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Allan Haldane

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Allan Haldane

  • College of Science and Technology

    • Physics

      • Research Associate Professor

Selected Publications

Recent

  • McGee, F., Hauri, S., Novinger, Q., Vucetic, S., Levy, R., Carnevale, V., & Haldane, A. (2021). The generative capacity of probabilistic protein sequence models. Nature Communications, 12(1). doi: 10.1038/s41467-021-26529-9.

  • Haldane, A. & Levy, R. (2021). Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis. Computer Physics Communications, 260. doi: 10.1016/j.cpc.2020.107312.

  • Do, H., Haldane, A., Levy, R., & Miao, Y. (2021). Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins: Structure, Function and Bioinformatics. doi: 10.1002/prot.26256.

  • Harris, C., Millman, K., Walt, S.v.d., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N., Kern, R., Picus, M., Hoyer, S., Kerkwijk, M.v., Brett, M., Haldane, A., Río, J.d., Wiebe, M., Peterson, P., Gérard-Marchant, P., Sheppard, K., Reddy, T., Weckesser, W., Abbasi, H., Gohlke, C., & Oliphant, T. (2020). Array programming with NumPy. Nature, 585(7825), 357-362. doi: 10.1038/s41586-020-2649-2.

  • Biswas, A., Haldane, A., Arnold, E., & Levy, R. (2019). Epistasis and entrenchment of drug resistance in HIV-1 subtype B. ELife, 8. doi: 10.7554/eLife.50524.

  • Haldane, A. & Levy, R. (2019). Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation. Physical Review E, 99(3). doi: 10.1103/PhysRevE.99.032405.

  • Arasteh, S., He, P., Haldane, A., & Levy, R.M. (2019). Protein Kinase Free Energy Landscapes: The Role of the Activation Loop. BIOPHYSICAL JOURNAL, 116(3), 436A-436A. 10.1016/j.bpj.2018.11.2348

  • Haldane, A., He, P., Flynn, W.F., & Levy, R.M. (2019). Coevolutionary Landscapes of Kinase Family Proteins. BIOPHYSICAL JOURNAL, 116(3), 168A-168A. 10.1016/j.bpj.2018.11.936

  • Haldane, A., Flynn, W., He, P., & Levy, R. (2018). Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs. Biophysical Journal, 114(1), 21-31. doi: 10.1016/j.bpj.2017.10.028.

  • Flynn, W., Haldane, A., Torbett, B., & Levy, R. (2017). Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease. Molecular Biology and Evolution, 34(6), 1291-1306. doi: 10.1093/molbev/msx095.

  • Levy, R., Haldane, A., & Flynn, W. (2017). Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness. Current Opinion in Structural Biology, 43, 55-62. doi: 10.1016/j.sbi.2016.11.004.