NanoParticle Ontology for cancer nanotechnology research. - Dennis G. Thomas; Rohit V. Pappu; Nathan A. Baker (J. Biomed. Informatics, 2011)

Annotating the structure and components of a nanoparticle formulation using computable string expressions. - Dennis G. Thomas; Satish Chikkagoudar; Alan R. Chappell; Nathan A. Baker (BIBM Workshops, 2012)

Parameterization of a geometric flow implicit solvation model. - Dennis G. Thomas; Jaehun Chun; Zhan Chen; Guowei Wei 001; Nathan A. Baker (J. Comput. Chem., 2013)

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. - Jian Ma; Cameron P. Casey; Xueyun Zheng; Yehia M. Ibrahim; Christopher S. Wilkins; Ryan S. Renslow; Dennis G. Thomas; Samuel H. Payne; Matthew E. Monroe; Richard D. Smith; Justin G. Teeguarden; Erin S. Baker; et al. (Bioinform., 2017)

An automated framework for NMR chemical shift calculations of small organic molecules. - Yasemin Yesiltepe; Jamie R. Nuñez; Sean M. Colby; Dennis G. Thomas; Mark I. Borkum; Patrick Reardon; Nancy M. Washton; Thomas O. Metz; Justin G. Teeguarden; Niranjan Govind; Ryan S. Renslow (J. Cheminformatics, 2018)

Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples. - Jamie R. Nuñez; Sean M. Colby; Dennis G. Thomas; Malak M. Tfaily; Nikola Tolic; Elin M. Ulrich; Jon R. Sobus; Thomas O. Metz; Justin G. Teeguarden; Ryan S. Renslow (J. Chem. Inf. Model., 2019)

User Role Identification in Software Vulnerability Discussions over Social Networks. - Rebecca Jones; Daniel Fortin; Samrat Chatterjee; Dennis G. Thomas; Lisa Newburn (ISI, 2021)

A tri-level optimization model for interdependent infrastructure network resilience against compound hazard events. - Matthew R. Oster; Ilya Amburg; Samrat Chatterjee; Daniel A. Eisenberg; Dennis G. Thomas; Feng Pan; Auroop R. Ganguly (Int. J. Crit. Infrastructure Prot., 2024)

NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials. - Richard Overstreet; Dennis G. Thomas; John R. Cort (J. Chem. Inf. Model., 2024)