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

Rezultaty

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

Publikacje

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

Autorzy: 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
Opublikowane w: Toxicology, Numer 458, 2021, Strona(/y) 152846, ISSN 0300-483X
Wydawca: Elsevier BV
DOI: 10.1016/j.tox.2021.152846

Unsupervised Representation Learning for Proteochemometric Modeling

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

Scientific validation of human Neurosphere Assays for Developmental Neurotoxicity evaluation

Autorzy: Koch K, Bartmann K, Hartmann J, Kapr J, Klose J, Kuchovská E, Pahl M, Schlüppmann K, Zühr E and Fritsche E
Opublikowane w: The Frontiers in toxicology/Section Neurotoxicology, Numer 4/816370, 2022, Strona(/y) 1-26, ISSN 2673-3080
Wydawca: 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

Autorzy: 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
Opublikowane w: Journal of Biomedical Informatics, Numer Volume 145, September 2023, 2023, Strona(/y) 104465, ISSN 1532-0464
Wydawca: 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

Autorzy: Marie Corradi, Alyanne de Haan, Bernard Staumont, Aldert Piersma, Liesbet Geris, Raymond Pieters, Cyrille Krul, Marc Teunis
Opublikowane w: Biosystems and Biomaterials, Numer 26665344, 2022, ISSN 2666-5344
Wydawca: Elsevier BV
DOI: 10.1016/j.bbiosy.2022.100061

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

Autorzy: Thomas Hartung
Opublikowane w: ALTEX, Numer 4/yr, 2023, Strona(/y) 559-570, ISSN 1868-8551
Wydawca: Springer Spektrum
DOI: 10.14573/altex.2309191

A call for a Human Exposome Project.

Autorzy: Thomas Hartung
Opublikowane w: ALTEX, Numer 4/yr, 2023, Strona(/y) 4–33, ISSN 1868-8551
Wydawca: Springer Spektrum
DOI: 10.14573/altex.2301061

Img2Mol – accurate SMILES recognition from molecular graphical depictions

Autorzy: Djork-Arné Clevert, Tuan Le, Robin Winter, Floriane Montanari
Opublikowane w: Chemical Science, Numer 12/42, 2021, Strona(/y) 14174-14181, ISSN 2041-6520
Wydawca: 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

Autorzy: 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
Opublikowane w: ATLA, Numer Jan, 2024, 2024, ISSN 0261-1929
Wydawca: 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

Autorzy: Gianluca Selvestrel, Giovanna J. Lavado, Alla P. Toropova, Andrey A. Toropov, Domenico Gadaleta, Marco Marzo, Diego Baderna and Emilio Benfenati
Opublikowane w: International Journal of Molecular Sciences, Numer 14220067, 2022, Strona(/y) 6615, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23126615

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

Autorzy: Breanne Kincaid , Przemyslaw Piechota, Emily Golden, Mikhail Maertens, Thomas Hartung, and Alexandra Maertens
Opublikowane w: Frontier in Artificial Intelligence, Numer 6/yr, 2023, Strona(/y) 1-16, ISSN 0922-6389
Wydawca: IOS Press
DOI: 10.3389/ftox.2023.1216802

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

Autorzy: Mihajlović M and Vinken M
Opublikowane w: International Journal of Molecular Sciences, Numer 23(6), 3315, 2022, Strona(/y) 1-37, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23063315

In Vitro Liver Toxicity Testing of Chemicals: A Pragmatic Approach

Autorzy: 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
Opublikowane w: International Journal of Molecular Sciences, Numer 22/9, 2021, Strona(/y) 5038, ISSN 1422-0067
Wydawca: 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.

Autorzy: Jian Jiang, Jonas van Ertvelde, Gökhan Ertaylan, Ralf Peeters, Danyel Jennen, Theo M. de Kok, Mathieu Vinken
Opublikowane w: Archives of Toxicology, Numer volume 91, 2023, 2023, Strona(/y) 2969-2981, ISSN 1432-0738
Wydawca: Springer
DOI: 10.1007/s00204-023-03583-4

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

Autorzy: Fenna Sillé, Thomas Hartung
Opublikowane w: Metabolites, Numer 14(2), 98, 2024, ISSN 2218-1989
Wydawca: MDPI
DOI: 10.3390/metabo14020098

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

Autorzy: Alexandra Maertens, Thomas Luechtefeld, Jean Knight, Thomas Hartung
Opublikowane w: ALTEX, Numer Vol. 41 No. 1, 2024, ISSN 1868-8551
Wydawca: Springer International Publishing AG
DOI: 10.14573/altex.2312291

AI as the New Frontier in Chemical Risk Assessment

Autorzy: Thomas Hartung
Opublikowane w: Frontiers in Artificial Intelligence, 2023, Strona(/y) 1-4, ISSN 0922-6389
Wydawca: IOS Press
DOI: 10.3389/frai.2023.1269932

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

Autorzy: Jean Knight, Thomas Hartung, Costanza Rovida
Opublikowane w: ALTEX, Numer 4/yr, 2023, Strona(/y) 389-407, ISSN 1868-8551
Wydawca: Springer Spektrum
DOI: 10.14573/altex.2303201

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

Autorzy: Caloni F, De Angelis I, Hartung T
Opublikowane w: Archives of Toxicology, Numer 96, 2022, Strona(/y) 1935–1950, ISSN 0340-5761
Wydawca: 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

Autorzy: Domenico Gadaleta, Nicoleta Spînu, Alessandra Roncaglioni, Mark T. D. Cronin, Emilio Benfenati
Opublikowane w: International Journal of Molecular Sciences, Numer 14220067, 2022, Strona(/y) 3053, ISSN 1422-0067
Wydawca: 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

Autorzy: Susana Proença, Nick van Sabben, Juliette Legler, Jorke H. Kamstra, Nynke I. Kramer
Opublikowane w: Toxicology, Numer Volume 485, February 2023, 153411, 2023, ISSN 0300-483X
Wydawca: Elsevier BV
DOI: 10.1016/j.tox.2022.153411

G × E interactions as a basis for toxicological uncertainty

Autorzy: 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
Opublikowane w: Archives of Toxicology, 2023, Strona(/y) 2035–2049, ISSN 0340-5761
Wydawca: 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)

Autorzy: Nicole Kleinstreuer, Thomas Hartung
Opublikowane w: Archives of Toxicology, Numer Vol 98, 2024, Strona(/y) 735–754, ISSN 0340-5761
Wydawca: Springer Verlag
DOI: 10.1007/s00204-023-03666-2

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

Autorzy: Marina Garcia de Lomana, Paula Andrea Marin Zapata, and Floriane Montanari
Opublikowane w: Chemical Research in Toxicology, Numer Volume 36, issue 7, 2023, Strona(/y) 1107–1120, ISSN 0893-228X
Wydawca: American Chemical Society
DOI: 10.1021/acs.chemrestox.3c00086

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

Autorzy: Costanza Rovida, Francois Busquet, Marcel Leist, Thomas Hartung
Opublikowane w: ALTEX, Numer 4/yr, 2023, Strona(/y) 367-388, ISSN 1868-8551
Wydawca: Springer Spektrum
DOI: 10.14573/altex.2307121

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

Autorzy: 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
Opublikowane w: ALTEX, Numer 4/yr, 2023, Strona(/y) 706–712, ISSN 1868-8551
Wydawca: Springer Spektrum
DOI: 10.14573/altex.2310021

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

Autorzy: Kaat Leroy, Alanah Pieters, Axelle Cooreman, Raf Van Campenhout, Bruno Cogliati, Mathieu Vinken
Opublikowane w: International Journal of Molecular Sciences, Numer 22/21, 2021, Strona(/y) 11724, ISSN 1422-0067
Wydawca: 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

Autorzy: Emily Golden, Daniel C. Ukaegbu, Peter Ranslow, Robert H. Brown, Thomas Hartung, and Alexandra Maertens
Opublikowane w: Chemical Research in Toxicology, 2023, Strona(/y) 734 - 746, ISSN 0893-228X
Wydawca: American Chemical Society
DOI: 10.1021/acs.chemrestox.2c00383

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

Autorzy: Alasdair R. Irvine, Damiën van Berlo, Rawan Shekhani, Rosalinde Masereeuw
Opublikowane w: Current Opinion in Toxicology, Numer 27, 2021, Strona(/y) 18-26, ISSN 2468-2020
Wydawca: Elsevier
DOI: 10.1016/j.cotox.2021.06.001

The probable future of toxicology - probabilistic risk assessment

Autorzy: 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
Opublikowane w: ALTEX, Numer N/A, 2024, Strona(/y) N/A, ISSN 1868-8551
Wydawca: Springer International Publishing AG
DOI: 10.14573/altex.2310301

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

Autorzy: Vânia Vilas-Boas, Eva Gijbels, Kaat Leroy, Alanah Pieters, Audrey Baze, Céline Parmentier, Mathieu Vinken
Opublikowane w: International Journal of Molecular Sciences, Numer 22/20, 2021, Strona(/y) 11005, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222011005

Development of an adverse outcome pathway network for nephrotoxicity

Autorzy: D A Barnes, J W Firman, S J Belfield, M T D Cronin, M Vinken, M J Janssen, R Masereeuw
Opublikowane w: Archives of Toxicology, Numer Volume 98, 2024, Strona(/y) 929-942, ISSN 0340-5761
Wydawca: Springer Verlag
DOI: 10.1007/s00204-023-03637-7

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

Autorzy: Eliska Kuchovska, Alessio Gamba, Luiz Carlos Maia Ladeira, Bernard Staumont, Raphaëlle Lesage, Inger-Lise Steffensen, Graciela Lopez Soop
Opublikowane w: 21st International Congress ESTIV Abstract Book, Numer annual, 2022, Strona(/y) 48-49, ISBN 978-80-969474-8-5
Wydawca: ESTIV

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

Autorzy: Alessio Gamba, Luiz Carlos Maia Ladeira, Raphaëlle Lesage, Devon Barnes, Daniël Roodzant, Marc Teunis, Manoe Janssen, Rosalinde Masereeuw, Liesbet Geris, Bernard Staumont
Opublikowane w: Toxicology Letters, Numer Volume 368, Supplement, 1 September 2022, 2022, Strona(/y) S101, ISSN 0378-4274
Wydawca: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.290

Physiological Map to Study Kidney Toxicity in the ONTOX Project.

Autorzy: Alessio Gamba, Luiz Carlos Maia Ladeira, Raphaëlle Lesage, Daniël Roodzant, Devon Barnes, Manoe Janssen, Marc Teunis, Rosalinde Masereeuw, Liesbet Geris, Bernard Staumont
Opublikowane w: 21st International Congress ESTIV Abstract Book, Numer annual, 2022, Strona(/y) 120-121, ISBN 978-80-969474-8-5
Wydawca: ESTIV

Development of an Adverse Outcome Pathway for Kidney Tubular Necrosis

Autorzy: Devon Barnes, Alasdair Irvine, Alessio Gamba, Luiz Carlos Maia Ladeira, Bernard Staumont, Huan Yang, Inger-Lise Steffensen, Liesbet Geris, Manoe Janssen, and Rosalinde Masereeuw
Opublikowane w: 21st International Congress ESTIV Abstract Book, Numer annual, 2022, Strona(/y) 186-187, ISBN 978-80-969474-8-5
Wydawca: ESTIV

Protocol for a systematic scoping review

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

P17-07 Computational modelling of neural tube closure defects

Autorzy: Job H Berkhout, Aldert H Piersma, Juliette Legler, Harm J Heusinkveld
Opublikowane w: Toxicology letters, Numer Volume 368, Supplement, 1 September 2022, 2022, Strona(/y) S229, ISSN 0378-4274
Wydawca: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.617

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

Autorzy: Devon Barnes, A. Irvine, Alessio Gamba, Bernard Staumont, Luiz C Maia Ladeira, Huan Yang, Inger-Lise Stffensen, Liesbet Geris, Manoe Janssen, Roos Masereeuw
Opublikowane w: Toxicology Letters, Numer Volume 368, Supplement, 1 September 2022, 2022, Strona(/y) S86-S87, ISSN 0378-4274
Wydawca: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.251

Designing Physiological Maps as a Tool to Study Liver Toxicology

Autorzy: 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.
Opublikowane w: 21st International Congress ESTIV Abstract Book, Numer annual, 2022, Strona(/y) 123-124, ISBN 978-80-969474-8-5
Wydawca: ESTIV

Computational Modelling of Neural Tube Closure Defects

Autorzy: Job Berkhout, Aldert Piersma, Juliette Legler, Alessio Gamba, Luiz Carlos Maia Ladeira, Bernard Staumont, Raphaëlle Lesage, Liesbet Geris, and Harm Heuseinkveld
Opublikowane w: 21st International Congress ESTIV Abstract Book, Numer annual, 2022, Strona(/y) 127, ISBN 978-80-969474-8-5
Wydawca: ESTIV

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

Autorzy: 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
Opublikowane w: Toxicology Letters, Numer Volume 368, Supplement, 1 September 2022, 2022, Strona(/y) S165-S166, ISSN 0378-4274
Wydawca: 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

Autorzy: 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
Opublikowane w: Toxicology Letters, Numer Volume 368, Supplement, 1 September 2022, 2022, Strona(/y) S77-S78, ISSN 0378-4274
Wydawca: ELSEVIER BV
DOI: 10.1016/j.toxlet.2022.07.228

Multi-task Proteochemometric Modelling

Autorzy: Anastasia Pentina, and Djork-Arné Clevert
Opublikowane w: ChemRxiv, Numer 25732293, 2022, ISSN 2573-2293
Wydawca: Cambridge Open Engage
DOI: 10.26434/chemrxiv-2022-d5tzd

Probabilistic Risk Assessment –The Keystone for the Future of Toxicology

Autorzy: Maertens A, Golden E, Luechtefeld T, Hoffmann S, Tsaioun K
Opublikowane w: Altex- Alternatives to animal experimentation, Numer 39/1, 2022, Strona(/y) 3–29, ISSN 1868-8551
Wydawca: Springer-Spektrum
DOI: 10.14573/altex.2201081

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