Immune digital twins for complex human pathologies: applications, limitations, and challenges.

Autor: Niarakis A; Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France. anna.niaraki@univ-tlse3.fr.; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France. anna.niaraki@univ-tlse3.fr., Laubenbacher R; Department of Medicine, University of Florida, Gainesville, FL, USA., An G; Department of Surgery, University of Vermont Larner College of Medicine, Vermont, USA., Ilan Y; Faculty of Medicine Hebrew University, Hadassah Medical Center, Jerusalem, Israel., Fisher J; UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK., Flobak Å; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.; The Cancer Clinic, St Olav's University Hospital, Trondheim, Norway.; Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway., Reiche K; Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.; Institute of Clinical Immunology, Medical Faculty, University Hospital, University of Leipzig, Leipzig, Germany.; Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden/Leipzig, Germany., Rodríguez Martínez M; Department of Biomedical Informatics & Data Science, Yale School of Medicine, New Haven, CT, USA., Geris L; Prometheus Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium.; Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.; Biomechanics Research Unit, GIGA Molecular and Computational Biology, University of Liège, Liège, Belgium., Ladeira L; Biomechanics Research Unit, GIGA Molecular and Computational Biology, University of Liège, Liège, Belgium., Veschini L; Faculty of Dentistry Oral & Craniofacial Sciences, King's College London, London, UK.; Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, 47408, USA., Blinov ML; Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, 06030, USA., Messina F; Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases 'Lazzaro Spallanzani' - I.R.C.C.S., Rome, Italy., Fonseca LL; Department of Medicine, University of Florida, Gainesville, FL, USA., Ferreira S; Mathematics Department and Center of Mathematics, University of Beira Interior, Covilhã, Portugal., Montagud A; Barcelona Supercomputing Center (BSC), Barcelone, Spain.; Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, Valencia, Spain., Noël V; Institut Curie, Université PSL, F-75005, Paris, France.; INSERM, U900, F-75005, Paris, France.; Mines ParisTech, Université PSL, F-75005, Paris, France., Marku M; Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France., Tsirvouli E; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway., Torres MM; Department of Mathematics and Statistics, University of Richmond, Richmond, VA, USA., Harris LA; Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA.; Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA.; Cancer Biology Program, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Sego TJ; Department of Medicine, University of Florida, Gainesville, FL, USA., Cockrell C; Department of Surgery, University of Vermont Larner College of Medicine, Vermont, USA., Shick AE; Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL, USA., Balci H; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands., Salazar A; INRIA Paris/CNRS/École Normale Supérieure/PSL Research University, Paris, France., Rian K; Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain., Hemedan AA; Bioinformatics Core Unit, Luxembourg Centre of Systems Biomedicine LCSB, Luxembourg University, Esch-sur-Alzette, Luxembourg., Esteban-Medina M; Andalusian Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain., Staumont B; Biomechanics Research Unit, GIGA Molecular and Computational Biology, University of Liège, Liège, Belgium., Hernandez-Vargas E; Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, 83844-1103, USA., Martis B S; Novadiscovery, Lyon, France., Madrid-Valiente A; Barcelona Supercomputing Center (BSC), Barcelone, Spain., Karampelesis P; Department of Electrical and Computer Engineering, University of Patras, Patras, Greece., Sordo Vieira L; Department of Medicine, University of Florida, Gainesville, FL, USA., Harlapur P; Department of Bioengineering, Indian Institute of Science, Bengaluru, India., Kulesza A; Novadiscovery, Lyon, France., Nikaein N; School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-70182, Örebro, Sweden.; X-HiDE - Exploring Inflammation in Health and Disease Consortium, Örebro University, Örebro, Sweden., Garira W; Multiscale Mathematical Modelling of Living Systems program (M3-LSP), Kimberley, South Africa.; Department of Mathematical Sciences, Sol Plaatje University, Kimberley, South Africa.; Private Bag X5008, Kimberley, 8300, South Africa., Malik Sheriff RS; European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, Cambridge, UK.; Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK., Thakar J; Department of Microbiology & Immunology and Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, USA., Tran VDT; Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland., Carbonell-Caballero J; Barcelona Supercomputing Center (BSC), Barcelone, Spain., Safaei S; Institute of Biomedical Engineering and Technology, Ghent University, Gent, Belgium.; Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand., Valencia A; Barcelona Supercomputing Center (BSC), Barcelone, Spain.; ICREA, 23 Passeig Lluís Companys, 08010, Barcelona, Spain., Zinovyev A; In silico R&D, Evotec, 31400, Toulouse, France., Glazier JA; Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, 47408, USA.

Publikováno v: NPJ systems biology and applications [NPJ Syst Biol Appl] 2024 Nov 30; Vol. 10 (1), pp. 141. Date of Electronic Publication: 2024 Nov 30.

SimService: a lightweight library for building simulation services in Python.

Autor: Sego TJ; Department of Medicine, University of Florida, Gainesville, FL 32610-0225, United States.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Jan 02; Vol. 40 (1).

Tissue Forge: Interactive biological and biophysics simulation environment.

Autor: Sego TJ; Department of Medicine, University of Florida, Gainesville, Florida, United States of America., Sluka JP; Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America., Sauro HM; Department of Bioengineering, University of Washington, Seattle, Washington, United States of America., Glazier JA; Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America.

Publikováno v: PLoS computational biology [PLoS Comput Biol] 2023 Oct 23; Vol. 19 (10), pp. e1010768. Date of Electronic Publication: 2023 Oct 23 (Print Publication: 2023).

Modeling the roles of cohesotaxis, cell-intercalation, and tissue geometry in collective cell migration of Xenopus mesendoderm.

Autor: Comlekoglu T, Dzamba BJ, Pacheco GG, Shook DR, Sego TJ, Glazier JA, Peirce SM, DeSimone DW

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2023 Oct 17. Date of Electronic Publication: 2023 Oct 17.

Building digital twins of the human immune system: toward a roadmap.

Autor: Laubenbacher R; Department of Medicine, University of Florida, Gainesville, FL, USA. reinhard.laubenbacher@medicine.ufl.edu., 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, 91120, Palaiseau, France., Helikar T; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA., An G; Department of Surgery, Larner College of Medicine, University of Vermont, Burlington, VT, USA., Shapiro B; Department of Medicine, University of Florida, Gainesville, FL, USA., Malik-Sheriff RS; European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, Cambridge, UK., Sego TJ; Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA., Knapp A; Department of Medicine, University of Florida, Gainesville, FL, USA., Macklin P; Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA., Glazier JA; Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.

Publikováno v: NPJ digital medicine [NPJ Digit Med] 2022 May 20; Vol. 5 (1), pp. 64. Date of Electronic Publication: 2022 May 20.