Local deformations of polymers with nonplanar rigid main-chain internal coordinates. - Aaron R. Dinner (J. Comput. Chem., 2000)

Monte Carlo simulations of biomolecules: The MC module in CHARMM. - Jie Hu; Ao Ma; Aaron R. Dinner (J. Comput. Chem., 2006)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

Discovering transcription factor regulatory targets using gene expression and binding data. - Mark Maienschein-Cline; Jie Zhou; Kevin P. White; Roger Sciammas; Aaron R. Dinner (Bioinform., 2012)

Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle. - Yihan Lin; Ying Li; Sean Crosson; Aaron R. Dinner; Norbert F. Scherer (PLoS Comput. Biol., 2012)

Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data. - Alan L. Hutchison; Mark Maienschein-Cline; Andrew H. Chiang; S. M. Ali Tabei; Herman Gudjonson; Neil Bahroos; Ravi Allada; Aaron R. Dinner (PLoS Comput. Biol., 2015)

Trajectory Stratification of Stochastic Dynamics. - Aaron R. Dinner; Jonathan C. Mattingly; Jeremy O. B. Tempkin; Brian Van Koten; Jonathan Weare (SIAM Rev., 2018)

Stratification as a General Variance Reduction Method for Markov Chain Monte Carlo. - Aaron R. Dinner; Erik H. Thiede; Brian Van Koten; Jonathan Weare (SIAM/ASA J. Uncertain. Quantification, 2020)

Error Bounds for Dynamical Spectral Estimation. - Robert J. Webber; Erik H. Thiede; Douglas Dow; Aaron R. Dinner; Jonathan Weare (SIAM J. Math. Data Sci., 2021)

Transformers are efficient hierarchical chemical graph learners. - Zihan Pengmei; Zimu Li; Chih-chan Tien; Risi Kondor; Aaron R. Dinner (CoRR, 2023)

Predicting rare events using neural networks and short-trajectory data. - John Strahan; Justin Finkel; Aaron R. Dinner; Jonathan Weare (J. Comput. Phys., 2023)

Pervasive, conserved secondary structure in highly charged protein regions. - Catherine G. Triandafillou; Rosalind Wenshan Pan; Aaron R. Dinner; D. Allan Drummond (PLoS Comput. Biol., 2023)

geom2vec: pretrained GNNs as geometric featurizers for conformational dynamics. - Zihan Pengmei; Chatipat Lorpaiboon; Spencer C. Guo; Jonathan Weare; Aaron R. Dinner (CoRR, 2024)

Sampling Parameters of Ordinary Differential Equations with Constrained Langevin Dynamics. - Chris Chi; Jonathan Weare; Aaron R. Dinner (SIAM/ASA J. Uncertain. Quantification, 2025)

Mitigating mode collapse in normalizing flows by annealing with an adaptive schedule: Application to parameter estimation. - Yihang Wang; Chris Chi; Aaron R. Dinner (CoRR, 2025)