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A Method to Infer Changed Activity of Metabolic Function from Transcript Profiles
ModeScore: A Method to Infer Changed Activity of Metabolic Function from Transcript Profiles Andreas Hoppe and Hermann-Georg Holzhütter Charité University Medicine Berlin, Institute for Biochemistry, Computational Systems Biochemistry Group [email protected] Abstract Genome-wide transcript profiles are often the only available quantitative data for a particular perturbation of a cellular system and their interpretation with respect to the metabolism is a major challenge in systems biology, especially beyond on/off distinction of genes. We present a method that predicts activity changes of metabolic functions by scoring reference flux distributions based on relative transcript profiles, providing a ranked list of most regulated functions. Then, for each metabolic function, the involved genes are ranked upon how much they represent a specific regulation pattern. Compared with the naïve pathway-based approach, the reference modes can be chosen freely, and they represent full metabolic functions, thus, directly provide testable hypotheses for the metabolic study. In conclusion, the novel method provides promising functions for subsequent experimental elucidation together with outstanding associated genes, solely based on transcript profiles. 1998 ACM Subject Classification J.3 Life and Medical Sciences Keywords and phrases Metabolic network, expression profile, metabolic function Digital Object Identifier 10.4230/OASIcs.GCB.2012.1 1 Background The comprehensive study of the cell’s metabolism would include measuring metabolite concentrations, reaction fluxes, and enzyme activities on a large scale. Measuring fluxes is the most difficult part in this, for a recent assessment of techniques, see [31]. Although mass spectrometry allows to assess metabolite concentrations in a more comprehensive way, the larger the set of potential metabolites, the more difficult [8]. -
RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY
RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press ISSN: 1790-5125 www.wseas.org ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press www.wseas.org Copyright © 2009, by WSEAS Press All the copyright of the present book belongs to the World Scientific and Engineering Academy and Society Press. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the Editor of World Scientific and Engineering Academy and Society Press. All papers of the present volume were peer reviewed -
The Kyoto Encyclopedia of Genes and Genomes (KEGG)
Kyoto Encyclopedia of Genes and Genome Minoru Kanehisa Institute for Chemical Research, Kyoto University HFSPO Workshop, Strasbourg, November 18, 2016 The KEGG Databases Category Database Content PATHWAY KEGG pathway maps Systems information BRITE BRITE functional hierarchies MODULE KEGG modules KO (KEGG ORTHOLOGY) KO groups for functional orthologs Genomic information GENOME KEGG organisms, viruses and addendum GENES / SSDB Genes and proteins / sequence similarity COMPOUND Chemical compounds GLYCAN Glycans Chemical information REACTION / RCLASS Reactions / reaction classes ENZYME Enzyme nomenclature DISEASE Human diseases DRUG / DGROUP Drugs / drug groups Health information ENVIRON Health-related substances (KEGG MEDICUS) JAPIC Japanese drug labels DailyMed FDA drug labels 12 manually curated original DBs 3 DBs taken from outside sources and given original annotations (GENOME, GENES, ENZYME) 1 computationally generated DB (SSDB) 2 outside DBs (JAPIC, DailyMed) KEGG is widely used for functional interpretation and practical application of genome sequences and other high-throughput data KO PATHWAY GENOME BRITE DISEASE GENES MODULE DRUG Genome Molecular High-level Practical Metagenome functions functions applications Transcriptome etc. Metabolome Glycome etc. COMPOUND GLYCAN REACTION Funding Annual budget Period Funding source (USD) 1995-2010 Supported by 10+ grants from Ministry of Education, >2 M Japan Society for Promotion of Science (JSPS) and Japan Science and Technology Agency (JST) 2011-2013 Supported by National Bioscience Database Center 0.8 M (NBDC) of JST 2014-2016 Supported by NBDC 0.5 M 2017- ? 1995 KEGG website made freely available 1997 KEGG FTP site made freely available 2011 Plea to support KEGG KEGG FTP academic subscription introduced 1998 First commercial licensing Contingency Plan 1999 Pathway Solutions Inc. -
3 13437143.Pdf
Title Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones Imanishi, Tadashi; Itoh, Takeshi; Suzuki, Yutaka; O'Donovan, Claire; Fukuchi, Satoshi; Koyanagi, Kanako O.; Barrero, Roberto A.; Tamura, Takuro; Yamaguchi-Kabata, Yumi; Tanino, Motohiko; Yura, Kei; Miyazaki, Satoru; Ikeo, Kazuho; Homma, Keiichi; Kasprzyk, Arek; Nishikawa, Tetsuo; Hirakawa, Mika; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Ashurst, Jennifer; Jia, Libin; Nakao, Mitsuteru; Thomas, Michael A.; Mulder, Nicola; Karavidopoulou, Youla; Jin, Lihua; Kim, Sangsoo; Yasuda, Tomohiro; Lenhard, Boris; Eveno, Eric; Suzuki, Yoshiyuki; Yamasaki, Chisato; Takeda, Jun-ichi; Gough, Craig; Hilton, Phillip; Fujii, Yasuyuki; Sakai, Hiroaki; Tanaka, Susumu; Amid, Clara; Bellgard, Matthew; Bonaldo, Maria de Fatima; Bono, Hidemasa; Bromberg, Susan K.; Brookes, Anthony J.; Bruford, Elspeth; Carninci, Piero; Chelala, Claude; Couillault, Christine; Souza, Sandro J. de; Debily, Marie-Anne; Devignes, Marie-Dominique; Dubchak, Inna; Endo, Toshinori; Estreicher, Anne; Eyras, Eduardo; Fukami-Kobayashi, Kaoru; R. Gopinath, Gopal; Graudens, Esther; Hahn, Yoonsoo; Han, Michael; Han, Ze-Guang; Hanada, Kousuke; Hanaoka, Hideki; Harada, Erimi; Hashimoto, Katsuyuki; Hinz, Ursula; Hirai, Momoki; Hishiki, Teruyoshi; Hopkinson, Ian; Imbeaud, Sandrine; Inoko, Hidetoshi; Kanapin, Alexander; Kaneko, Yayoi; Kasukawa, Takeya; Kelso, Janet; Kersey, Author(s) Paul; Kikuno, Reiko; Kimura, Kouichi; Korn, Bernhard; Kuryshev, Vladimir; Makalowska, Izabela; Makino, Takashi; Mano, Shuhei; -
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. -
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; -
ISMB 2008 Toronto
ISMB 2008 Toronto The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Linial, Michal, Jill P. Mesirov, B. J. Morrison McKay, and Burkhard Rost. 2008. ISMB 2008 Toronto. PLoS Computational Biology 4(6): e1000094. Published Version doi:10.1371/journal.pcbi.1000094 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11213310 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 Message from ISCB ISMB 2008 Toronto Michal Linial1,2, Jill P. Mesirov1,3, BJ Morrison McKay1*, Burkhard Rost1,4 1 International Society for Computational Biology (ISCB), University of California San Diego, La Jolla, California, United States of America, 2 Sudarsky Center, The Hebrew University of Jerusalem, Jerusalem, Israel, 3 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, 4 Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America the integration of students, and for the of ISMB. One meeting in South Asia support of young leaders in the field. (InCoB; http://incob.binfo.org.tw/) has ISMB has also become a forum for already been sponsored by ISCB, and reviewing the state of the art in the many another one in North Asia is going to fields of this growing discipline, for follow. ISMB itself has also been held in introducing new directions, and for an- Australia (2003) and Brazil (2006). -
Curriculum Vitae – Prof. Anders Krogh Personal Information
Curriculum Vitae – Prof. Anders Krogh Personal Information Date of Birth: May 2nd, 1959 Private Address: Borgmester Jensens Alle 22, st th, 2100 København Ø, Denmark Contact information: Dept. of Biology, Univ. of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. +45 3532 1329, [email protected] Web: https://scholar.google.com/citations?user=-vGMjmwAAAAJ Education Sept 1991 Ph.D. (Physics), Niels Bohr Institute, Univ. of Copenhagen, Denmark June 1987 Cand. Scient. [M. Sc.] (Physics and mathematics), NBI, Univ. of Copenhagen Professional / Work Experience (since 2000) 2018 – Professor of Bionformatics, Dept of Computer Science (50%) and Dept of Biology (50%), Univ. of Copenhagen 2002 – 2018 Professor of Bionformatics, Dept of Biology, Univ. of Copenhagen 2009 – 2018 Head of Section for Computational and RNA Biology, Dept. of Biology, Univ. of Copenhagen 2000–2002 Associate Prof., Technical Univ. of Denmark (DTU), Copenhagen Prices and Awards 2017 – Fellow of the International Society for Computational Biology https://www.iscb.org/iscb- fellows-program 2008 – Fellow, Royal Danish Academy of Sciences and Letters Public Activities & Appointments (since 2009) 2014 – Board member, Elixir, European Infrastructure for Life Science. 2014 – Steering committee member, Danish Elixir Node. 2012 – 2016 Board member, Bioinformatics Infrastructure for Life Sciences (BILS), Swedish Research Council 2011 – 2016 Director, Centre for Computational and Applied Transcriptomics (COAT) 2009 – Associate editor, BMC Bioinformatics Publications § Google Scholar: https://scholar.google.com/citations?user=-vGMjmwAAAAJ § ORCID: 0000-0002-5147-6282. ResearcherID: M-1541-2014 § Co-author of 130 peer-reviewed papers and 2 monographs § 63,000 citations and h-index of 74 (Google Scholar, June 2019) § H-index of 54 in Web of science (June 2019) § Publications in high-impact journals: Nature (5), Science (1), Cell (1), Nature Genetics (2), Nature Biotechnology (2), Nature Communications (4), Cell (1, to appear), Genome Res. -
Genbank by Walter B
GenBank by Walter B. Goad o understand the significance of the information stored in memory—DNA—to the stuff of activity—proteins. The idea that GenBank, you need to know a little about molecular somehow the bases in DNA determine the amino acids in proteins genetics. What that field deals with is self-replication—the had been around for some time. In fact, George Gamow suggested in T process unique to life—and mutation and 1954, after learning about the structure proposed for DNA, that a recombination—the processes responsible for evolution-at the triplet of bases corresponded to an amino acid. That suggestion was fundamental level of the genes in DNA. This approach of working shown to be true, and by 1965 most of the genetic code had been from the blueprint, so to speak, of a living system is very powerful, deciphered. Also worked out in the ’60s were many details of what and studies of many other aspects of life—the process of learning, for Crick called the central dogma of molecular genetics—the now example—are now utilizing molecular genetics. firmly established fact that DNA is not translated directly to proteins Molecular genetics began in the early ’40s and was at first but is first transcribed to messenger RNA. This molecule, a nucleic controversial because many of the people involved had been trained acid like DNA, then serves as the template for protein synthesis. in the physical sciences rather than the biological sciences, and yet These great advances prompted a very distinguished molecular they were answering questions that biologists had been asking for geneticist to predict, in 1969, that biology was just about to end since years. -
2015 Wattiezm Memoire
Institutional Repository - Research Portal Dépôt Institutionnel - Portail de la Recherche University of Namurresearchportal.unamur.be THESIS / THÈSE MASTER IN COMPUTER SCIENCE Design of a support system for modelling gene regulatory networks Author(s) - Auteur(s) : Wattiez, Morgan Award date: 2015 Awarding institution: University of Namur Supervisor - Co-Supervisor / Promoteur - Co-Promoteur : Link to publication Publication date - Date de publication : Permanent link - Permalien : Rights / License - Licence de droit d’auteur : General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. BibliothèqueDownload date: Universitaire 04. oct.. 2021 Moretus Plantin University of Namur Faculty of Computer Science Academic Year 2014{2015 Design of a support system for modelling gene regulatory networks Morgan WATTIEZ Supervisor: (Signed for Release Approval Jean-Marie JACQUET Study Rules art. 40) Thesis submitted in partial fulfillment of the requirements for the degree of Master in Computer Science at the University of Namur Abstract The understanding of gene regulatory networks depends upon the solving of ques- tions related to the interactions in those networks.