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Making PBPK models more reproducible in practice.

Autor: Domínguez-Romero E; Department of Bioinformatics-BiGCaT, School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.; RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic., Mazurenko S; Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91, Brno, Czech Republic., Scheringer M; RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic., Martins Dos Santos VAP; Laboratory of Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands., Evelo CT; Department of Bioinformatics-BiGCaT, School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands., Anton M; ELIXIR, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom.; Department of Life Sciences, National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Chalmers University of Technology, Kemigården 1, Gothenburg SE-412 96, Sweden., Hancock JM; Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia., Županič A; Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia., Suarez-Diez M; Laboratory of Systems and Synthetic Biology (SSB), Wageningen University and Research, Agrotechnology and Food Sciences, Stippeneng 4, 6708 WE Wageningen, The Netherlands.

Publikováno v: Briefings in bioinformatics [Brief Bioinform] 2024 Sep 23; Vol. 25 (6).

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.

Autor: Niarakis A; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France., Ostaszewski M; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Mazein A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Kuperstein I; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Kutmon M; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands., Gillespie ME; Ontario Institute for Cancer Research, Toronto, ON, Canada.; St. John's University, Queens, NY, United States., Funahashi A; Department of Biosciences and Informatics, Keio University, Kanagawa, Japan., Acencio ML; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Hemedan A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Aichem M; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany., Klein K; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany., Czauderna T; Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany., Burtscher F; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Yamada TG; Department of Biosciences and Informatics, Keio University, Kanagawa, Japan., Hiki Y; Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa, Japan., Hiroi NF; Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa, Japan.; Keio University School of Medicine, Tokyo, Japan., Hu F; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., Pham N; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., Ehrhart F; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., Willighagen EL; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., Valdeolivas A; Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany., Dugourd A; Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany., Messina F; Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases' Lazzaro Spallanzani' - IRCCS, Rome, Italy., Esteban-Medina M; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.; Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain., Peña-Chilet M; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.; Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain.; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain., Rian K; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain., Soliman S; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France., Aghamiri SS; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States., Puniya BL; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States., Naldi A; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France., Helikar T; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States., Singh V; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France., Fernández MF; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway., Bermudez V; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway., Tsirvouli E; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway., Montagud A; Barcelona Supercomputing Center (BSC.), Barcelona, Spain., Noël V; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Ponce-de-Leon M; Barcelona Supercomputing Center (BSC.), Barcelona, Spain., Maier D; Labvantage-Biomax GmbH, Planegg, Germany., Bauch A; Labvantage-Biomax GmbH, Planegg, Germany., Gyori BM; Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States., Bachman JA; Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States., Luna A; Computational Biology Branch, National Library of Medicine, Bethesda, MD, United States.; Department of Systems Biology, Harvard Medical School, Boston, MA, United States., Piñero J; Medbioinformatics Solutions SL, Barcelona, Spain.; Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain., Furlong LI; Medbioinformatics Solutions SL, Barcelona, Spain.; Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain., Balaur I; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Rougny A; Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan.; Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan., Jarosz Y; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Overall RW; Institute for Biology, Humboldt University of Berlin, Berlin, Germany., Phair R; Integrative Bioinformatics, Inc., Mountain View, CA, United States., Perfetto L; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy., Matthews L; Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States., Rex DAB; Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Derlakatte, Mangalore, India., Orlic-Milacic M; Ontario Institute for Cancer Research, Toronto, ON, Canada., Gomez LCM; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., De Meulder B; Association E.I.S.B.M, Brignais, France., Ravel JM; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Jassal B; Ontario Institute for Cancer Research, Toronto, ON, Canada., Satagopam V; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.; Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany., Wu G; Oregon Health Sciences University, Portland, OR, United States., Golebiewski M; Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany., Gawron P; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Calzone L; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Beckmann JS; University of Lausanne, Lausanne, Switzerland., Evelo CT; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., D'Eustachio P; Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States., Schreiber F; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.; Faculty of Information Technology, Monash University, Clayton, Victoria, VIC, Australia., Saez-Rodriguez J; Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany., Dopazo J; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.; Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain.; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain.; FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain., Kuiper M; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway., Valencia A; Barcelona Supercomputing Center (BSC.), Barcelona, Spain.; I.C.R.E.A., Pg. Lluís Companys 23, Barcelona, Spain., Wolkenhauer O; Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany.; Leibniz Institute for Food Systems Biology, at the Technical University Munich, Munich, Germany., Kitano H; Systems Biology Institute, Tokyo, Japan., Barillot E; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Auffray C; Association E.I.S.B.M, Brignais, France., Balling R; Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany., Schneider R; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.

Publikováno v: Frontiers in immunology [Front Immunol] 2024 Feb 13; Vol. 14, pp. 1282859. Date of Electronic Publication: 2024 Feb 13 (Print Publication: 2023).