Translational quantitative systems toxicology to improve the understanding of the safety of medicines - Sofia: 116030 | TransQST | Project | Results | H2020 | CORDIS

Publications

Homeostasis, injury and recovery dynamics at multiple scales in a self-organizing mouse intestinal crypt

Auteurs: Louis Gall, Carrie Duckworth, Ferran Jardi, Lieve Lammens, Aimee Parker, Ambra Bianco, Holly Kimko, David Mark Pritchard, Carmen Pin
Publié dans: eLife, 2023, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.85478

Genetic polymorphism in ATIC is associated with effectiveness and toxicity of pemetrexed in non-small-cell lung cancer

Auteurs: Sabine Visser, Stijn Koolen, Nadine van Donk, Nico van Walree, Cor van der Leest, Robin Cornelissen, Ron van Schaik, Ron Mathijssen, Joachim Aerts, Bruno H Stricker
Publié dans: Thorax, Numéro 76/11, 2021, Page(s) 1150-1153, ISSN 0040-6376
Éditeur: BMJ Publishing Group
DOI: 10.1136/thoraxjnl-2020-216504

Dysregulated mesenchymal PDGFR‐β drives kidney fibrosis

Auteurs: Eva M Buhl, Sonja Djudjaj, Barbara M Klinkhammer, Katja Ermert, Victor G Puelles, Maja T Lindenmeyer, Clemens D Cohen, Chaoyong He, Erawan Borkham‐Kamphorst, Ralf Weiskirchen, Bernd Denecke, Panuwat Trairatphisan, Julio Saez‐Rodriguez, Tobias B Huber, Lorin E Olson, Jürgen Floege, Peter Boor
Publié dans: EMBO Molecular Medicine, Numéro 12/3, 2020, ISSN 1757-4676
Éditeur: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.201911021

Utilization of Pharmacokinetic/ Pharmacodynamic Modeling in Pharmacoepidemiological Studies: ASystematic Review on Antiarrhythmic and Glucose-Lowering Medicines

Auteurs: Soroush Mohammadi Jouabadi, Mitra Nekouei Shahraki, Payam Peymani, Bruno H. Stricker and Fariba Ahmadizar
Publié dans: Frontiers in Pharmacology, 2022, ISSN 1663-9812
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fphar.2022.908538

The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment

Auteurs: Giulia Callegaro, Steven J. Kunnen, Panuwat Trairatphisan, Solène Grosdidier, Marije Niemeijer, Wouter den Hollander, Emre Guney, Janet Piñero Gonzalez, Laura Furlong, Yue W. Webster, Julio Saez-Rodriguez, Jeffrey J. Sutherland, Jennifer Mollon, James L. Stevens, Bob van de Water
Publié dans: Archives of Toxicology, Numéro 95/12, 2021, Page(s) 3745-3775, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-021-03141-w

Benchmarking post-GWAS analysis tools in major depression: Challenges and implications

Auteurs: Judith Pérez-Granado, Janet Piñero and Laura I. Furlong
Publié dans: Frontiers in Genetics, Numéro 16648021, 2022, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2022.1006903

Applying the CiPA Approach to Evaluate Cardiac Proarrhythmia Risk of some Antimalarials Used Off‐label in the First Wave of COVID‐19

Auteurs: Annie Delaunois, Matthew Abernathy, Warren D. Anderson, Kylie A. Beattie, Khuram W. Chaudhary, Julie Coulot, Vitalina Gryshkova, Simon Hebeisen, Mark Holbrook, James Kramer, Yuri Kuryshev, Derek Leishman, Isabel Lushbough, Elisa Passini, Will S. Redfern, Blanca Rodriguez, Eric I. Rossman, Cristian Trovato, Caiyun Wu, Jean‐Pierre Valentin
Publié dans: Clinical and Translational Science, 2021, ISSN 1752-8054
Éditeur: Wiley-Blackwell
DOI: 10.1111/cts.13011

The virtual assay software for human in silico drug trials to augment drug cardiac testing

Auteurs: Elisa Passini, Xin Zhou, Cristian Trovato, Oliver J Britton, Alfonso Bueno-Orovio, Blanca Rodriguez
Publié dans: Journal of Computational Science, 2020, Page(s) 101202, ISSN 1877-7503
Éditeur: Elsevier BV
DOI: 10.1016/j.jocs.2020.101202

Path4Drug: Data Science Workflow for Identification of Tissue-Specific Biological Pathways Modulated by Toxic Drugs

Auteurs: Barbara Füzi, Jana Gurinova, Henning Hermjakob, Gerhard F. Ecker, Rahuman Sheriff
Publié dans: Frontiers in Pharmacology, Numéro 12, 2021, ISSN 1663-9812
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fphar.2021.708296

Blinded In Silico Drug Trial Reveals the Minimum Set of Ion Channels for Torsades de Pointes Risk Assessment

Auteurs: Xin Zhou, Yusheng Qu, Elisa Passini, Alfonso Bueno-Orovio, Yang Liu, Hugo M. Vargas, Blanca Rodriguez
Publié dans: Frontiers in Pharmacology, Numéro 10, 2020, ISSN 1663-9812
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fphar.2019.01643

Parallel ant colony optimization for the training of cell signaling networks

Auteurs: Patricia González, Roberto Prado-Rodriguez, Attila Gábor, Julio Saez-Rodriguez, Julio R.Banga, Ramón Doallo
Publié dans: Expert Systems with Applications, 2022, ISSN 0957-4174
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.eswa.2022.118199

A novel cardiovascular systems model to quantify drugs effects on the inter-relationship between contractility and other hemodynamic variables

Auteurs: Yu Fu, Hadi Taghvafard, Medhat M Said, Eric I Rossman, Teresa A Collins, Stéphanie Billiald-Desquand, Derek Leishman, Piet H van der Graaf, J G Coen van Hasselt, Nelleke Snelder
Publié dans: CPT: pharmacometrics & systems pharmacology, 2022, ISSN 2163-8306
Éditeur: Nature Publishing Group
DOI: 10.1002/psp4.12774

Mouse organoids as an in vitro tool to study the in vivo intestinal response to cytotoxicants

Auteurs: F Jardi, C Kelly, C Teague, H Fowler-Williams, D C Sevin, D Rodrigues, H Jo, S Ferreira, B Herpers, M Van Heerden, T de Kok, C Pin, A Lynch, C A Duckworth, S De Jonghe, L Lammens, D M Pritchard
Publié dans: Archives of Toxicology, Numéro 03405761, 2022, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-022-03374-3

All-Optical Electrophysiology Refines Populations of In Silico Human iPSC-CMs for Drug Evaluation

Auteurs: Michelangelo Paci, Elisa Passini, Aleksandra Klimas, Stefano Severi, Jari Hyttinen, Blanca Rodriguez, Emilia Entcheva
Publié dans: Biophysical Journal, Numéro 118/10, 2020, Page(s) 2596-2611, ISSN 0006-3495
Éditeur: Biophysical Society
DOI: 10.1016/j.bpj.2020.03.018

BioModels—15 years of sharing computational models in life science

Auteurs: Rahuman S Malik-Sheriff, Mihai Glont, Tung V N Nguyen, Krishna Tiwari, Matthew G Roberts, Ashley Xavier, Manh T Vu, Jinghao Men, Matthieu Maire, Sarubini Kananathan, Emma L Fairbanks, Johannes P Meyer, Chinmay Arankalle, Thawfeek M Varusai, Vincent Knight-Schrijver, Lu Li, Corina Dueñas-Roca, Gaurhari Dass, Sarah M Keating, Young M Park, Nicola Buso, Nicolas Rodriguez, Michael Hucka, Henning Herm
Publié dans: Nucleic Acids Research, 2019, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz1055

Reproducibility in systems biology modelling

Auteurs: Krishna Tiwari, Sarubini Kananathan, Matthew G Roberts, Johannes P Meyer, Mohammad Umer Sharif Shohan, Ashley Xavier, Matthieu Maire, Ahmad Zyoud, Jinghao Men, Szeyi Ng, Tung V N Nguyen, Mihai Glont, Henning Hermjakob, Rahuman S Malik‐Sheriff
Publié dans: Molecular Systems Biology, Numéro 17/2, 2021, ISSN 1744-4292
Éditeur: Nature Publishing Group
DOI: 10.15252/msb.20209982

Unravelling Mechanisms of Doxorubicin-Induced Toxicity in 3D Human Intestinal Organoids

Auteurs: Daniela Rodrigues, Luke Coyle,Barbara Füzi, Sofia Ferreira, Heeseung Jo, Bram Herpers, Seung-Wook Chung, Ciarán Fisher, Jos C. S. Kleinjans, Danyel Jennen and Theo M. de Kok
Publié dans: International Journal of Molecular Sciences, Numéro 2022: 23(3), 2022, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23031286

Sex-Based Difference in the Effect of Metoprolol on Heart Rate and Bradycardia in a Population-Based Setting

Auteurs: Linda C. Hendriksen,Grace Omes-Smit, Birgit C. P. Koch, M. Arfan Ikram, Bruno H. Stricker and Loes E. Visser
Publié dans: MDPI, Numéro 20754701, 2022, ISSN 2075-4701
Éditeur: MDPI
DOI: 10.3390/jpm12060870

QTc-interval prolongation and increased risk of sudden cardiac death associated with hydroxychloroquine

Auteurs: Fariba Ahmadizar, Negin Soroush, M Arfan Ikram, Jan A Kors, Maryam Kavousi, Bruno H Stricker
Publié dans: European Journal of Preventive Cardiology, 2020, ISSN 2047-4873
Éditeur: SAGE Publications Ltd
DOI: 10.1093/eurjpc/zwaa118

A NOS1AP gene variant is associated with a paradoxical increase of the QT-interval shortening effect of digoxin

Auteurs: Negin Soroush, Albert-Jan Aarnoudse, Maryam Kavousi, Jan A. Kors, M. Arfan Ikram, Christopher Newton-Cheh, Fariba Ahmadizar, Bruno H. Stricker
Publié dans: The Pharmacogenomics Journal, 2021, ISSN 1470-269X
Éditeur: Nature Publishing Group
DOI: 10.1038/s41397-021-00256-2

Genome-wide expression changes induced by bisphenol A, F and S in human stem cell derived hepatocyte-like cells

Auteurs: Lucendo-Villarin, B.; Nell, Patrick; Hellwig, Birte; Filis, P.; Feuerborn, David; O'Shaughnessy, P.J.; Godoy, Patricio; Rahnenführer, Jörg; Hengstler, Jan G.; Cherianidou, A.; Sachinidis, A.; Fowler, P.A.; Hay, David C.
Publié dans: 1611-2156, Numéro 1, 2020, ISSN 1611-2156
Éditeur: University of Mainz
DOI: 10.17179/excli2020-2934/supplementary_tables

Systems Modeling to Quantify Safety Risks in Early Drug Development: Using Bifurcation Analysis and Agent-Based Modeling as Examples

Auteurs: Carmen Pin, Teresa Collins, Megan Gibbs, Holly Kimko
Publié dans: The AAPS Journal, Numéro 23/4, 2021, ISSN 1550-7416
Éditeur: Springer New York
DOI: 10.1208/s12248-021-00580-2

Drug Safety Data Curation and Modeling in ChEMBL: Boxed Warnings and Withdrawn Drugs

Auteurs: Fiona M.I. Hunter, A. Patrícia Bento, Nicolas Bosc, Anna Gaulton, Anne Hersey, Andrew R. Leach
Publié dans: Chemical Research in Toxicology, Numéro 34/2, 2021, Page(s) 385-395, ISSN 0893-228X
Éditeur: American Chemical Society
DOI: 10.1021/acs.chemrestox.0c00296

Scientific and regulatory evaluation of mechanistic in silico drug and disease models in drug development: Building model credibility.

Auteurs: Musuamba FT, Skottheim Rusten I, Lesage R, Russo G, Bursi R, Emili L, Wangorsch G, Manolis E, Karlsson KE, Kulesza A, Courcelles E, Boissel JP, Rousseau CF, Voisin EM, Alessandrello R, Curado N8, Dall'ara E, Rodriguez B, Pappalardo F, Geris L
Publié dans: CPT: Pharmacometrics & Systems Pharmacology, 2021, ISSN 2163-8306
Éditeur: Nature Publishing Group
DOI: 10.1002/psp4.12669

KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study.

Auteurs: Füzi B, Malik-Sheriff RS, Manners EJ, Hermjakob H, Ecker GF
Publié dans: Journal of Cheminformatics, 2022, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-022-00615-6

Flame: an open source framework for model development, hosting, and usage in production environments

Auteurs: Manuel Pastor, José Carlos Gómez-Tamayo, Ferran Sanz
Publié dans: Journal of Cheminformatics, Numéro 13/1, 2021, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-021-00509-z

Improving prediction of torsadogenic risk in the CiPA in silico model by appropriately accounting for clinical exposure

Auteurs: Derek J. Leishman
Publié dans: Journal of Pharmacological and Toxicological Methods, Numéro 101, 2020, Page(s) 106654, ISSN 1056-8719
Éditeur: Elsevier BV
DOI: 10.1016/j.vascn.2019.106654

Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein–Protein Interaction Data

Auteurs: Patricia Mirela-Bota, Joaquim Aguirre-Plans, Alberto Meseguer, Cristiano Galletti, Joan Segura, Joan Planas-Iglesias, Javi Garcia-Garcia, Emre Guney, Baldo Oliva, Narcis Fernandez-Fuentes
Publié dans: Journal of Molecular Biology, 2020, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2020.09.015

The DisGeNET cytoscape app: Exploring and visualizing disease genomics data

Auteurs: Janet Piñero, Josep Saüch, Ferran Sanz, Laura I. Furlong
Publié dans: Computational and Structural Biotechnology Journal, Numéro 19, 2021, Page(s) 2960-2967, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2021.05.015

Genome-wide expression changes induced by bisphenol A, F and S in human stem cell derived hepatocyte-like cells

Auteurs: B. Lucendo-Villarin, P. Nell, B. Hellwig, P. Filis, D. Feuerborn, P.J. O'Shaughnessy, P. Godoy, J. Rahnenführer, J.G. Hengstler, A. Cherianidou, A. Sachinidis, P.A. Fowler, and D.C. Hay*
Publié dans: EXCLI Journal, 2020, ISSN 1611-2156
Éditeur: University of Mainz
DOI: 10.17179/excli2020-2934

Gene expression responses reflecting 5-FU-induced toxicity: Comparison between patient colon tissue and 3D human colon organoids

Auteurs: Daniela Rodrigues, Roelvan Kampen, Ad A.van Bodegraven, Jos C.S.Kleinjans, Danyel G.J.Jennen, Theo M.de Kok
Publié dans: Toxicology Letters, Numéro 03784274, 2022, ISSN 0378-4274
Éditeur: Elsevier BV
DOI: 10.1016/j.toxlet.2022.09.013

Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare

Auteurs: Davide Cirillo, Silvina Catuara-Solarz, Czuee Morey, Emre Guney, Laia Subirats, Simona Mellino, Annalisa Gigante, Alfonso Valencia, María José Rementeria, Antonella Santuccione Chadha, Nikolaos Mavridis
Publié dans: npj Digital Medicine, Numéro 3/1, 2020, ISSN 2398-6352
Éditeur: Springer Nature in partnership with Seoul National University Bundang Hospital
DOI: 10.1038/s41746-020-0288-5

Human In Silico Drug Trials Demonstrate Higher Accuracy than Animal Models in Predicting Clinical Pro-Arrhythmic Cardiotoxicity

Auteurs: Elisa Passini, Oliver J. Britton, Hua Rong Lu, Jutta Rohrbacher, An N. Hermans, David J. Gallacher, Robert J. H. Greig, Alfonso Bueno-Orovio, Blanca Rodriguez
Publié dans: Frontiers in Physiology, Numéro 8, 2017, ISSN 1664-042X
Éditeur: Frontiers Research Foundation
DOI: 10.3389/fphys.2017.00668

Integration of Genome Scale Metabolic Networks and Gene Regulation of Metabolic Enzymes With Physiologically Based Pharmacokinetics

Auteurs: Elaina M. Maldonado, Vytautas Leoncikas, Ciarán P. Fisher, J. Bernadette Moore, Nick J. Plant, Andrzej M. Kierzek
Publié dans: CPT: Pharmacometrics & Systems Pharmacology, Numéro 6/11, 2017, Page(s) 732-746, ISSN 2163-8306
Éditeur: Nature Publishing Group
DOI: 10.1002/psp4.12230

In silico models in drug development: where we are

Auteurs: Janet Piñero, Laura I Furlong, Ferran Sanz
Publié dans: Current Opinion in Pharmacology, Numéro 42, 2018, Page(s) 111-121, ISSN 1471-4892
Éditeur: Elsevier BV
DOI: 10.1016/j.coph.2018.08.007

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response

Auteurs: Janet Piñero, Abel Gonzalez-Perez, Emre Guney, Joaquim Aguirre-Plans, Ferran Sanz, Baldo Oliva, Laura I. Furlong
Publié dans: Frontiers in Genetics, Numéro 9, 2018, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2018.00412

Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury

Auteurs: Terezinha Souza, Panuwat Trairatphisan, Janet Piñero, Laura I. Furlong, Julio Saez-Rodriguez, Jos Kleinjans, Danyel Jennen
Publié dans: Frontiers in Genetics, Numéro 9, 2018, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2018.00527

Development of an Infrastructure for the Prediction of Biological Endpoints in Industrial Environments. Lessons Learned at the eTOX Project

Auteurs: Manuel Pastor, Jordi Quintana, Ferran Sanz
Publié dans: Frontiers in Pharmacology, Numéro 9, 2018, ISSN 1663-9812
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fphar.2018.01147

Quantitative systems pharmacology analysis of drug combination and scaling to humans: the interaction between noradrenaline and vasopressin in vasoconstriction

Auteurs: Anyue Yin, Akihiro Yamada, Wiro B Stam, Johan G C van Hasselt, Piet H van der Graaf
Publié dans: British Journal of Pharmacology, Numéro 175/16, 2018, Page(s) 3394-3406, ISSN 0007-1188
Éditeur: Wiley-Blackwell
DOI: 10.1111/bph.14385

Characterisation of the NRF2 transcriptional network and its response to chemical insult in primary human hepatocytes: implications for prediction of drug-induced liver injury

Auteurs: Ian M. Copple, Wouter den Hollander, Giulia Callegaro, Fiona E. Mutter, James L. Maggs, Amy L. Schofield, Lucille Rainbow, Yongxiang Fang, Jeffrey J. Sutherland, Ewa C. Ellis, Magnus Ingelman-Sundberg, Stephen W. Fenwick, Christopher E. Goldring, Bob van de Water, James L. Stevens, B. Kevin Park
Publié dans: Archives of Toxicology, Numéro 93/2, 2019, Page(s) 385-399, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-018-2354-1

GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets

Auteurs: Joaquim Aguirre-Plans, Janet Piñero, Ferran Sanz, Laura I. Furlong, Narcis Fernandez-Fuentes, Baldo Oliva, Emre Guney
Publié dans: Journal of Molecular Biology, Numéro 431/13, 2019, Page(s) 2477-2484, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2019.02.027

Prediction of human drug-induced liver injury (DILI) in relation to oral doses and blood concentrations

Auteurs: Wiebke Albrecht, Franziska Kappenberg, Tim Brecklinghaus, Regina Stoeber, Rosemarie Marchan, Mian Zhang, Kristina Ebbert, Hendrik Kirschner, Marianna Grinberg, Marcel Leist, Wolfgang Moritz, Cristina Cadenas, Ahmed Ghallab, Jörg Reinders, Nachiket Vartak, Christoph van Thriel, Klaus Golka, Laia Tolosa, José V. Castell, Georg Damm, Daniel Seehofer, Alfonso Lampen, Albert Braeuning, Thorsten Buhrk
Publié dans: Archives of Toxicology, Numéro 93/6, 2019, Page(s) 1609-1637, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-019-02492-9

Development, calibration, and validation of a novel human ventricular myocyte model in health, disease, and drug block

Auteurs: Jakub Tomek, Alfonso Bueno-Orovio, Elisa Passini, Xin Zhou, Ana Minchole, Oliver Britton, Chiara Bartolucci, Stefano Severi, Alvin Shrier, Laszlo Virag, Andras Varro, Blanca Rodriguez
Publié dans: eLife, Numéro 8, 2019, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.48890

Drug‐induced shortening of the electromechanical window is an effective biomarker for in silico prediction of clinical risk of arrhythmias

Auteurs: Elisa Passini, Cristian Trovato, Pierre Morissette, Frederick Sannajust, Alfonso Bueno‐Orovio, Blanca Rodriguez
Publié dans: British Journal of Pharmacology, Numéro 176/19, 2019, Page(s) 3819-3833, ISSN 0007-1188
Éditeur: Wiley-Blackwell
DOI: 10.1111/bph.14786

Drug-induced gene expression profile changes in relation to intestinal toxicity: State-of-the-art and new approaches

Auteurs: Daniela Rodrigues, Terezinha Souza, Danyel G.J. Jennen, Lieve Lemmens, Jos C.S. Kleinjans, Theo M. de Kok
Publié dans: Cancer Treatment Reviews, Numéro 77, 2019, Page(s) 57-66, ISSN 0305-7372
Éditeur: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.ctrv.2019.06.004

Quantitative Systems Toxicology Modeling To Address Key Safety Questions in Drug Development: A Focus of the TransQST Consortium

Auteurs: Sofia Ferreira, Ciarán Fisher, Laura I. Furlong, Loic Laplanche, Brian Kevin Park, Carmen Pin, Julio Saez-Rodriguez, Panuwat Trairatphisan
Publié dans: Chemical Research in Toxicology, Numéro 33/1, 2020, Page(s) 7-9, ISSN 0893-228X
Éditeur: American Chemical Society
DOI: 10.1021/acs.chemrestox.9b00499

From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL

Auteurs: Anika Liu, Panuwat Trairatphisan, Enio Gjerga, Athanasios Didangelos, Jonathan Barratt, Julio Saez-Rodriguez
Publié dans: npj Systems Biology and Applications, Numéro 5/1, 2019, ISSN 2056-7189
Éditeur: Nature
DOI: 10.1038/s41540-019-0118-z

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology

Auteurs: Joaquim Aguirre-Plans, Janet Piñero, Jörg Menche, Ferran Sanz, Laura Furlong, Harald Schmidt, Baldo Oliva, Emre Guney
Publié dans: Pharmaceuticals, Numéro 11/3, 2018, Page(s) 61, ISSN 1424-8247
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ph11030061

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

Auteurs: N. del-Toro, M. Duesbury, M. Koch, L. Perfetto, A. Shrivastava, D. Ochoa, O. Wagih, J. Piñero, M. Kotlyar, C. Pastrello, P. Beltrao, L. I. Furlong, I. Jurisica, H. Hermjakob, S. Orchard, P. Porras
Publié dans: Nature Communications, Numéro 10/1, 2019, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-018-07709-6

Human Purkinje in silico model enables mechanistic investigations into automaticity and pro-arrhythmic abnormalities

Auteurs: Cristian Trovato, Elisa Passini, Norbert Nagy, András Varró, Najah Abi-Gerges, Stefano Severi, Blanca Rodriguez
Publié dans: Journal of Molecular and Cellular Cardiology, Numéro 142, 2020, Page(s) 24-38, ISSN 0022-2828
Éditeur: Academic Press
DOI: 10.1016/j.yjmcc.2020.04.001

Application of High-Throughput Transcriptomics for Mechanism-Based Biological Read-Across of Short-Chain Carboxylic Acid Analogues of Valproic Acid

Auteurs: Nanette G. Vrijenhoek, Matthias M. Wehr, Steven J. Kunnen, Lukas S. Wijaya, Giulia Callegaro, Martijn J. Moné, Sylvia E. Escher and Bob van de Water
Publié dans: ALTEX, 2022, ISSN 1868-8551
Éditeur: Pringer
DOI: 10.14573/altex.2107261

Women are started on a lower daily dose of metoprolol than men irrespective of dose recommendations: A potential source of confounding by contraindication in pharmacoepidemiology

Auteurs: Linda C. Hendriksen, Katia M. C. Verhamme, Paul D. Van der Linden, Bruno H. Stricker, Loes E. Visser
Publié dans: Pharmacoepidemiology and Drug Safety, 2021, ISSN 1053-8569
Éditeur: John Wiley & Sons Inc.
DOI: 10.1002/pds.5220

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Auteurs: Niarakis A, Waltemath D, Glazier J, Schreiber F, Keating SM, Nickerson D, Chaouiya C, Siegel A, Noël V, Hermjakob H, Helikar T, Soliman S,Calzona L
Publié dans: Briefings in Bioinformatics, 2022, ISSN 1467-5463
Éditeur: Oxford University Press
DOI: 10.1093/bib/bbac212

Cross clinical-experimental-computational qualification of in silico drug trials on human cardiac purkinje cells for proarrhythmia risk prediction

Auteurs: Cristian Trovato, Marcel Mohr, Friedemann Schmidt, Elisa Passini, Blanca Rodriguez
Publié dans: Frontiers in Toxicology, Numéro 26733080, 2022, ISSN 2673-3080
Éditeur: Frontiers in Toxicology
DOI: 10.3389/ftox.2022.992650

A Transcriptomic Approach to Elucidate the Mechanisms of Gefitinib-Induced Toxicity in Healthy Human Intestinal Organoids

Auteurs: Daniela Rodrigues,* Bram Herpers,Sofia Ferreira, Heeseung Jo, Ciarán Fisher, Luke Coyle, Seung-Wook Chung, Jos C. S. Kleinjans, Danyel G. J. Jennen, and Theo M. de Kok
Publié dans: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23042213

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis

Auteurs: Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio‐Escat, Michal Klein, Olga Ivanova, Márton Ölbei, Attila Gábor, Fabian Theis, Dezső Módos, Tamás Korcsmáros, Julio Saez‐Rodriguez
Publié dans: Molecular Systems Biology, Numéro 17/3, 2021, ISSN 1744-4292
Éditeur: Nature Publishing Group
DOI: 10.15252/msb.20209923

In-silico human electro-mechanical ventricular modelling and simulation for drug-induced pro-arrhythmia and inotropic risk assessment

Auteurs: Francesca Margara, Zhinuo J. Wang, Francesc Levrero-Florencio, Alfonso Santiago, Mariano Vázquez, Alfonso Bueno-Orovio, Blanca Rodriguez
Publié dans: Progress in Biophysics and Molecular Biology, 2020, ISSN 0079-6107
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.pbiomolbio.2020.06.007

Converting networks to predictive logic models from perturbation signalling data with CellNOpt

Auteurs: Enio Gjerga, Panuwat Trairatphisan, Attila Gabor, Hermann Koch, Celine Chevalier, Franceco Ceccarelli, Aurelien Dugourd, Alexander Mitsos, Julio Saez-Rodriguez
Publié dans: Bioinformatics, 2020, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btaa561

Integration of temporal single cell cellular stress response activity with logic-ODE modeling reveals activation of ATF4-CHOP axis as a critical predictor of drug-induced liver injury

Auteurs: Lukas Surya Wijaya, Panuwat Trairatphisan, Attila Gabor, Marije Niemeijer, Jason Keet, Ariadna Alcalà Morera, Kirsten E. Snijders, Steven Wink, Huan Yang, Stefan Schildknecht, James L. Stevens, Peter Bouwman, Hennicke Kamp, Jan Hengstler, Joost Beltman, Marcel Leist, Sylvia Le Dévédec, Julio Saez-Rodriguez, Bob van de Water
Publié dans: Biochemical Pharmacology, Numéro 190, 2021, Page(s) 114591, ISSN 0006-2952
Éditeur: Elsevier BV
DOI: 10.1016/j.bcp.2021.114591

Functional Genomics Analysis to Disentangle the Role of Genetic Variants in Major Depression

Auteurs: Judith Pérez-Granado, Janet Piñero, Alejandra Medina-Rivera, and Laura I. Furlong
Publié dans: MDPI, Numéro 20754701, 2022, ISSN 2075-4701
Éditeur: MDPI
DOI: 10.3390/genes13071259

New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids.

Auteurs: Daniela Rodrigues*, Terezinha de Souza, Luke Coyle, Matteo Di Piazza, Bram Herpers, Sofia Ferreira, Mian Zhang, Daniel Sevin, Anthony Lynch, Attila Gabor, Seung-Wook Chung, Julio Saez-Rodriguez, Danyel G.J. Jennen1, Jos C.S. Kleinjans, Theo M. de Kok.
Publié dans: Archives of Toxicology, 2021, ISSN 1432-0738
Éditeur: Springer Science+Business Media
DOI: 10.1007/s00204-021-03092-2

Human biventricular electromechanical simulations on the progression of electrocardiographic and mechanical abnormalities in post-myocardial infarction

Auteurs: Zhinuo J Wang, Alfonso Santiago, Xin Zhou, Lei Wang, Francesca Margara, Francesc Levrero-Florencio, Arka Das, Chris Kelly, Erica Dall'Armellina, Mariano Vazquez, Blanca Rodriguez
Publié dans: EP Europace, Numéro 23/Supplement_1, 2021, Page(s) i143-i152, ISSN 1099-5129
Éditeur: Oxford University Press
DOI: 10.1093/europace/euaa405

Comparison of the Simulated Response of Three in Silico Human Stem Cell-Derived Cardiomyocytes Models and in Vitro Data Under 15 Drug Actions

Auteurs: Michelangelo Paci, Jussi T. Koivumäki, Hua Rong Lu, David J. Gallacher, Elisa Passini, Blanca Rodriguez
Publié dans: Frontiers in Pharmacology, Numéro 12, 2021, ISSN 1663-9812
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fphar.2021.604713

BioModels Parameters: a treasure trove of parameter values from published systems biology models

Auteurs: Mihai Glont, Chinmay Arankalle, Krishna Tiwari, Tung V N Nguyen, Henning Hermjakob, Rahuman S Malik-Sheriff
Publié dans: Bioinformatics, 2020, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btaa560

Model-based translation of DNA damage signaling dynamics across cell types

Auteurs: Muriel M. Heldring,Lukas S. Wijaya,Marije Niemeijer,Huan Yang,Talel Lakhal,Sylvia E. Le Dévédec,Bob van de Water,Joost B. Beltman
Publié dans: PLoS Comput Biol, 2022, ISSN 1553-734X
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1010264

Accurate in silico simulation of the rabbit Purkinje fiber electrophysiological assay to facilitate early pharmaceutical cardiosafety assessment: Dream or reality?

Auteurs: Marcel Mohr, Jean-Marie Chambard, Véronique Ballet, Friedemann Schmidt
Publié dans: J Pharmacol Toxicol Methods ., 2022, ISSN 1056-8719
Éditeur: Elsevier BV
DOI: 10.1016/j.vascn.2022.107172

Transcriptomic Cross‐Species Analysis of Chronic Liver Disease Reveals Consistent Regulation Between Humans and Mice

Auteurs: Christian H. Holland, Ricardo O. Ramirez Flores, Maiju Myllys, Reham Hassan, Karolina Edlund, Ute Hofmann, Rosemarie Marchan, Cristina Cadenas, Jörg Reinders, Stefan Hoehme, Abdel‐latif Seddek, Steven Dooley, Verena Keitel, Patricio Godoy, Brigitte Begher‐Tibbe, Christian Trautwein, Christian Rupp, Sebastian Mueller, Thomas Longerich, Jan G. Hengstler, Julio Saez‐Rodriguez, Ahmed Ghallab
Publié dans: Hepatology Communications, 2021, ISSN 2471-254X
Éditeur: Wiley
DOI: 10.1002/hep4.1797

The DisGeNET knowledge platform for disease genomics: 2019 update

Auteurs: Janet Piñero, Juan Manuel Ramírez-Anguita, Josep Saüch-Pitarch, Francesco Ronzano, Emilio Centeno, Ferran Sanz, Laura I Furlong
Publié dans: Nucleic Acids Research, 2019, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz1021

Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury

Auteurs: Panuwat Trairatphisan, Terezinha Maria de Souza, Jos Kleinjans, Danyel Jennen, Julio Saez-Rodriguez
Publié dans: Toxicology Letters, 2021, ISSN 0378-4274
Éditeur: Elsevier BV
DOI: 10.1016/j.toxlet.2021.06.020

An ensemble learning approach for modeling the systems biology of drug-induced injury

Auteurs: Joaquim Aguirre-Plans, Janet Piñero, Terezinha Souza, Giulia Callegaro, Steven J. Kunnen, Ferran Sanz, Narcis Fernandez-Fuentes, Laura I. Furlong, Emre Guney, Baldo Oliva
Publié dans: Biology Direct, Numéro 16/1, 2021, ISSN 1745-6150
Éditeur: BioMed Central
DOI: 10.1186/s13062-020-00288-x

SARS-CoV-2-Specific Antibody Profiles Distinguish Patients with Moderate from Severe COVID-19

Auteurs: de Campos Mata L, Piñero J, Vaquero ST, Tachó-Piñot R, Kuksin M, Aldea IA, Melero NR, Carolis C, Furlong L, Cerutti A, Villar-García J, Magri G
Publié dans: medRxiv, 2020
Éditeur: medRxiv
DOI: 10.1101/2020.12.18.20248461

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