Dr James Firman

Journal article

Achar J, Firman JW, Cronin MTD, Öberg G. 2024. A framework for categorizing sources of uncertainty in in silico toxicology methods: considerations for chemical toxicity predictions Regulatory Toxicology and Pharmacology, 154 DOI Author Url Publisher Url Public Url

Firman JW, Boobis A, Hollnagel HM, Kaiser S, Lovell DP, Moretto A, Mueller S, Rider CV, Schmidt F, Stice S, Wijeyesakere SJ, Borja G, Patlewicz G. 2024. Evaluating the consistency of judgments derived through both in silico and expert application of the Cramer classification scheme Food and Chemical Toxicology, 194 DOI Author Url Publisher Url Public Url

Achar J, Firman JW, Tran C, Kim D, Cronin MTD, Öberg G. 2024. Analysis of implicit and explicit uncertainties in QSAR prediction of chemical toxicity: A case study of neurotoxicity Regulatory Toxicology and Pharmacology, 154 :105716-105716 DOI Author Url Publisher Url Public Url

de Souza IR, Iulini M, Galbiati V, Rodrigues AC, Gradia DF, Andrade AJM, Firman JW, Pestana C, Leme DM, Corsini E. 2024. The evaluation of skin sensitization potential of the UVCB substance diisopentyl phthalate by in silico and in vitro methods. Archives of Toxicology, DOI Author Url Publisher Url Public Url

Achar J, Cronin MTD, Firman JW, Öberg G. 2024. A problem formulation framework for the application of in silico toxicology methods in chemical risk assessment Archives of Toxicology, DOI Author Url Publisher Url Public Url

Barnes D, Firman JW, Belfield SJ, Cronin MTD, Vinken M, Janssem M, Masereeuw R. 2024. Development of an adverse outcome pathway network for nephrotoxicity Archives of Toxicology, DOI Author Url Publisher Url Public Url

Furuhama A, Kitazawa A, Yao Y, Matos dos Santos CE, Rathman J, Yang C, Ribeiro JV, Cross K, Myatt G, Raitano G, Benfenati E, Jeliazkova N, Saiakhov R, Chakravarti S, Foster RS, Bossa C, Laura Battistelli C, Benigni R, Sawada T, Wasada H, Hashimoto T, Wu M, Barzilay R, Daga PR, Clark RD, Mestres J, Montero A, Gregori- Puigjané E, Petkov P, Ivanova H, Mekenyan O, Matthews S, Guan D, Spicer J, Lui R, Uesawa Y, Kurosaki K, Matsuzaka Y, Sasaki S, Cronin M, Belfield J, Firman JW, Spînu N, Qiu M, Keca JM, Gini G, Li T, Tong W, Hong H, Liu Z, Igarashi Y, Yamada H, Sugiyama K-L, Honma M. 2023. Evaluation of QSAR models for predicting mutagenicity: outcome of the Second Ames/QSAR international challenge project SAR and QSAR in Environmental Research, 34 :983-1001 DOI Author Url Publisher Url Public Url

Yang C, Rathman JF, Ribeiro V, Batke M, Escher SE, Firman JW, Hobocienski B, Kellner R, Mostrag A, Przybylak KR, Cronin MTD. 2023. Update of the Cancer Potency Database (CPDB) to enable derivations of Thresholds Of Toxicological Concern (TTC) for cancer potency Food and Chemical Toxicology, 182 DOI Author Url Publisher Url Public Url

Belfield SJ, Cronin MTD, Enoch SJ, Firman JW. 2023. Guidance for good practice in the application of machine learning in development of toxicological quantitative structure-activity relationships (QSARs) Tayara H. PLOS ONE, 18 DOI Author Url Publisher Url Public Url

Yang C, Rathman JF, Bienfait B, Burbank M, Detroyer A, Enoch SJ, Firman JW, Gutsell S, Hewitt NJ, Hobocienski B, Mostrag-Szlichtyng A, Krueger CT, Lester C, Mahoney C, Najjar A, Ouédraogo G, Przybylak KR, Ribeiro JF, Cronin M. 2023. The role of a molecular informatics platform to support next generation risk assessment Computational Toxicology, 26 DOI Publisher Url Public Url

Cronin M, Belfield SJ, Briggs K, Enoch SJ, Firman JW, Frericks M, Garrard C, MacCallum P, Madden JC, Pastor M, Sanz F, Soininen I, Sousoni D. 2023. Making in silico predictive models for toxicology FAIR Regulatory Toxicology and Pharmacology, 140 DOI Author Url Publisher Url Public Url

Firman JW, Ebbrell DJ, Bauer FJ, Sapounidou M, Hodges G, Campos B, Roberts J, Gutsell S, Thomas PC, Bonnell M, Cronin MTD. 2022. Construction of an In Silico Structural Profiling Tool Facilitating Mechanistically Grounded Classification of Aquatic Toxicants. Environmental Science and Technology, DOI Author Url Publisher Url Public Url

Belfield SJ, Firman JW, Enoch SJ, Madden JC, Erik Tollefsen K, Cronin MTD. 2022. A Review of Quantitative Structure-Activity Relationship Modelling Approaches to Predict the Toxicity of Mixtures Computational Toxicology, :100251-100251 DOI Publisher Url Public Url

Cronin MTD, Bauer FJ, Bonnell M, Campos B, Ebbrell DJ, Firman JW, Gutsell S, Hodges G, Patlewicz G, Sapounidou M, Spinu N, Thomas PC, Worth AP. 2022. A scheme to evaluate structural alerts to predict toxicity – Assessing confidence by characterising uncertainties Regulatory Toxicology and Pharmacology, 135 DOI Author Url Publisher Url Public Url

Pestana C, Enoch SJ, Firman JW, Madden JC, Spinu N, Cronin MTD. 2022. A Strategy to Define Applicability Domains for Read-Across Computational Toxicology, 22 DOI Publisher Url Public Url

Firman JW, Cronin MTD, Rowe P, Semenova E, Doe JE. 2022. The use of Bayesian methodology in the development and validation of a tiered assessment approach towards prediction of rat acute oral toxicity Archives of Toxicology, DOI Author Url Publisher Url Public Url

Thompson C, Firman JW, Goldsmith M, Grulke C, Tan Y-M, Paini A, Penson P, Sayre R, Webb S, 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 :197-208 DOI Author Url Publisher Url Public Url

Arnesdotter E, Spinu N, Firman JW, Ebbrell DJ, Cronin MTD, Vanhaecke T, Vinken M. 2021. Derivation, characterisation and analysis of an adverse outcome pathway network for human hepatotoxicity Toxicology, DOI Author Url Publisher Url Public Url

Belfield SJ, Enoch SJ, Firman JW, Madden JC, Schultz TW, 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 DOI Author Url Publisher Url Public Url

Bury D, Alexander-White C, Clewell H, Cronin MTD, Desprez B, Detroyer A, Efremenko A, Firman JW, Hack E, Hewitt NJ, Kenna G, Klaric M, Lester C, Mahoney C, Ouédraogo G, Paini A, Schepky A. 2021. New Framework for a Non-Animal Approach Adequately Assures the Safety of Cosmetic Ingredients – A Case Study on Caffeine Regulatory Toxicology and Pharmacology, 123 DOI Author Url Publisher Url Public Url

Sapounidou M, Ebbrell DJ, Bonnell M, Campos B, Firman J, Gitsell S, Cronin MTD. 2021. Development of an Enhanced Mechanistically-Driven Mode of Action Classification Scheme for Adverse Effects in Environmental Species Environmental Science and Technology, 55 :1897-1907 DOI Author Url Publisher Url Public Url

Pestana C, Firman JW, Cronin MTD. 2020. Incorporating Lines of Evidence from New Approach Methodologies (NAMs) to Reduce Uncertainties in a Category Based Read-Across: A Case Study for Repeated Dose Toxicity Regulatory Toxicology and Pharmacology, 120 DOI Author Url Publisher Url Public Url

Firman JW, Pestana CB, Rathman JF, Vinken M, Yang C, Cronin MTD. 2020. A robust, mechanistically-based in silico structural profiler for hepatic cholestasis Chemical Research in Toxicology, 34 :641-655 DOI Author Url Publisher Url Public Url

Firman JW, Punt A, Cronin MTD, Boobis AR, Wilks MF, Hepburn PA, Thief A, Fussell KC. 2020. Exploring the Potential of ToxCast Data in Supporting Read-across for Evaluation of Food Chemical Safety Chemical Research in Toxicology, 34 :300-312 DOI Author Url Publisher Url Public Url

Mellor CL, Tollefsen K-E, LaLone C, Cronin MTD, Firman JW. 2020. In silico identification of chemicals capable of binding to the ecdysone receptor Environmental Toxicology and Chemistry, 39 :1438-1450 DOI Author Url Publisher Url Public Url

Punt A, Firman J, Boobis A, Cronin MTD, Gosling JP, Wilks MF, Hepburn PA, Thiel A, Fussell K. 2020. Potential of ToxCast data in the safety assessment of food chemicals Toxicological Sciences, DOI Author Url Publisher Url Public Url

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

Tomlinson L, Hyndman L, Firman J, Bentley R, Kyffin J, Webb S, McGinty S, Sharma P. 2019. In vitro Liver Zonation of Primary Rat Hepatocytes Frontiers in Bioengineering and Biotechnology, 7 DOI Author Url Publisher Url Public Url

Firman JW, Belfield SJ, Chen G, Jackson M, Lam FH, Richmond C, Smith J, Steinmetz FP, Cronin MTD. 2019. Chemoinformatic Consideration of Novel Psychoactive Substances: Compilation and Preliminary Analysis of a Categorised Dataset Molecular Informatics, 38 DOI Author Url Publisher Url Public Url

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

Pletz J, Enoch SJ, Jais DM, Mellor CL, Pawar G, Madden JC, Webb SD, Tagliati C, 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, DOI Author Url Publisher Url Public Url

Firman J, Patel A, Date M, Cronin MTD, Schultz TW. 2018. Read-across of 90-day rodent repeated-dose toxicity: A case study for selected simple aryl alcohol alkyl carboxylic acid esters Computational Toxicology, 7 :1-8 DOI Author Url Publisher Url Public Url

La Pensee L, Sabbani S, Sharma R, Bhamra I, Shore E, Chadwick AE, Berry NG, Firman J, Araujo NC, Cabral L, Cristiano MLS, Bateman C, Janneh O, Gavrila A, Wu YH, Hussain A, Ward SA, Stocks PA, Cosstick R, O'Neill PM. 2013. Artemisinin-Polypyrrole Conjugates: Synthesis, DNA Binding Studies and Preliminary Antiproliferative Evaluation CHEMMEDCHEM, 8 :709-718 DOI Author Url Publisher Url

Copple I, Mercer A, Firman JW, Donegan G, Herpers B, Wong M, Chadwick J, Bringela A, Cristiano M, van de Water B, Ward S, O'Neill P, Park BK. 2012. Examination of the Cytotoxic and Embryotoxic Potential and Underlying Mechanisms of Next-Generation Synthetic Trioxolane and Tetraoxane Antimalarials Molecular Medicine, 18 :1045-1055 DOI Author Url Publisher Url Public Url

Conference publication

Cronin M, Belfield S, Chavan S, Enoch S, Firman J, Luijten M, Madden J, Marx-Stoelting P, Pradeep P, Steinbach A-M, Wilenbockel C-T, Zgheib E. 2023. Making Quantitative AOP Networks into Usable Tools for Risk Assessment Toxicology Letters, Eurotox 2023 :S48-S48

Cronin MT, Firman JW, Ebbrell D, Enoch SJ, Madden JC, Rathman JF, Yang C. 2021. Developing and Assessing In Silico Profilers for Organ-Level Toxicity Using Non-Standard Data TOXICOLOGY LETTERS, 56th Congress of the European-Societies-of-Toxicology (EUROTOX) - Toxicology of the Next Generation 350 :S49-S49 Author Url

Yang C, Cronin MT, Ebbrell D, Firman JW, Kawamoto T, Madden JC, Magdziarz T, Mostrag A, Rathman JF, Theophilus EH. 2019. novel methods for estimating noael confidence bounds and optimising similarity measures for read-across workflows TOXICOLOGY LETTERS, 55th Congress of the European-Societies-of-Toxicology (EUROTOX) - Toxicology - Science Providing Solutions 314 :S259-S260 Author Url

Cronin MTD, Bienfait B, Ebbrell DJ, Enoch SJ, Firman JW, Madden JC, Mostrag-Szlichtyng A, Rathman JF, Vitcheva V, Yang C. 2018. An extended mechanistically-based in silico profiler for liver toxicity TOXICOLOGY LETTERS, 54th Congress of the European-Societies-of-Toxicology (EUROTOX) - Toxicology Out of the Box 295 :S101-S101 DOI Author Url Publisher Url

Pletz J, Ebbrell DJ, Enoch SJ, Firman JW, Madden JC, Webb SD, Cronin MTD. 2018. Development of a Robust In Silico Profiler to Screen for Nephrotoxicity Endpoints TOXICOLOGY LETTERS, 54th Congress of the European-Societies-of-Toxicology (EUROTOX) - Toxicology Out of the Box 295 :S97-S97 DOI Author Url Publisher Url

Nepelska M, Cronin MTD, Cubberley R, Dent M, Firman JW, Fisher J, Kenna G, Mahony C, Nicol B, Piechota S, Przybylak K, Schepky A, Tozer S, Troutman J, Desprez B. 2018. Cosmetic Europe's long range science strategy - A non-animal safety assessment case study for phenoxyethanol, a cosmetic ingredient TOXICOLOGY LETTERS, 54th Congress of the European-Societies-of-Toxicology (EUROTOX) - Toxicology Out of the Box 295 :S171-S171 DOI Author Url Publisher Url

Cronin M, Belfield S, Escher S, Firman J, Lieu J, Marsaux C, Mostrag-Szlichtyng A, Przybylak K, Rathman J, Tarkhov A, Yang C. 2017. Extension of the carcinogen dose-response database for threshold of toxicological concern TOXICOLOGY LETTERS, 53rd Congress of the European-Societies-of-Toxicology (EUROTOX) 280 :S284-S284 DOI Author Url Publisher Url

Firman J, Cain K, Park BK, MacFarlane M, Chadwick A. 2014. Investigating the roles of lysosomal iron and reactive oxygen species in the onset of mitochondrial toxicity induced through endoperoxide antimalarial drugs Toxicology Letters, 229 :S61-S62 DOI Publisher Url

Firman JW, MacFarlane M, Park BK, Mercer AE. 2011. Assessing the cytotoxic profile of novel endoperoxide derivatives Toxicology, 290 :138-138 DOI Publisher Url

Chapters

Ebbrell D, Cronin M, Ellison C, Firman J, Madden J. Development of Baseline Quantitative Structure-Activity Relationships (QSARs) for the Effects of Active Pharmaceutical Ingredients (APIs) to Aquatic Species Roy K. Ecotoxicological QSARs Springer 978-1-0716-0149-5 DOI Publisher Url