Publication Topic

Snyder K, Greene N, De Nieu M, Anger L, Shah F. Developing predictive models to facilitate interpretation of toxicology study results. Symposium co-chair, Symposium S04, American College of Toxicology (ACT) 46^th Annual Meeting, Phoenix, AZ, November 2025.

Seal S, Trapotsi M, Subramanian V, Spjuth O, Greene N, Bender A. 2025. PKSmart: An open-source computational model to predict in vivo pharmacokinetics of small molecules. J Cheminform 17(1):147; doi: 10.1186/s13321-025-01066-5.

Hanser T, Ahlberg E, Amberg A, Anger LT, Barber C, Brennan RJ, Brigo A,…, Greene N, et al. 2025. Data-driven federated learning in drug discovery with knowledge distillation. Nat Mach Intell 7(Mar):423–436; doi: 10.1038/s42256-025-00991-2.

Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. 2025. Cell painting: A decade of discovery and innovation in cellular imaging. Nat Meth 22(2):254-268; doi: 10.1038/s41592-024-02528-8. PMID: 39639168.

Hagan B, Patlewicz G, Shah I. Metabolic similarity in read-across prediction: A case study using graph convolutional networks to predict genotoxicity outcomes from metabolic networks. Abstract 62, American Society for Cellular and Computation Toxicology 13th Annual Meeting, Research Triangle Park, NC, October 2024.

Leary AJ, Patlewicz G, Shah I. An exploration of the use of hybrid fingerprints in generalized read-across and their impact on predictive performance for selected in vivo toxicity outcomes. Abstract 42, American Society for Cellular and Computation Toxicology 13th Annual Meeting, Research Triangle Park, NC, October 2024.

Van Herwerden D, Kant E, Jackson M, Fender CL, Garcia-Jaramillo M, O’Brien J, Thomas K, Samanipour S. 2024. Modular open-access and open-source Julia language toolbox for processing of HRMS data: jHRMSToolbox. ChemRxiv; doi: 10.26434/chemrxiv-2024-b713v. Under revision in Environ Sci Technol.

Wright PSR, Briggs KA, Thomas R, Smith GF, Maglennon G, Mikulskis P, Chapman M, Greene N, et al. 2023. Statistical analysis of preclinical interspecies concordance of histopathological findings in the eTOX database. Regul Toxicol Pharmacol 138(Feb):105308; doi: 10.1016/j.yrtph.2022.105308. PMID: 36481279.

Zwickl CM, Graham JC, Holly RA, Bassan A, Ahlberg E, Amberg A, Anger LT,.., Patlewicz G, et al. 2022. Principles and procedures for assessment of acute toxicity incorporating in silico methods. Comput Toxicol 24(Nov):100237; doi: 10.1016/j.comtox.2022.100237. PMID: 36818760.

Patlewicz G, Nelms MN, Rua D. 2022. Evaluating the utility of the Threshold of Toxicological Concern (TTC) and its exclusions in the biocompatibility assessment of extractable chemical substances from medical devices. Comput Toxicol 24(Nov):100246; doi: 10.1016/j.comtox.2022.100246. PMID: 36405647.

Nicolas CI, Linakis MW, Minto MS, Mansouri K, Clewell RA, Yoon M, Wambaugh JF, Patlewicz G, et al. 2022. Estimating provisional margins of exposure for data poor chemicals using high throughput computational methods. Front Pharmacol 13(Oct 7):980747; doi: 10.3389/fphar.2022.980747. PMID: 36278238.

Roell K, Koval LE, Boyles R, Patlewicz G, Ring C, Rider CV, Ward-Caviness C, Reif D, et al. 2022. Development of the intelligence and machine learning toolkit (TAME) for introductory data science, chemical-biological analyses, predictive modelling, and database mining for environmental health research. Front Toxicol 4(Jun 22):893924; doi: 10.3389/ftox.2022.893924. PMID: 35812168.

Fender CL, Good S, Jaramillo-Garcia M. Exploring the impacts of evaporation on chemical trends in a regional river and irrigation canal, using nontarget LCMS approaches. Poster presentation at Pacific Northwest Water Symposium, Corvallis, OR, 2022.

Fender CL, Good S, Jaramillo-Garcia M. Using nontarget LCMS and in silico toxicological approaches for the detection and prioritization of contaminant mixtures is a regional irrigation canal. Poster presentation at SETAC Nontarget Special Topics Session, Durham, NC, 2022.

Fender CL, Honneffer J, Morshead M, Bionaz M, Ates S, Duringer J, Garcia-Jaramillo M. Targeted and non-targeted high-resolution LCMS lipidomics analysis of adipose tissue from lambs fed with spent hemp biomass. Poster presentation at Metabolomics Association of North America, Edmonton, Alberta, Canada, 2022.

Patlewicz G. 2022. Editorial: Reflections of the QSAR2021 meeting. Comput Toxicol 22(May):100221; doi: 10.1016/j.comtox.2022.100221. PMID: 35252631.

Patlewicz G, Worth AP, Yang C, Zhu T. 2022. Editorial: Advances and refinements in the development and application of threshold of toxicological concern. Front Toxicol 4(Apr 28):882321; doi: 10.3389/ftox.2022.882321. PMID: 35573274.

Williams AJ, Gaines LG, Grulke CM, Lowe CN, Sinclair G, Samano V, Thillainadarajah I, Meyer B, Patlewicz G, Richard AM. 2022. Assembly and curation of list of per- and polyfluoroalkyl substances (PFAS) to support environmental science research. Front Environ Sci 10(Apr 5):1-13; doi: 10.3389/fenvs.2022.850019. PMID: 35936994.

Bai P, Miljković F, Ge Y, Greene N, John B, Lu H. Hierarchical clustering split for low-bias evaluation of drug-target interaction prediction. IEEE International Conference on Bioinformatics and Biomedicine (BIBM); doi: 10.1109/BIBM52615.2021.966915. Houston, TX, December 2021.

Bassan A, Alves VM, Amberg A, Anger LT, Auerbach S, Beilke L, Bender A…, Greene N, et al. 2021. In silico approaches in organ toxicity hazard assessment: Current status and future needs in predicting liver toxicity. Computation Toxicol 20(Nov):100187; doi: 10.1016/j.comtox.2021.100187. PMID: 35340402.