Applications of Multimodal Artificial Intelligence in Non-Hodgkin Lymphoma B Cells.

Autor: Isavand P; Department of Radiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan 4513956184, Iran., Aghamiri SS; Department of Biochemistry, University of Nebraska, Lincoln, NE 68503, USA., Amin R; Department of Biochemistry, University of Nebraska, Lincoln, NE 68503, USA.

Publikováno v: Biomedicines [Biomedicines] 2024 Aug 05; Vol. 12 (8). Date of Electronic Publication: 2024 Aug 05.

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery.

Autor: Bessell B; Department of Biochemistry, University of Nebraska-Lincoln, NE, USA., Loecker J; Department of Biochemistry, University of Nebraska-Lincoln, NE, USA., Zhao Z; Department of Biochemistry, University of Nebraska-Lincoln, NE, USA., Aghamiri SS; Department of Biochemistry, University of Nebraska-Lincoln, NE, USA., Mohanty S; Department of Biochemistry, University of Nebraska-Lincoln, NE, USA., Amin R; Department of Biochemistry, University of Nebraska-Lincoln, NE, USA., Helikar T; Department of Biochemistry, University of Nebraska-Lincoln, NE, USA., Puniya BL; Department of Biochemistry, University of Nebraska-Lincoln, NE, USA.

Publikováno v: Briefings in bioinformatics [Brief Bioinform] 2023 Sep 22; Vol. 24 (6).

Recent applications of quantitative systems pharmacology and machine learning models across diseases.

Autor: Aghamiri SS; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA., Amin R; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA. raminali2@unl.edu., Helikar T; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA. thelikar2@unl.edu.

Publikováno v: Journal of pharmacokinetics and pharmacodynamics [J Pharmacokinet Pharmacodyn] 2022 Feb; Vol. 49 (1), pp. 19-37. Date of Electronic Publication: 2021 Oct 20.

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Autor: 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.

Publikováno v: Molecular systems biology [Mol Syst Biol] 2021 Oct; Vol. 17 (10), pp. e10387.

Automated inference of Boolean models from molecular interaction maps using CaSQ.

Autor: Aghamiri SS; GenHotel, Département de Biologie, Univ. èvry, Université Paris-Saclay, Genopole, èvry 91025, France., Singh V; GenHotel, Département de Biologie, Univ. èvry, Université Paris-Saclay, Genopole, èvry 91025, France., Naldi A; Département de Biologie, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), ècole Normale Supérieure, CNRS, INSERM, Université PSL, Paris 75005, France., Helikar T; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA., Soliman S; Lifeware Group, Inria Saclay-île de France, Palaiseau 91120, France., Niarakis A; GenHotel, Département de Biologie, Univ. èvry, Université Paris-Saclay, Genopole, èvry 91025, France.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2020 Aug 15; Vol. 36 (16), pp. 4473-4482.