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

Deliverables

Report on existing in vitro assays to detect MIEs and KEs in the qAOP networks on liver steatosis and cholestasis
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

Publications

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

Author(s): 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
Published in: Toxicology, Issue 458, 2021, Page(s) 152846, ISSN 0300-483X
Publisher: Elsevier BV
DOI: 10.1016/j.tox.2021.152846

Unsupervised Representation Learning for Proteochemometric Modeling

Author(s): Kim, Paul T., Robin Winter, and Djork-Arné Clevert
Published in: International Journal of Molecular Sciences, 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222312882

Scientific validation of human Neurosphere Assays for Developmental Neurotoxicity evaluation

Author(s): Koch K, Bartmann K, Hartmann J, Kapr J, Klose J, Kuchovská E, Pahl M, Schlüppmann K, Zühr E and Fritsche E
Published in: The Frontiers in toxicology/Section Neurotoxicology, Issue 4/816370, 2022, Page(s) 1-26, ISSN 2673-3080
Publisher: 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

Author(s): 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
Published in: Journal of Biomedical Informatics, Issue Volume 145, September 2023, 2023, Page(s) 104465, ISSN 1532-0464
Publisher: 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

Author(s): Marie Corradi, Alyanne de Haan, Bernard Staumont, Aldert Piersma, Liesbet Geris, Raymond Pieters, Cyrille Krul, Marc Teunis
Published in: Biosystems and Biomaterials, Issue 26665344, 2022, ISSN 2666-5344
Publisher: Elsevier BV
DOI: 10.1016/j.bbiosy.2022.100061

https://www.altex.org/index.php/altex/article/view/2692

Author(s): Thomas Hartung
Published in: ALTEX, Issue 4/yr, 2023, Page(s) 559-570, ISSN 1868-8551
Publisher: Springer Spektrum
DOI: 10.14573/altex.2309191

A call for a Human Exposome Project.

Author(s): Thomas Hartung
Published in: ALTEX, Issue 4/yr, 2023, Page(s) 4–33, ISSN 1868-8551
Publisher: Springer Spektrum
DOI: 10.14573/altex.2301061

Img2Mol – accurate SMILES recognition from molecular graphical depictions

Author(s): Djork-Arné Clevert, Tuan Le, Robin Winter, Floriane Montanari
Published in: Chemical Science, Issue 12/42, 2021, Page(s) 14174-14181, ISSN 2041-6520
Publisher: 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

Author(s): 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
Published in: ATLA, Issue Jan, 2024, 2024, ISSN 0261-1929
Publisher: 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

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

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

Author(s): Breanne Kincaid , Przemyslaw Piechota, Emily Golden, Mikhail Maertens, Thomas Hartung, and Alexandra Maertens
Published in: Frontier in Artificial Intelligence, Issue 6/yr, 2023, Page(s) 1-16, ISSN 0922-6389
Publisher: IOS Press
DOI: 10.3389/ftox.2023.1216802

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

Author(s): Mihajlović M and Vinken M
Published in: International Journal of Molecular Sciences, Issue 23(6), 3315, 2022, Page(s) 1-37, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23063315

In Vitro Liver Toxicity Testing of Chemicals: A Pragmatic Approach

Author(s): 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
Published in: International Journal of Molecular Sciences, Issue 22/9, 2021, Page(s) 5038, ISSN 1422-0067
Publisher: 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.

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

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

Author(s): Fenna Sillé, Thomas Hartung
Published in: Metabolites, Issue 14(2), 98, 2024, ISSN 2218-1989
Publisher: MDPI
DOI: 10.3390/metabo14020098

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

Author(s): Alexandra Maertens, Thomas Luechtefeld, Jean Knight, Thomas Hartung
Published in: ALTEX, Issue Vol. 41 No. 1, 2024, ISSN 1868-8551
Publisher: Springer International Publishing AG
DOI: 10.14573/altex.2312291

AI as the New Frontier in Chemical Risk Assessment

Author(s): Thomas Hartung
Published in: Frontiers in Artificial Intelligence, 2023, Page(s) 1-4, ISSN 0922-6389
Publisher: IOS Press
DOI: 10.3389/frai.2023.1269932

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

Author(s): Jean Knight, Thomas Hartung, Costanza Rovida
Published in: ALTEX, Issue 4/yr, 2023, Page(s) 389-407, ISSN 1868-8551
Publisher: Springer Spektrum
DOI: 10.14573/altex.2303201

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

Author(s): Caloni F, De Angelis I, Hartung T
Published in: Archives of Toxicology, Issue 96, 2022, Page(s) 1935–1950, ISSN 0340-5761
Publisher: Springer Verlag
DOI: 10.1007/s00204-022-03299-x

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

Author(s): Domenico Gadaleta, Nicoleta Spînu, Alessandra Roncaglioni, Mark T. D. Cronin, Emilio Benfenati
Published in: International Journal of Molecular Sciences, Issue 14220067, 2022, Page(s) 3053, ISSN 1422-0067
Publisher: 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

Author(s): Susana Proença, Nick van Sabben, Juliette Legler, Jorke H. Kamstra, Nynke I. Kramer
Published in: Toxicology, Issue Volume 485, February 2023, 153411, 2023, ISSN 0300-483X
Publisher: Elsevier BV
DOI: 10.1016/j.tox.2022.153411

G × E interactions as a basis for toxicological uncertainty

Author(s): 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
Published in: Archives of Toxicology, 2023, Page(s) 2035–2049, ISSN 0340-5761
Publisher: 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)

Author(s): Nicole Kleinstreuer, Thomas Hartung
Published in: Archives of Toxicology, Issue Vol 98, 2024, Page(s) 735–754, ISSN 0340-5761
Publisher: Springer Verlag
DOI: 10.1007/s00204-023-03666-2

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

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

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

Author(s): Costanza Rovida, Francois Busquet, Marcel Leist, Thomas Hartung
Published in: ALTEX, Issue 4/yr, 2023, Page(s) 367-388, ISSN 1868-8551
Publisher: Springer Spektrum
DOI: 10.14573/altex.2307121

https://altex.org/index.php/altex/article/view/2696

Author(s): Anna-Katharina Holzer, Nadine Dreser, Giorgia Pallocca, Aswin Mangerich, Glyn Stacey, Michele Dipalo, Bob van de Water, Costanza Rovida, Petra H. Wirtz, Barbara van Vugt, Giulia Panzarella, Thomas Hartung, Andrea Terron, Iris Mangas, Matthias Herzler, Philip Marx-Stoelting, Sandra Coecke, Marcel Leist
Published in: ALTEX, Issue 4/yr, 2023, Page(s) 706–712, ISSN 1868-8551
Publisher: Springer Spektrum
DOI: 10.14573/altex.2310021

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

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

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

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

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

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

The probable future of toxicology - probabilistic risk assessment

Author(s): 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
Published in: ALTEX, Issue N/A, 2024, Page(s) N/A, ISSN 1868-8551
Publisher: Springer International Publishing AG
DOI: 10.14573/altex.2310301

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

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

Development of an adverse outcome pathway network for nephrotoxicity

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

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

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

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

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

Physiological Map to Study Kidney Toxicity in the ONTOX Project.

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

Development of an Adverse Outcome Pathway for Kidney Tubular Necrosis

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

Protocol for a systematic scoping review

Author(s): Trine Husøy, Michael Guy Diemar, Erwin Roggen, Maria Kalyva, Hubert Dirven, Gunn Elisabeth Vist
Published in: Methods and tools for assessing chemical exposure in humans: protocol for a systematic scoping review - prosjektbeskrivelse, 2021
Publisher: NIPH

P17-07 Computational modelling of neural tube closure defects

Author(s): Job H Berkhout, Aldert H Piersma, Juliette Legler, Harm J Heusinkveld
Published in: Toxicology letters, Issue Volume 368, Supplement, 1 September 2022, 2022, Page(s) S229, ISSN 0378-4274
Publisher: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.617

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

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

Designing Physiological Maps as a Tool to Study Liver Toxicology

Author(s): 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.
Published in: 21st International Congress ESTIV Abstract Book, Issue annual, 2022, Page(s) 123-124, ISBN 978-80-969474-8-5
Publisher: ESTIV

Computational Modelling of Neural Tube Closure Defects

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

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

Author(s): 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
Published in: Toxicology Letters, Issue Volume 368, Supplement, 1 September 2022, 2022, Page(s) S165-S166, ISSN 0378-4274
Publisher: 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

Author(s): 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
Published in: Toxicology Letters, Issue Volume 368, Supplement, 1 September 2022, 2022, Page(s) S77-S78, ISSN 0378-4274
Publisher: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.228

Multi-task Proteochemometric Modelling

Author(s): Anastasia Pentina, and Djork-Arné Clevert
Published in: ChemRxiv, Issue 25732293, 2022, ISSN 2573-2293
Publisher: Cambridge Open Engage
DOI: 10.26434/chemrxiv-2022-d5tzd

Probabilistic Risk Assessment –The Keystone for the Future of Toxicology

Author(s): Maertens A, Golden E, Luechtefeld T, Hoffmann S, Tsaioun K
Published in: Altex- Alternatives to animal experimentation, Issue 39/1, 2022, Page(s) 3–29, ISSN 1868-8551
Publisher: Springer-Spektrum
DOI: 10.14573/altex.2201081

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