FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping.

Andrew L. Ferguson https://orcid.org/0000-0002-8829-9726 https://www.wikidata.org/entity/Q41049915

Michael S. Jones Smayan Khanna Andrew L. Ferguson FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping. 672-692 2025 65 J. Chem. Inf. Model. 2 https://doi.org/10.1021/acs.jcim.4c02046 db/journals/jcisd/jcisd65.html#JonesKF25 streams/journals/jcisd

Ellis R. Crabtree Juan M. Bello-Rivas Andrew L. Ferguson Ioannis G. Kevrekidis GANs and Closures: Micro-Macro Consistency in Multiscale Modeling. 1122-1146 2023 September 21 Multiscale Model. Simul. 3 https://doi.org/10.1137/22m1517834 db/journals/mmas/mmas21.html#CrabtreeBFK23

Michael S. Jones Kirill Shmilovich Andrew L. Ferguson DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces. 2023 abs/2307.12451 CoRR https://doi.org/10.48550/arXiv.2307.12451 db/journals/corr/corr2307.html#abs-2307-12451

Ellis R. Crabtree Juan M. Bello-Rivas Andrew L. Ferguson Ioannis G. Kevrekidis GANs and Closures: Micro-Macro Consistency in Multiscale Modeling. 2022 abs/2208.10715 CoRR https://doi.org/10.48550/arXiv.2208.10715 db/journals/corr/corr2208.html#abs-2208-10715

Kirill Shmilovich Rachael A. Mansbach Hythem Sidky Olivia E. Dunne Sayak Subhra Panda John D. Tovar Andrew L. Ferguson Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation. 2020 abs/2002.01563 CoRR https://arxiv.org/abs/2002.01563 db/journals/corr/corr2002.html#abs-2002-01563

Wei Chen 0044 Hythem Sidky Andrew L. Ferguson Nonlinear Discovery of Slow Molecular Modes using Hierarchical Dynamics Encoders. 2019 abs/1902.03336 CoRR http://arxiv.org/abs/1902.03336 db/journals/corr/corr1902.html#abs-1902-03336

Wei Chen 0044 Hythem Sidky Andrew L. Ferguson Capabilities and Limitations of Time-lagged Autoencoders for Slow Mode Discovery in Dynamical Systems. 2019 abs/1906.00325 CoRR http://arxiv.org/abs/1906.00325 db/journals/corr/corr1906.html#abs-1906-00325

Wei Chen 0044 Andrew L. Ferguson Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration. 2079-2102 2018 39 J. Comput. Chem. 25 https://doi.org/10.1002/jcc.25520 https://www.wikidata.org/entity/Q62658299 db/journals/jcc/jcc39.html#ChenF18

Andrew L. Ferguson BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method. 1583-1605 2017 38 J. Comput. Chem. 18 https://doi.org/10.1002/jcc.24800 https://www.wikidata.org/entity/Q36364393 db/journals/jcc/jcc38.html#Ferguson17

Jingtian Hu Andrew L. Ferguson Global graph matching using diffusion maps. 637-654 2016 20 Intell. Data Anal. 3 https://doi.org/10.3233/IDA-160824 https://www.wikidata.org/entity/Q62658328 db/journals/ida/ida20.html#HuF16

Jaclyn K. Mann John P. Barton Andrew L. Ferguson Saleha Omarjee Bruce D. Walker Arup Chakraborty Thumbi Ndung'u The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by <i>In Vitro</i> Testing. 2014 10 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1003776 https://www.wikidata.org/entity/Q34015177 db/journals/ploscb/ploscb10.html#MannBFOWCN14

John P. Barton Juan M. Bello-Rivas Arup Chakraborty Wei Chen 0044 Ellis R. Crabtree Olivia E. Dunne Jingtian Hu Michael S. Jones Ioannis G. Kevrekidis Smayan Khanna Jaclyn K. Mann Rachael A. Mansbach Thumbi Ndung'u Saleha Omarjee Sayak Subhra Panda Kirill Shmilovich Hythem Sidky John D. Tovar Bruce D. Walker