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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. -
Microblogging the ISMB: a New Approach to Conference Reporting
Message from ISCB Microblogging the ISMB: A New Approach to Conference Reporting Neil Saunders1*, Pedro Beltra˜o2, Lars Jensen3, Daniel Jurczak4, Roland Krause5, Michael Kuhn6, Shirley Wu7 1 School of Molecular and Microbial Sciences, University of Queensland, St. Lucia, Brisbane, Queensland, Australia, 2 Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America, 3 Novo Nordisk Foundation Center for Protein Research, Panum Institute, Copenhagen, Denmark, 4 Department of Bioinformatics, University of Applied Sciences, Hagenberg, Freistadt, Austria, 5 Max-Planck-Institute for Molecular Genetics, Berlin, Germany, 6 European Molecular Biology Laboratory, Heidelberg, Germany, 7 Stanford Medical Informatics, Stanford University, Stanford, California, United States of America Cameron Neylon entitled FriendFeed for Claire Fraser-Liggett opened the meeting Scientists: What, Why, and How? (http:// with a review of metagenomics and an blog.openwetware.org/scienceintheopen/ introduction to the human microbiome 2008/06/12/friendfeed-for-scientists-what- project (http://friendfeed.com/search?q = why-and-how/) for an introduction. room%3Aismb-2008+microbiome+OR+ We—a group of science bloggers, most fraser). The subsequent Q&A session of whom met in person for the first time at covered many of the exciting challenges The International Conference on Intel- ISMB 2008—found FriendFeed a remark- for those working in this field. Clearly, ligent Systems for Molecular Biology -
Complete Vertebrate Mitogenomes Reveal Widespread Gene Duplications and Repeats
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.30.177956; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats Giulio Formenti+*1,2,3, Arang Rhie4, Jennifer Balacco1, Bettina Haase1, Jacquelyn Mountcastle1, Olivier Fedrigo1, Samara Brown2,3, Marco Capodiferro5, Farooq O. Al-Ajli6,7,8, Roberto Ambrosini9, Peter Houde10, Sergey Koren4, Karen Oliver11, Michelle Smith11, Jason Skelton11, Emma Betteridge11, Jale Dolucan11, Craig Corton11, Iliana Bista11, James Torrance11, Alan Tracey11, Jonathan Wood11, Marcela Uliano-Silva11, Kerstin Howe11, Shane McCarthy12, Sylke Winkler13, Woori Kwak14, Jonas Korlach15, Arkarachai Fungtammasan16, Daniel Fordham17, Vania Costa17, Simon Mayes17, Matteo Chiara18, David S. Horner18, Eugene Myers13, Richard Durbin12, Alessandro Achilli5, Edward L. Braun19, Adam M. Phillippy4, Erich D. Jarvis*1,2,3, and The Vertebrate Genomes Project Consortium +First author *Corresponding authors; [email protected]; [email protected] Author affiliations 1. The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA 2. Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA 3. The Howards Hughes Medical Institute, Chevy Chase, MD, USA 4. Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA 5. Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy 6. Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia 7. -
PROGRAM CHAIR: Eben Rosenthal, MD PROFFERED PAPERS CHAIR: Ellie Maghami, MD POSTER CHAIR: Maie St
AHNS 10TH INTERNATIONAL CONFERENCE ON HEAD & NECK CANCER “Survivorship through Quality & Innovation” JULY 22-25, 2021 • VIRTUAL CONFERENCE AHNS PRESIDENT: Cherie-Ann Nathan, MD, FACS CONFERENCE/DEVELOPMENT CHAIR: Robert Ferris, MD, PhD PROGRAM CHAIR: Eben Rosenthal, MD PROFFERED PAPERS CHAIR: Ellie Maghami, MD POSTER CHAIR: Maie St. John, MD Visit www.ahns2021.org for more information. WELCOME LETTER Dear Colleagues, The American Head and Neck Society (AHNS) is pleased to invite you to the virtual AHNS 10th International Conference on Head and Neck Cancer, which will be held July 22-25, 2021. The theme is Survivorship through Quality & Innovation and the scientific program has been thoughtfully designed to bring together all disciplines related to the treatment of head and neck cancer. Our assembled group of renowned head and neck surgeons, radiologists and oncologists have identified key areas of interest and major topics for us to explore. The entire conference will be presented LIVE online July 22-25, 2021. We encourage you to attend the live sessions in order to engage with the faculty and your colleagues. After the live meeting, all of the meeting content will be posted on the conference site and remain open for on-demand viewing through October 1, 2021. Attendees may earn up to 42.25 AMA PRA Category 1 Credit(s)TM as well as earn re- quired annual part II self-assessment credit in the American Board of Otolaryngology – Head and Neck Surgery’s Continu- ing Certification program (formerly known as MOC). At the conclusion of the activity, -
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. -
1993 Human Genome Program Report
Please address queries on this publication to: Human Genome Program U.S. Department of Energy Office of Health and Environmental Research ER-72 GTN Washington, DC 20585 301/903-6488, Fax: 301/903-8521 Internet: [email protected] Human Genome Management Information System Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge, TN 37831-6050 615/576-6669, Fax: 615/574-9888 BITNET: bkq@ornlstc Internet: [email protected] This report has been reproduced directly frorn the best obtainable copy. Available to DOE and DOE contractors from the Office of Scientific and Technical Information; P.O. Box 62; Oak Ridge, TN 37831. Price information: 615/576-8401 . Available to the public from the National Technical Information Service; U.S. Department of Commerce; 5285 Port Royal Road; Springfield, VA 22161. DOE/ER-0611 P uman nome 1993 Program Report Date Published: March 1994 U.S. Department of Energy Office of Energy Research Office of Health and Environmental Research Washington, D.C. 20585 Preface he purpose of this report is to update the Human Genome 1991-92 Program Report T (DOE/ER-0544P, published June 1992) and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward the 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes. -
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. -
The Johns Hopkins University
THE JOHNS HOPKINS UNIVERSITY COMMENCEMENT 2019 Conferring of degrees at the close of the 143rd academic year MAY 23, 2019 CONTENTS Order of Candidate Procession ......................................................... 11 Order of Procession .......................................................................... 12 Order of Events ................................................................................. 13 Conferring of Degrees ....................................................................... 14 Honorary Degrees ............................................................................. 17 Academic Garb .................................................................................. 14 Awards ............................................................................................... 16 Honor Societies ................................................................................. 28 Student Honors ................................................................................. 34 Candidates for Degrees ..................................................................... 43 Divisional Ceremonies Information ............................................... 121 Please note that while all degrees are conferred, only doctoral and bachelor’s graduates process across the stage. Taking photos from your seats during the ceremony is allowed, but we request that guests respect one another’s comfort and enjoyment by not standing and blocking other people’s views. Photos of graduates can be purchased from GradImages®: gradimages.com -
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