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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 -
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, -
Cancer Immunology of Cutaneous Melanoma: a Systems Biology Approach
Cancer Immunology of Cutaneous Melanoma: A Systems Biology Approach Mindy Stephania De Los Ángeles Muñoz Miranda Doctoral Thesis presented to Bioinformatics Graduate Program at Institute of Mathematics and Statistics of University of São Paulo to obtain Doctor of Science degree Concentration Area: Bioinformatics Supervisor: Prof. Dr. Helder Takashi Imoto Nakaya During the project development the author received funding from CAPES São Paulo, September 2020 Mindy Stephania De Los Ángeles Muñoz Miranda Imunologia do Câncer de Melanoma Cutâneo: Uma abordagem de Biologia de Sistemas VERSÃO CORRIGIDA Esta versão de tese contém as correções e alterações sugeridas pela Comissão Julgadora durante a defesa da versão original do trabalho, realizada em 28/09/2020. Uma cópia da versão original está disponível no Instituto de Matemática e Estatística da Universidade de São Paulo. This thesis version contains the corrections and changes suggested by the Committee during the defense of the original version of the work presented on 09/28/2020. A copy of the original version is available at Institute of Mathematics and Statistics at the University of São Paulo. Comissão Julgadora: • Prof. Dr. Helder Takashi Imoto Nakaya (Orientador, Não Votante) - FCF-USP • Prof. Dr. André Fujita - IME-USP • Profa. Dra. Patricia Abrão Possik - INCA-Externo • Profa. Dra. Ana Carolina Tahira - I.Butantan-Externo i FICHA CATALOGRÁFICA Muñoz Miranda, Mindy StephaniaFicha de Catalográfica los Ángeles M967 Cancer immunology of cutaneous melanoma: a systems biology approach = Imuno- logia do câncer de melanoma cutâneo: uma abordagem de biologia de sistemas / Mindy Stephania de los Ángeles Muñoz Miranda, [orientador] Helder Takashi Imoto Nakaya. São Paulo : 2020. 58 p. -
2018 Program Book.Indd
32nd Annual Symposium BOSTON July 9 - 12, 2018 Program www.proteinsociety.org Table of Contents #PS32 2 Welcome Mission 3 Program Planning Committee 4 Committees The Protein Society is a not-for-profi t scholarly society 7 Corporate Support with a mission to advance state-of-the-art science through international forums that promote commu- 8 Registration nication, cooperation, and collaboration among scientists involved in the study of proteins. 9 Hotel Floor Plan For 32 years, The Protein Society has served as the in- 11 General Information tellectual home of investigators across all disciplines - and from around the world - involved in the study 16 2018 Protein Society Award Winners of protein structure, function, and design. The Soci- ety provides forums for scientifi c collaboration and 22 Travel Awards communication and supports professional growth of young investigators through workshops, networking 24 At-A-Glance opportunities, and by encouraging junior research- ers to participate fully in the Annual Symposium. In 26 Program addition to our Symposium, the Society’s prestigious journal, Protein Science, serves as an ideal platform 40 Exhibitor Director to further the science of proteins in the broadest sense possible. 50 Poster Presentation Schedule 64 Abstracts: TPS Award Winners & Invited Speakers 86 Posters #PS32 1986 - 2018 1 Welcome Program Planning Committee #PS32 Welcome to Boston and to the 2018 32nd Boston | July 9 - 12, 2018 Annual Symposium of the Protein Society! We are excited to bring you this year’s Annual Symposium comprising twelve exceptional scien- tifi c sessions that cover a wide range of scientifi c achievement in the fi eld of protein science. -
Mutational Scanning Symposium Virtual Event
MUTATIONAL SCANNING SYMPOSIUM VIRTUAL EVENT APRIL 5-7, 2021 1 TABLE OF CONTENTS Welcome 3 Agenda Day 1; April 5 4 Agenda Day 2; April 6 5 Agenda Day 3; April 7 6 Keynote Speakers 7 Artist Alex Cagan 8 Speaker Bios 6 Grace R. Anderson Atina Cote Erika DeBenedictis John Doench Maitreya Dunham Doug Fowler Meghan Garrett Matt Hurles Martin Kampmann Rachel Karchin Ben Lehner (Keynote Speaker) Prashant Mali Deborah Marks Kenneth Matreyek Beatriz Adriana Osuna Maria-Jesus Martin Erik Procko Kimberly A. Reynolds (Keynote Speaker) Frederick (Fritz) Roth Alan Rubin Avtar Singh Lea Starita Tyler N. Starr Clare Turnbull Organizing Committee 17 Virtual Meeting Information 18 Sponsors 19 2 Multiplex Assays of Variant Effects Multiplex Assays of Variant Effects (MAVEs) are key to variant interpretation and are transforming our understanding of the human genome. This annual symposium is sponsored by the Center for the Multiplex Assessment of Phenotype , Illumina, Octant, Wellcome Sanger, and the Brotman Baty Institute. Experts in the field of mutational scanning come from around the world meet to present their work and provide insights on the future of this science for this three-day event which will be held virtually, April 5th-7th 2021. Register to attend HERE 3 Mutational Scanning Symposium April 5-7 2021 All times April 5, 2021 Agenda Pacific Standard Time Lea Starita, PhD | UW 8:00 -08:10 am Welcome, Opening Remarks Kim Reynolds, PhD | UTSW, Dallas (KEYNOTE/featured speaker) 8:10 - 8:55 am Mapping sequence constraints in an essential metabolic enzyme Maitreya Dunham, PhD | UW 8:55 - 9:20 am Deep mutational scanning of pharmacogenes using yeast activity assays. -
Mutational Scanning Symposium
MUTATIONAL SCANNING SYMPOSIUM VIRTUAL EVENT APRIL 5-7, 2021 1 TABLE OF CONTENTS Welcome 3 Agenda Day 1; April 5 4 Agenda Day 2; April 6 5 Agenda Day 3; April 7 6 Keynote Speakers 7 Artist Alex Cagan 8 Speaker Bios 6 Grace R. Anderson Atina Cote Erika DeBenedictis John Doench Maitreya Dunham Doug Fowler Meghan Garrett Matt Hurles Martin Kampmann Rachel Karchin Ben Lehner (Keynote Speaker) Prashant Mali Deborah Marks Kenneth Matreyek Beatriz Adriana Osuna Maria-Jesus Martin Erik Procko Kimberly A. Reynolds (Keynote Speaker) Frederick (Fritz) Roth Alan Rubin Avtar Singh Lea Starita Tyler N. Starr Clare Turnbull Organizing Committee 17 Virtual Meeting Information 18 Sponsors 19 2 Multiplex Assays of Variant Effects Multiplex Assays of Variant Effects (MAVEs) are key to variant interpretation and are transforming our understanding of the human genome. This annual symposium is sponsored by the Center for the Multiplex Assessment of Phenotype , Illumina, Octant, Wellcome Sanger, and the Brotman Baty Institute. Experts in the field of mutational scanning come from around the world meet to present their work and provide insights on the future of this science for this three-day event which will be held virtually, April 5th-7th 2021. Register to attend HERE 3 Mutational Scanning Symposium April 5-7 2021 All times April 5, 2021 Agenda Pacific Standard Time Lea Starita, PhD | UW 8:00 -08:10 am Welcome, Opening Remarks Kim Reynolds, PhD | UTSW, Dallas (KEYNOTE/featured speaker) 8:10 - 8:55 am Mapping sequence constraints in an essential metabolic enzyme Maitreya Dunham, PhD | UW 8:55 - 9:20 am Deep mutational scanning of pharmacogenes using yeast Activity assays. -
Bio::Graphics HOWTO Lincoln Stein Cold Spring Harbor Laboratory1 [email protected]
Bio::Graphics HOWTO Lincoln Stein Cold Spring Harbor Laboratory1 [email protected] This HOWTO describes how to render sequence data graphically in a horizontal map. It applies to a variety of situations ranging from rendering the feature table of a GenBank entry, to graphing the positions and scores of a BLAST search, to rendering a clone map. It describes the programmatic interface to the Bio::Graphics module, and discusses how to create dynamic web pages using Bio::DB::GFF and the gbrowse package. Table of Contents Introduction ...........................................................................................................................3 Preliminaries..........................................................................................................................3 Getting Started ......................................................................................................................3 Adding a Scale to the Image ...............................................................................................5 Improving the Image............................................................................................................7 Parsing Real BLAST Output...............................................................................................8 Rendering Features from a GenBank or EMBL File ....................................................12 A Better Version of the Feature Renderer ......................................................................14 Summary...............................................................................................................................18 -
UCLA UCLA Electronic Theses and Dissertations
UCLA UCLA Electronic Theses and Dissertations Title Bipartite Network Community Detection: Development and Survey of Algorithmic and Stochastic Block Model Based Methods Permalink https://escholarship.org/uc/item/0tr9j01r Author Sun, Yidan Publication Date 2021 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Bipartite Network Community Detection: Development and Survey of Algorithmic and Stochastic Block Model Based Methods A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Statistics by Yidan Sun 2021 © Copyright by Yidan Sun 2021 ABSTRACT OF THE DISSERTATION Bipartite Network Community Detection: Development and Survey of Algorithmic and Stochastic Block Model Based Methods by Yidan Sun Doctor of Philosophy in Statistics University of California, Los Angeles, 2021 Professor Jingyi Li, Chair In a bipartite network, nodes are divided into two types, and edges are only allowed to connect nodes of different types. Bipartite network clustering problems aim to identify node groups with more edges between themselves and fewer edges to the rest of the network. The approaches for community detection in the bipartite network can roughly be classified into algorithmic and model-based methods. The algorithmic methods solve the problem either by greedy searches in a heuristic way or optimizing based on some criteria over all possible partitions. The model-based methods fit a generative model to the observed data and study the model in a statistically principled way. In this dissertation, we mainly focus on bipartite clustering under two scenarios: incorporation of node covariates and detection of mixed membership communities. -
Stein Gives Bioinformatics Ten Years to Live
O'Reilly Network: Stein Gives Bioinformatics Ten Years to Live http://www.oreillynet.com/lpt/a/3205 Published on O'Reilly Network (http://www.oreillynet.com/) http://www.oreillynet.com/pub/a/network/biocon2003/stein.html See this if you're having trouble printing code examples Stein Gives Bioinformatics Ten Years to Live by Daniel H. Steinberg 02/05/2003 Lincoln Stein's keynote at the O'Reilly Bioinformatics Technology Conference was provocatively titled "Bioinformatics: Gone in 2012." Despite the title, Stein is optimistic about the future for people doing bioinformatics. But he explained that "the field of bioinformatics will be gone by 2012. The field will be doing the same thing but it won't be considered a field." His address looked at what bioinformatics is and what its future is likely to be in the context of other scientific disciplines. He also looked at career prospects for people doing bioinformatics and provided advice for those looking to enter the field. What Is Bioinformatics: Take One Stein, of the Cold Spring Harbor Laboratory, began his keynote by examining what is meant by bioinformatics. In the past such a talk would begin with a definition displayed from an authoritative dictionary. The modern approach is to appeal to an FAQ from an authoritative web site. Take a look at the FAQ at bioinformatics.org and you'll find several definitions. Stein summarized Fedj Tekaia of the Institut Pasteur--that bioinformatics is DNA and protein analysis. Stein also summarized Richard Durbin of the Sanger Institute--that bioinformatics is managing data sets. Stein's first pass at a definition of bioinformatics is that it is "Biologists using computers or the other way around." He followed by observing that whatever it is, it's growing. -
Thesis Reference
Thesis Analysis of large biological data: metabolic network modularization and prediction of N-terminal acetylation CHARPILLOZ, Christophe Abstract During last decades, biotechnology advances allowed to gather a huge amount of biological data. This data ranges from genome composition to the chemical interactions occurring in the cell. Such huge amount of information requires the application of complex algorithms to reveal how they are organized in order to understand the underlying biology. The metabolism forms a class of very complex data and the graphs that represent it are composed of thousands of nodes and edges. In this thesis we propose an approach to modularize such networks to reveal their internal organization. We have analyzed red blood cells' networks corresponding to pathological states and the obtained in-silico results were corroborated by known in-vitro analysis. In the second part of the thesis we describe a learning method that analyzes thousands of sequences from the UniProt database to predict the N-alpha-terminal acetylation. This is done by automatically discovering discriminant motifs that are combined in a binary decision tree manner. Prediction performances on N-alpha-terminal acetylation are higher than the other published classifiers. Reference CHARPILLOZ, Christophe. Analysis of large biological data: metabolic network modularization and prediction of N-terminal acetylation. Thèse de doctorat : Univ. Genève, 2015, no. Sc. 4883 URN : urn:nbn:ch:unige-860463 DOI : 10.13097/archive-ouverte/unige:86046 Available