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    Wyświetlanie 1-11 z 11
    Tytuł:
    Automated assembly of molecular mechanisms at scale from text mining and curated databases.
    Autorzy:
    Bachman JA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
    Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
    Sorger PK; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.; Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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    Źródło:
    Molecular systems biology [Mol Syst Biol] 2023 May 09; Vol. 19 (5), pp. e11325. Date of Electronic Publication: 2023 Mar 20.
    Typ publikacji:
    Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
    MeSH Terms:
    Data Mining*
    Natural Language Processing*
    Humans ; Reproducibility of Results ; Databases, Factual
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    A roadmap for the functional annotation of protein families: a community perspective.
    Autorzy:
    de Crécy-Lagard V; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
    Amorin de Hegedus R; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
    Arighi C; Department of Computer and Information Sciences, University of Delaware, Newark, DE 19713, USA.
    Babor J; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
    Bateman A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
    Blaby I; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
    Blaby-Haas C; Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
    Bridge AJ; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva 4 CH-1211, Switzerland.
    Burley SK; RCSB Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
    Cleveland S; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
    Colwell LJ; Departmenf of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
    Conesa A; Spanish National Research Council, Institute for Integrative Systems Biology, Paterna, Valencia 46980, Spain.
    Dallago C; TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology, i12, Boltzmannstr. 3, Garching/Munich 85748, Germany.
    Danchin A; School of Biomedical Sciences, Li KaShing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, SAR Hong Kong 999077, China.
    de Waard A; Research Collaboration Unit, Elsevier, Jericho, VT 05465, USA.
    Deutschbauer A; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
    Dias R; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
    Ding Y; Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, USA.
    Fang G; NYU-Shanghai, Shanghai 200120, China.
    Friedberg I; Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.
    Gerlt J; Institute for Genomic Biology and Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
    Goldford J; Physics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
    Gorelik M; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
    Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
    Henry C; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
    Hutinet G; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
    Jaroch M; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
    Karp PD; Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.
    Kondratova L; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
    Lu Z; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA.
    Marchler-Bauer A; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA.
    Martin MJ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
    McWhite C; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA.
    Moghe GD; Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
    Monaghan P; Department of Agricultural Education and Communication, University of Florida, Gainesville, FL 32611, USA.
    Morgat A; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva 4 CH-1211, Switzerland.
    Mungall CJ; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
    Natale DA; Georgetown University Medical Center, Washington, DC 20007, USA.
    Nelson WC; Biological Sciences Division, Pacific Northwest National Laboratories, Richland, WA 99354, USA.
    O'Donoghue S; School of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW 2052, Australia.
    Orengo C; Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
    O'Toole KH; New England Biolabs, Ipswich, MA 01938, USA.
    Radivojac P; Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA.
    Reed C; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
    Roberts RJ; New England Biolabs, Ipswich, MA 01938, USA.
    Rodionov D; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
    Rodionova IA; Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA 92093-0412, USA.
    Rudolf JD; Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
    Saleh L; New England Biolabs, Ipswich, MA 01938, USA.
    Sheynkman G; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
    Thibaud-Nissen F; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA.
    Thomas PD; Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA.
    Uetz P; Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA.
    Vallenet D; LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry 91057, France.
    Carter EW; Department of Plant Pathology, University of Florida Citrus Research and Education Center, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA.
    Weigele PR; New England Biolabs, Ipswich, MA 01938, USA.
    Wood V; Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
    Wood-Charlson EM; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
    Xu J; Department of Plant Pathology, University of Florida Citrus Research and Education Center, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA.
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    Źródło:
    Database : the journal of biological databases and curation [Database (Oxford)] 2022 Aug 12; Vol. 2022.
    Typ publikacji:
    Journal Article; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, N.I.H., Intramural
    MeSH Terms:
    Genomics*
    Proteins*
    Base Sequence ; Computational Biology ; Genome ; Molecular Sequence Annotation
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    A Simple Standard for Sharing Ontological Mappings (SSSOM).
    Autorzy:
    Matentzoglu N; Semanticly Ltd, London WC2H 9JQ, UK.
    Balhoff JP; RENCI, University of North Carolina, Chapel Hill, NC 27517, USA.
    Bello SM; The Jackson Laboratory, Bar Harbor, ME 04609, USA.
    Bizon C; RENCI, University of North Carolina, Chapel Hill, NC 27517, USA.
    Brush M; University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA.
    Callahan TJ; University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA.
    Chute CG; Johns Hopkins University, Baltimore, MD 21210, USA.
    Duncan WD; Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
    Evelo CT; Maastricht University, Maastricht 6211 LK, The Netherlands.
    Gabriel D; Johns Hopkins University, Baltimore, MD 21210, USA.
    Graybeal J; Stanford University, Stanford, CA 94305, USA.
    Gray A; Department of Computer Science, Heriot-Watt University, Edinburgh, Currie EH14 4AS, UK.
    Gyori BM; Harvard Medical School, Boston, MA 02115, USA.
    Haendel M; University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA.
    Harmse H; European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.
    Harris NL; Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
    Harrow I; Pistoia Alliance Inc, USA.
    Hegde HB; Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
    Hoyt AL; Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
    Hoyt CT; Harvard Medical School, Boston, MA 02115, USA.
    Jiao D; Johns Hopkins University, Baltimore, MD 21210, USA.
    Jiménez-Ruiz E; City University of London, London EC1V 0HB, UK.; University of Oslo, Oslo 0315, Norway.
    Jupp S; SciBite Limited, Bio Data Innovation Centre, Wellcome Genome Campus, Hinxton, Saffron Walden CB10 1DR, UK.
    Kim H; Robert Bosch LLC, Sunnyvale, CA 94085, USA.
    Koehler S; Ada Health GmbH, Berlin 10178, Germany.
    Liener T; Pistoia Alliance Inc, USA.
    Long Q; Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
    Malone J; BenchSci, 25 York St Suite 1100, Toronto, ON M5J 2V5, Canada.
    McLaughlin JA; European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.
    McMurry JA; University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA.
    Moxon S; Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
    Munoz-Torres MC; University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA.
    Osumi-Sutherland D; European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.
    Overton JA; Knocean Inc., Toronto, ON M6P 2T3, Canada.
    Peters B; La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
    Putman T; University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA.
    Queralt-Rosinach N; Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
    Shefchek K; University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA.
    Solbrig H; Johns Hopkins University, Baltimore, MD 21210, USA.
    Thessen A; University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA.
    Tudorache T; Independent Scholar.
    Vasilevsky N; University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA.
    Wagner AH; The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA.; The Ohio State University College of Medicine, Columbus, OH 43210, USA.
    Mungall CJ; Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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    Źródło:
    Database : the journal of biological databases and curation [Database (Oxford)] 2022 May 25; Vol. 2022.
    Typ publikacji:
    Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
    MeSH Terms:
    Metadata*
    Semantic Web*
    Data Management ; Databases, Factual ; Workflow
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    Gilda: biomedical entity text normalization with machine-learned disambiguation as a service.
    Autorzy:
    Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
    Hoyt CT; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
    Steppi A; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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    Źródło:
    Bioinformatics advances [Bioinform Adv] 2022 May 11; Vol. 2 (1), pp. vbac034. Date of Electronic Publication: 2022 May 11 (Print Publication: 2022).
    Typ publikacji:
    Journal Article
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment.
    Autorzy:
    Scholten B; Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands.; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands.
    Simón LG; Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands.
    Krishnan S; Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands.
    Vermeulen R; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands.
    Pronk A; Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands.
    Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
    Bachman JA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
    Vlaanderen J; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands.
    Stierum R; Research Group Risk Analysis for Products in Development, The Netherlands Organisation for applied scientific research, Utrecht, Netherlands.
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    Źródło:
    Environmental health perspectives [Environ Health Perspect] 2022 Mar; Vol. 130 (3), pp. 37002. Date of Electronic Publication: 2022 Mar 03.
    Typ publikacji:
    Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
    MeSH Terms:
    Carcinogens*/toxicity
    Neoplasms*/chemically induced
    Neoplasms*/epidemiology
    Benzene ; Databases, Factual ; Humans ; Risk Assessment
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
    Autorzy:
    Ostaszewski M
    Niarakis A
    Mazein A
    Kuperstein I
    Phair R
    Orta-Resendiz A
    Singh V
    Aghamiri SS
    Acencio ML
    Glaab E
    Ruepp A
    Fobo G
    Montrone C
    Brauner B
    Frishman G
    Monraz Gómez LC
    Somers J
    Hoch M
    Kumar Gupta S
    Scheel J
    Borlinghaus H
    Czauderna T
    Schreiber F
    Montagud A
    Ponce de Leon M
    Funahashi A
    Hiki Y
    Hiroi N
    Yamada TG
    Dräger A
    Renz A
    Naveez M
    Bocskei Z
    Messina F
    Börnigen D
    Fergusson L
    Conti M
    Rameil M
    Nakonecnij V
    Vanhoefer J
    Schmiester L
    Wang M
    Ackerman EE
    Shoemaker JE
    Zucker J
    Oxford K
    Teuton J
    Kocakaya E
    Summak GY
    Hanspers K
    Kutmon M
    Coort S
    Eijssen L
    Ehrhart F
    Rex DAB
    Slenter D
    Martens M
    Pham N
    Haw R
    Jassal B
    Matthews L
    Orlic-Milacic M
    Senff-Ribeiro A
    Rothfels K
    Shamovsky V
    Stephan R
    Sevilla C
    Varusai T
    Ravel JM
    Fraser R
    Ortseifen V
    Marchesi S
    Gawron P
    Smula E
    Heirendt L
    Satagopam V
    Wu G
    Riutta A
    Golebiewski M
    Owen S
    Goble C
    Hu X
    Overall RW
    Maier D
    Bauch A
    Gyori BM
    Bachman JA
    Vega C
    Grouès V
    Vazquez M
    Porras P
    Licata L
    Iannuccelli M
    Sacco F
    Nesterova A
    Yuryev A
    de Waard A
    Turei D
    Luna A
    Babur O
    Soliman S
    Valdeolivas A
    Esteban-Medina M
    Peña-Chilet M
    Rian K
    Helikar T
    Puniya BL
    Modos D
    Treveil A
    Olbei M
    De Meulder B
    Ballereau S
    Dugourd A
    Naldi A
    Noël V
    Calzone L
    Sander C
    Demir E
    Korcsmaros T
    Freeman TC
    Augé F
    Beckmann JS
    Hasenauer J
    Wolkenhauer O
    Willighagen EL
    Pico AR
    Evelo CT
    Gillespie ME
    Stein LD
    Hermjakob H
    D'Eustachio P
    Saez-Rodriguez J
    Dopazo J
    Valencia A
    Kitano H
    Barillot E
    Auffray C
    Balling R
    Schneider R
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    Corporate Authors:
    COVID-19 Disease Map Community
    Źródło:
    Molecular systems biology [Mol Syst Biol] 2021 Dec; Vol. 17 (12), pp. e10851.
    Typ publikacji:
    Published Erratum
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
    Autorzy:
    Ostaszewski M; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Niarakis A; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.; Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France.
    Mazein A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Kuperstein I; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France.
    Phair R; Integrative Bioinformatics, Inc., Mountain View, CA, USA.
    Orta-Resendiz A; Institut Pasteur, Université de Paris, Unité HIV, Inflammation et Persistance, Paris, France.; Bio Sorbonne Paris Cité, Université de Paris, Paris, France.
    Singh V; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.
    Aghamiri SS; Inserm- Institut national de la santé et de la recherche médicale, Paris, France.
    Acencio ML; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Glaab E; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Ruepp A; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
    Fobo G; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
    Montrone C; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
    Brauner B; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
    Frishman G; Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
    Monraz Gómez LC; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France.
    Somers J; Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, OR, USA.
    Hoch M; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
    Kumar Gupta S; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
    Scheel J; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
    Borlinghaus H; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
    Czauderna T; Faculty of Information Technology, Department of Human-Centred Computing, Monash University, Clayton, Vic., Australia.
    Schreiber F; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.; Faculty of Information Technology, Department of Human-Centred Computing, Monash University, Clayton, Vic., Australia.
    Montagud A; Barcelona Supercomputing Center (BSC), Barcelona, Spain.
    Ponce de Leon M; Barcelona Supercomputing Center (BSC), Barcelona, Spain.
    Funahashi A; Department of Biosciences and Informatics, Keio University, Yokohama, Japan.
    Hiki Y; Department of Biosciences and Informatics, Keio University, Yokohama, Japan.
    Hiroi N; Graduate School of Media and Governance, Research Institute at SFC, Keio University, Kanagawa, Japan.
    Yamada TG; Department of Biosciences and Informatics, Keio University, Yokohama, Japan.
    Dräger A; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.; Department of Computer Science, University of Tübingen, Tübingen, Germany.; German Center for Infection Research (DZIF), partner site, Tübingen, Germany.
    Renz A; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.; Department of Computer Science, University of Tübingen, Tübingen, Germany.
    Naveez M; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.; Institute of Applied Computer Systems, Riga Technical University, Riga, Latvia.
    Bocskei Z; Sanofi R&D, Translational Sciences, Chilly-Mazarin, France.
    Messina F; Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.S., Rome, Italy.; COVID-19 INMI Network Medicine for IDs Study Group, National Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.S, Rome, Italy.
    Börnigen D; Bioinformatics Core Facility, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
    Fergusson L; Royal (Dick) School of Veterinary Medicine, The University of Edinburgh, Edinburgh, UK.
    Conti M; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
    Rameil M; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
    Nakonecnij V; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
    Vanhoefer J; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.
    Schmiester L; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany.; Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching, Germany.
    Wang M; Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
    Ackerman EE; Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
    Shoemaker JE; Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA.; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
    Zucker J; Pacific Northwest National Laboratory, Richland, WA, USA.
    Oxford K; Pacific Northwest National Laboratory, Richland, WA, USA.
    Teuton J; Pacific Northwest National Laboratory, Richland, WA, USA.
    Kocakaya E; Stem Cell Institute, Ankara University, Ankara, Turkey.
    Summak GY; Stem Cell Institute, Ankara University, Ankara, Turkey.
    Hanspers K; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
    Kutmon M; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands.
    Coort S; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
    Eijssen L; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.; Maastricht University Medical Centre, Maastricht, The Netherlands.
    Ehrhart F; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.; Maastricht University Medical Centre, Maastricht, The Netherlands.
    Rex DAB; Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India.
    Slenter D; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
    Martens M; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
    Pham N; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
    Haw R; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.
    Jassal B; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.
    Matthews L; NYU Grossman School of Medicine, New York, NY, USA.
    Orlic-Milacic M; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.
    Senff Ribeiro A; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.; Universidade Federal do Paraná, Curitiba, Brasil.
    Rothfels K; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.
    Shamovsky V; NYU Grossman School of Medicine, New York, NY, USA.
    Stephan R; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.
    Sevilla C; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK.
    Varusai T; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK.
    Ravel JM; INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, Nancy, France.; Laboratoire de génétique médicale, CHRU Nancy, Nancy, France.
    Fraser R; Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK.
    Ortseifen V; Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
    Marchesi S; Department of Surgical Science, Uppsala University, Uppsala, Sweden.
    Gawron P; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.; Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
    Smula E; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Heirendt L; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Satagopam V; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Wu G; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA.
    Riutta A; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
    Golebiewski M; Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
    Owen S; Department of Computer Science, The University of Manchester, Manchester, UK.
    Goble C; Department of Computer Science, The University of Manchester, Manchester, UK.
    Hu X; Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
    Overall RW; German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany.; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.; Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
    Maier D; Biomax Informatics AG, Planegg, Germany.
    Bauch A; Biomax Informatics AG, Planegg, Germany.
    Gyori BM; Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, USA.
    Bachman JA; Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, USA.
    Vega C; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Grouès V; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Vazquez M; Barcelona Supercomputing Center (BSC), Barcelona, Spain.
    Porras P; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK.
    Licata L; Department of Biology, University of Rome Tor Vergata, Rome, Italy.
    Iannuccelli M; Department of Biology, University of Rome Tor Vergata, Rome, Italy.
    Sacco F; Department of Biology, University of Rome Tor Vergata, Rome, Italy.
    Nesterova A; Elsevier, Philadelphia, PA, USA.
    Yuryev A; Elsevier, Philadelphia, PA, USA.
    de Waard A; Research Collaborations Unit, Elsevier, Jericho, VT, USA.
    Turei D; Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.
    Luna A; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
    Babur O; Computer Science Department, University of Massachusetts Boston, Boston, MA, USA.
    Soliman S; Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France.
    Valdeolivas A; Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.
    Esteban-Medina M; Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, Spain.; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain.
    Peña-Chilet M; Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, Spain.; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain.; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Sevilla, Spain.
    Rian K; Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, Spain.; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain.
    Helikar T; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
    Puniya BL; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
    Modos D; Quadram Institute Bioscience, Norwich, UK.; Earlham Institute, Norwich, UK.
    Treveil A; Quadram Institute Bioscience, Norwich, UK.; Earlham Institute, Norwich, UK.
    Olbei M; Quadram Institute Bioscience, Norwich, UK.; Earlham Institute, Norwich, UK.
    De Meulder B; European Institute for Systems Biology and Medicine (EISBM), Vourles, France.
    Ballereau S; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
    Dugourd A; Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.; Institute of Experimental Medicine and Systems Biology, Faculty of Medicine, RWTH, Aachen University, Aachen, Germany.
    Naldi A; Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France.
    Noël V; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France.
    Calzone L; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France.
    Sander C; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
    Demir E; Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, OR, USA.
    Korcsmaros T; Quadram Institute Bioscience, Norwich, UK.; Earlham Institute, Norwich, UK.
    Freeman TC; The Roslin Institute, University of Edinburgh, Edinburgh, UK.
    Augé F; Sanofi R&D, Translational Sciences, Chilly-Mazarin, France.
    Beckmann JS; University of Lausanne, Lausanne, Switzerland.
    Hasenauer J; Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.; Interdisciplinary Research Unit Mathematics and Life Sciences, University of Bonn, Bonn, Germany.
    Wolkenhauer O; Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
    Wilighagen EL; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
    Pico AR; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
    Evelo CT; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands.
    Gillespie ME; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.; St. John's University College of Pharmacy and Health Sciences, Queens, NY, USA.
    Stein LD; MaRS Centre, Ontario Institute for Cancer Research, Toronto, ON, Canada.; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
    Hermjakob H; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK.
    D'Eustachio P; NYU Grossman School of Medicine, New York, NY, USA.
    Saez-Rodriguez J; Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.
    Dopazo J; Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, Sevilla, Spain.; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain.; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Sevilla, Spain.; FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain.
    Valencia A; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
    Kitano H; Systems Biology Institute, Tokyo, Japan.; Okinawa Institute of Science and Technology Graduate School, Okinawa, Japan.
    Barillot E; Institut Curie, PSL Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, Paris, France.
    Auffray C; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
    Balling R; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
    Schneider R; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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    Corporate Authors:
    COVID-19 Disease Map Community
    Źródło:
    Molecular systems biology [Mol Syst Biol] 2021 Oct; Vol. 17 (10), pp. e10387.
    Typ publikacji:
    Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
    MeSH Terms:
    Databases, Factual*
    Software*
    COVID-19/*immunology
    Computational Biology/*methods
    SARS-CoV-2/*immunology
    Antiviral Agents/therapeutic use ; COVID-19/genetics ; COVID-19/virology ; Computer Graphics ; Cytokines/genetics ; Cytokines/immunology ; Data Mining/statistics & numerical data ; Gene Expression Regulation ; Host Microbial Interactions/genetics ; Host Microbial Interactions/immunology ; Humans ; Immunity, Cellular/drug effects ; Immunity, Humoral/drug effects ; Immunity, Innate/drug effects ; Lymphocytes/drug effects ; Lymphocytes/immunology ; Lymphocytes/virology ; Metabolic Networks and Pathways/genetics ; Metabolic Networks and Pathways/immunology ; Myeloid Cells/drug effects ; Myeloid Cells/immunology ; Myeloid Cells/virology ; Protein Interaction Mapping ; SARS-CoV-2/drug effects ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; Signal Transduction ; Transcription Factors/genetics ; Transcription Factors/immunology ; Viral Proteins/genetics ; Viral Proteins/immunology ; COVID-19 Drug Treatment
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    Robustness and parameter geography in post-translational modification systems.
    Autorzy:
    Nam KM; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.
    Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America.
    Amethyst SV; Department of Mathematics, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, United States of America.
    Bates DJ; Department of Mathematics, United States Naval Academy, Annapolis, Maryland, United States of America.
    Gunawardena J; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.
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    Źródło:
    PLoS computational biology [PLoS Comput Biol] 2020 May 04; Vol. 16 (5), pp. e1007573. Date of Electronic Publication: 2020 May 04 (Print Publication: 2020).
    Typ publikacji:
    Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
    MeSH Terms:
    Computational Biology/*methods
    Protein Processing, Post-Translational/*physiology
    Algorithms ; Gene Expression/genetics ; Gene Expression/physiology ; Gene Regulatory Networks/genetics ; Gene Regulatory Networks/physiology ; Models, Biological ; Models, Theoretical ; Protein Processing, Post-Translational/genetics
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.
    Autorzy:
    Hoyt CT; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.; Bonn-Aachen International Center for Information Technology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
    Domingo-Fernández D; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.; Bonn-Aachen International Center for Information Technology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
    Aldisi R; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.; Bonn-Aachen International Center for Information Technology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
    Xu L; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.; Bonn-Aachen International Center for Information Technology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
    Kolpeja K; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.
    Spalek S; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.
    Wollert E; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.
    Bachman J; Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, USA.
    Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, USA.
    Greene P; Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, USA.
    Hofmann-Apitius M; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.; Bonn-Aachen International Center for Information Technology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
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    Źródło:
    Database : the journal of biological databases and curation [Database (Oxford)] 2019 Jan 01; Vol. 2019.
    Typ publikacji:
    Journal Article; Research Support, Non-U.S. Gov't
    MeSH Terms:
    Data Mining*
    MEDLINE*
    Pattern Recognition, Automated*
    Semantics*
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.
    Autorzy:
    Bachman JA; Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA.
    Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA.
    Sorger PK; Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA. peter_.
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    Źródło:
    BMC bioinformatics [BMC Bioinformatics] 2018 Jun 28; Vol. 19 (1), pp. 248. Date of Electronic Publication: 2018 Jun 28.
    Typ publikacji:
    Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
    MeSH Terms:
    Data Mining/*methods
    Proteins/*metabolism
    Humans
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
    Tytuł:
    From word models to executable models of signaling networks using automated assembly.
    Autorzy:
    Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
    Bachman JA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
    Subramanian K; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
    Muhlich JL; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
    Galescu L; Institute for Human and Machine Cognition, Pensacola, FL, USA.
    Sorger PK; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA peter_.
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    Źródło:
    Molecular systems biology [Mol Syst Biol] 2017 Nov 24; Vol. 13 (11), pp. 954. Date of Electronic Publication: 2017 Nov 24.
    Typ publikacji:
    Journal Article
    MeSH Terms:
    Gene Expression Regulation, Neoplastic*
    Models, Genetic*
    Natural Language Processing*
    Neural Networks, Computer*
    Melanoma/*genetics
    Skin Neoplasms/*genetics
    Antineoplastic Agents/therapeutic use ; Cell Line, Tumor ; Computer Simulation ; DNA Damage ; Drug Resistance, Neoplasm/genetics ; Enzyme Inhibitors/therapeutic use ; Humans ; Indoles/therapeutic use ; Language ; Melanoma/drug therapy ; Melanoma/metabolism ; Melanoma/pathology ; Proto-Oncogene Proteins B-raf/genetics ; Proto-Oncogene Proteins B-raf/metabolism ; Proto-Oncogene Proteins p21(ras)/genetics ; Proto-Oncogene Proteins p21(ras)/metabolism ; Signal Transduction ; Skin Neoplasms/drug therapy ; Skin Neoplasms/metabolism ; Skin Neoplasms/pathology ; Sulfonamides/therapeutic use ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism ; Vemurafenib
    Czasopismo naukowe
    Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
      Wyświetlanie 1-11 z 11

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