| Identifying who has long COVID in the USA: a machine learning approach using N3C data ER Pfaff, AT Girvin, TD Bennett, A Bhatia, IM Brooks, RR Deer, ... The Lancet Digital Health 4 (7), e532-e541, 2022 | 170 | 2022 |
| Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets W Chen, H Sidky, AL Ferguson The Journal of chemical physics 150 (21), 2019 | 145 | 2019 |
| Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation H Sidky, W Chen, AL Ferguson Molecular Physics 118 (5), e1737742, 2020 | 136 | 2020 |
| SSAGES: software suite for advanced general ensemble simulations H Sidky, YJ Colón, J Helfferich, BJ Sikora, C Bezik, W Chu, F Giberti, ... The Journal of chemical physics 148 (4), 2018 | 130 | 2018 |
| Role of associative charging in the entropy–energy balance of polyelectrolyte complexes VS Rathee, H Sidky, BJ Sikora, JK Whitmer Journal of the American Chemical Society 140 (45), 15319-15328, 2018 | 127 | 2018 |
| Discovery of self-assembling π-conjugated peptides by active learning-directed coarse-grained molecular simulation K Shmilovich, RA Mansbach, H Sidky, OE Dunne, SS Panda, JD Tovar, ... The Journal of Physical Chemistry B 124 (19), 3873-3891, 2020 | 100 | 2020 |
| Learning free energy landscapes using artificial neural networks H Sidky, JK Whitmer The Journal of chemical physics 148 (10), 2018 | 78 | 2018 |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support J Moore, D Basurto-Lozada, S Besson, J Bogovic, J Bragantini, EM Brown, ... Histochemistry and Cell Biology 160 (3), 223-251, 2023 | 74 | 2023 |
| Weak polyelectrolyte complexation driven by associative charging VS Rathee, AJ Zervoudakis, H Sidky, BJ Sikora, JK Whitmer The Journal of Chemical Physics 148 (11), 2018 | 67 | 2018 |
| High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnets H Sidky, W Chen, AL Ferguson The Journal of Physical Chemistry B 123 (38), 7999-8009, 2019 | 65 | 2019 |
| Adaptive enhanced sampling by force-biasing using neural networks AZ Guo, E Sevgen, H Sidky, JK Whitmer, JA Hubbell, JJ De Pablo The Journal of chemical physics 148 (13), 2018 | 60 | 2018 |
| Molecular latent space simulators H Sidky, W Chen, AL Ferguson Chemical Science 11 (35), 9459-9467, 2020 | 55 | 2020 |
| Explicit ion effects on the charge and conformation of weak polyelectrolytes VS Rathee, H Sidky, BJ Sikora, JK Whitmer Polymers 11 (1), 183, 2019 | 46 | 2019 |
| Capabilities and limitations of time-lagged autoencoders for slow mode discovery in dynamical systems W Chen, H Sidky, AL Ferguson The Journal of Chemical Physics 151 (6), 2019 | 44 | 2019 |
| In Silico Measurement of Elastic Moduli of Nematic Liquid Crystals H Sidky, JJ de Pablo, JK Whitmer Physical review letters 120 (10), 107801, 2018 | 28 | 2018 |
| Simulating the thermodynamics of charging in weak polyelectrolytes: the Debye–Hückel limit VS Rathee, BJ Sikora, H Sidky, JK Whitmer Materials Research Express 5 (1), 014010, 2018 | 28 | 2018 |
| Hierarchical coupling of first-principles molecular dynamics with advanced sampling methods E Sevgen, F Giberti, H Sidky, JK Whitmer, G Galli, F Gygi, JJ de Pablo Journal of Chemical Theory and Computation 14 (6), 2881-2888, 2018 | 26 | 2018 |
| Combined force-frequency sampling for simulation of systems having rugged free energy landscapes E Sevgen, AZ Guo, H Sidky, JK Whitmer, JJ De Pablo Journal of chemical theory and computation 16 (3), 1448-1455, 2020 | 21 | 2020 |
| Assessing the effect of selective serotonin reuptake inhibitors in the prevention of post-acute sequelae of COVID-19 H Sidky, KA Hansen, AT Girvin, N Hotaling, SG Michael, K Gersing, ... Computational and Structural Biotechnology Journal 24, 115-125, 2024 | 20 | 2024 |
| Elastic properties of common Gay–Berne nematogens from density of states (DOS) simulations H Sidky, JK Whitmer Liquid Crystals 43 (13-15), 2285-2299, 2016 | 17 | 2016 |
Jonathan K. WhitmerAssociate Professor of Chemical and Biomolecular Engineering, University of Notre DameVerificeret mail på nd.edu