The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing. - Jaclyn K. Mann; John P. Barton; Andrew L. Ferguson; Saleha Omarjee; Bruce D. Walker; Arup Chakraborty; Thumbi Ndung'u (PLoS Comput. Biol., 2014)

Global graph matching using diffusion maps. - Jingtian Hu; Andrew L. Ferguson (Intell. Data Anal., 2016)

BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method. - Andrew L. Ferguson (J. Comput. Chem., 2017)

Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration. - Wei Chen 044; Andrew L. Ferguson (J. Comput. Chem., 2018)

Nonlinear Discovery of Slow Molecular Modes using Hierarchical Dynamics Encoders. - Wei Chen 044; Hythem Sidky; Andrew L. Ferguson (CoRR, 2019)

Capabilities and Limitations of Time-lagged Autoencoders for Slow Mode Discovery in Dynamical Systems. - Wei Chen 044; Hythem Sidky; Andrew L. Ferguson (CoRR, 2019)

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation. - Kirill Shmilovich; Rachael A. Mansbach; Hythem Sidky; Olivia E. Dunne; Sayak Subhra Panda; John D. Tovar; Andrew L. Ferguson (CoRR, 2020)

DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces. - Michael S. Jones; Kirill Shmilovich; Andrew L. Ferguson (CoRR, 2023)

GANs and Closures: Micro-Macro Consistency in Multiscale Modeling. - Ellis R. Crabtree; Juan M. Bello-Rivas; Andrew L. Ferguson; Ioannis G. Kevrekidis (Multiscale Model. Simul., 2023)

FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping. - Michael S. Jones; Smayan Khanna; Andrew L. Ferguson (J. Chem. Inf. Model., 2025)