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

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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
DOI: 10.1016/j.yjmcc.2020.04.001