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

Author(s): Louis Gall, Carrie Duckworth, Ferran Jardi, Lieve Lammens, Aimee Parker, Ambra Bianco, Holly Kimko, David Mark Pritchard, Carmen Pin
Published in: eLife, 2023, ISSN 2050-084X
Publisher: 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

Author(s): 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
Published in: Thorax, Issue 76/11, 2021, Page(s) 1150-1153, ISSN 0040-6376
Publisher: BMJ Publishing Group
DOI: 10.1136/thoraxjnl-2020-216504

Dysregulated mesenchymal PDGFR‐β drives kidney fibrosis

Author(s): 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
Published in: EMBO Molecular Medicine, Issue 12/3, 2020, ISSN 1757-4676
Publisher: 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

Author(s): Soroush Mohammadi Jouabadi, Mitra Nekouei Shahraki, Payam Peymani, Bruno H. Stricker and Fariba Ahmadizar
Published in: Frontiers in Pharmacology, 2022, ISSN 1663-9812
Publisher: 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

Author(s): 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
Published in: Archives of Toxicology, Issue 95/12, 2021, Page(s) 3745-3775, ISSN 0340-5761
Publisher: Springer Verlag
DOI: 10.1007/s00204-021-03141-w

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

Author(s): Judith Pérez-Granado, Janet Piñero and Laura I. Furlong
Published in: Frontiers in Genetics, Issue 16648021, 2022, ISSN 1664-8021
Publisher: 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

Author(s): 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
Published in: Clinical and Translational Science, 2021, ISSN 1752-8054
Publisher: Wiley-Blackwell
DOI: 10.1111/cts.13011

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

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

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

Author(s): Barbara Füzi, Jana Gurinova, Henning Hermjakob, Gerhard F. Ecker, Rahuman Sheriff
Published in: Frontiers in Pharmacology, Issue 12, 2021, ISSN 1663-9812
Publisher: 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

Author(s): Xin Zhou, Yusheng Qu, Elisa Passini, Alfonso Bueno-Orovio, Yang Liu, Hugo M. Vargas, Blanca Rodriguez
Published in: Frontiers in Pharmacology, Issue 10, 2020, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2019.01643

Parallel ant colony optimization for the training of cell signaling networks

Author(s): Patricia González, Roberto Prado-Rodriguez, Attila Gábor, Julio Saez-Rodriguez, Julio R.Banga, Ramón Doallo
Published in: Expert Systems with Applications, 2022, ISSN 0957-4174
Publisher: 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

Author(s): 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
Published in: CPT: pharmacometrics & systems pharmacology, 2022, ISSN 2163-8306
Publisher: Nature Publishing Group
DOI: 10.1002/psp4.12774

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

Author(s): 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
Published in: Archives of Toxicology, Issue 03405761, 2022, ISSN 0340-5761
Publisher: Springer Verlag
DOI: 10.1007/s00204-022-03374-3

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

Author(s): Michelangelo Paci, Elisa Passini, Aleksandra Klimas, Stefano Severi, Jari Hyttinen, Blanca Rodriguez, Emilia Entcheva
Published in: Biophysical Journal, Issue 118/10, 2020, Page(s) 2596-2611, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2020.03.018

BioModels—15 years of sharing computational models in life science

Author(s): 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
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1055

Reproducibility in systems biology modelling

Author(s): 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
Published in: Molecular Systems Biology, Issue 17/2, 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20209982

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

Author(s): 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
Published in: International Journal of Molecular Sciences, Issue 2022: 23(3), 2022, ISSN 1422-0067
Publisher: 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

Author(s): Linda C. Hendriksen,Grace Omes-Smit, Birgit C. P. Koch, M. Arfan Ikram, Bruno H. Stricker and Loes E. Visser
Published in: MDPI, Issue 20754701, 2022, ISSN 2075-4701
Publisher: MDPI
DOI: 10.3390/jpm12060870

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

Author(s): Fariba Ahmadizar, Negin Soroush, M Arfan Ikram, Jan A Kors, Maryam Kavousi, Bruno H Stricker
Published in: European Journal of Preventive Cardiology, 2020, ISSN 2047-4873
Publisher: 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

Author(s): Negin Soroush, Albert-Jan Aarnoudse, Maryam Kavousi, Jan A. Kors, M. Arfan Ikram, Christopher Newton-Cheh, Fariba Ahmadizar, Bruno H. Stricker
Published in: The Pharmacogenomics Journal, 2021, ISSN 1470-269X
Publisher: 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

Author(s): 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.
Published in: 1611-2156, Issue 1, 2020, ISSN 1611-2156
Publisher: 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

Author(s): Carmen Pin, Teresa Collins, Megan Gibbs, Holly Kimko
Published in: The AAPS Journal, Issue 23/4, 2021, ISSN 1550-7416
Publisher: Springer New York
DOI: 10.1208/s12248-021-00580-2

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

Author(s): Fiona M.I. Hunter, A. Patrícia Bento, Nicolas Bosc, Anna Gaulton, Anne Hersey, Andrew R. Leach
Published in: Chemical Research in Toxicology, Issue 34/2, 2021, Page(s) 385-395, ISSN 0893-228X
Publisher: 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.

Author(s): 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
Published in: CPT: Pharmacometrics & Systems Pharmacology, 2021, ISSN 2163-8306
Publisher: 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.

Author(s): Füzi B, Malik-Sheriff RS, Manners EJ, Hermjakob H, Ecker GF
Published in: Journal of Cheminformatics, 2022, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-022-00615-6

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

Author(s): Manuel Pastor, José Carlos Gómez-Tamayo, Ferran Sanz
Published in: Journal of Cheminformatics, Issue 13/1, 2021, ISSN 1758-2946
Publisher: 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

Author(s): Derek J. Leishman
Published in: Journal of Pharmacological and Toxicological Methods, Issue 101, 2020, Page(s) 106654, ISSN 1056-8719
Publisher: Elsevier BV
DOI: 10.1016/j.vascn.2019.106654

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

Author(s): 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
Published in: Journal of Molecular Biology, 2020, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2020.09.015

The DisGeNET cytoscape app: Exploring and visualizing disease genomics data

Author(s): Janet Piñero, Josep Saüch, Ferran Sanz, Laura I. Furlong
Published in: Computational and Structural Biotechnology Journal, Issue 19, 2021, Page(s) 2960-2967, ISSN 2001-0370
Publisher: 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

Author(s): 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*
Published in: EXCLI Journal, 2020, ISSN 1611-2156
Publisher: 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

Author(s): Daniela Rodrigues, Roelvan Kampen, Ad A.van Bodegraven, Jos C.S.Kleinjans, Danyel G.J.Jennen, Theo M.de Kok
Published in: Toxicology Letters, Issue 03784274, 2022, ISSN 0378-4274
Publisher: Elsevier BV
DOI: 10.1016/j.toxlet.2022.09.013

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

Author(s): 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
Published in: npj Digital Medicine, Issue 3/1, 2020, ISSN 2398-6352
Publisher: 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

Author(s): 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
Published in: Frontiers in Physiology, Issue 8, 2017, ISSN 1664-042X
Publisher: 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

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

In silico models in drug development: where we are

Author(s): Janet Piñero, Laura I Furlong, Ferran Sanz
Published in: Current Opinion in Pharmacology, Issue 42, 2018, Page(s) 111-121, ISSN 1471-4892
Publisher: Elsevier BV
DOI: 10.1016/j.coph.2018.08.007

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

Author(s): Janet Piñero, Abel Gonzalez-Perez, Emre Guney, Joaquim Aguirre-Plans, Ferran Sanz, Baldo Oliva, Laura I. Furlong
Published in: Frontiers in Genetics, Issue 9, 2018, ISSN 1664-8021
Publisher: 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

Author(s): Terezinha Souza, Panuwat Trairatphisan, Janet Piñero, Laura I. Furlong, Julio Saez-Rodriguez, Jos Kleinjans, Danyel Jennen
Published in: Frontiers in Genetics, Issue 9, 2018, ISSN 1664-8021
Publisher: 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

Author(s): Manuel Pastor, Jordi Quintana, Ferran Sanz
Published in: Frontiers in Pharmacology, Issue 9, 2018, ISSN 1663-9812
Publisher: 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

Author(s): Anyue Yin, Akihiro Yamada, Wiro B Stam, Johan G C van Hasselt, Piet H van der Graaf
Published in: British Journal of Pharmacology, Issue 175/16, 2018, Page(s) 3394-3406, ISSN 0007-1188
Publisher: 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

Author(s): 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
Published in: Archives of Toxicology, Issue 93/2, 2019, Page(s) 385-399, ISSN 0340-5761
Publisher: 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

Author(s): Joaquim Aguirre-Plans, Janet Piñero, Ferran Sanz, Laura I. Furlong, Narcis Fernandez-Fuentes, Baldo Oliva, Emre Guney
Published in: Journal of Molecular Biology, Issue 431/13, 2019, Page(s) 2477-2484, ISSN 0022-2836
Publisher: 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

Author(s): 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
Published in: Archives of Toxicology, Issue 93/6, 2019, Page(s) 1609-1637, ISSN 0340-5761
Publisher: 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

Author(s): 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
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
Publisher: 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

Author(s): Elisa Passini, Cristian Trovato, Pierre Morissette, Frederick Sannajust, Alfonso Bueno‐Orovio, Blanca Rodriguez
Published in: British Journal of Pharmacology, Issue 176/19, 2019, Page(s) 3819-3833, ISSN 0007-1188
Publisher: 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

Author(s): Daniela Rodrigues, Terezinha Souza, Danyel G.J. Jennen, Lieve Lemmens, Jos C.S. Kleinjans, Theo M. de Kok
Published in: Cancer Treatment Reviews, Issue 77, 2019, Page(s) 57-66, ISSN 0305-7372
Publisher: 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

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

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

Author(s): Anika Liu, Panuwat Trairatphisan, Enio Gjerga, Athanasios Didangelos, Jonathan Barratt, Julio Saez-Rodriguez
Published in: npj Systems Biology and Applications, Issue 5/1, 2019, ISSN 2056-7189
Publisher: Nature
DOI: 10.1038/s41540-019-0118-z

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology

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

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

Author(s): 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
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-07709-6

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

Author(s): Cristian Trovato, Elisa Passini, Norbert Nagy, András Varró, Najah Abi-Gerges, Stefano Severi, Blanca Rodriguez
Published in: Journal of Molecular and Cellular Cardiology, Issue 142, 2020, Page(s) 24-38, ISSN 0022-2828
Publisher: 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

Author(s): 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
Published in: ALTEX, 2022, ISSN 1868-8551
Publisher: 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

Author(s): Linda C. Hendriksen, Katia M. C. Verhamme, Paul D. Van der Linden, Bruno H. Stricker, Loes E. Visser
Published in: Pharmacoepidemiology and Drug Safety, 2021, ISSN 1053-8569
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/pds.5220

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

Author(s): 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
Published in: Briefings in Bioinformatics, 2022, ISSN 1467-5463
Publisher: 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

Author(s): Cristian Trovato, Marcel Mohr, Friedemann Schmidt, Elisa Passini, Blanca Rodriguez
Published in: Frontiers in Toxicology, Issue 26733080, 2022, ISSN 2673-3080
Publisher: 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

Author(s): 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
Published in: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23042213

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis

Author(s): 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
Published in: Molecular Systems Biology, Issue 17/3, 2021, ISSN 1744-4292
Publisher: 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

Author(s): Francesca Margara, Zhinuo J. Wang, Francesc Levrero-Florencio, Alfonso Santiago, Mariano Vázquez, Alfonso Bueno-Orovio, Blanca Rodriguez
Published in: Progress in Biophysics and Molecular Biology, 2020, ISSN 0079-6107
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.pbiomolbio.2020.06.007

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

Author(s): Enio Gjerga, Panuwat Trairatphisan, Attila Gabor, Hermann Koch, Celine Chevalier, Franceco Ceccarelli, Aurelien Dugourd, Alexander Mitsos, Julio Saez-Rodriguez
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: 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

Author(s): 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
Published in: Biochemical Pharmacology, Issue 190, 2021, Page(s) 114591, ISSN 0006-2952
Publisher: Elsevier BV
DOI: 10.1016/j.bcp.2021.114591

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

Author(s): Judith Pérez-Granado, Janet Piñero, Alejandra Medina-Rivera, and Laura I. Furlong
Published in: MDPI, Issue 20754701, 2022, ISSN 2075-4701
Publisher: 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.

Author(s): 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.
Published in: Archives of Toxicology, 2021, ISSN 1432-0738
Publisher: 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

Author(s): 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
Published in: EP Europace, Issue 23/Supplement_1, 2021, Page(s) i143-i152, ISSN 1099-5129
Publisher: 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

Author(s): Michelangelo Paci, Jussi T. Koivumäki, Hua Rong Lu, David J. Gallacher, Elisa Passini, Blanca Rodriguez
Published in: Frontiers in Pharmacology, Issue 12, 2021, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2021.604713

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

Author(s): Mihai Glont, Chinmay Arankalle, Krishna Tiwari, Tung V N Nguyen, Henning Hermjakob, Rahuman S Malik-Sheriff
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa560

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

Author(s): Muriel M. Heldring,Lukas S. Wijaya,Marije Niemeijer,Huan Yang,Talel Lakhal,Sylvia E. Le Dévédec,Bob van de Water,Joost B. Beltman
Published in: PLoS Comput Biol, 2022, ISSN 1553-734X
Publisher: 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?

Author(s): Marcel Mohr, Jean-Marie Chambard, Véronique Ballet, Friedemann Schmidt
Published in: J Pharmacol Toxicol Methods ., 2022, ISSN 1056-8719
Publisher: Elsevier BV
DOI: 10.1016/j.vascn.2022.107172

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

Author(s): 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
Published in: Hepatology Communications, 2021, ISSN 2471-254X
Publisher: Wiley
DOI: 10.1002/hep4.1797

The DisGeNET knowledge platform for disease genomics: 2019 update

Author(s): Janet Piñero, Juan Manuel Ramírez-Anguita, Josep Saüch-Pitarch, Francesco Ronzano, Emilio Centeno, Ferran Sanz, Laura I Furlong
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1021

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

Author(s): Panuwat Trairatphisan, Terezinha Maria de Souza, Jos Kleinjans, Danyel Jennen, Julio Saez-Rodriguez
Published in: Toxicology Letters, 2021, ISSN 0378-4274
Publisher: Elsevier BV
DOI: 10.1016/j.toxlet.2021.06.020

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

Author(s): Joaquim Aguirre-Plans, Janet Piñero, Terezinha Souza, Giulia Callegaro, Steven J. Kunnen, Ferran Sanz, Narcis Fernandez-Fuentes, Laura I. Furlong, Emre Guney, Baldo Oliva
Published in: Biology Direct, Issue 16/1, 2021, ISSN 1745-6150
Publisher: BioMed Central
DOI: 10.1186/s13062-020-00288-x

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

Author(s): 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
Published in: medRxiv, 2020
Publisher: medRxiv
DOI: 10.1101/2020.12.18.20248461

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Translational quantitative systems toxicology to improve the understanding of the safety of medicines - Sofia: 116030

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