Ontology-driven and artificial intelligence-based repeated dose toxicity testing of chemicals for next generation risk assessment

Livrables

Report on existing in vitro assays to detect MIEs and KEs in the qAOP networks on liver steatosis and cholestasis
Report on existing and novel in vitro assays to detect MIEs and KEs in the qAOP network on cognitive function defects
Report on existing in vitro assays to detect MIEs and KEs in the qAOP networks on tubular necrosis and crystallopathy
Report on the definition of and contact with target audiences

Project website

Computational model for neural tube closure defects

Publications

Safer chemicals using less animals: kick-off of the European ONTOX project

Auteurs: Mathieu Vinken, Emilio Benfenati, François Busquet, José Castell, Djork-Arné Clevert, Theo M. de Kok, Hubert Dirven, Ellen Fritsche, Liesbet Geris, Rafael Gozalbes, Thomas Hartung, Danyel Jennen, Ramiro Jover, Helena Kandarova, Nynke Kramer, Cyrille Krul, Thomas Luechtefeld, Rosalinde Masereeuw, Erwin Roggen, Stephan Schaller, Tamara Vanhaecke, Chihae Yang, Aldert H. Piersma
Publié dans: Toxicology, Numéro 458, 2021, Page(s) 152846, ISSN 0300-483X
Éditeur: Elsevier BV
DOI: 10.1016/j.tox.2021.152846

Unsupervised Representation Learning for Proteochemometric Modeling

Auteurs: Kim, Paul T., Robin Winter, and Djork-Arné Clevert
Publié dans: International Journal of Molecular Sciences, 2021, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222312882

Scientific validation of human Neurosphere Assays for Developmental Neurotoxicity evaluation

Auteurs: Koch K, Bartmann K, Hartmann J, Kapr J, Klose J, Kuchovská E, Pahl M, Schlüppmann K, Zühr E and Fritsche E
Publié dans: The Frontiers in toxicology/Section Neurotoxicology, Numéro 4/816370, 2022, Page(s) 1-26, ISSN 2673-3080
Éditeur: Frontiers Media S.A.
DOI: 10.3389/ftox.2022.816370

Optimization of an adverse outcome pathway network on chemical-induced cholestasis using an artificial intelligence-assisted data collection and confidence level quantification approach

Auteurs: Jonas van Ertvelde, Anouk Verhoeven, Amy Maerten, Axelle Cooreman, Bruna dos Santos Rodrigues, Julen Sanz-Serrano, Milos Mihajlovic, Ignacio Tripodi, Marc Teunis, Ramiro Jover, Thomas Luechtefeld, Tamara Vanhaecke, Jian Jiang, Mathieu Vinken
Publié dans: Journal of Biomedical Informatics, Numéro Volume 145, September 2023, 2023, Page(s) 104465, ISSN 1532-0464
Éditeur: Academic Press
DOI: 10.1016/j.jbi.2023.104465

Natural language processing in toxicology: Delineating adverse outcome pathways and guiding the application of new approach methodologies

Auteurs: Marie Corradi, Alyanne de Haan, Bernard Staumont, Aldert Piersma, Liesbet Geris, Raymond Pieters, Cyrille Krul, Marc Teunis
Publié dans: Biosystems and Biomaterials, Numéro 26665344, 2022, ISSN 2666-5344
Éditeur: Elsevier BV
DOI: 10.1016/j.bbiosy.2022.100061

ToxAIcology - The evolving role of artificial intelligence in advancing toxicology and modernizing regulatory science

Auteurs: Thomas Hartung
Publié dans: ALTEX, Numéro 4/yr, 2023, Page(s) 559-570, ISSN 1868-8551
Éditeur: Springer Spektrum
DOI: 10.14573/altex.2309191

A call for a Human Exposome Project.

Auteurs: Thomas Hartung
Publié dans: ALTEX, Numéro 4/yr, 2023, Page(s) 4–33, ISSN 1868-8551
Éditeur: Springer Spektrum
DOI: 10.14573/altex.2301061

Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing

Auteurs: Malene Lislien, Eliska Kuchovska, Julia Kapr, Nur Duale, Jill Mari Andersen, Hubert Dirven, Oddvar Myhre, Ellen Fritsche, Katharina Koch, Marcin W. Wojewodzic
Publié dans: Toxicology, Numéro 510, 2024, Page(s) 154000, ISSN 0300-483X
Éditeur: Elsevier BV
DOI: 10.1016/j.tox.2024.154000

Img2Mol – accurate SMILES recognition from molecular graphical depictions

Auteurs: Djork-Arné Clevert, Tuan Le, Robin Winter, Floriane Montanari
Publié dans: Chemical Science, Numéro 12/42, 2021, Page(s) 14174-14181, ISSN 2041-6520
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d1sc01839f

Report of the First ONTOX Stakeholder Network Meeting: Digging Under the Surface of ONTOX Together With the Stakeholders

Auteurs: Michael Diemar, Mathieu Vinken, Marc Teunis, Cyrille Krul, François Busquet, Julia Dominika Zajac, Helena Kandarova, Raffaella Corvi, Matteo Z. Russo, Anastasiia Kharina, Louise Bryndum, Michael Santillo, Denise Bloch, Olena Kucheryavenko, Demosthenes Panagiotakos, Vera Rogiers, Manon Beekhuijzen, Arianna Giusti, Abdulkarim Najjar, Carol CourageShow lessTorben Koenig, Susanne Kolle, Harrie Boonen
Publié dans: ATLA, Numéro Jan, 2024, 2024, ISSN 0261-1929
Éditeur: Fund for the Replacement of Animals in Medical Experiments
DOI: 10.1177/02611929231225730

Monte Carlo Models for Sub-Chronic Repeated-Dose Toxicity: Systemic and Organ-Specific Toxicity

Auteurs: Gianluca Selvestrel, Giovanna J. Lavado, Alla P. Toropova, Andrey A. Toropov, Domenico Gadaleta, Marco Marzo, Diego Baderna and Emilio Benfenati
Publié dans: International Journal of Molecular Sciences, Numéro 14220067, 2022, Page(s) 6615, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23126615

Mitochondria as the Target of Hepatotoxicity and Drug-Induced Liver Injury: Molecular Mechanisms and Detection Methods

Auteurs: Mihajlović M and Vinken M
Publié dans: International Journal of Molecular Sciences, Numéro 23(6), 3315, 2022, Page(s) 1-37, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23063315

In Vitro Liver Toxicity Testing of Chemicals: A Pragmatic Approach

Auteurs: Andrés Tabernilla, Bruna dos Santos Rodrigues, Alanah Pieters, Anne Caufriez, Kaat Leroy, Raf Van Campenhout, Axelle Cooreman, Ana Rita Gomes, Emma Arnesdotter, Eva Gijbels, Mathieu Vinken
Publié dans: International Journal of Molecular Sciences, Numéro 22/9, 2021, Page(s) 5038, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22095038

Unraveling the mechanisms underlying drug-induced cholestatic liver injury: identifying key genes using machine learning techniques on human on in vitro data sets.

Auteurs: Jian Jiang, Jonas van Ertvelde, Gökhan Ertaylan, Ralf Peeters, Danyel Jennen, Theo M. de Kok, Mathieu Vinken
Publié dans: Archives of Toxicology, Numéro volume 91, 2023, 2023, Page(s) 2969-2981, ISSN 1432-0738
Éditeur: Springer
DOI: 10.1007/s00204-023-03583-4

The application of natural language processing for the extraction of mechanistic information in toxicology

Auteurs: Marie Corradi, Thomas Luechtefeld, Alyanne M. de Haan, Raymond Pieters, Jonathan H. Freedman, Tamara Vanhaecke, Mathieu Vinken, Marc Teunis
Publié dans: Frontiers in Toxicology, Numéro 6, 2024, ISSN 2673-3080
Éditeur: Frontiers
DOI: 10.3389/ftox.2024.1393662

Metabolomics in Preclinical Drug Safety Assessment: Current Status and Future Trends

Auteurs: Fenna Sillé, Thomas Hartung
Publié dans: Metabolites, Numéro 14(2), 98, 2024, ISSN 2218-1989
Éditeur: MDPI
DOI: 10.3390/metabo14020098

Using in silico tools to predict flame retardant metabolites for more informative exposomics-based approaches

Auteurs: Breanne Kincaid, Przemyslaw Piechota, Emily Golden, Mikhail Maertens, Thomas Hartung, Alexandra Maertens
Publié dans: Frontiers in Toxicology, Numéro 5, 2023, Page(s) 45307, ISSN 2673-3080
Éditeur: Frontiers
DOI: 10.3389/ftox.2023.1216802

Alternative methods go green! Green toxicology as a sustainable approach for assessing chemical safety and designing safer chemicals

Auteurs: Alexandra Maertens, Thomas Luechtefeld, Jean Knight, Thomas Hartung
Publié dans: ALTEX, Numéro Vol. 41 No. 1, 2024, ISSN 1868-8551
Éditeur: Springer International Publishing AG
DOI: 10.14573/altex.2312291

AI as the New Frontier in Chemical Risk Assessment

Auteurs: Thomas Hartung
Publié dans: Frontiers in Artificial Intelligence, 2023, Page(s) 1-4, ISSN 0922-6389
Éditeur: IOS Press
DOI: 10.3389/frai.2023.1269932

4.2 million and counting… The animal toll for REACH systemic toxicity studies

Auteurs: Jean Knight, Thomas Hartung, Costanza Rovida
Publié dans: ALTEX, Numéro 4/yr, 2023, Page(s) 389-407, ISSN 1868-8551
Éditeur: Springer Spektrum
DOI: 10.14573/altex.2303201

Replacement of animal testing by integrated approaches to testingand assessment (IATA): a call for in vivitrosi

Auteurs: Caloni F, De Angelis I, Hartung T
Publié dans: Archives of Toxicology, Numéro 96, 2022, Page(s) 1935–1950, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-022-03299-x

The Good, The Bad, and The Perplexing: Structural Alerts and Read-Across for Predicting Skin Sensitization Using Human Data

Auteurs: Emily Golden, Daniel C. Ukaegbu, Peter Ranslow, Robert H. Brown, Thomas Hartung, Alexandra Maertens
Publié dans: Chemical Research in Toxicology, Numéro 36, 2023, Page(s) 734-746, ISSN 0893-228X
Éditeur: American Chemical Society
DOI: 10.1021/acs.chemrestox.2c00383

Prediction of the Neurotoxic Potential of Chemicals Based on Modelling of Molecular Initiating Events Upstream of the Adverse Outcome Pathways of (Developmental) Neurotoxicity

Auteurs: Domenico Gadaleta, Nicoleta Spînu, Alessandra Roncaglioni, Mark T. D. Cronin, Emilio Benfenati
Publié dans: International Journal of Molecular Sciences, Numéro 14220067, 2022, Page(s) 3053, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23063053

The effects of hexabromocyclododecane on the transcriptome and hepatic enzyme activity in three human HepaRG-based models

Auteurs: Susana Proença, Nick van Sabben, Juliette Legler, Jorke H. Kamstra, Nynke I. Kramer
Publié dans: Toxicology, Numéro Volume 485, February 2023, 153411, 2023, ISSN 0300-483X
Éditeur: Elsevier BV
DOI: 10.1016/j.tox.2022.153411

G × E interactions as a basis for toxicological uncertainty

Auteurs: Ilinca Suciu, David Pamies, Roberta Peruzzo, Petra H. Wirtz, Lena Smirnova, Giorgia Pallocca, Christof Hauck, Mark T. D. Cronin, Jan G. Hengstler, Thomas Brunner, Thomas Hartung, Ivano Amelio, and Marcel Leist
Publié dans: Archives of Toxicology, 2023, Page(s) 2035–2049, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-023-03500-9

Artificial intelligence (AI)—it’s the end of the tox as we know it (and I feel fine)

Auteurs: Nicole Kleinstreuer, Thomas Hartung
Publié dans: Archives of Toxicology, Numéro Vol 98, 2024, Page(s) 735–754, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-023-03666-2

Predicting the Mitochondrial Toxicity of Small Molecules: Insights from Mechanistic Assays and Cell Painting Data

Auteurs: Marina Garcia de Lomana, Paula Andrea Marin Zapata, and Floriane Montanari
Publié dans: Chemical Research in Toxicology, Numéro Volume 36, issue 7, 2023, Page(s) 1107–1120, ISSN 0893-228X
Éditeur: American Chemical Society
DOI: 10.1021/acs.chemrestox.3c00086

REACH out-numbered! The future of REACH and animal numbers

Auteurs: Costanza Rovida, Francois Busquet, Marcel Leist, Thomas Hartung
Publié dans: ALTEX, Numéro 4/yr, 2023, Page(s) 367-388, ISSN 1868-8551
Éditeur: Springer Spektrum
DOI: 10.14573/altex.2307121

Connexin-Based Channel Activity Is Not Specifically Altered by Hepatocarcinogenic Chemicals

Auteurs: Kaat Leroy, Alanah Pieters, Axelle Cooreman, Raf Van Campenhout, Bruno Cogliati, Mathieu Vinken
Publié dans: International Journal of Molecular Sciences, Numéro 22/21, 2021, Page(s) 11724, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222111724

A systematic review of in vitro models of drug-induced kidney injury

Auteurs: Alasdair R. Irvine, Damiën van Berlo, Rawan Shekhani, Rosalinde Masereeuw
Publié dans: Current Opinion in Toxicology, Numéro 27, 2021, Page(s) 18-26, ISSN 2468-2020
Éditeur: Elsevier
DOI: 10.1016/j.cotox.2021.06.001

The probable future of toxicology - probabilistic risk assessment

Auteurs: Alexandra Maertens, Eric Antignac, Emilio Benfenati, Denise Bloch, Ellen Fritsche, Sebastian Hoffmann, Joanna Jaworska, George Loizou, Kevin McNally, Przemyslaw Piechota, Erwin L. Roggen, Marc Teunis, Thomas Hartung
Publié dans: ALTEX, Numéro N/A, 2024, Page(s) N/A, ISSN 1868-8551
Éditeur: Springer International Publishing AG
DOI: 10.14573/altex.2310301

Primary Human Hepatocyte Spheroids as Tools to Study the Hepatotoxic Potential of Non-Pharmaceutical Chemicals

Auteurs: Vânia Vilas-Boas, Eva Gijbels, Kaat Leroy, Alanah Pieters, Audrey Baze, Céline Parmentier, Mathieu Vinken
Publié dans: International Journal of Molecular Sciences, Numéro 22/20, 2021, Page(s) 11005, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222011005

Development of an adverse outcome pathway network for nephrotoxicity

Auteurs: D A Barnes, J W Firman, S J Belfield, M T D Cronin, M Vinken, M J Janssen, R Masereeuw
Publié dans: Archives of Toxicology, Numéro Volume 98, 2024, Page(s) 929-942, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-023-03637-7

First steps for creating an ontology for cognitivefunction defects for regulatory application

Auteurs: Eliska Kuchovska, Alessio Gamba, Luiz Carlos Maia Ladeira, Bernard Staumont, Raphaëlle Lesage, Inger-Lise Steffensen, Graciela Lopez Soop
Publié dans: 21st International Congress ESTIV Abstract Book, Numéro annual, 2022, Page(s) 48-49, ISBN 978-80-969474-8-5
Éditeur: ESTIV

P04-06 New approaches for evaluating kidney toxicity using physiological maps

Auteurs: Alessio Gamba, Luiz Carlos Maia Ladeira, Raphaëlle Lesage, Devon Barnes, Daniël Roodzant, Marc Teunis, Manoe Janssen, Rosalinde Masereeuw, Liesbet Geris, Bernard Staumont
Publié dans: Toxicology Letters, Numéro Volume 368, Supplement, 1 September 2022, 2022, Page(s) S101, ISSN 0378-4274
Éditeur: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.290

Physiological Map to Study Kidney Toxicity in the ONTOX Project.

Auteurs: Alessio Gamba, Luiz Carlos Maia Ladeira, Raphaëlle Lesage, Daniël Roodzant, Devon Barnes, Manoe Janssen, Marc Teunis, Rosalinde Masereeuw, Liesbet Geris, Bernard Staumont
Publié dans: 21st International Congress ESTIV Abstract Book, Numéro annual, 2022, Page(s) 120-121, ISBN 978-80-969474-8-5
Éditeur: ESTIV

Development of an Adverse Outcome Pathway for Kidney Tubular Necrosis

Auteurs: Devon Barnes, Alasdair Irvine, Alessio Gamba, Luiz Carlos Maia Ladeira, Bernard Staumont, Huan Yang, Inger-Lise Steffensen, Liesbet Geris, Manoe Janssen, and Rosalinde Masereeuw
Publié dans: 21st International Congress ESTIV Abstract Book, Numéro annual, 2022, Page(s) 186-187, ISBN 978-80-969474-8-5
Éditeur: ESTIV

Protocol for a systematic scoping review

Auteurs: Trine Husøy, Michael Guy Diemar, Erwin Roggen, Maria Kalyva, Hubert Dirven, Gunn Elisabeth Vist
Publié dans: Methods and tools for assessing chemical exposure in humans: protocol for a systematic scoping review - prosjektbeskrivelse, 2021
Éditeur: NIPH

P17-07 Computational modelling of neural tube closure defects

Auteurs: Job H Berkhout, Aldert H Piersma, Juliette Legler, Harm J Heusinkveld
Publié dans: Toxicology letters, Numéro Volume 368, Supplement, 1 September 2022, 2022, Page(s) S229, ISSN 0378-4274
Éditeur: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.617

P01-07 Development of an adverse outcome pathway for kidney tubular necrosis

Auteurs: Devon Barnes, A. Irvine, Alessio Gamba, Bernard Staumont, Luiz C Maia Ladeira, Huan Yang, Inger-Lise Stffensen, Liesbet Geris, Manoe Janssen, Roos Masereeuw
Publié dans: Toxicology Letters, Numéro Volume 368, Supplement, 1 September 2022, 2022, Page(s) S86-S87, ISSN 0378-4274
Éditeur: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.251

Designing Physiological Maps as a Tool to Study Liver Toxicology

Auteurs: Luiz Carlos Maia Ladeira, Alessio Gamba, Raphaëlle Lesage, Anouk Verhoeven, Jonas van Ertvelde, Jian Jiang, Daniël Roodzant, Marc Teunis, Ramiro Jover, Tamara Vanhaecke, Mathieu Vinken, Harm Heusinkveld, Liesbet Geris, Bernard Staumont.
Publié dans: 21st International Congress ESTIV Abstract Book, Numéro annual, 2022, Page(s) 123-124, ISBN 978-80-969474-8-5
Éditeur: ESTIV

Computational Modelling of Neural Tube Closure Defects

Auteurs: Job Berkhout, Aldert Piersma, Juliette Legler, Alessio Gamba, Luiz Carlos Maia Ladeira, Bernard Staumont, Raphaëlle Lesage, Liesbet Geris, and Harm Heuseinkveld
Publié dans: 21st International Congress ESTIV Abstract Book, Numéro annual, 2022, Page(s) 127, ISBN 978-80-969474-8-5
Éditeur: ESTIV

P11-09 Physiology-based framework to study chemical-induced cholestasis

Auteurs: Luiz Carlos Maia Ladeira, Alessio Gamba, Raphaëlle Lesage, Jonas van Ertvelde, Jian Jiang, Anouk Verhoeven, Daniël Roodzant, Marc Teunis, Ramiro Jover, Tamara Vanhaecke, Mathieu Vinken, Liesbet Geris, Bernard Staumont
Publié dans: Toxicology Letters, Numéro Volume 368, Supplement, 1 September 2022, 2022, Page(s) S165-S166, ISSN 0378-4274
Éditeur: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.459

SOC-VI-08 Physiological maps: a benchmark tool for adverse outcome pathways and a cornerstone for the development of disease ontologies

Auteurs: Bernard Staumont, Luiz Carlos Maia Ladeira, Alessio Gamba, Raphaëlle Lesage, Anouk Verhoeven, Jian Jiang, Jonas van Ertvelde, Devon Barnes, Manoe Janssen, Eliska Kuchovska, Job Berkhout, Daniël Roodzant, Marc Teunis, Thomas Bozada Jr, Thomas Luechtefeld, Ramiro Jover, Tamara Vanhaecke, Mathieu Vinken, Rosalinde Masereeuw, Ellen Fritsche, Aldert Piersma, Harm Heusinkveld, Liesbet Geris
Publié dans: Toxicology Letters, Numéro Volume 368, Supplement, 1 September 2022, 2022, Page(s) S77-S78, ISSN 0378-4274
Éditeur: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.228

Multi-task Proteochemometric Modelling

Auteurs: Anastasia Pentina, and Djork-Arné Clevert
Publié dans: ChemRxiv, Numéro 25732293, 2022, ISSN 2573-2293
Éditeur: Cambridge Open Engage
DOI: 10.26434/chemrxiv-2022-d5tzd

Probabilistic Risk Assessment –The Keystone for the Future of Toxicology

Auteurs: Maertens A, Golden E, Luechtefeld T, Hoffmann S, Tsaioun K
Publié dans: Altex- Alternatives to animal experimentation, Numéro 39/1, 2022, Page(s) 3–29, ISSN 1868-8551
Éditeur: Springer-Spektrum
DOI: 10.14573/altex.2201081

Adverse outcome pathway networks as the basis for the development of new approach methodologies: Liver toxicity as a case study

Auteurs: Mathieu Vinken
Publié dans: Current Opinion in Toxicology, Numéro 40, 2024, Page(s) 100504, ISSN 2468-2020
Éditeur: Elsevier
DOI: 10.1016/j.cotox.2024.100504

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