CPM's 20Th Anniversary: a Statistical Retrospective
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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 -
On the Suffix Automaton with Mismatches
On the suffix automaton with mismatches Maxime Crochemore, Chiara Epifanio, Alessandra Gabriele, Filippo Mignosi To cite this version: Maxime Crochemore, Chiara Epifanio, Alessandra Gabriele, Filippo Mignosi. On the suffix au- tomaton with mismatches. 12th International Conference on Implementation and Application of Automata (CIAA’07), 2007, Prague, Czech Republic. pp.144-156, 10.1007/978-3-540-76336-9_15. hal-00620159 HAL Id: hal-00620159 https://hal-upec-upem.archives-ouvertes.fr/hal-00620159 Submitted on 3 Oct 2016 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. On the Su±x Automaton with mismatches ? Maxime Crochemore1, Chiara Epifanio2, Alessandra Gabriele2, Filippo Mignosi3 1 Institut Gaspard-Monge, Universit¶ede Marne-la-Vall¶ee,France and King's College London, UK, [email protected] 2 Dipartimento di Matematica e Applicazioni, Universit`adi Palermo, Italy (epifanio,sandra)@math.unipa.it 3 Dipartimento di Informatica, Universit`adell'Aquila, Italy [email protected] Abstract. In this paper we focus on the construction of the minimal deterministic ¯nite automaton S k that recognizes the set of su±xes of a word w up to k errors. We present an algorithm that makes use of the automaton S k in order to accept in an e±cient way the language of all su±xes of w up to k errors in every windows of size r, where r is the value of the repetition index of w. -
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, -
Accelerating Dynamic Programming Oren Weimann
Accelerating Dynamic Programming by Oren Weimann Submitted to the Department of Electrical Engineering and Computer Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY June 2009 c Massachusetts Institute of Technology 2009. All rights reserved. Author................................................................... Department of Electrical Engineering and Computer Science February 5, 2009 Certified by . Erik D. Demaine Associate Professor of Electrical Engineering and Computer Science Thesis Supervisor Accepted by . Professor Terry P. Orlando Chairman, Department Committee on Graduate Students 2 Accelerating Dynamic Programming by Oren Weimann Submitted to the Department of Electrical Engineering and Computer Science on February 5, 2009, in partial fulfillment of the requirements for the degree of Doctor of Philosophy Abstract Dynamic Programming (DP) is a fundamental problem-solving technique that has been widely used for solving a broad range of search and optimization problems. While DP can be invoked when more specialized methods fail, this generality often incurs a cost in efficiency. We explore a unifying toolkit for speeding up DP, and algorithms that use DP as subroutines. Our methods and results can be summarized as follows. – Acceleration via Compression. Compression is traditionally used to efficiently store data. We use compression in order to identify repeats in the table that imply a redundant computation. Utilizing these repeats requires a new DP, and often different DPs for different compression schemes. We present the first provable speedup of the celebrated Viterbi algorithm (1967) that is used for the decoding and training of Hidden Markov Models (HMMs). Our speedup relies on the compression of the HMM’s observable sequence. -
Arxiv:0707.3619V21 [Cs.DS] 23 Nov 2013
Semi-local string comparison: Algorithmic techniques and applications Alexander Tiskin1 September 13, 2021 arXiv:0707.3619v21 [cs.DS] 23 Nov 2013 1Department of Computer Science, University of Warwick, Coventry CV4 7AL, United Kingdom. Research supported by the Centre for Discrete Mathematics and Its Applications (DIMAP), University of Warwick, and by the Royal Society Leverhulme Trust Senior Research Fellowship. Abstract A classical measure of string comparison is given by the longest common sub- sequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string- related problems. The semi-local LCS problem asks for the LCS scores for each of the input strings against every substring of the other input string, and for every prefix of each input string against every suffix of the other input string. Such a comparison pattern provides a much more detailed picture of string similarity than a single LCS score; it also arises naturally in many string-related problems. In fact, the semi-local LCS problem turns out to be fundamental for string comparison, providing a powerful and flex- ible alternative to classical dynamic programming. It is especially useful when the input to a string comparison problem may not be available all at once: for example, comparison of dynamically changing strings; comparison of compressed strings; parallel string comparison. The same approach can also be applied to permutation strings, providing efficient solutions for local versions of the longest increasing subsequence (LIS) problem, and for the problem of computing a maximum clique in a circle graph. -
A High-Quality Digital Library Supporting Computing Education: the Ensemble Approach
A High-quality Digital Library Supporting Computing Education: The Ensemble Approach Yinlin Chen Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Computer Science & Application Edward A. Fox, Chair Sanmay Das Weiguo Fan Christopher L. North Ricardo Da Silva Torres July 27, 2017 Blacksburg, Virginia 24061 Keywords: Educational Digital Library; ACM Classification System; Amazon Mechanical Turk; Classification; Transfer learning; Active learning; YouTube; SlideShare; Digital Library Service Quality; Cloud Computing Copyright 2017 Yinlin Chen A High-quality Digital Library Supporting Computing Education: The Ensemble Approach Yinlin Chen ABSTRACT Educational Digital Libraries (DLs) are complex information systems which are designed to support individuals' information needs and information seeking behavior. To have a broad impact on the communities in education and to serve for a long period, DLs need to structure and organize the resources in a way that facilitates the dissemination and the reuse of resources. Such a digital library should meet defined quality dimensions in the 5S (Societies, Scenarios, Spaces, Structures, Streams) framework - including completeness, consistency, efficiency, extensibility, and reliability - to ensure that a good quality DL is built. In this research, we addressed both external and internal quality aspects of DLs. For internal qualities, we focused on completeness and consistency of the collection, catalog, and repos- itory. We developed an application pipeline to acquire user-generated computing-related resources from YouTube and SlideShare for an educational DL. We applied machine learn- ing techniques to transfer what we learned from the ACM Digital Library dataset. -
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 -
Timeline of the European Commission, U.S
Google’s Anti-Competitive Search Manipulation Practices A Timeline of the European Commission, U.S. FTC, DOJ, and State AG Antitrust Probes, Prohibition Decisions & Lawsuits By Adam Raff and Shivaun Raff Co-founders of Foundem and SearchNeutrality.org First Published: 15 April 2015 Last Updated: 3 March 2021 Table of Contents Jun 2006 Foundem’s Google Search Penalty 3 May 2007 Google Launches Universal Search 6 Nov 2009 Foundem’s Competition Complaint to the European Commission (EC) 14 Feb 2010 Launch of the EC’s Informal Investigation / Foundem’s Updated Complaint 16 Nov 2010 Launch of the EC’s Formal Investigation 19 Apr 2011 Official Launch of the U.S. FTC’s Investigation 22 May 2012 Commissioner Almunia Commences Settlement Negotiations with Google 27 Jan 2013 Premature Closure of the U.S. FTC’s Investigation 34 Jan 2013 Origins of the Even-Handed / Equal-Treatment Remedy 35 Apr 2013 Google’s 1st Commitment Proposals 38 Oct 2013 Google’s 2nd Commitment Proposals 41 Jan 2014 Google’s 3rd Commitment Proposals 43 Jul 2014 The European Commission’s Dramatic U-Turn 50 Nov 2014 Commissioner Vestager Takes Office 53 Mar 2015 Inadvertent Release of the FTC’s Damning Internal Final Report 54 Apr 2015 Statement of Objections (SO) in the Google Search Case 57 Jul 2016 Supplementary Statement of Objections (SSO) in the Google Search Case 62 Jun 2017 EC Prohibition Decision (Guilty Verdict) in the Google Search Case 65 Sep 2017 Google’s Brazenly Non-Compliant CSS Auction 67 Jul 2018 EC Prohibition Decision in the Google Android Case 69 Jun 2019 Launch of the U.S. -
LNBI 9044), Entitled “Advances on Computational Intelligence
Lecture Notes in Bioinformatics 9044 Subseries of Lecture Notes in Computer Science LNBI 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 LNBI Editorial Board Alberto Apostolico Georgia Institute of Technology, Atlanta, GA, USA 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, 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, 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 Francisco Ortuño Ignacio Rojas (Eds.) Bioinformatics and Biomedical Engineering Third International Conference, IWBBIO 2015 Granada, Spain, April 15-17, 2015 Proceedings, Part II 13 Volume Editors Francisco Ortuño Ignacio Rojas Universidad de Granada Dpto. de Arquitectura y Tecnología de Computadores (ATC) E.T.S. de Ingenierías en Informática y Telecomunicación, CITIC-UGR Granada, Spain E-mail: {fortuno, irojas}@ugr.es ISSN 0302-9743 e-ISSN 1611-3349 ISBN 978-3-319-16479-3 e-ISBN 978-3-319-16480-9 DOI 10.1007/978-3-319-16480-9 Springer Cham Heidelberg New York Dordrecht London Library of Congress Control Number: 2015934926 LNCS Sublibrary: SL 8 – Bioinformatics © Springer International Publishing Switzerland 2015 This work is subject to copyright. -
Lecture Notes in Computer Science 2676 Edited by G
Lecture Notes in Computer Science 2676 Edited by G. Goos, J. Hartmanis, and J. van Leeuwen 3 Berlin Heidelberg New York Barcelona Hong Kong London Milan Paris Tokyo Ricardo Baeza-Yates Edgar Chávez Maxime Crochemore (Eds.) Combinatorial Pattern Matching 14th Annual Symposium, CPM 2003 Morelia, Michoacán, Mexico, June 25-27, 2003 Proceedings 13 Series Editors Gerhard Goos, Karlsruhe University, Germany Juris Hartmanis, Cornell University, NY, USA Jan van Leeuwen, Utrecht University, The Netherlands Volume Editors Ricardo Baeza-Yates Universidad de Chile Depto. de Ciencias de la Computación Blanco Encalada 2120 Santiago 6511224, Chile E-mail: [email protected] Edgar Chávez Universidad Michoacana Escuela de Ciencias Físico-Matemáticas Edificio "B", ciudad universitaria Morelia, Michoacán, Mexico E-mail: elchavez@fismat.umich.mx Maxime Crochemore Université de Marne-la-Vallée 77454 Marne-la-Vallée CEDEX 2, France E-mail: [email protected] Cataloging-in-Publication Data applied for A catalog record for this book is available from the Library of Congress. Bibliographic information published by Die Deutsche Bibliothek Die Deutsche Bibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data is available in the Internet at <http://dnb.ddb.de>. CR Subject Classification (1998): F.2.2, I.5.4, I.5.0, I.7.3, H.3.3, E.4, G.2.1 ISSN 0302-9743 ISBN 3-540-40311-6 Springer-Verlag Berlin Heidelberg New York This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, re-use of illustrations, recitation, broadcasting, reproduction on microfilms or in any other way, and storage in data banks.