hao Wu (2002): The Cellular Dimensions of Immunity . .58 Ajay Chawla (2003): Beyond Immunity . 61 Christopher Lima (2003): Structure Meets Function . 64 Laura Johnston (2004): How Life Shapes Up . .67 Senthil Muthuswamy (2004): Tackling Cancer in Three Dimensions . .70 David Sabatini (2004): Fueling Cell Growth . .73 David Tuveson (2004): Decoding a Cryptic Cancer . 76 Hilary Coller (2005): When Cells Sleep . .79 Diana Bautista (2010): An Itch for Knowledge . .82 David Prober (2010): Sleeping Like the Fishes . -
Program Book PACIFIC SYMPOSIUM on BIOCOMPUTING 2018 Big Island of Hawaii, January 3-7, 2018
Pacific Symposium on Biocomputing 2018 January 3-7, 2018 Big Island of Hawaii Program Book PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018 Big Island of Hawaii, January 3-7, 2018 Welcome to PSB 2018! We have prepared this program book to give you quick access to information you need for PSB 2018. Enclosed you will find • Logistics information • Menus for PSB hosted meals • Full conference schedule • Call for Session and Workshop Proposals for PSB 2019 • Poster/abstract titles and authors • Participant List Conference materials are also available online at http://psb.stanford.edu/conference-materials/. PSB 2018 gratefully acknowledges the support the Institute for Computational Biology, a collaborative effort of Case Western Reserve University, the Cleveland Clinic Foundation, and University Hospitals; Pfizer; the Institute for Informatics (I2), Washington University School of Medicine; the National Institutes of Health (NIH); and the International Society for Computational Biology (ISCB). If you or your institution are interested in sponsoring, PSB, please contact Tiffany Murray at [email protected] If you have any questions, the PSB registration staff (Tiffany Murray, Kasey Miller, BJ Morrison-McKay, and Cindy Paulazzo) are happy to help you. Aloha! Russ Altman Keith Dunker Larry Hunter Teri Klein Maryln Ritchie The PSB 2018 Organizers PSB 2018 Program Book 1 PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018 Big Island of Hawaii, January 3-7, 2018 SPEAKER INFORMATION Oral presentations of accepted proceedings papers will take place in Salon 2 & 3. Speakers are allotted 10 minutes for presentation and 5 minutes for questions for a total of 15 minutes. Instructions for uploading talks were sent to authors with oral presentations. -
A Guide to the Archival Collection of the Robert Cook-Deegan Human
Bioethics Research Library The Joseph and Rose Kennedy Institute of Ethics bioethics.georgetown.edu A Guide to the Archival Collection of The Robert Cook-Deegan Human Genome Archive Set 2 April, 2013 Bioethics Research Library Joseph and Rose Kennedy Institute of Ethics Georgetown University Washington, D.C. Overview The Robert Cook-Deegan Human Genome Archive is founded on the bibliography of The Gene Wars: Science, Politics, and the Human Genome. The archive encompasses both physical and digital materials related to The Human Genome Project (HGP) and includes correspondence, government reports, background information, and oral histories from prominent participants in the project. Hosted by the Bioethics Research Library at Georgetown University the archive is comprised of 20.85 linear feet of materials currently and is expected to grow as new materials are processed and added to the collection. Most of the materials comprising the archive were obtained between the years 1986 and 1994. However, several of the documents are dated earlier. Introduction This box listing was created in order to assist the Bioethics Research Library in its digitization effort for the archive and is being shared as a resource to our patrons to assist in their use of the collection. The archive consists of 44 separate archive boxes broken down into three separate sets. Set one is comprised of nine boxes, set two is comprised of seven boxes, and set three is comprised of 28 boxes. Each set corresponds to a distinct addition to the collection in the order in which they were given to the library. No value should be placed on the importance of any given set, or the order the boxes are in, as each was accessed, processed, and kept in the order in which they were received. -
Immunological Bioinformatics Sorin Istrail, Pavel Pevzner, and Michael Waterman, Editors
Immunological Bioinformatics Sorin Istrail, Pavel Pevzner, and Michael Waterman, editors Computational molecular biology is a new discipline, bringing together computational, statistical, experimental, and technological methods, which is energizing and dramatically accelerating the discovery of new technologies and tools for molecular biology. The MIT Press Series on Computational Molecular Biology is intended to provide a unique and effective venue for the rapid publication of monographs, textbooks, edited collections, reference works, and lecture notes of the highest quality. Computational Molecular Biology: An Algorithmic Approach Pavel A. Pevzner, 2000 Computational Methods for Modeling Biochemical Networks James M. Bower and Hamid Bolouri, editors, 2001 Current Topics in Computational Molecular Biology Tao Jiang, Ying Xu, and Michael Q. Zhang, editors, 2002 Gene Regulation and Metabolism: Postgenomic Computation Approaches Julio Collado-Vides, editor, 2002 Microarrays for an Integrative Genomics Isaac S. Kohane, Alvin Kho, and Atul J. Butte, 2002 Kernel Methods in Computational Biology Bernhard Schölkopf, Koji Tsuda and Jean-Philippe Vert, editors, 2004 An Introduction to Bioinformatics Algorithms Neil C. Jones and Pavel A. Pevzner, 2004 Immunological Bioinformatics Ole Lund, Morten Nielsen, Claus Lundegaard, Can Ke¸smirand Søren Brunak, 2005 Ontologies for Bioinformatics Kenneth Baclawski and Tianhua Niu, 2005 Immunological Bioinformatics Ole Lund Morten Nielsen Claus Lundegaard Can Ke¸smir Søren Brunak The MIT Press Cambridge, Massachusetts London, England c 2005 Massachusetts Institute of Technology All rights reserved. No part of this book may be reproduced in any form by any electronic or mechanical means (including photocopying, recording, or information storage and retrieval) without permission in writing from the publisher. MIT press books may be purchased at special quantity discounts for business or sales promotional use. -
Reading Genomes Bit by Bit
Reading genomes bit by bit Sean Eddy HHMI Janelia Farm Ashburn, Virginia Why did we sequence so many different flies? the power of comparative genome sequence analysis Why did we sequence a single-celled pond protozooan? exploiting unusual adaptations and unusual genomes Oxytricha trifallax Symbolic texts can be cracked by statistical analysis “Cryptography has contributed a new weapon to the student of unknown scripts.... the basic principle is the analysis and indexing of coded texts, so that underlying patterns and regularities can be discovered. If a number of instances can be collected, it may appear that a certain group of signs in the coded text has a particular function....” John Chadwick, The Decipherment of Linear B Cambridge University Press, 1958 Linear B, from Mycenae ca. 1500-1200 BC deciphered by Michael Ventris and John Chadwick, 1953 How much data are we talking about, really? STORAGE TIME TO COST/YEAR DOWNLOAD raw images 30 TB $36,000 20 days unassembled reads 100 GB $120 1 hr mapped reads 100 GB $120 1 hr assembled genome 6 GB $7 5 min differences 4 MB $0.005 0.2 sec my coffee coaster selab:/misc/data0/genomes 3 GB 450 GB JFRC computing, available disk ~ 1 petabyte (1000 TB) 1000 Genomes Project pilot 5 TB (30 GB/genome) selab:~eddys/Music/iTunes 128 albums 3 MB 15 GB NCBI Short Read Archive 200 TB + 10-20 TB/mo GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGG CGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATG -
Gene Pioneers: Donald Brown and Thomas Maniatis Win the 2012 Lasker~Koshland Special Achievement Award in Medical Science
Gene pioneers: Donald Brown and Thomas Maniatis win the 2012 Lasker~Koshland Special Achievement Award in Medical Science Kathryn Claiborn J Clin Invest. 2012;122(10):3383-3386. https://doi.org/10.1172/JCI66476. News The 2012 Lasker~Koshland Special Achievement Award in Medical Science recognizes Donald Brown (Carnegie Institute of Washington) and Thomas Maniatis (Columbia University) (Figure 1), two scientists whose career-long contributions were seminal to our understanding of what genes are and our ability to study and manipulate them, and whose commitment to mentorship have had tremendous impact on a generation of scientists. What is a gene? In the nineteenth century, an Austrian monk began a set of experiments in a small garden plot. Gregor Mendel’s detailed study of garden peas led him to understand that visible traits, such as the height or color of a plant, were determined by the combined inheritance of two physical particles from the two parent plants. Decades later, Theodor Boveri and Walter Sutton, analyzing meiotic cell divisions in grasshopper testes with the help of a microscope, hypothesized that Mendel’s hereditary factors — genes — could be carried on chromosomes. The groundwork was thus laid for a basic understanding of inheritance, but the question remained: what is a gene, exactly? Further understanding these entities — both their molecular makeup and their regulation — would require the dedication of innumerable scientific careers, as well as technical innovations that allowed the isolation and manipulation their sequences.Development -
SKIING the SUN New Mexico Essays by Michael Waterman
SKIING THE SUN New Mexico Essays ——————————————————— by Michael Waterman ....he will eat dried buffalo meat and frijoles with chili, and he will be glad to drink water when he can get it. From the novel Death Comes for the Archbishop, written by Willa Cather in 1926-1927. In recent years I have written several essays about New Mexico, only one of which has appeared in print. The truth is that my motivation has not been to tell others these stories and thoughts, but instead to articulate them to myself. That is harder than it looks, at least it is when I do it! After the memorial article about Gian-Carlo Rota appeared in the Notices of the AMS (here it is titled “Silhouettes on the Mesa”), several people expressed an interest in Rota, Ulam and Metropolis, so I decided to post this material. As this appears on my scientific web page, I have only included the essays that relate to science and mathematics, or more accurately, to scientists and mathematicians. The only formulas in the manuscript appear in “Silhouettes” and should be easy to skip over. The title comes from a 1970s slogan advertising New Mexico, “Ski the Sun,” that referred to the fact that the New Mexico weather was so good that people didn’t need to ski in bad weather. Coming from Idaho where there wasn’t much sunshine in the winter, I was struck by the reluctance of people to venture outdoors in anything but ideal conditions. Then again there is an obvious connection to be made with that incredible ball of fire when the bomb exploded at White Sands on July 16, 1945. -
From MRC-Cambridge to Madison, Wisconsin
C HA P TER 5 From MRC-Cambridge to Madison, Wisconsin William Dove and Alexandra Shedlovsky McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI Figure 5.1. Bill Dove. Figure 5.2. Alexandra Shedlovsky. PROLOGue – a STYLE OF DOING SCIENCE Our experience in the early 1960s as postdoctoral fellows in the MRC Unit for Molecular Biology led to our understanding the following principle: science is effectively driven by an idea when the seed is nourished by dialogue between con- trasting outlooks. We shall share our experiences that illustrate this ‘core principle’ 57 M ERIESM O AND C ONSEQUEN C E S by which the MRC unit thrived in that era. Since science does not function in a vacuum we include our perceptions of the cultural context that stimulated the growth of ideas through dialogue. This dialogue led to the remarkable edifice of molecular biology that emerged from the unit and its progeny around the world. Our comments are strictly matters of personal perception; however, Horace Judson’s Eighth Day of Creation gives a more global view of this and surrounding eras,1 while Sidney Altman wrote from a personal perspective of his experiences in the unit a decade later [‘RNA processing: a postdoc in a great laboratory’2]. Finally, the core principle is revealed in the essay written by the physical chemist John Platt [‘Strong Inference: Certain systematic methods of scientific thinking may produce much more rapid progress than others’3]. The messenger RNA experiments, the demonstration of the ‘triplet code’, and Marshall Nirenberg’s polyU encoding polyPhe experiment were all published by the middle of 1961.