DOCSLIB.ORG

Alignment-Free Phylogeny Reconstruction Based on Quartet Trees

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Alignment-Free Phylogeny Reconstruction Based on Quartet Trees Alignment-free Phylogeny Reconstruction Based On Quartet Trees Dissertation for the award of the degree „Doctor rerum naturalium“ of the Georg-August-Universität Göttingen within the doctoral program „Computer Science“ (PCS) of the Georg-August-University School of Science (GAUSS) submitted by Thomas Dencker from Nordenham January 27, 2020 Members of the Thesis Committee Prof. Dr. Burkhard Morgenstern (1st Referee) Institute for Microbiology and Genetics, Georg-August-Universität Göttingen Prof. Dr. Stephan Waack (2nd Referee) Institute for Computer Science, Georg-August-Universität Göttingen Dr. Johannes Söding Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry Göttingen Further Members of the Examination Board Prof. Dr. Christoph Bleidorn Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-Universität Göttingen Prof. Dr. Anja Sturm Institute for Mathematical Stochastics, Georg-August-Universität Göttingen Prof. Dr. Jan de Vries Institute for Microbiology and Genetics, Georg-August-Universität Göttingen Date of the oral examination: March 4 th 2020 ii Affidavit I hereby confirm that this thesis has been written independently and with no other sources and aids than quoted. Göttingen, 27. January 2020 Thomas Dencker iii Danksagung An dieser Stelle möchte ich mich bei allen bedanken, die mich in den letzten Jahren be- gleitet und unterstützt haben. Zuallererst bedanke ich mich bei meinem Doktorvater Prof. Dr. Burkhard Morgenstern für die Betreuung dieser Doktorarbeit und die andauernde Unterstützung seit der Bache- lorarbeit. Ohne ihn wäre ich gar nicht in der Bioinformatik gelandet. Besonders dankbar ich bin für die vielen Ratschläge, mit denen ich vor allem meine Präsentationsfähigkeiten verbessern konnte. Außerdem hat er mir die Möglichkeit gegeben, an der RECOMB-CG in Kanada teilzunehmen und viele neue Erfahrungen zu sammeln. An die gemeinsame Zeit werde ich mich noch lange positiv erinnern. Außerdem danke ich Dr. Soeding und Prof. Dr. Waack für die konstruktive Kritik in den Komiteetreffen. Des Weiteren möchte ich mich auch bei Dr. Peter Meinecke, Heiner Klingenberg, Lars Hahn und Matthias Blanke für die vielen hilfreichen Diskussion und das gute Feedback bei meinen Präsentationen bedanken. Ganz besonders bedanke ich mich bei meinem Freund und ehemaligen Kollegen Chris Leimeister dafür, dass er mir immer mit gutem Rat zur Seite stand und für die vielen hilfreichen Gesprache, die mich immer wieder motiviert haben. Mein ganz besonderer Dank gilt auch meinen Eltern, die mich während des gesamten Studiums unterstützt und immer an mich geglaubt haben. v Contents 1 Introduction 5 1.1 Sequence alignment . .6 1.2 Tree building methods . .9 1.3 Supertree methods . 12 1.4 Alignment-free methods . 16 1.5 Filtered spaced word matches . 22 1.6 Objectives of this thesis and overview . 25 2 ‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruc- tion using multiple spaced-word matches and quartet trees 27 3 Insertions and deletions as a phylogenetic signal in an alignment-free context 39 4 Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points. 67 5 Further improvements and experiments 77 5.1 SH-like support values . 77 5.1.1 Correctness and RF . 79 5.2 Neighbor-Joining . 83 5.2.1 Test results . 83 5.3 Bootstrapping . 87 vii 6 Discussion 89 6.1 Alignment-free methods based on micro-alignments . 91 6.2 Limitations . 94 7 Conclusion and outlook 96 7.1 Possible improvements . 96 7.2 Further applications . 98 viii Publication List Journal Papers • Thomas Dencker, Chris-André Leimeister, Michael Gerth, Christoph Bleidorn, Sagi Snir, Burkhard Morgenstern. ‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees NAR Genomics and Bioinformatics, 2:lqz013, 2020. • Thomas Dencker, Niklas Birth und Burkhard Morgenstern. Insertions and dele- tions as a phylogenetic signal in an alignment-free context. Prepared for submission. • Chris-Andre Leimeister, Thomas Dencker, and Burkhard Morgenstern. Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points. Bioinformatics, 35(2):211–218, 2019. • Andrzej Zielezinski, Hani Z Girgis, Guillaume Bernard, Chris-Andre Leimeister, Kujin Tang, Thomas Dencker, Anna Katharina Lau, Sophie Röhling, Jae Jin Choi, Michael S Waterman, Matteo Comin, Sung-Hou Kim, Susana Vinga, Jonas S Almeida, Cheong Xin Chan, Benjamin T James, Fengzhu Sun, Burkhard Morgen- stern, Wojciech M Karlowski Benchmarking of alignment-free sequence comparison methods. Genome Biol., 20(1):144, 2019. • Sophie Röhling, Alexander Linne, Jendrik Schellhorn, Morteza Hosseini, Thomas Dencker and Burkhard Morgenstern. The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances. PLOS ONE, in press, 2020. Conference Papers (peer reviewed) • Thomas Dencker, Chris-Andre Leimeister, Michael Gerth, Christoph Bleidorn, Sagi Snir, and Burkhard Morgenstern. Multi-SpaM: a Maximum-Likelihood ap- proach to phylogeny reconstruction using multiple spaced-word matches and quartet trees. In Comparative Genomics, pages 227–241. Springer International Publishing, 2018. 1 Abstract Traditional methods for phylogeny reconstruction are based on multiple sequence align- ments and character-based methods. This combination of computationally expensive meth- ods leads to very accurate results, but it is ill-suited to handle the enormous amount of sequence data that is available today. As a consequence, very fast alignment-free methods have been developed. These methods calculate pairwise distances in order to build phy- logenetic trees. However, current alignment-free methods are generally less accurate than traditional methods. In this thesis, I developed Multi-SpaM which is a novel alignment-free approach that tries to combine the best of both worlds. This method quickly finds small gap-free ‘micro- alignments’ – so-called blocks – involving four sequences. A binary pattern defines at which positions the nucleotides have to match. At the remaining don’t care positions, the possibly mismatching nucleotides are first used to remove random matches with a filtering procedure previously introduced by Filtered Spaced-Word Matches (FSWM). Then, the character-based method RAxML is used to find the optimal quartet tree for each block. Subsequently, all quartet trees are amalgamated into a supertree with Quartet MaxCut. This approach can be used to build phylogenetic trees of high quality. Furthermore, I showed multiple ways that could help to improve Multi-SpaM. The distances between two adjacent blocks involving the same four sequences can be used to identify pu- tative insertions and deletions from which accurate quartet trees can be derived. These trees could be used both on their own and in combination with the quartet trees pro- duced by Multi-SpaM to build or improve phylogenetic trees using Quartet MaxCut. As an alternative, we also used Maximum-Parsimony to infer accurate phylogenies from these pu- tative insertions and deletions. In other experiments, I tried to give the individual quartet trees weights based on SH-like support values and tried to use Neighbor-Joining in order to speed up Multi-SpaM. Moreover, I contributed to another extension of the FSWM approach. Here, we used these matches as anchor points for a genome alignment tool called mugsy. We found that a higher number of homologous pairs could be aligned for more distantly related species in comparison to other anchor points used with the same alignment program. 3 1 Introduction Evolution is a central concept in biology. A formal theory of evolution was first formulated by Charles Darwin in his book “On the Origin of Species” [23]. We now believe that all species [89] ultimately evolved from a common ancestor [137]. The evolutionary history of a group of species is called a phylogeny. It is commonly visualized as a phylogenetic tree. In some cases, the phylogeny is depicted as a phylogenetic network [58] to take even more complex relationships into account. Reconstructing phylogenies is a fundamental task in the life sciences. Ultimately, it is one major goal to identify the evolutionary relationships between all species and thus reconstruct the tree of life [53]. For the longest time, relationships between species were determined purely by morpho- logical features such as bone structures. Based on these features, species can be assigned to certain taxa. Taxa are groups of species on different levels (domain, kingdom, phylum, class, order, family, genus, and species) and can be thought of as subtrees of the tree of life. Reconstructing phylogenies based on morphological features can be a challenging task. One problem is that a feature can appear independently in different taxa. The ability to fly was developed by both birds and bats and is a common example for convergent evolution. Such a feature is also called a homoplasy [8]. In contrast, features are called homologies when they exist due to divergent evolution, i.e. they were inherited from a shared ances- tor. In order to reconstruct the correct phylogeny, it has to be based on sufficiently many homologies. However, the morphological approach reaches its limits when homologies are hard to find. For example, for certain taxa, such as closely related bacteria, it is difficult to make out any differences. In such a case, the genetic material can provide
Load more

Recommended publications
  • Proquest Dissertations
    Automated learning of protein involvement in pathogenesis using integrated queries Eithon Cadag A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2009 Program Authorized to Offer Degree: Department of Medical Education and Biomedical Informatics UMI Number: 3394276 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI Dissertation Publishing UMI 3394276 Copyright 2010 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. uest ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 University of Washington Graduate School This is to certify that I have examined this copy of a doctoral dissertation by Eithon Cadag and have found that it is complete and satisfactory in all respects, and that any and all revisions required by the final examining committee have been made. Chair of the Supervisory Committee: Reading Committee: (SjLt KJ. £U*t~ Peter Tgffczy-Hornoch In presenting this dissertation in partial fulfillment of the requirements for the doctoral degree at the University of Washington, I agree that the Library shall make its copies freely available for inspection. I further agree that extensive copying of this dissertation is allowable only for scholarly purposes, consistent with "fair use" as prescribed in the U.S.
    [Show full text]
  • Molecular Biology for Computer Scientists
    CHAPTER 1 Molecular Biology for Computer Scientists Lawrence Hunter “Computers are to biology what mathematics is to physics.” — Harold Morowitz One of the major challenges for computer scientists who wish to work in the domain of molecular biology is becoming conversant with the daunting intri- cacies of existing biological knowledge and its extensive technical vocabu- lary. Questions about the origin, function, and structure of living systems have been pursued by nearly all cultures throughout history, and the work of the last two generations has been particularly fruitful. The knowledge of liv- ing systems resulting from this research is far too detailed and complex for any one human to comprehend. An entire scientific career can be based in the study of a single biomolecule. Nevertheless, in the following pages, I attempt to provide enough background for a computer scientist to understand much of the biology discussed in this book. This chapter provides the briefest of overviews; I can only begin to convey the depth, variety, complexity and stunning beauty of the universe of living things. Much of what follows is not about molecular biology per se. In order to 2ARTIFICIAL INTELLIGENCE & MOLECULAR BIOLOGY explain what the molecules are doing, it is often necessary to use concepts involving, for example, cells, embryological development, or evolution. Bi- ology is frustratingly holistic. Events at one level can effect and be affected by events at very different levels of scale or time. Digesting a survey of the basic background material is a prerequisite for understanding the significance of the molecular biology that is described elsewhere in the book.
    [Show full text]
  • Ontology-Based Methods for Analyzing Life Science Data
    Habilitation a` Diriger des Recherches pr´esent´ee par Olivier Dameron Ontology-based methods for analyzing life science data Soutenue publiquement le 11 janvier 2016 devant le jury compos´ede Anita Burgun Professeur, Universit´eRen´eDescartes Paris Examinatrice Marie-Dominique Devignes Charg´eede recherches CNRS, LORIA Nancy Examinatrice Michel Dumontier Associate professor, Stanford University USA Rapporteur Christine Froidevaux Professeur, Universit´eParis Sud Rapporteure Fabien Gandon Directeur de recherches, Inria Sophia-Antipolis Rapporteur Anne Siegel Directrice de recherches CNRS, IRISA Rennes Examinatrice Alexandre Termier Professeur, Universit´ede Rennes 1 Examinateur 2 Contents 1 Introduction 9 1.1 Context ......................................... 10 1.2 Challenges . 11 1.3 Summary of the contributions . 14 1.4 Organization of the manuscript . 18 2 Reasoning based on hierarchies 21 2.1 Principle......................................... 21 2.1.1 RDF for describing data . 21 2.1.2 RDFS for describing types . 24 2.1.3 RDFS entailments . 26 2.1.4 Typical uses of RDFS entailments in life science . 26 2.1.5 Synthesis . 30 2.2 Case study: integrating diseases and pathways . 31 2.2.1 Context . 31 2.2.2 Objective . 32 2.2.3 Linking pathways and diseases using GO, KO and SNOMED-CT . 32 2.2.4 Querying associated diseases and pathways . 33 2.3 Methodology: Web services composition . 39 2.3.1 Context . 39 2.3.2 Objective . 40 2.3.3 Semantic compatibility of services parameters . 40 2.3.4 Algorithm for pairing services parameters . 40 2.4 Application: ontology-based query expansion with GO2PUB . 43 2.4.1 Context . 43 2.4.2 Objective .
    [Show full text]
  • The International Society for Computational Biology 10Th Anniversary Lawrence Hunter, Russ B
    Message from ISCB The International Society for Computational Biology 10th Anniversary Lawrence Hunter, Russ B. Altman, Philip E. Bourne* Introduction training programs in bioinformatics or significant part of the original computational biology. By 1996, motivation for founding the Society PLoS Computational Biology is the however, high throughput molecular was to provide a stable financial home official journal of the International biology and the attendant need for for the ISMB conference. The first few Society for Computational Biology informatics had clearly arrived. In conferences were sufficiently successful (ISCB), a partnership that was formed addition to the founding of ISCB, 1996 to create a financial nest egg that was during the Journal’s conception in saw the sequencing of the first genome used each year to start the process of 2005. With ISCB being the only of a free-living organism (yeast) and planning and executing the next year’s international body representing Affymetrix’s release of its first meeting. Initially, relatively modest computational biologists, it made commercial DNA chip. checks were cut and sent from one perfect sense for PLoS Computational The hot topics in bioinformatics organizer to another informally. As the Biology to be closely affiliated. The circa 1996, at least as reflected by the size of these checks increased, the Society had to take more of a chance conference on Intelligent Systems for organizers (and their home than similar societies, choosing to step Molecular Biology (ISMB) at institutions) became increasingly away from an existing financially Washington University in St. Louis, uncomfortable exchanging them beneficial subscription journal to align included issues which have largely been informally, and decided that they with an open access publication as a solved (such as gene finding or needed an organization—thus, ISCB.
    [Show full text]
  • Biocuration 2016 - Posters
    Biocuration 2016 - Posters Source: http://www.sib.swiss/events/biocuration2016/posters 1 RAM: A standards-based database for extracting and analyzing disease-specified concepts from the multitude of biomedical resources Jinmeng Jia and Tieliu Shi Each year, millions of people around world suffer from the consequence of the misdiagnosis and ineffective treatment of various disease, especially those intractable diseases and rare diseases. Integration of various data related to human diseases help us not only for identifying drug targets, connecting genetic variations of phenotypes and understanding molecular pathways relevant to novel treatment, but also for coupling clinical care and biomedical researches. To this end, we built the Rare disease Annotation & Medicine (RAM) standards-based database which can provide reference to map and extract disease-specified information from multitude of biomedical resources such as free text articles in MEDLINE and Electronic Medical Records (EMRs). RAM integrates disease-specified concepts from ICD-9, ICD-10, SNOMED-CT and MeSH (http://www.nlm.nih.gov/mesh/MBrowser.html) extracted from the Unified Medical Language System (UMLS) based on the UMLS Concept Unique Identifiers for each Disease Term. We also integrated phenotypes from OMIM for each disease term, which link underlying mechanisms and clinical observation. Moreover, we used disease-manifestation (D-M) pairs from existing biomedical ontologies as prior knowledge to automatically recognize D-M-specific syntactic patterns from full text articles in MEDLINE. Considering that most of the record-based disease information in public databases are textual format, we extracted disease terms and their related biomedical descriptive phrases from Online Mendelian Inheritance in Man (OMIM), National Organization for Rare Disorders (NORD) and Orphanet using UMLS Thesaurus.
    [Show full text]
  • Scalable Approaches for Auditing the Completeness of Biomedical Ontologies
    University of Kentucky UKnowledge Theses and Dissertations--Computer Science Computer Science 2021 Scalable Approaches for Auditing the Completeness of Biomedical Ontologies Fengbo Zheng University of Kentucky, [email protected] Author ORCID Identifier: https://orcid.org/0000-0001-5902-0186 Digital Object Identifier: https://doi.org/10.13023/etd.2021.128 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Zheng, Fengbo, "Scalable Approaches for Auditing the Completeness of Biomedical Ontologies" (2021). Theses and Dissertations--Computer Science. 105. https://uknowledge.uky.edu/cs_etds/105 This Doctoral Dissertation is brought to you for free and open access by the Computer Science at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Computer Science by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known.
    [Show full text]
  • Development and Application of Ligand-Based Cheminformatics Tools for Drug Discovery from Natural Products
    Development and application of ligand-based cheminformatics tools for drug discovery from natural products Entwicklung und Anwendung von ligandenbasierten Cheminformatik-Programmen für die Identifizierung von Arzneimitteln aus Naturstoffen INAUGURALDISSERTATION zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Albert-Ludwigs-Universität Freiburg im Breisgau vorgelegt von Kiran Kumar Telukunta aus Hyderabad, Indien Juli 2018 Dekan: Prof. Dr. Manfred Jung Universität Freiburg Institut für Pharmazeutische Wissenschaften Chemische Epigenetik Albertstraße 25 79104 Freiburg Vorsitzender: Prof. Dr. Stefan Weber des Promotionsausschusses Universität Freiburg Institut für Physikalische Chemie Physikalishe Chemie Albertstraße 21 79104 Freiburg Referent: Prof. Dr. Stefan Günther Universität Freiburg Institut für Pharmazeutische Wissenschaften Pharmazeutische Bioinformatik Hermann-Herder-Straße 9 79104 Freiburg Korreferent: Prof. Dr. Rolf Backofen Universität Freiburg Institut für Informatik Lehrstuhl für Bioinformatik Georges-Köhler-Allee 106 79110 Freiburg Drittprüfer: Prof. Dr. Andreas Bechthold Universität Freiburg Institut für Pharmazeutische Wissenschaften Pharmazeutische Biologie und Biotechnologie Stefan-Meier-Straße 19 79104 Freiburg Prüfungsdatum: 30 Aug 2018 Eidesstattliche Erklärung Hiermit erkläre ich, dass ich diese Arbeit allein und ausschließlich unter Nutzung der direkt oder sinngemäß gekennzeichneten Zitate geschrieben habe. Weiterhin versichere ich, dass diese Arbeit in keinem anderen Prüfungsverfahren eingereicht
    [Show full text]
  • BMC Bioinformatics Biomed Central
    BMC Bioinformatics BioMed Central Proceedings Open Access NIPS workshop on New Problems and Methods in Computational Biology Gal Chechik*1, Christina Leslie2, William Stafford Noble3, Gunnar Rätsch4, Quaid Morris5 and Koji Tsuda6 Address: 1Computer Science Department, Stanford University, 353 Serra Mall, Stanford University, Stanford, CA 94305, USA, 2Computational Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 460, New York, NY 10065, USA, 3Department of Genome Sciences, University of Washington, 1705 NE Pacific St, Seattle, WA 98109, USA, 4Friedrich Miescher Laboratory of the Max Planck Society, Spemannstr. 39, 72076 Tübingen, Germany, 5Terrence Donnelley Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada and 6Max Planck Institute for Biological Cybernetics, Spemannstr. 38, 72076 Tübingen, Germany Email: Gal Chechik* - [email protected]; Christina Leslie - [email protected]; William Stafford Noble - [email protected]; Gunnar Rätsch - [email protected]; Quaid Morris - [email protected]; Koji Tsuda - [email protected] * Corresponding author from NIPS workshop on New Problems and Methods in Computational Biology Whistler, Canada. 8 December 2006 Published: 21 December 2007 BMC Bioinformatics 2007, 8(Suppl 10):S1 doi:10.1186/1471-2105-8-S10-S1 <supplement> <title> <p>Neural Information Processing Systems (NIPS) workshop on New Problems and Methods in Computational Biology</p> </title> <editor>Gal Chechik, Christina Leslie, William Stafford Noble, Gunnar Rätsch, Quiad Morris and Koji Tsuda</editor> <note>Proceedings</note> <url>http://www.biomedcentral.com/content/pdf/1471-2105-8-S10-info.pdf</url> </supplement> This article is available from: http://www.biomedcentral.com/1471-2105/8/S10/S1 © 2007 Chechik et al; licensee BioMed Central Ltd.
    [Show full text]
  • Pacific Symposium on Biocomputing 2008
    PACIFIC SYMPOSIUM ON BIOCOMPUTING 2008 This year, PSB returns to its most common venue, the Fairmont Orchid on the Big Island of Hawaii. We are now in our thirteenth year, and had a record number of both proposed sessions (we accepted 9) as well as submissions to the conference this year (150). Many sessions at PSB have a lifetime of approximately three years. The first year is a test of the interest in the field, and the ability to attract a critical mass of papers. With success, the second year is usually a larger, more competitive session. The third (and rarely fourth years) usually come as the subdiscipline is recognized at the general biocomputing meetings such as ISMB, RECOMB and others, and often this is when the PSB organizers conclude that their work is done, and the session can be “retired.” PSB aficionados will notice new sessions this year in next-generation sequencing, tiling array analysis, multiscale modeling, small regulatory RNAs, and other areas. The richness of exciting new areas has led us to have more total sessions, and thus the average session size is smaller. We consider this an experiment, and look forward to seeing how it goes. We would like to thank our keynote speakers. Dr. Andrew McCulloch, Professor and Chair, Department of Bioengineering, University of California, San Diego, will talk about “Systems biology and multi-scale modeling of the heart.” Our keynote in the area of Ethical, Legal and Social implications of technology will be John Dupre, Director of Egenis (ESRC Centre for Genomics in Society) and Professor of Philosophy of Science, University of Exeter.
    [Show full text]
  • 2016 National Library of Medicine Informatics Training Confernece
    National Library of Medicine Informatics Training Conference June 27-28, 2016 The Ohio State University The Ohio Union Columbus, Ohio TABLE OF CONTENTS Agenda ..................................................................................................................................................... 1 Day 1 in Detail ......................................................................................................................................... 1 Day 2 in Detail ......................................................................................................................................... 6 Attendee and Presenter Information Full Training Conference Attendee and Presenters List ......................................................................... 9 Administrative Contacts for Each Program ............................................................................................. 13 Plenary/Focus Session Presentations List ................................................................................................ 14 Poster Presentations List ......................................................................................................................... 15 Open Mic Presentations List .................................................................................................................... 17 Abstracts for Presentations and Posters ....................................................................................... 19 Plenary Sessions (Days 1 and 2) Day 1 Plenary Session #1 ......................................................................................................................
    [Show full text]
  • Pacific Symposium on Biocomputing 2020 January 3-7, 2020 Big Island of Hawaii
    Pacific Symposium on Biocomputing 2020 January 3-7, 2020 Big Island of Hawaii Program Book PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020 Big Island of Hawaii, January 3-7, 2020 Welcome to PSB 2020! We have prepared this program book to give you quick access to information you need for PSB 2020. Enclosed you will find: • Logistics information • Medical services information • Full conference schedule (see website for the latest version) • Agendas for workshops and JBrowse demo • Call for Session and Workshop Proposals for PSB 2021 • Poster/abstract titles and author index • Participant list The latest conference materials are available online at http://psb.stanford.edu/conference-materials/. PSB 2020 gratefully acknowledges the support of the Cleveland Institute for Computational Biology; UPenn Institute for Biomedical Informatics; Variant Bio; Penn Center for Precision Medicine, Penn Medicine; Cipherome; Translational Bioinformatics Conference (TBC); 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 2020 Organizers PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020 Big Island of Hawaii, January 3-7, 2020 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.
    [Show full text]
  • I S C B N E W S L E T T
    ISCB NEWSLETTER FOCUS ISSUE {contents} President’s Letter 2 Member Involvement Encouraged Register for ISMB 2002 3 Registration and Tutorial Update Host ISMB 2004 or 2005 3 David Baker 4 2002 Overton Prize Recipient Overton Endowment 4 ISMB 2002 Committees 4 ISMB 2002 Opportunities 5 Sponsor and Exhibitor Benefits Best Paper Award by SGI 5 ISMB 2002 SIGs 6 New Program for 2002 ISMB Goes Down Under 7 Planning Underway for 2003 Hot Jobs! Top Companies! 8 ISMB 2002 Job Fair ISCB Board Nominations 8 Bioinformatics Pioneers 9 ISMB 2002 Keynote Speakers Invited Editorial 10 Anna Tramontano: Bioinformatics in Europe Software Recommendations11 ISCB Software Statement volume 5. issue 2. summer 2002 Community Development 12 ISCB’s Regional Affiliates Program ISCB Staff Introduction 12 Fellowship Recipients 13 Awardees at RECOMB 2002 Events and Opportunities 14 Bioinformatics events world wide INTERNATIONAL SOCIETY FOR COMPUTATIONAL BIOLOGY A NOTE FROM ISCB PRESIDENT This newsletter is packed with information on development and dissemination of bioinfor- the ISMB2002 conference. With over 200 matics. Issues arise from recommendations paper submissions and over 500 poster submis- made by the Society’s committees, Board of sions, the conference promises to be a scientific Directors, and membership at large. Important feast. On behalf of the ISCB’s Directors, staff, issues are defined as motions and are discussed EXECUTIVE COMMITTEE and membership, I would like to thank the by the Board of Directors on a bi-monthly Philip E. Bourne, Ph.D., President organizing committee, local organizing com- teleconference. Motions that pass are enacted Michael Gribskov, Ph.D., mittee, and program committee for their hard by the Executive Committee which also serves Vice President work preparing for the conference.
    [Show full text]