Article

Thompson, CV, Webb, SD, Leedale, JA, Penson, PE, Paini, A, Ebbrell, DJ and Madden, JC (2023) Using Read-Across to Build Physiologically-Based Kinetic Models: Part 2. Case Studies for atenolol and flumioxazin. Computational Toxicology, 29. p. 100293. ISSN 2468-1113

Thompson, CV, Webb, SD, Leedale, JA, Penson, PE, Paini, A, Ebbrell, D and Madden, JC (2023) Using read-across to build physiologically-based kinetic models: Part 1. Development of a KNIME workflow to assist analogue selection for PBK modelling. Computational Toxicology, 29. p. 100292. ISSN 2468-1113

Cronin, M, Belfield, SJ, Briggs, K, Enoch, SJ, Firman, JW, Frericks, M, Garrard, C, MacCallum, P, Madden, JC, Pastor, M, Sanz, F, Soininen, I and Sousoni, D (2023) Making in silico predictive models for toxicology FAIR. Regulatory Toxicology and Pharmacology, 140. ISSN 0273-2300

Belfield, SJ, Firman, JW, Enoch, SJ, Madden, JC, Erik Tollefsen, K and Cronin, MTD (2022) A Review of Quantitative Structure-Activity Relationship Modelling Approaches to Predict the Toxicity of Mixtures. Computational Toxicology. p. 100251. ISSN 2468-1113

Krebs, C, Camp, C, Constantino, H, Courtot, L, Kavanagh, O, Batista Leite, S, Madden, JC, Paini, A, Poojary, B, Tripodi, IJ and Trunnell, ER (2022) Proceedings of a workshop to address animal methods bias in scientific publishing. ALTEX. ISSN 1868-596X

Pestana, C, Enoch, SJ, Firman, JW, Madden, JC, Spinu, N and Cronin, MTD (2022) A Strategy to Define Applicability Domains for Read-Across. Computational Toxicology, 22. ISSN 2468-1113

Cronin, MTD, Enoch, SJ, Madden, JC, Rathman, JF, Richarz, AN and Yang, C (2022) A Review of In Silico Toxicology Approaches to Support the Safety Assessment of Cosmetics-Related Materials. Computational Toxicology, 21. ISSN 2468-1113

Spinu, N, Cronin, MTD, Lao, J, Bal-Price, A, Campia, I, Enoch, SJ, Madden, JC, Lagares, LM, Novič, M, Pamies, D, Scholz, S, Villeneuve, DL and Worth, A (2021) Probabilistic Modelling of Developmental Neurotoxicity based on a Simplified Adverse Outcome Pathway Network. Computational Toxicology, 21. ISSN 2468-1113

Spinu, N, Cronin, MTD, Madden, JC and Worth, A (2021) A Matter of Trust: Learning Lessons About Causality Will Make qAOPs Credible. Computational Toxicology, 21. ISSN 2468-1113

Thompson, C, Firman, JW, Goldsmith, M, Grulke, C, Tan, Y-M, Paini, A, Penson, P, Sayre, R, Webb, S and Madden, JC (2021) A systematic review of published physiologically-based kinetic models and an assessment of their chemical space coverage. Alternatives to Laboratory Animals, 49 (5). pp. 197-208. ISSN 0261-1929

Yang, C, Cronin, MTD, Arvidson, K, Bienfait, B, Enoch, SJ, Heldreth, B, Hobocienski, B, Muldoon-Jacobs, K, Lan, Y, Madden, JC, Magdziarz, T, Marusczyk, J, Mostrag, A, Nelms, MD, Przybylak, KR, Rathman, JF, Richarz, A-N, Richard, AM, Ribeiro, JV, Sacher, O et al, Schwab, C, Vitcheva, P, Volarath, P and Worth, AP (2021) COSMOS Next Generation – a public knowledge base leveraging chemical and biological data to support the regulatory assessment of chemicals. Computational Toxicology, 19. ISSN 2468-1113

Pletz, J, Allen, T, Madden, JC, Cronin, MTD and Webb, SD (2021) A Mechanistic Model to Study the Kinetics and Toxicity of Salicylic Acid in the Kidney of Four Virtual Individuals. Computational Toxicology, 19. ISSN 2468-1113

Belfield, SJ, Enoch, SJ, Firman, JW, Madden, JC, Schultz, TW and Cronin, MTD (2021) Determination of “Fitness-for-Purpose” of Quantitative Structure-Activity Relationship (QSAR) Models to Predict (Eco-)Toxicological Endpoints for Regulatory Use. Regulatory Toxicology and Pharmacology, 123. ISSN 0273-2300

Paini, A, Worth, A, Kulkarni, S, Ebbrell, DJ and Madden, JC (2021) Assessment of the predictive capacity of a physiologically based kinetic model using a read-across approach. Computational Toxicology, 18. ISSN 2468-1113

Madden, JC, Enoch, SJ, Paini, A and Cronin, MTD (2020) A Review of In Silico Tools as Alternatives to Animal Testing: Principles, Resources and Applications. Alternatives to Laboratory Animals. ISSN 0261-1929

Madden, JC (2020) Comment from the New Editor-in-Chief: A Journey to Replacement and the Inevitable Question. Alternatives to Laboratory Animals. ISSN 0261-1929

Spinu, N, Cronin, MTD, Enoch, SJ, Madden, JC and Worth, A (2020) Quantitative Adverse Outcome Pathway (qAOP) models for toxicity prediction. Archives of Toxicology, 94. pp. 1497-1510. ISSN 0340-5761

Ball, N, Madden, JC, Paini, A, Mathea, M, Palmer, A, Sperber, S, Hartung, T and van Ravenzwaay, B (2020) Key Read Across Framework Components and Biology Based Improvements. Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 853. ISSN 1383-5718

Ebbrell, DJ, Madden, JC, Cronin, MTD, Schultz, T and Enoch, SJ (2019) Development of a fragment-based in silico profiler for SN2 thiol reactivity and its application in predicting toxicity of chemicals towards Tetrahymena pyriformis. Computational Toxicology, 13. ISSN 2468-1113

Madden, JC, Tan, Y-M, Blaauboer, B and Paini, A (2019) Development and Application of Physiologically-Based Kinetic (PBK) Models. Computational Toxicology, 13. ISSN 2468-1113

Spinu, N, Bal-Price, A, Cronin, MTD, Enoch, SJ, Madden, JC and Worth, A (2019) Development and Analysis of an Adverse Outcome Pathway Network for Human Neurotoxicity. Archives of Toxicology, 93 (10). pp. 2759-2772. ISSN 0340-5761

Pawar, G, Madden, JC, Ebbrell, DJ, Firman, JW and Cronin, MTD (2019) In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. Frontiers in Pharmacology, 10. ISSN 1663-9812

Madden, JC, Pawar, G, Cronin, MTD, Webb, SD, Tan, Y-M and Paini, A (2019) In Silico Resources to Assist in the Development and Evaluation of Physiologically-Based Kinetic Models. Computational Toxicology, 11. pp. 33-49. ISSN 2468-1113

Lukac, I, Abdelhakim, H, Ward, RA, St-Gallay, SA, Madden, JC and Leach, AG (2019) Predicting protein–ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A. Chemical Science, 10 (7). pp. 2218-2227. ISSN 2041-6520

Cronin, MTD, Madden, JC, Yang, C and Worth, A (2018) Unlocking the Potential of In Silico Chemical Safety Assessment – A Report on a Cross-Sector Symposium on Current Opportunities and Future Challenges. Computational Toxicology, 10. pp. 38-43. ISSN 2468-1113

Mellor, CL, Marchese Robinson, RL, Benigni, R, Ebbrell, DJ, Enoch, SJ, Firman, JW, Madden, JC, Pawar, G, Yang, C and Cronin, MTD (2018) Molecular Fingerprint-Derived Similarity Measures for Toxicological Read-Across: Recommendations for Optimal Use. Regulatory Toxicology and Pharmacology, 101. pp. 121-134. ISSN 0273-2300

Paini, A, Leonard, JA, Joossens, E, Bessems, JGM, Desalegn, A, Dorne, JL, Gosling, JP, Heringa, MB, Klaric, M, Kliment, T, Kramer, NI, Loizou, G, Louisse, J, Lumen, A, Madden, JC, Patterson, EA, Proença, S, Punt, A, Setzer, RW, Suciu, N et al, Troutman, J, Yoon, M, Worth, A and Tan, YM (2018) Next generation physiologically based kinetic (NG-PBK) models in support of regulatory decision making. Computational Toxicology, 9. pp. 61-72. ISSN 2468-1113

Pletz, J, Enoch, SJ, Jais, DM, Mellor, CL, Pawar, G, Madden, JC, Webb, SD, Tagliati, C and Cronin, MTD (2018) A Critical Review of Adverse Effects to the Kidney: Mechanisms, Data Sources and In Silico Tools to Assist Prediction. Expert Opinion on Drug Metabolism and Toxicology. ISSN 1744-7607

Nelms, M, Mellor, C, Enoch, SJ, Judson, R, Patlewicz, G, Richard, A, Madden, JC, Cronin, MTD and Edwards, S (2018) A Mechanistic Framework for Integrating Chemical Structure and High-Throughput Screening Results to Improve Toxicity Predictions. Computational Toxicology, 8. ISSN 2468-1113

Patel, M, Chilton, M, Sartini, A, Gibson, L, Barber, C, Covey-Crump, L, Przybylak, KR, Cronin, MTD and Madden, JC (2018) Assessment and Reproducibility of Quantitative Structure-Activity Relationship Models by the Nonexpert. Journal of Chemical Information and Modeling, 58 (3). pp. 673-682. ISSN 1549-9596

Lukac, I, Zarnecka, J, Griffen, EJ, Dossetter, AG, St-Gallay, SA, Enoch, SJ, Madden, JC and Leach, AG (2017) Turbocharging Matched Molecular Pair Analysis: Optimizing the Identification and Analysis of Pairs. Journal of Chemical Information Modeling. ISSN 1549-9596

Cronin, MTD, Enoch, SJ, Mellor, CL, Przybylak, KR, Richarz, AN and Madden, JC (2017) In Silico Prediction of Organ Level Toxicity: Linking Chemistry to Adverse Effects. Toxicological Research, 33 (3). pp. 173-182. ISSN 1976-8257

Madden, JC, Webb, SD, Enoch, SJ, Colley, H, Murdoch, C, Shipley, R, Sharma, P, Yang, C and Cronin, MTD (2017) In silico prediction of skin metabolism and its implication in toxicity assessment. Computational Toxicology. ISSN 2468-1113

Przybylak, KR, Madden, JC, Covey-Crump, E, Gibson, L, Barber, C, Patel, M and Cronin, MTD (2017) Characterisation of data resources for in silico modelling: benchmark datasets for ADME properties. Expert Opinion on Drug Metabolism and Toxicology. ISSN 1744-7607

Ebbrell, DJ, Madden, JC, Cronin, MTD, Schultz, TW and Enoch, SJ (2017) Validation of a fragment-based profiler for thiol reactivity for the prediction of toxicity: skin sensitisation and tetrahymena pyriformis. Chemical Research in Toxicology, 30 (2). pp. 604-613. ISSN 0893-228X

Ebbrell, DJ, Madden, JC, Cronin, MTD, Schultz, TW and Enoch, SJ (2016) Development of a Fragment-Based in Silico Profiler for Michael Addition Thiol Reactivity. Chemical Research in Toxicology, 29 (6). pp. 1073-1081. ISSN 1520-5010

Ates, G, Steinmetz, FP, Doktorova, TY, Madden, JC and Rogiers, V (2016) Linking existing in vitro dermal absorption data to physicochemical properties: Contribution to the design of a weight-of-evidence approach for the safety evaluation of cosmetic ingredients with low dermal bioavailability. Regulatory Toxicology and Pharmacology, 76. pp. 74-78. ISSN 1096-0295

Ellison, CM, Piechota, P, Madden, JC, Enoch, SJ and Cronin, MTD (2016) Adverse Outcome Pathway (AOP) Informed Modeling of Aquatic Toxicology: QSARs, Read-Across, and Interspecies Verification of Modes of Action. Environmental Science & Technology, 50 (7). pp. 3995-4007. ISSN 1520-5851

Steinmetz, FP, Madden, JC and Cronin, MTD (2015) Data quality in the human and environmental health sciences: Using statistical confidence scoring to improve QSAR/QSPR modeling. Journal of Chemical Information and Modeling, 55 (8). pp. 1739-1746. ISSN 1549-960X

Ellison, CM, Madden, JC, Cronin, MTD and Enoch, SJ (2015) Investigation of the Verhaar scheme for predicting acute aquatic toxicity: improving predictions obtained from Toxtree ver. 2.6. Chemosphere, 139. pp. 146-154. ISSN 1879-1298

Wen, Y, Su, L, Qin, W, Zhao, Y, Madden, JC, Steinmetz, FP and Cronin, MTD (2015) Investigation of Critical Body Residues and Modes of Toxic Action Based on Injection and Aquatic Exposure in Fish. WATER AIR AND SOIL POLLUTION, 226 (6). pp. 1-11. ISSN 0049-6979

Nelms, MD, Ates, G, Madden, JC, Vinken, M, Cronin, MTD, Rogiers, V and Enoch, SJ (2015) Proposal of an in silico profiler for categorisation of repeat dose toxicity data of hair dyes. ARCHIVES OF TOXICOLOGY, 89 (5). pp. 733-741. ISSN 0340-5761

Hewitt, M, Ellison, CM, Cronin, MTD, Madden, JC, Pastor, M, Steger-Hartmann, T, Munoz-Muriendas, J and Pognan, F (2015) Ensuring confidence in predictions: A scheme to assess the scientific validity of in silico models. Advanced Drug Delivery Reviews, 86. pp. 101-111. ISSN 0169-409X

Richarz, A-N, Madden, JC, Marchese Robinson, RL, Lubiński, Ł, Mokshina, E, Urbaszek, P, Kuz׳min, VE, Puzyn, T and Cronin, MTD (2015) Development of computational models for the prediction of the toxicity of nanomaterials. Perspectives in Science, 3 (1-4). pp. 27-29. ISSN 2213-0209

Enoch, SJ, Roberts, DW, Madden, JC and Cronin, MTD (2014) Development of an In Silico Profiler for Respiratory Sensitisation. Alternatives to the Laboratory Animals, 42 (6). pp. 367-375. ISSN 0261-1929

Madden, JC, Rogiers, V and Vinken, M (2014) Application of in silico and in vitro methods in the development of adverse outcome pathway constructs in wildlife. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 369 (1656). ISSN 0962-8436

Hutchinson, TH, Madden, JC, Naidoo, V and Walker, CH (2014) Comparative metabolism as a key driver of wildlife species sensitivity to human and veterinary pharmaceuticals. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 369 (1656). ISSN 0962-8436

Rodriguez-Sanchez, N, Cronin, MTD, Lillicrap, A, Madden, JC, Piechota, P and Tollefsen, KE (2014) DEVELOPMENT OF A LIST OF REFERENCE CHEMICALS FOR EVALUATING ALTERNATIVE METHODS TO IN VIVO FISH BIOACCUMULATION TESTS. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, 33 (12). ISSN 0730-7268

Monograph

Paini, A, Joossens, E, Bessems, J, Desalegn, A, Dorne, JL, Gosling, JP, Heringa, MB, Klaric, M, Kramer, N, Loizou, G, Louisse, J, Lumen, A, Madden, JC, Patterson, EA, Proenca, S, Punt, A, Setzer, RW, Suciu, N, Troutman, J, Yoon, M et al, Worth, A and Tan, YM (2017) EURL ECVAM Workshop on New Generation of Physiologically-Based Kinetic Models in Risk Assessment. Other. Publications Office of the European Union, Luxembourg.