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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 -
Experimental and Computational Requirements for Post-Genomic Integrative Cellular Physiology John Wikswo
VANDERBILT INSTITUTE FOR INTEGRATIVE BIOSCIENCE RESEARCH AND EDUCATION (VIIBRE) Experimental and Computational Requirements for Post-Genomic Integrative Cellular Physiology John Wikswo Instrumenting and the Single Cell Controlling 1 Topics • The advantages of micro/nanoscale instruments • Cellular complexity • The need for closed-loop control • How to identify early manifestations of disease – Modeling – Interactive, dynamical analysis – Mining dynamics data 2 Topics • The advantages of micro/nanoscale instruments • Cellular complexity • The need for closed-loop control • How to identify early manifestations of disease – Modeling – Interactive, dynamical analysis – Mining dynamics data 3 Reductionism in Science Thermodynamics Bulk solids Anatomy Statistical Devices Physiology mechanics Continuum Organ Molecular/atomic models dynamics Cell Microscopic Electrodynamics models Protein Quantum Atomic physics Genome Chromodynamics 4 Historical Evolution of Spatial Resolution in Biology and Physiology 3000 • Genomics Molecular Physiology Biology Cell 2000 –Structural Molecule Cell genomics 1000 X-Ray / SEM / STM … Optical microscope 0 • Proteomics Tissue –Structural -1000 Magnifying glass proteomics -2000 –Functional HistoricalYears Time, proteomics Unaided eye AnimalAnimal -3000 … • What is next? 10-9 10-6 10-3 100 Resolution, Meters 5 TheThe raterate atat whichwhich DNADNA sequencessequences beganbegan accumulatingaccumulating waswas exponentialexponential 14,000,000 ~13 million 12,000,000 sequence entries 10,000,000 in GenBank 8,000,000 Nearly 13 billion 6,000,000 bases from Human Genome Rapid DNA 4,000,000 Project begun ~50,000 species sequencing invented 2,000,000 GB 0 1965 1970 1975 1980 1985 1990 1995 2001 Year National Library of Medicine Courtesy of Mark Boguski 6 Hypotheses I and II I. The explosion in genomic and proteomic knowledge and measurement techniques will revolutionize the early detection of diseases II. -
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, -
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 -
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. -
Download This PDF File
SpecialSpecial iissuessue EMBnetEMBnet CConferenceonference 22008008 – 2200thth AnniversaryAnniversary CCelebration:elebration: ProgrammeProgramme aandnd AAbstractbstract BBookook 2 EMBnet Volume 14 Nr. 3 Editorial Contents The present volume is a special number for Editorial .............................................................. 2 several reasons. Our 20th aniversary may be Nils-Einar Eriksson: “EMBnet, a brief history and a the most important one. But, for our readers it current picture” .................................................. 3 represents a chance of getting the abstracts, the program and the list of participants in the Pedro Fernandes: “The spirit of EMBnet and its 2008 EMBnet conference, on top of our usual human dimension” ............................................ 6 set of articles. In this issue we tried to obtain Laurent Falquet : “The fabulous destiny of texts about EMBnet's early steps and its role EMBnet.news ”.................................................... 8 for so many Bioinformatics users and profes- sionals, with its presence, its spirit as a support José R. Valverde: “The EMBnet e-learning server”. 9 provider, and its outreach, mainly obtained Conference Programme ................................. 15 with EMBnet.news. An article on EMBnet's - Committees..................................................... 16 e-learning portal brings you up to date with Welcome letter ................................................ 17 what our community is doing in this area. As- usual feel free to comment on -
Existing and Emerging Information Technologies That Affect Genomic Data Sharing
Existing and Emerging Information Technologies that Affect Genomic Data Sharing Joyce A. Mitchell, PhD Associate Vice President, Health Sciences IT Professor and Chair, Dept of Biomedical Informatics University of Utah, Salt Lake City, UT Genomics • You know a lot about Genomics – Human Genome Project complete in 2003 25,000 genes, perhaps 1,000,000 proteins – HapMap completed in 2005 More than 1 million SNPs – Now over 5000 genomes available online – Incredible information is available online Public data repositories are routine 2 Genomics (cont) – Almost 1900 specific genetic tests available – 1 million SNP chip studies are routine – GWAS studies are rapidly expanding knowledge (looking for G2P associations) – Gene expression studies are impacting clinical care Gene function can be measured and used diagnostically – Next Generation Sequencing has arrived. Avg variant file for a complete human sequence is 3.1 – 4.5 M SNPs, and about 10% more for INDELs, etc. Science 2009. 19892942 3 Consumer Demand for Genetics Information is Exploding! What is the GHR? http://ghr.nlm.nih.gov/ • An information system focusing on the health implications of research arising from the Human Genome Project – Targets the public – Bridges consumer health information and bioinformatics data – Links to existing resources (NLM and other) 5 6 Genetics Home Reference statistics • 500 health conditions • 700 curated + 1800 auto- generated gene summaries • 215 million hits per year As of 11-2009 7 Direct to Consumer Genetic Testing A huge force for changing the -
Signature of Author
An Analysis of Representations for Protein Structure Prediction by Barbara K. Moore Bryant S.B., S.M., Massachusetts Institute of Technology (1986) 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 September 1994 ( Massachusetts Institute of Technology 1994 SignatureofAuthor ............. ,...... ........-.. .. Department of Electrical Engineering and Computer Science September 2, 1994 Certified by... ..... -- Patrick. H. Winston Professor, Electrical Engineering and Computer Science This Supervisor %-"ULfrtifioAvL.Lv--k &y ho, . Tomas o) no-Perez and Computer Science L! Thp.i. .,nPrvi.qnr Accepted by .. ... , a. ,- · F' drY................... / Frederic~) R. Morgenthaler Departmental /Committee on Graduate Students Iv:r tfF:r _ ;: ! --.. t.8r'(itr i-7etFr An Analysis of Representations for Protein Structure Prediction by Barbara K. Moore Bryant Submitted to the Department of Electrical Engineering and Computer Science on September 2, 1994, in partial fulfillment of the requirements for the degree of Doctor of Philosophy Abstract Protein structure prediction is a grand challenge in' the fields of biology and computer science. Being able to quickly determine the structure of a protein from its amino acid sequence would be extremely useful to biologists interested in elucidating the mechanisms of life and finding ways to cure disease. In spite of a wealth of knowl- edge about proteins and their structure, the structure prediction problem has gone unsolved in the nearly forty years since the first determination of a protein structure by X-ray crystallography. In this thesis, I discuss issues in the representation of protein structure and se- quence for algorithms which perform structure prediction. -
Graphical Pangenomics
Graphical pangenomics Erik Peter Garrison Wellcome Sanger Institute University of Cambridge This dissertation is submitted for the degree of Doctor of Philosophy Fitzwilliam College September 2018 for E2 & E3 Declaration I hereby declare that except where specific reference is made to the work of others, the contents of this dissertation are original and have not been submitted in whole or in part for consideration for any other degree or qualification in this, or any other university. This dissertation is my own work and contains nothing which is the outcome of work done in collaboration with others, except as specified in the text and Acknowledgements. This dissertation contains fewer than 65,000 words including appendices, bibliography, footnotes, tables and equations and has fewer than 150 figures. Erik Peter Garrison September 2018 Graphical pangenomics Erik Peter Garrison Completely sequencing genomes is expensive, and to save costs we often analyze new genomic data in the context of a reference genome. This approach distorts our image of the inferred genome, an effect which we describe as reference bias. To mitigate reference bias, I repurpose graphical models previously used in genome assembly and alignment to serve as a reference system in resequencing. To do so I formalize the concept of a variation graph to link genomes to a graphical model of their mutual alignment that is capable of representing any kind of genomic variation, both small and large. As this model combines both sequence and variation information in one structure it serves as a natural basis for resequencing. By indexing the topology, sequence space, and haplotype space of these graphs and developing generalizations of sequence alignment suitable to them, I am able to use them as reference systems in the analysis of a wide array of genomic systems, from large vertebrate genomes to microbial pangenomes. -
Connecting the Dots
© 1999 Nature America Inc. • http://genetics.nature.com editorial volume 23 no. 3 november 1999 Connecting the dots As expressed by Francis Collins (director of the National Human Genome Research Institute (NHGRI)) in The Chipping Forecast1, it is too early to predict the ultimate impact of microarrays on our understanding of biology, and genetics in particular. Data presented at a recent Nature Genetics conference* indicate that estimates of impact and rate of progress should not be conservative. Two previous microarray meetings2 focused more heavily on technological aspects. Whereas aspects of the technology received some airtime at this year’s meeting, the substan- http://genetics.nature.com • tive nature of presentations that focused on biological questions indicates that the field, such as it is, is advancing quickly. Abstracts of oral and poster presentations are freely available (http://genetics.nature.com/microarray). Comprehensive analysis in yeast. The most extensive array analyses have been carried out in Saccharomyces cerevisiae, where approximately 250 sequence-spe- cific regulators interact with at least 100 components of the transcription appara- tus to effect the expression of over 6000 genes3. The hope is that microarray analysis will permit a detailed understanding of the transcriptional pathways that Carina Dennis 1999 Nature America Inc. © underlie cellular metabolism. From the data to hand, it is clear that gene expres- Mark Boguski scans the horizon. sion patterns are clustered; groups of genes are expressed in similar patterns throughout the cell cycle and under a variety of environmental conditions. The hypothesis that these genes are co-regulated at the transcriptional level is corrobo- rated by a growing number of studies.