| Array programming with NumPy CR Harris, KJ Millman, SJ Van Der Walt, R Gommers, P Virtanen, ... Nature 585 (7825), 357-362, 2020 | 21586 | 2020 |
| del R’ıo CR Harris, KJ Millman, SJ Van Der Walt, R Gommers, P Virtanen, ... JF, Wiebe, M., Peterson, P., G’erard-Marchant, P., Sheppard, K., Reddy, T …, 2020 | 104 | 2020 |
| Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness RM Levy, A Haldane, WF Flynn Current opinion in structural biology 43, 55-62, 2017 | 95 | 2017 |
| Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease WF Flynn, A Haldane, BE Torbett, RM Levy Molecular biology and evolution 34 (6), 1291-1306, 2017 | 61 | 2017 |
| Structural propensities of kinase family proteins from a Potts model of residue co‐variation A Haldane, WF Flynn, P He, RSK Vijayan, RM Levy Protein Science 25 (8), 1378-1384, 2016 | 61 | 2016 |
| Biophysical fitness landscapes for transcription factor binding sites A Haldane, M Manhart, AV Morozov PLoS computational biology 10 (7), e1003683, 2014 | 45 | 2014 |
| The generative capacity of probabilistic protein sequence models F McGee, S Hauri, Q Novinger, S Vucetic, RM Levy, V Carnevale, ... Nature communications 12 (1), 6302, 2021 | 37 | 2021 |
| Epistasis and entrenchment of drug resistance in HIV-1 subtype B A Biswas, A Haldane, E Arnold, RM Levy Elife 8, e50524, 2019 | 37 | 2019 |
| Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation A Haldane, RM Levy Physical Review E 99 (3), 032405, 2019 | 29 | 2019 |
| Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants M Li, D Oliveira Passos, Z Shan, SJ Smith, Q Sun, A Biswas, I Choudhuri, ... Science Advances 9 (29), eadg5953, 2023 | 26 | 2023 |
| Coevolutionary landscape of kinase family proteins: sequence probabilities and functional motifs A Haldane, WF Flynn, P He, RM Levy Biophysical journal 114 (1), 21-31, 2018 | 26 | 2018 |
| Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis A Haldane, RM Levy Computer Physics Communications 260, 107312, 2021 | 20 | 2021 |
| del R’io CR Harris, KJ Millman, SJ Van Der Walt, R Gommers, P Virtanen, ... JF, Wiebe, M., Peterson, P., G’erard-Marchant, P., Sheppard, K., Reddy, T …, 2020 | 18 | 2020 |
| A universal scaling law determines time reversibility and steady state of substitutions under selection M Manhart, A Haldane, AV Morozov Theoretical population biology 82 (1), 66-76, 2012 | 16 | 2012 |
| Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases J Gizzio, A Thakur, A Haldane, RM Levy Elife 11, e83368, 2022 | 13 | 2022 |
| Unique features of different classes of G‐protein‐coupled receptors revealed from sequence coevolutionary and structural analysis HN Do, A Haldane, RM Levy, Y Miao Proteins: Structure, Function, and Bioinformatics 90 (2), 601-614, 2022 | 10 | 2022 |
| Limits to detecting epistasis in the fitness landscape of HIV A Biswas, A Haldane, RM Levy Plos one 17 (1), e0262314, 2022 | 9 | 2022 |
| Contingency and entrenchment of drug-resistance mutations in HIV viral proteins I Choudhuri, A Biswas, A Haldane, RM Levy The Journal of Physical Chemistry B 126 (50), 10622-10636, 2022 | 8 | 2022 |
| Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure A Biswas, I Choudhuri, E Arnold, D Lyumkis, A Haldane, RM Levy Proceedings of the National Academy of Sciences 121 (15), e2316662121, 2024 | 4 | 2024 |
| Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases J Gizzio, A Thakur, A Haldane, CB Post, RM Levy bioRxiv, 2024 | 3 | 2024 |
