The Application of Hadoop in Structural Bioinformatics
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Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
Gene Prediction: the End of the Beginning Comment Colin Semple
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central http://genomebiology.com/2000/1/2/reports/4012.1 Meeting report Gene prediction: the end of the beginning comment Colin Semple Address: Department of Medical Sciences, Molecular Medicine Centre, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK. E-mail: [email protected] Published: 28 July 2000 reviews Genome Biology 2000, 1(2):reports4012.1–4012.3 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2000/1/2/reports/4012 © GenomeBiology.com (Print ISSN 1465-6906; Online ISSN 1465-6914) Reducing genomes to genes reports A report from the conference entitled Genome Based Gene All ab initio gene prediction programs have to balance sensi- Structure Determination, Hinxton, UK, 1-2 June, 2000, tivity against accuracy. It is often only possible to detect all organised by the European Bioinformatics Institute (EBI). the real exons present in a sequence at the expense of detect- ing many false ones. Alternatively, one may accept only pre- dictions scoring above a more stringent threshold but lose The draft sequence of the human genome will become avail- those real exons that have lower scores. The trick is to try and able later this year. For some time now it has been accepted increase accuracy without any large loss of sensitivity; this deposited research that this will mark a beginning rather than an end. A vast can be done by comparing the prediction with additional, amount of work will remain to be done, from detailing independent evidence. -
Current Topics in Computational Molecular Biology Edited by Tao Jiang Ying Xu Michael Q. Zhang a Bradford Book the MIT Press
Current Topics in Computational Molecular Biology edited by Tao Jiang Ying Xu Michael Q. Zhang A Bradford Book The MIT Press Cambridge, Massachusetts London, England Contents Preface vii I INTRODUCTION 1 1 The Challenges Facing Genomic Informatics 3 Temple F. Smith H COMPARATIVE SEQUENCE AND GENOME ANALYSIS 9 2 Bayesian Modeling and Computation in Bioinformatics Research 11 Jun S. Liu 3 Bio-Sequence Comparison and Applications 45 Xiaoqiu Huang 4 Algorithmic Methods for Multiple Sequence Alignment 71 Tao Jiang and Lusheng Wang 5 Phylogenetics and the Quartet Method 111 Paul Kearney 6 Genome Rearrangement 135 David Sankoff and Nadia El-Mabrouk 7 Compressing DNA Sequences 157 Ming Li HI DATA MINING AND PATTERN DISCOVERY 173 8 Linkage Analysis of Quantitative Traits 175 Shizhong Xu , 9 Finding Genes by Computer: Probabilistic and Discriminative Approaches 201 Victor V. Solovyev 10 Computational Methods for Promoter Recognition 249 Michael Q. Zhang 11 Algorithmic Approaches to Clustering Gene Expression Data 269 Ron Shamir and Roded Sharan 12 KEGG for Computational Genomics 301 Minoru Kanehisa and Susumu Goto vi Contents 13 Datamining: Discovering Information from Bio-Data 317 Limsoon Wong IV COMPUTATIONAL STRUCTURAL BIOLOGY 343 14 RNA Secondary Structure Prediction 345 Zhuozhi Wang and Kaizhong Zhang 15 Properties and Prediction of Protein Secondary Structure 365 Victor V. Solovyev and Ilya N. Shindyalov 16 Computational Methods for Protein Folding: Scaling a Hierarchy of Complexities 403 Hue Sun Chan, Huseyin Kaya, and Seishi Shimizu 17 Protein Structure Prediction by Comparison: Homology-Based Modeling 449 Manuel C. Peitsch, Torsten Schwede, Alexander Diemand, and Nicolas Guex 18 Protein Structure Prediction by Protein Threading and Partial Experimental Data 467 Ying Xu and Dong Xu 19 Computational Methods for Docking and Applications to Drug Design: Functional Epitopes and Combinatorial Libraries 503 Ruth Nussinov, Buyong Ma, and Haim J. -
Meeting Review: Bioinformatics and Medicine – from Molecules To
Comparative and Functional Genomics Comp Funct Genom 2002; 3: 270–276. Published online 9 May 2002 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.178 Feature Meeting Review: Bioinformatics And Medicine – From molecules to humans, virtual and real Hinxton Hall Conference Centre, Genome Campus, Hinxton, Cambridge, UK – April 5th–7th Roslin Russell* MRC UK HGMP Resource Centre, Genome Campus, Hinxton, Cambridge CB10 1SB, UK *Correspondence to: Abstract MRC UK HGMP Resource Centre, Genome Campus, The Industrialization Workshop Series aims to promote and discuss integration, automa- Hinxton, Cambridge CB10 1SB, tion, simulation, quality, availability and standards in the high-throughput life sciences. UK. The main issues addressed being the transformation of bioinformatics and bioinformatics- based drug design into a robust discipline in industry, the government, research institutes and academia. The latest workshop emphasized the influence of the post-genomic era on medicine and healthcare with reference to advanced biological systems modeling and simulation, protein structure research, protein-protein interactions, metabolism and physiology. Speakers included Michael Ashburner, Kenneth Buetow, Francois Cambien, Cyrus Chothia, Jean Garnier, Francois Iris, Matthias Mann, Maya Natarajan, Peter Murray-Rust, Richard Mushlin, Barry Robson, David Rubin, Kosta Steliou, John Todd, Janet Thornton, Pim van der Eijk, Michael Vieth and Richard Ward. Copyright # 2002 John Wiley & Sons, Ltd. Received: 22 April 2002 Keywords: bioinformatics; -
Bonnie Berger Named ISCB 2019 ISCB Accomplishments by a Senior
F1000Research 2019, 8(ISCB Comm J):721 Last updated: 09 APR 2020 EDITORIAL Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient [version 1; peer review: not peer reviewed] Diane Kovats 1, Ron Shamir1,2, Christiana Fogg3 1International Society for Computational Biology, Leesburg, VA, USA 2Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel 3Freelance Writer, Kensington, USA First published: 23 May 2019, 8(ISCB Comm J):721 ( Not Peer Reviewed v1 https://doi.org/10.12688/f1000research.19219.1) Latest published: 23 May 2019, 8(ISCB Comm J):721 ( This article is an Editorial and has not been subject https://doi.org/10.12688/f1000research.19219.1) to external peer review. Abstract Any comments on the article can be found at the The International Society for Computational Biology (ISCB) honors a leader in the fields of computational biology and bioinformatics each year with the end of the article. Accomplishments by a Senior Scientist Award. This award is the highest honor conferred by ISCB to a scientist who is recognized for significant research, education, and service contributions. Bonnie Berger, Simons Professor of Mathematics and Professor of Electrical Engineering and Computer Science at the Massachusetts Institute of Technology (MIT) is the 2019 recipient of the Accomplishments by a Senior Scientist Award. She is receiving her award and presenting a keynote address at the 2019 Joint International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology in Basel, Switzerland on July 21-25, 2019. Keywords ISCB, Bonnie Berger, Award This article is included in the International Society for Computational Biology Community Journal gateway. -
The Ethos and Effects of Data-Sharing Rules: Examining The
Informed consent for: "The ethos and effects of data-sharing rules: Examining the history of the 'Bermuda principles' and their effects on 21 st century science" University of Adelaide Duke University Researchers at the University of Adelaide, Australia, and the IGSP Center for Genome Ethics, Law & Policy, Duke University, are engaged in research on the Bermuda Principles for sharing DNA sequence data from high-volume sequencing centers. You have been selected for an interview because we believe that the recollections you may have of your experiences with the International Strategy Meetings for Human Genome Sequencing (1996-1998) will be interesting and helpful for our project. We expect that interviews will last from 30 minutes to much longer, but you may stop your interview at any time. Your participation is strictly voluntary, and you do not have to answer every question asked. Your interview is being recorded and we may take written notes during the interview. After your interview, we may prepare a typed transcript of the interview. If we prepare a transcript, you will have an opportunity to review it and to make deletions and corrections. Unless you indicate otherwise, the information that you provide in this interview will be "on the record"-that is, it can be attributed to you in the various articles and chapters that we plan to write, and thus could become public through these channels. Jf, however, at some point in the interview you want to provide us with information that might be useful for us to know, but which you do not want to have attributed to you, you should tell us that you wish to go "off the record" and we will stop the recording. -
ISMB 99 August 6 – 10, 1999 Heidelberg, Germany the Seventh
______________________________________ Welcome to ISMB 99 August 6 – 10, 1999 Heidelberg, Germany The Seventh International Conference on Intelligent Systems for Molecular Biology ______________________________________ Final Program and Detailed Schedule Friday, August 6, 1999 Tutorial Day The tutorials will take place in the following rooms: 8:30 – 12:30 (Coffee break around 10:30) Tutorial #1 Trübnersaal Piere Baldi Probabilistic graphical models Tutorial #2 Robert-Schumann-Zimmer Douglas L. Brutlag Bioinformatics and Molecular Biology Tutorial #3 Ballsaal Martin Reese The challenge of annotating a complete eukaryotic genome: A case study in Drosophila melanogaster Tutorial #4 Gustav-Mahler-Zimmer Tandy Warnow Computational and statistical Junhyong Kim challenges involved in reconstructing evolutionary trees Tutorial #5 Sebastian-Münster-Saal Thomas Werner The biology and bioinformatics of regulatory regions in genomes Lunch (on this day served in "Grosser Saal" on the ground floor) 13:30 – 17:30 (Coffee break around 15:30) Tutorial #6 Sebastian-Münster-Saal Rob Miller EST Clustering Alan Christoffels Winston Hide Tutorial #7 Trübnersaal Kevin Karplus Getting the most out of hidden Markov Melissa Cline models Christian Barrett Tutorial #8 Robert-Schumann-Zimmer Arthur Lesk Sequence-structure relationships and evolutionary structure changes in proteins Tutorial #9 Gustav-Mahler-Zimmer David States PERL abstractions for databases and Brian Dunford distributed computing Shore Tutorial # 10 Ballsaal Zoltan Szallasi Genetic network analysis -
Contcenter for Genomic Regul
CONTCENTER FOR GENOMIC REGUL CRG SCIENTIFIC STRUCTURE . 4 CRG MANAGEMENT STRUCTURE . 6 CRG SCIENTIFIC ADVISORY BOARD (SAB) . 8 CRG BUSINESS BOARD . 9 YEAR RETROSPECT BY THE DIRECTOR OF THE CRG: MIGUEL BEATO . 10 GENE REGULATION. 14 p Chromatin and gene expression .....................16 p Transcriptional regulation and chromatin remodelling .....19 p Regulation of alternative pre-mRNA splicing during cell . 22 differentiation, development and disease p RNA interference and chromatin regulation . 26 p RNA-protein interactions and regulation . 30 p Regulation of protein synthesis in eukaryotes . 33 p Translational control of gene expression . 36 DIFFERENTIATION AND CANCER ...........................40 p Hematopoietic differentiation and stem cell biology..........42 p Myogenesis.....................................46 p Epigenetics events in cancer.......................49 p Epithelial homeostasis and cancer ...................52 ENTSATION ANNUAL REPORT 2006 GENES AND DISEASE .................................56 p Genetic causes of disease .............................58 p Gene therapy ......................................63 p Murine models of disease .............................66 p Neurobehavioral phenotyping of mouse models of disease .....68 p Gene function ......................................73 p Associated Core Facility: Genotyping Unit..................76 BIOINFORMATICS AND GENOMICS ..........................80 p Bioinformatics and genomics ...........................82 p Genomic analysis of development and disease ..............86 -
Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: a European Perspective
1 Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective Attwood, T.K.1, Gisel, A.2, Eriksson, N-E.3 and Bongcam-Rudloff, E.4 1Faculty of Life Sciences & School of Computer Science, University of Manchester 2Institute for Biomedical Technologies, CNR 3Uppsala Biomedical Centre (BMC), University of Uppsala 4Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences 1UK 2Italy 3,4Sweden 1. Introduction The origins of bioinformatics, both as a term and as a discipline, are difficult to pinpoint. The expression was used as early as 1977 by Dutch theoretical biologist Paulien Hogeweg when she described her main field of research as bioinformatics, and established a bioinformatics group at the University of Utrecht (Hogeweg, 1978; Hogeweg & Hesper, 1978). Nevertheless, the term had little traction in the community for at least another decade. In Europe, the turning point seems to have been circa 1990, with the planning of the “Bioinformatics in the 90s” conference, which was held in Maastricht in 1991. At this time, the National Center for Biotechnology Information (NCBI) had been newly established in the United States of America (USA) (Benson et al., 1990). Despite this, there was still a sense that the nation lacked a “long-term biology ‘informatics’ strategy”, particularly regarding postdoctoral interdisciplinary training in computer science and molecular biology (Smith, 1990). Interestingly, Smith spoke here of ‘biology informatics’, not bioinformatics; and the NCBI was a ‘center for biotechnology information’, not a bioinformatics centre. The discipline itself ultimately grew organically from the needs of researchers to access and analyse (primarily biomedical) data, which appeared to be accumulating at alarming rates simultaneously in different parts of the world. -
Computational Biology: Plus C'est La Même Chose, Plus Ça Change
Computational biology: plus c'est la même chose, plus ça change The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Huttenhower, Curtis. 2011. Computational biology: plus c'est la même chose, plus ça change. Genome Biology 12(8): 307. Published Version doi:10.1186/gb-2011-12-8-307 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:10576037 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Huttenhower Genome Biology 2011, 12:307 http://genomebiology.com/2011/12/8/307 MEETING REPORT Computational biology: plus c’est la même chose, plus ça change Curtis Huttenhower* The data deluge: still keeping our heads above water Abstract Bioinformatics has been dealing with an exponential A report on the joint 19th Annual International growth in data since its coalescence as a field in the Conference on Intelligent Systems for Molecular 1980s, making the Senior Scientist Award keynote with Biology (ISMB)/10th Annual European Conference which Michael Ashburner closed the conference on Computational Biology (ECCB) meetings and particularly appropriate. This retrospective by the ‘father the 7th International Society for Computational of ontologies in biology’, to quote the introduction by Biology Student Council Symposium, Vienna, Austria, ISCB president Burkhard Rost, detailed the remarkable 15‑19 July 2011. expansion of computational biology since Ashburner’s start as a Cambridge undergraduate 50 years ago. -
CSHL Audio Visual Collection Inventory
CSHL AV Collection Inventory 1 CSHL Audio Visual Collection Inventory BOX VIDEOTAPE TITLE TITLE # TAPE # DATE CATEGORY FORMAT 1 ZEBRA FISH 419 #1 1/1/1996 Fish Hi8 1 ZEBRA FISH 420 #2 1/1/1996 Fish Hi8 1 TRINKAUS 421 1/1/1996 Lecture Hi8 1 GENOME 423 #1 1/1/1996 Genome Hi8 1 GENOME 424 #2 1/1/1996 Genome Hi8 1 THE CELL CYCLE 425 #1 5/15/1996 Cell Hi8 1 THE CELL CYCLE 426 #2 5/15/1996 Cell Hi8 1 RETROVIRUSES 427 5/21/1996 Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NE RVOUS SYSTEM 428 #1 5/29/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 429 #2 5/30/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 430 #3 5/30/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 431 #4 5/31/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 432 #5 5/31/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 433 #6 6/1/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 434 #7 6/1/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 435 #8 7/9/1998 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 436 #9 6/2/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 437 #10 6/2/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 438 #11 6/3/1996 Symposium Hi8 SYMPOSIUM 96: FUNCTION & DISFUNCTION OF 1 THE NERVOUS SYSTEM 439 #12 6/3/1996 Symposium Hi8 CSHL AV Collection Inventory 2 -
Flymine: an Integrated Database for Drosophila and Anopheles Genomics
Open Access Software2007LyneetVolume al. 8, Issue 7, Article R129 FlyMine: an integrated database for Drosophila and Anopheles comment genomics Rachel Lyne*, Richard Smith*, Kim Rutherford*, Matthew Wakeling*, Andrew Varley*, Francois Guillier*, Hilde Janssens*, Wenyan Ji*, Peter Mclaren*, Philip North*, Debashis Rana*, Tom Riley*, Julie Sullivan*, Xavier Watkins*, Mark Woodbridge*, Kathryn Lilley†, Steve Russell*, Michael Ashburner*, Kenji Mizuguchi†‡§ and Gos Micklem*‡ reviews Addresses: *Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK. †Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK. ‡Cambridge Computational Biology Institute, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 OWA, UK. §National Institute of Biomedical Innovation 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan. Correspondence: Gos Micklem. Email: [email protected] reports Published: 5 July 2007 Received: 15 November 2006 Revised: 6 March 2007 Genome Biology 2007, 8:R129 (doi:10.1186/gb-2007-8-7-r129) Accepted: 5 June 2007 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2007/8/7/R129 deposited research © 2007 Lyne et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The<p>Thissophila FlyMine </it>and novel database web-based <it>Anopheles</it>.</p> database provides unique accessibility and querying of integrated genomic and proteomic data for <it>Dro- Abstract refereed research refereed FlyMine is a data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data.