Discovery and Analysis of Aligned Pattern Clusters from Protein Family Sequences
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SD Gross BFI0403
Janet Thornton Bioinformatician avant la lettre Michael Gross B ioinformatics is very much a buzzword of our time, with new courses and institutes dedicated to it sprouting up almost everywhere. Most significantly, the flood of genome data has raised the gen- eral awareness of the need to deve-lop new computational approaches to make sense of all the raw information collected. Professor Janet Thornton, the current director of the European Bioinformatics Institute (EBI), an EMBL outpost based at the Hinxton campus near Cambridge, has been in the field even before there was a word for it. Coming to structural biology with a physics degree from the University of Nottingham, she was already involved with computer-generated structural im- ages in the 1970s, when personal comput- ers and user-friendly programs had yet to be invented. The Early Years larities. Within 15 minutes, the software From there to the EBI, her remarkable Janet Thornton can check all 2.4 billion possible re- career appears to be organised in lationships and pick the ones relevant decades. During the 1970s, she did doc- software to compare structures to each to the question at hand. In comparison toral and post-doctoral research at other, recognise known folds and spot to publicly available bioinformatics the Molecular Biophysics Laboratory in new ones. Such work provides both packages such as Blast or Psiblast, Oxford and at the National Institute for fundamental insights into the workings Biopendium can provide an additional Medical Research in Mill Hill, near Lon- of evolution on a molecular level, and 30 % of annotation, according to Inphar- don. -
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. -
The EMBL-European Bioinformatics Institute the Hub for Bioinformatics in Europe
The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe Blaise T.F. Alako, PhD [email protected] www.ebi.ac.uk What is EMBL-EBI? • Part of the European Molecular Biology Laboratory • International, non-profit research institute • Europe’s hub for biological data, services and research The European Molecular Biology Laboratory Heidelberg Hamburg Hinxton, Cambridge Basic research Structural biology Bioinformatics Administration Grenoble Monterotondo, Rome EMBO EMBL staff: 1500 people Structural biology Mouse biology >60 nationalities EMBL member states Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia Who we are ~500 members of staff ~400 work in services & support >53 nationalities ~120 focus on basic research EMBL-EBI’s mission • Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • Contribute to the advancement of biology through basic investigator-driven research in bioinformatics • Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • Help disseminate cutting-edge technologies to industry • Coordinate biological data provision throughout Europe Services Data and tools for molecular life science www.ebi.ac.uk/services Browse our services 9 What services do we provide? Labs around the -
Functional Effects Detailed Research Plan
GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data. -
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; -
The London Diplomatic List
UNCLASSIFIED THE LONDON DIPLOMATIC LIST Alphabetical list of the representatives of Foreign States & Commonwealth Countries in London with the names & designations of the persons returned as composing their Diplomatic Staff. Representatives of Foreign States & Commonwealth Countries & their Diplomatic Staff enjoy privileges & immunities under the Diplomatic Privileges Act, 1964. Except where shown, private addresses are not available. m Married * Married but not accompanied by wife or husband AFGHANISTAN Embassy of the Islamic Republic of Afghanistan 31 Princes Gate SW7 1QQ 020 7589 8891 Fax 020 7584 4801 [email protected] www.afghanistanembassy.org.uk Monday-Friday 09.00-16.00 Consular Section 020 7589 8892 Fax 020 7581 3452 [email protected] Monday-Friday 09.00-13.30 HIS EXCELLENCY DR MOHAMMAD DAUD YAAR m Ambassador Extraordinary & Plenipotentiary (since 07 August 2012) Mrs Sadia Yaar Mr Ahmad Zia Siamak m Counsellor Mr M Hanif Ahmadzai m Counsellor Mr Najibullah Mohajer m 1st Secretary Mr M. Daud Wedah m 1st Secretary Mrs Nazifa Haqpal m 2nd Secretary Miss Freshta Omer 2nd Secretary Mr Hanif Aman 3rd Secretary Mrs Wahida Raoufi m 3rd Secretary Mr Yasir Qanooni 3rd Secretary Mr Ahmad Jawaid m Commercial Attaché Mr Nezamuddin Marzee m Acting Military Attaché ALBANIA Embassy of the Republic of Albania 33 St George’s Drive SW1V 4DG 020 7828 8897 Fax 020 7828 8869 [email protected] www.albanianembassy.co.uk HIS EXELLENCY MR MAL BERISHA m Ambassador Extraordinary & Plenipotentiary (since 18 March 2013) Mrs Donika Berisha UNCLASSIFIED S:\Protocol\DMIOU\UNIVERSAL\Administration\Lists of Diplomatic Representation\LDL\RESTORED LDL Master List - Please update this one!.doc UNCLASSIFIED Dr Teuta Starova m Minister-Counsellor Ms Entela Gjika Counsellor Mrs Gentjana Nino m 1st Secretary Dr Xhoana Papakostandini m 3rd Secretary Col. -
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 . -
Contents and Society
8 EMBL August 2001 &cetera Newsletter of the European Molecular Biology Laboratory published by the Office of Information and Public Affairs EMBL appoints heads for Hinxton and Monterotondo MBLhas appointed new heads of the EBI in Hinxton and the A priority for both scientists will be to boost research activities at EMouse Biology Programme in Monterotondo. Nadia their units. Past funding limitations have prevented the EBI from Rosenthal, Associate Professor at Harvard and consulting editor developing a full research programme, although there have been at the New England Journal of Medicine, has taken charge of the a few very active groups since the site was opened. New funds Mouse Biology Programme, assuming the post vacated by Klaus from the EMBL member states will permit the addition of a full Rajewsky in June. Janet Thornton, Professor at the University complement of research teams, just as Cameron and his col- College of London and Fellow of the Royal Society, will direct leagues have been extremely successful in obtaining major fund- activities at the EBI, especially research. She succeeds Michael ing from the EC and the Wellcome Trust to bolster the EBI data- Ashburner, who has served as Co-Head of the Institute alongside bases and related services. Graham Cameron since the EBI was launched five years ago. Monterotondo, which opened in 1999, has been waiting for the "The new five-year scientific plan at EMBL stresses functional g reen light from EMBL's Council to reach critical mass. genomics and foresees substantial expansion of the EBI and the Rosenthal’s appointment comes at a time when a partner on the Mouse Biology Programme at Monterotondo," says Director Monterotondo campus, the European Mutant Mouse Archive General Fotis C. -
PREDICTD: Parallel Epigenomics Data Imputation with Cloud-Based Tensor Decomposition
bioRxiv preprint doi: https://doi.org/10.1101/123927; this version posted April 4, 2017. 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 4.0 International license. PREDICTD: PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition Timothy J. Durham Maxwell W. Libbrecht Department of Genome Sciences Department of Genome Sciences University of Washington University of Washington J. Jeffry Howbert Jeff Bilmes Department of Genome Sciences Department of Electrical Engineering University of Washington University of Washington William Stafford Noble Department of Genome Sciences Department of Computer Science and Engineering University of Washington April 4, 2017 Abstract The Encyclopedia of DNA Elements (ENCODE) and the Roadmap Epigenomics Project have produced thousands of data sets mapping the epigenome in hundreds of cell types. How- ever, the number of cell types remains too great to comprehensively map given current time and financial constraints. We present a method, PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition (PREDICTD), to address this issue by computationally im- puting missing experiments in collections of epigenomics experiments. PREDICTD leverages an intuitive and natural model called \tensor decomposition" to impute many experiments si- multaneously. Compared with the current state-of-the-art method, ChromImpute, PREDICTD produces lower overall mean squared error, and combining methods yields further improvement. We show that PREDICTD data can be used to investigate enhancer biology at non-coding human accelerated regions. PREDICTD provides reference imputed data sets and open-source software for investigating new cell types, and demonstrates the utility of tensor decomposition and cloud computing, two technologies increasingly applicable in bioinformatics. -
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. -
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. -
Motif Selection Using Simulated Annealing Algorithm with Application to Identify Regulatory Elements
Motif Selection Using Simulated Annealing Algorithm with Application to Identify Regulatory Elements A thesis presented to the faculty of the Russ College of Engineering and Technology of Ohio University In partial fulfillment of the requirements for the degree Master of Science Liang Chen August 2018 © 2018 Liang Chen. All Rights Reserved. 2 This thesis titled Motif Selection Using Simulated Annealing Algorithm with Application to Identify Regulatory Elements by LIANG CHEN has been approved for the Department of Electrical Engineering and Computer Science and the Russ College of Engineering and Technology by Lonnie Welch Professor of Electrical Engineering and Computer Science Dennis Irwin Dean, Russ College of Engineering and Technology 3 Abstract CHEN, LIANG, M.S., August 2018, Computer Science Master Program Motif Selection Using Simulated Annealing Algorithm with Application to Identify Regulatory Elements (106 pp.) Director of Thesis: Lonnie Welch Modern research on gene regulation and disorder-related pathways utilize the tools such as microarray and RNA-Seq to analyze the changes in the expression levels of large sets of genes. In silico motif discovery was performed based on the gene expression profile data, which generated a large set of candidate motifs (usually hundreds or thousands of motifs). How to pick a set of biologically meaningful motifs from the candidate motif set is a challenging biological and computational problem. As a computational problem it can be modeled as motif selection problem (MSP). Building solutions for motif selection problem will give biologists direct help in finding transcription factors (TF) that are strongly related to specific pathways and gaining insights of the relationships between genes.