Publications Peer reviewed articles (69) 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 Other (1) 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 Searching for OpenAIRE data... There was an error trying to search data from OpenAIRE No results available
