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

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Publikacje

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

Autorzy: Louis Gall, Carrie Duckworth, Ferran Jardi, Lieve Lammens, Aimee Parker, Ambra Bianco, Holly Kimko, David Mark Pritchard, Carmen Pin
Opublikowane w: eLife, 2023, ISSN 2050-084X
Wydawca: 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

Autorzy: 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
Opublikowane w: Thorax, Numer 76/11, 2021, Strona(/y) 1150-1153, ISSN 0040-6376
Wydawca: BMJ Publishing Group
DOI: 10.1136/thoraxjnl-2020-216504

Dysregulated mesenchymal PDGFR‐β drives kidney fibrosis

Autorzy: 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
Opublikowane w: EMBO Molecular Medicine, Numer 12/3, 2020, ISSN 1757-4676
Wydawca: 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

Autorzy: Soroush Mohammadi Jouabadi, Mitra Nekouei Shahraki, Payam Peymani, Bruno H. Stricker and Fariba Ahmadizar
Opublikowane w: Frontiers in Pharmacology, 2022, ISSN 1663-9812
Wydawca: 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

Autorzy: 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
Opublikowane w: Archives of Toxicology, Numer 95/12, 2021, Strona(/y) 3745-3775, ISSN 0340-5761
Wydawca: Springer Verlag
DOI: 10.1007/s00204-021-03141-w

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

Autorzy: Judith Pérez-Granado, Janet Piñero and Laura I. Furlong
Opublikowane w: Frontiers in Genetics, Numer 16648021, 2022, ISSN 1664-8021
Wydawca: 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

Autorzy: 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
Opublikowane w: Clinical and Translational Science, 2021, ISSN 1752-8054
Wydawca: Wiley-Blackwell
DOI: 10.1111/cts.13011

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

Autorzy: Elisa Passini, Xin Zhou, Cristian Trovato, Oliver J Britton, Alfonso Bueno-Orovio, Blanca Rodriguez
Opublikowane w: Journal of Computational Science, 2020, Strona(/y) 101202, ISSN 1877-7503
Wydawca: Elsevier BV
DOI: 10.1016/j.jocs.2020.101202

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

Autorzy: Barbara Füzi, Jana Gurinova, Henning Hermjakob, Gerhard F. Ecker, Rahuman Sheriff
Opublikowane w: Frontiers in Pharmacology, Numer 12, 2021, ISSN 1663-9812
Wydawca: 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

Autorzy: Xin Zhou, Yusheng Qu, Elisa Passini, Alfonso Bueno-Orovio, Yang Liu, Hugo M. Vargas, Blanca Rodriguez
Opublikowane w: Frontiers in Pharmacology, Numer 10, 2020, ISSN 1663-9812
Wydawca: Frontiers Media S.A.
DOI: 10.3389/fphar.2019.01643

Parallel ant colony optimization for the training of cell signaling networks

Autorzy: Patricia González, Roberto Prado-Rodriguez, Attila Gábor, Julio Saez-Rodriguez, Julio R.Banga, Ramón Doallo
Opublikowane w: Expert Systems with Applications, 2022, ISSN 0957-4174
Wydawca: 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

Autorzy: 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
Opublikowane w: CPT: pharmacometrics & systems pharmacology, 2022, ISSN 2163-8306
Wydawca: Nature Publishing Group
DOI: 10.1002/psp4.12774

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

Autorzy: 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
Opublikowane w: Archives of Toxicology, Numer 03405761, 2022, ISSN 0340-5761
Wydawca: Springer Verlag
DOI: 10.1007/s00204-022-03374-3

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

Autorzy: Michelangelo Paci, Elisa Passini, Aleksandra Klimas, Stefano Severi, Jari Hyttinen, Blanca Rodriguez, Emilia Entcheva
Opublikowane w: Biophysical Journal, Numer 118/10, 2020, Strona(/y) 2596-2611, ISSN 0006-3495
Wydawca: Biophysical Society
DOI: 10.1016/j.bpj.2020.03.018

BioModels—15 years of sharing computational models in life science

Autorzy: 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
Opublikowane w: Nucleic Acids Research, 2019, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkz1055

Reproducibility in systems biology modelling

Autorzy: 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
Opublikowane w: Molecular Systems Biology, Numer 17/2, 2021, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.20209982

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

Autorzy: 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
Opublikowane w: International Journal of Molecular Sciences, Numer 2022: 23(3), 2022, ISSN 1422-0067
Wydawca: 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

Autorzy: Linda C. Hendriksen,Grace Omes-Smit, Birgit C. P. Koch, M. Arfan Ikram, Bruno H. Stricker and Loes E. Visser
Opublikowane w: MDPI, Numer 20754701, 2022, ISSN 2075-4701
Wydawca: MDPI
DOI: 10.3390/jpm12060870

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

Autorzy: Fariba Ahmadizar, Negin Soroush, M Arfan Ikram, Jan A Kors, Maryam Kavousi, Bruno H Stricker
Opublikowane w: European Journal of Preventive Cardiology, 2020, ISSN 2047-4873
Wydawca: 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

Autorzy: Negin Soroush, Albert-Jan Aarnoudse, Maryam Kavousi, Jan A. Kors, M. Arfan Ikram, Christopher Newton-Cheh, Fariba Ahmadizar, Bruno H. Stricker
Opublikowane w: The Pharmacogenomics Journal, 2021, ISSN 1470-269X
Wydawca: 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

Autorzy: 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.
Opublikowane w: 1611-2156, Numer 1, 2020, ISSN 1611-2156
Wydawca: 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

Autorzy: Carmen Pin, Teresa Collins, Megan Gibbs, Holly Kimko
Opublikowane w: The AAPS Journal, Numer 23/4, 2021, ISSN 1550-7416
Wydawca: Springer New York
DOI: 10.1208/s12248-021-00580-2

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

Autorzy: Fiona M.I. Hunter, A. Patrícia Bento, Nicolas Bosc, Anna Gaulton, Anne Hersey, Andrew R. Leach
Opublikowane w: Chemical Research in Toxicology, Numer 34/2, 2021, Strona(/y) 385-395, ISSN 0893-228X
Wydawca: 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.

Autorzy: 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
Opublikowane w: CPT: Pharmacometrics & Systems Pharmacology, 2021, ISSN 2163-8306
Wydawca: 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.

Autorzy: Füzi B, Malik-Sheriff RS, Manners EJ, Hermjakob H, Ecker GF
Opublikowane w: Journal of Cheminformatics, 2022, ISSN 1758-2946
Wydawca: Chemistry Central
DOI: 10.1186/s13321-022-00615-6

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

Autorzy: Manuel Pastor, José Carlos Gómez-Tamayo, Ferran Sanz
Opublikowane w: Journal of Cheminformatics, Numer 13/1, 2021, ISSN 1758-2946
Wydawca: 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

Autorzy: Derek J. Leishman
Opublikowane w: Journal of Pharmacological and Toxicological Methods, Numer 101, 2020, Strona(/y) 106654, ISSN 1056-8719
Wydawca: Elsevier BV
DOI: 10.1016/j.vascn.2019.106654

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

Autorzy: 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
Opublikowane w: Journal of Molecular Biology, 2020, ISSN 0022-2836
Wydawca: Academic Press
DOI: 10.1016/j.jmb.2020.09.015

The DisGeNET cytoscape app: Exploring and visualizing disease genomics data

Autorzy: Janet Piñero, Josep Saüch, Ferran Sanz, Laura I. Furlong
Opublikowane w: Computational and Structural Biotechnology Journal, Numer 19, 2021, Strona(/y) 2960-2967, ISSN 2001-0370
Wydawca: 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

Autorzy: 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*
Opublikowane w: EXCLI Journal, 2020, ISSN 1611-2156
Wydawca: 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

Autorzy: Daniela Rodrigues, Roelvan Kampen, Ad A.van Bodegraven, Jos C.S.Kleinjans, Danyel G.J.Jennen, Theo M.de Kok
Opublikowane w: Toxicology Letters, Numer 03784274, 2022, ISSN 0378-4274
Wydawca: Elsevier BV
DOI: 10.1016/j.toxlet.2022.09.013

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

Autorzy: 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
Opublikowane w: npj Digital Medicine, Numer 3/1, 2020, ISSN 2398-6352
Wydawca: 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

Autorzy: 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
Opublikowane w: Frontiers in Physiology, Numer 8, 2017, ISSN 1664-042X
Wydawca: 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

Autorzy: Elaina M. Maldonado, Vytautas Leoncikas, Ciarán P. Fisher, J. Bernadette Moore, Nick J. Plant, Andrzej M. Kierzek
Opublikowane w: CPT: Pharmacometrics & Systems Pharmacology, Numer 6/11, 2017, Strona(/y) 732-746, ISSN 2163-8306
Wydawca: Nature Publishing Group
DOI: 10.1002/psp4.12230

In silico models in drug development: where we are

Autorzy: Janet Piñero, Laura I Furlong, Ferran Sanz
Opublikowane w: Current Opinion in Pharmacology, Numer 42, 2018, Strona(/y) 111-121, ISSN 1471-4892
Wydawca: Elsevier BV
DOI: 10.1016/j.coph.2018.08.007

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

Autorzy: Janet Piñero, Abel Gonzalez-Perez, Emre Guney, Joaquim Aguirre-Plans, Ferran Sanz, Baldo Oliva, Laura I. Furlong
Opublikowane w: Frontiers in Genetics, Numer 9, 2018, ISSN 1664-8021
Wydawca: 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

Autorzy: Terezinha Souza, Panuwat Trairatphisan, Janet Piñero, Laura I. Furlong, Julio Saez-Rodriguez, Jos Kleinjans, Danyel Jennen
Opublikowane w: Frontiers in Genetics, Numer 9, 2018, ISSN 1664-8021
Wydawca: 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

Autorzy: Manuel Pastor, Jordi Quintana, Ferran Sanz
Opublikowane w: Frontiers in Pharmacology, Numer 9, 2018, ISSN 1663-9812
Wydawca: 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

Autorzy: Anyue Yin, Akihiro Yamada, Wiro B Stam, Johan G C van Hasselt, Piet H van der Graaf
Opublikowane w: British Journal of Pharmacology, Numer 175/16, 2018, Strona(/y) 3394-3406, ISSN 0007-1188
Wydawca: 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

Autorzy: 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
Opublikowane w: Archives of Toxicology, Numer 93/2, 2019, Strona(/y) 385-399, ISSN 0340-5761
Wydawca: 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

Autorzy: Joaquim Aguirre-Plans, Janet Piñero, Ferran Sanz, Laura I. Furlong, Narcis Fernandez-Fuentes, Baldo Oliva, Emre Guney
Opublikowane w: Journal of Molecular Biology, Numer 431/13, 2019, Strona(/y) 2477-2484, ISSN 0022-2836
Wydawca: 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

Autorzy: 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
Opublikowane w: Archives of Toxicology, Numer 93/6, 2019, Strona(/y) 1609-1637, ISSN 0340-5761
Wydawca: 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

Autorzy: 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
Opublikowane w: eLife, Numer 8, 2019, ISSN 2050-084X
Wydawca: 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

Autorzy: Elisa Passini, Cristian Trovato, Pierre Morissette, Frederick Sannajust, Alfonso Bueno‐Orovio, Blanca Rodriguez
Opublikowane w: British Journal of Pharmacology, Numer 176/19, 2019, Strona(/y) 3819-3833, ISSN 0007-1188
Wydawca: 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

Autorzy: Daniela Rodrigues, Terezinha Souza, Danyel G.J. Jennen, Lieve Lemmens, Jos C.S. Kleinjans, Theo M. de Kok
Opublikowane w: Cancer Treatment Reviews, Numer 77, 2019, Strona(/y) 57-66, ISSN 0305-7372
Wydawca: 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

Autorzy: Sofia Ferreira, Ciarán Fisher, Laura I. Furlong, Loic Laplanche, Brian Kevin Park, Carmen Pin, Julio Saez-Rodriguez, Panuwat Trairatphisan
Opublikowane w: Chemical Research in Toxicology, Numer 33/1, 2020, Strona(/y) 7-9, ISSN 0893-228X
Wydawca: American Chemical Society
DOI: 10.1021/acs.chemrestox.9b00499

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

Autorzy: Anika Liu, Panuwat Trairatphisan, Enio Gjerga, Athanasios Didangelos, Jonathan Barratt, Julio Saez-Rodriguez
Opublikowane w: npj Systems Biology and Applications, Numer 5/1, 2019, ISSN 2056-7189
Wydawca: Nature
DOI: 10.1038/s41540-019-0118-z

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology

Autorzy: Joaquim Aguirre-Plans, Janet Piñero, Jörg Menche, Ferran Sanz, Laura Furlong, Harald Schmidt, Baldo Oliva, Emre Guney
Opublikowane w: Pharmaceuticals, Numer 11/3, 2018, Strona(/y) 61, ISSN 1424-8247
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ph11030061

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

Autorzy: 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
Opublikowane w: Nature Communications, Numer 10/1, 2019, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-018-07709-6

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

Autorzy: Cristian Trovato, Elisa Passini, Norbert Nagy, András Varró, Najah Abi-Gerges, Stefano Severi, Blanca Rodriguez
Opublikowane w: Journal of Molecular and Cellular Cardiology, Numer 142, 2020, Strona(/y) 24-38, ISSN 0022-2828
Wydawca: 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

Autorzy: 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
Opublikowane w: ALTEX, 2022, ISSN 1868-8551
Wydawca: 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

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

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

Autorzy: 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
Opublikowane w: Briefings in Bioinformatics, 2022, ISSN 1467-5463
Wydawca: 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

Autorzy: Cristian Trovato, Marcel Mohr, Friedemann Schmidt, Elisa Passini, Blanca Rodriguez
Opublikowane w: Frontiers in Toxicology, Numer 26733080, 2022, ISSN 2673-3080
Wydawca: 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

Autorzy: 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
Opublikowane w: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23042213

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis

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

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

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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

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

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

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

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

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

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

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

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

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The DisGeNET knowledge platform for disease genomics: 2019 update

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

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

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

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