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Publications

*(Co)-corresponding author, #Equal contributions, Undergraduate

Preprints/In Review

  1. Hegde S, Akhter S, Tang Z, Qi C, Yu C, Lewicka A, Liu Y, Koirala K, Reibarkh M, Battaile KP, Cooper A, Lovell S, Holmstrom ED, Wang X, Piccirilli JA, Gao Q*, Miao Y*, & Wang J* (2024) bioRxiv:2024.2010.2014.618236.Ěý
  2. Burger WAC, Mobbs JI, Rana B, Wang J, Joshi K, Gentry PR, Yeasmin M, Venugopal H, Bender AM, Lindsley CW, Miao Y*, Christopoulos A*, Valant C*, & Thal DM* (2025) . bioRxiv: 2025.02.05.636602.

Reviews and Book Chapters

  1. Adediwura VA, Koirala K, Do HN, Wang J, & Miao Y* (2024) Understanding the impact of binding free energy and kinetics calculations in modern drug discovery. Expert Opin Drug Discov:1-12.
  2. Miao Y* & Wolfe MS* (2024) Neural Regeneration Research, Published Online.
  3. Koirala K, Joshi K, Adediwura V, Wang J, Do H, & Miao Y* (2024) Computational Drug Discovery and Design, Second Edition, Edited by Mohini Gore and Umesh B. Jagtap, Methods in Molecular Biology. 2714:187-202.
  4. Do HN, Wang J, Joshi K, Koirala K, & Miao Y* (2023) , Edited by Poongavanam V & Ramaswamy V (Wiley). 1: 21-43.
  5. Pawnikar S, Akhter S, & Miao Y* (2023) Vitamins and Hormones, Edited by Dr. Gerald Litwack G, Vitamins and Hormones, 123: 645-662.
  6. Wang J, Do HN, Koirala K & Miao Y* (2022) Journal of Chemical Theory and Computation, Cover Highlight, 19(8):2135-2148.
  7. Wang J, Bhattarai A, Do HN, & Miao Y* (2022) QRB Discovery, 3, E13.
  8. Wolfe MS & Miao Y (2022) Curr Opin Struct Biol, 74:102373.
  9. Wang J, Bhattarai A, Do H, Akhter S, & Miao Y* (2022) Molecules, 27(7):2054.
  10. Pawnikar S, Bhattarai A, Wang J and Miao Y.* (2022) Adv Appl Bioinform Chem, 15:1-19.
  11. Wang J, Arantes P, Bhattarai A, Hsu R, Pawnikar S, Huang Y-M, Palermo G* and Miao Y* (2021) WIREs Computational Molecular Science: e1521.
    • Advanced Science News:
  12. Wang, J.; Bhattarai, A.; Ahmad, W. I.; Farnan, T. S.; John, K. P.; Miao, Y., Elsevier book “GPCRs: Structure, Function, and Drug Discovery”, Edited by Dr. Paul Shin-Hyun Park and Dr. Beata Jastrzebska, 283-293.
  13. Wang, J., and Miao, Y.* (2019) Advances in Protein Chemistry and Structural Biology, 116, 397-419.

Research Articles

  1. Maxine Bi, Xudong Wang, Jinan Wang, Jun Xu, Wenkai Sun, Victor Ayo Adediwura, Yinglong Miao*, Yifan Cheng*, andĚýLibin Ye*. . Nature Communications, 16 (1), 1100.
  2. Joshi J and Miao Y.* (2024) , Biochemistry, 64(4):871-878.
  3. Liu S, Payne A, Wang J, Zhu L, Eng ET, Liu W, Miao Y, Hite RK, & Huang X-Y (2024) Nat. Struct. Mol. Biol.,Ěýhttps://doi.org/10.1038/s41594-024-01426-z.
  4. Pawnikar S, Magenheimer BS, Munoz EN, Haldane A, Maser RL*, & Miao Y* (2024) eLife, 13: RP95992.
  5. Lou J-S, Su M, Wang J, Do HN, Miao Y, & Huang X-Y (2024) Experimental & Molecular Medicine, 56: 1952–1966.Ěý
  6. Wang J, Koirala K, Do HN, & Miao Y* (2024) Journal of Physical Chemistry B, 128(30):7332-7340.
  7. Wang J & Miao Y* (2024) Journal of Chemical Theory and Computation, 20(14), 5829–5841.
  8. Woods KE, Akhter S, Rodriguez B, Townsend KA, Smith N, Smith B, Wambua A, Craddock V, Abisado-Duque RG, Santa EE, Manson DE, Oakley BR, Hancock LE, Miao Y, Blackwell HE, & Chandler JR (2024) Microbiology Spectrum, e00681-24.
  9. Hasse T, Mantei E, Shahoei R, Pawnikar S, Wang J, Miao Y, & Huang Y-M (2024) PLOS Computational Biology, 20(3):e1011955.
  10. Devkota S, Zhou R, Nagarajan V, Maesako M, Do H, Noorani A, Overmeyer C, Bhattarai S, Douglas JT, Saraf A, Miao Y, Ackley BD, Shi Y, & Wolfe MS (2024) Cell Rep, 43(2):113761.
  11. Adediwura VA & Miao Y* (2024) Molecules. 29(1):164.
  12. Akhter S, Tang Z, Wang J, Haboro M, Holmstrom ED, Wang J, & Miao Y* (2024) Journal of Chemical Information and Modeling, 64(3):1017-1029.
  13. Do HN#, Malvankar SR#, Wolfe MS*, & Miao Y* (2023) ACS Chemical Neurosciences, 14(23):4216-4226.Ěý
  14. Do HN, Wang J, & Miao Y* (2023) JACS Au, 3 (11): 3165–3180.
  15. Su, M.#, Wang, J.#, Xiang, G., Do, H.N., Levitz, J., Miao, Y.*, Huang, X.-Y.* (2023) Nature Communications. 14: 4819.Ěý ( | )
  16. Do HN & Miao Y* (2023). Journal of Physical Chemistry Letters, 14 (21): 4970-4982.
  17. Vuckovic Z#, Wang J#, Pham V#, Mobbs J#, Belousoff MJ, Bhattarai A, Nawaratne V, Leach K, Burger WAC, Westhuizen ETvd, Khajehali E, Thompson G, Yeasmin M, Liang Y-L, Glukhova A, Wootten D, Lindsley CW, Tobin AB, Sexton PM, Danev R, Valant C, Miao Y*, Christopoulos A*, & Thal DM* (2022) eLife, 12:e83477.Ěý (
  18. Pawnikar S, Bhattarai A, Ouyang SX, Vega R, Chen Y*, & Miao Y* (2023) J Phys Chem Lett, 14(11):2792-2799.
  19. Do HN#, Devkota S#, Bhattarai A, Wolfe MS*, & Miao Y* (2022) Communications Biology, 6(1):174.
  20. Wu X, Ramesh R, Wang J, Zheng Y, Armaly AM, Wei L, Xing M, Roy S, Lan L, Gao FP, Miao Y, Xu L, & Aube J (2023) J Med Chem, 66(3):2032-2053.
  21. Wang J & Miao Y* (2022) Journal of Chemical Theory and Computation, 19(3): 733–745.
  22. Copeland M#, Do HN#, Votapka L, Joshi K, Wang J, Amaro RE, & Miao Y* (2022) Journal of Physical Chemistry B, 126(31): 5810–5820.Ěý (
  23. Su M, Paknejad N, Zhu L, Wang J, Do HN, Miao Y, Liu W, Hite RK, & Huang X-Y (2022) Nature Communications, 13: 4095.
  24. Pawnikar, S., Magenheimer, B.S., Nevarez-Munoz, E., Maser, R.L.*, and Miao, Y.* (2022). Proc Natl Acad Sci U S A, 119(19):e2113786119.
  25. Bhattarai, A., Devkota, S., Do, H.N., Wang, J., Bhattarai, S., Wolfe, M.S.*, and Miao, Y.* (2022). Journal of American Chemical Society, 144(14): 6215-6226.
  26. Pawnikar S & Miao Y* (2022) Frontiers in Molecular Biosciences, 9:821055.
  27. Do HN, Wang J, Bhattarai A, & Miao Y* (2022) Journal of Chemical Theory and Computation, 18(3):1423-1436.
  28. Célerse F, Inizan TJ, Lagardère L, Adjoua O, Monmarché P, Miao Y, Derat E, & Piquemal J-P (2022) Journal of Chemical Theory and Computation, 18(2):968-977.
  29. Wang, J. and Miao, Y*, (2022) Journal of Chemical Theory and Computation, 18(3):1275-1285.
  30. Wang J, Lan L, Wu X, Xu L, & Miao Y* (2022) Current Research in Structural Biology, 4:10-20.
  31. Do HN, Haldane A*, Levy RM, & Miao Y* (2021) Proteins: Structure Function and Bioinformatics, 90(2):601-614.
  32. Draper-Joyce CJ, Bhola R, Wang J, Bhattarai A, Nguyen ATN, Cowie-Kent I, O’Sullivan K, Venugopal H, Valant C, Thal DM, Wootten D, Panel N, Carlsson J, Christie MJ, Scammells P, May LT, Sexton PM, Danev R, Miao Y, Glukhova A, Wendy L I, Christopoulos A (2021) Nature, 597 (7877): 571-576.
  33. Tang Z, Akhter S, Ramprasad A, Wang X, Reibarkh M, Wang J, Aryal S, Thota S, Zhao J, Douglas J, Gao P, Holmstrom E, Miao Y*, & Wang J* (2021) Nucleic Acids Research, 49(14):7870-7883.
  34. Bhattarai A, Pawnikar S, & Miao Y* (2021) J Phys Chem Lett, 12:4814-4822.
  35. Do, H. N., Akhter, S. & Miao, Y.*Ěý(2021) Frontiers in Molecular Biosciences 8, 242.
  36. Gao, Y.; Cao, D.; Pawnikar, S.; Akhter, S.; Miao, Y.*; Liang, B.*, (2021) STAR Protocols, 2(1), 100315.
  37. Conrad M, Soldner CA, Miao Y, & Sticht H (2020) International Journal of Molecular Sciences, 21(18):6693.
  38. Wang, J. and Miao, Y*, (2020) Journal of Chemical Physics,Ěý153, 154109.
  39. Miao, Y*, Bhattarai, A., and Wang, J. (2020) Journal of Chemical Theory and Computation, 16(9): 5526-5547.
  40. Gao, Y.; Cao, D.; Pawnikar, S.; John, K. P.; Ahn, H. M.; Hill, S.; Ha, J. M.; Parikh, P.; Ogilvie, C.; Swain, A.; Yang, A.; Bell, A.; Salazar, A.; Miao, Y.*; Liang, B.*, Structure, 28(9):979-990.
  41. Lan, L.; Liu, J.; Xing, M.; Smith, A.R.; Wang, J.; Wu, X.; Appelman, C.; Li, K.; Roy, A.; Gowthaman, R.; Karanicolas, J.; Somoza, A.D.; Wang, C.C.C.; Miao, Y.; De Guzman, R.; Oakley, B.R.; Neufeld, K.L.; Xu, L. (2020) Cancers, 12, 2221.
  42. Bhattarai, A., Devkota, S., Bhattarai, S., Wolfe, M. S.* & Miao, Y.* (2020) ACS Central Science, 6(6), 969-983.
  43. Pawnikar, S. and Miao, Y.* (2020) Future Medicinal Chemistry, 12(13):1213-1225.
  44. Bhattarai, A.#, Wang, J.#, and Miao, Y.* (2020) Special Issue “Advances in Computational Molecular Biophysics”, BBA – General Subjects, 6: 112.
  45. Wang, J., Alekseenko, A, Kozakov, D. and Miao, Y.* (2019) ĚýSpecial Issue “Multiscale Modeling from Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations”, ĚýFrontiers in Molecular Biosciences, 6: 112.
  46. Bhattarai, A.#, Wang, J.#, and Miao, Y.* (2019) J. Comp. Chem., Special Issue “Membrane Protein Simulations”, 41 (5), 460-471.
  47. Wang, J., and Miao, Y.* (2019) Journal of Physical Chemistry B, 123, 6462-6473.
    • “Specific G protein coupling to adenosine G-protein-coupled receptors revealed from all-atom enhanced sampling simulations: the adenosine A1 receptor (A1AR) prefers to bind the Gi protein to the Gs. The Gs could not stabilize adenosine binding in the active A1AR and vice versa. In contrast, the adenosine A2A receptor (A2AAR) could bind both the Gs and Gi proteins.”
  48. Ricci, C. G., Chen, J. S., Miao, Y., Jinek, M., Doudna, J. A., McCammon, J. A., and Palermo, G. (2019) ACS Central Science, 5(4): 651-662.
  49. Miao, Y.*, Bhattarai, A., Nguyen, A. T., Christopoulos, A., and May, L. T. (2018) Scientific Reports, 8:16836.
  50. Bhattarai, A., and Miao, Y.* (2018) Expert Opinion On Drug Discovery.13(11):1055-1065.
  51. Huang YM, Munguia J, Miao Y, Nizet V, & McCammon JA (2018) Chem Biol Drug Des., 93 (4), 647-652.
  52. Zhang, J., Wang, N., Miao, Y.*, Hauser, F., Rappel, W.-J., McCammon, J. A., and Schroeder, J.* (2018) Proc Natl Acad Sci, 115 (44) 11129-11137.
  53. Utesch, T., Catalina, A. d. M., Schattenberg, C., Paege, N., Schmieder, P., Krause, E., Miao, Y., McCammon, J. A., Meyer, V., Jung, S., and Mroginski, M. (2018) mSphere, 3(5), e00377-18.
  54. Miao, Y. (2018). Journal of Chemical Physics, 149(7): 072308.
  55. Amaro, R. E., J. Baudry, J. Chodera, Ă–. Demir, J. A. McCammon, Y. Miao and J. C. Smith (2018). Biophysical Journal,114(10): 2271-78.
  56. Huang, Y. M.*, J. A. McCammon and Y. Miao* (2018). J Chem Theory Comput, 14(4): 1853-64.
  57. Miao Y* & McCammon JA* (2018) Proc Natl Acad Sci U S A, 115(12): 3036-41.
    •Extreme Science and Engineering Discovery Environment (XSEDE) Science Stories: “XSEDE Helps Reveal How a Heart Drug Molecular Switch Is Turned On and Off”
    •San Diego Supercomputer News: “”
  58. Miao Y*, Huang YM*, Walker R, Chang C-eA, & McCammon JA (2018) Biochemistry, 57(9): 1533-41.

Software

  1. Case, D. A., K. Belfon, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, I. T.E. Cheatham, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, G. Giambasu, M. K. Gilson, H. Gohlke, A. W. Goetz, R. Harris, S. Izadi, K. K.-. jhala, A. Kovalenko, R. Krasny, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K. M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F. Pan, S. Pantano, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, N. Skrynnikov, J. Smith, J. Swails, R. C. Walker, J. Wang, L. Wilson, R. M. Wolf, X. Wu, D. M. York and P. A. Kollman (2022). AMBER 22, University of California, San Francisco.
  2. Case, D. A., K. Belfon, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, I. T.E. Cheatham, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, G. Giambasu, M. K. Gilson, H. Gohlke, A. W. Goetz, R. Harris, S. Izadi, K. K.-. jhala, A. Kovalenko, R. Krasny, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K. M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F. Pan, S. Pantano, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, N. Skrynnikov, J. Smith, J. Swails, R. C. Walker, J. Wang, L. Wilson, R. M. Wolf, X. Wu, D. M. York and P. A. Kollman (2020). AMBER 20, University of California, San Francisco.
  3. Case, D. A., I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, I. T.E. Cheatham, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, D. Ghoreishi, M. K. Gilson, H. Gohlke, A. W. Goetz, D. Greene, R. Harris, N. Homeyer, S. Izadi, A. Kovalenko, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D. J. Mermelstein, K. M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R. C. Walker, J. Wang, H. Wei, R. M. Wolf, X. Wu, L. Xiao, D. M. York and P. A. Kollman (2018). AMBER 18, University of California, San Francisco.

Editorials

  1. Miao Y*, Chang C-EA*, Zhu W*, & McCammon JA* (2023) Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning. Frontiers in Molecular Biosciences, 10.

Prior to KU:

Research Articles

  1. G Palermo, Y Miao, RC Walker, M Jinek, JA McCammon (2017), Proc Natl Acad Sci U S A, 114(28), 7260-7265.
    • UCSD News, Science Daily: “
  2. Caliman, A., Miao, Y., McCammon, J.A. (2017), Chemical Biology & Drug Design, DOI: 10.1111/cbdd.13053.
  3. Caliman, A., Miao, Y., McCammon, J.A. (2017), Protein Science, 26(6), 1150-1160.
  4. Pang, Y.T.#, Y. Miao#,*, Y. Wang* and J. A. McCammon* (2017) J Chemical Theory and Computation, 13(1): 9-19.
  5. Anderson, O. J., M. W. Risør, E. C. Poulsen, N. C. Nielsen, Y. Miao, J. J. Enghild and B. Schiøtt (2017), Biochemistry, 56 (4): 634–646.
  6. Grouleff, J., H. Koldsø, Y. Miao and B. Schiøtt (2017), ACS Chemical Neuroscience, 8 (3): 619–628.
  7. Miao Y.* and McCammon, J. A. (2016) Proc Natl Acad Sci U S A, 113(43): 12162–12167.
  8. Miao Y.*,#, Goldfeld D, Moo EV, Sexton PM, Christopoulos A, McCammon J. A.* and Valant C.*,# (2016) Proc Natl Acad Sci U S A 113(38): E5675–E5684.
    • UCSD News, Science Daily: “
    • Health Medicinet:
  9. G Palermo, Y Miao, RC Walker, M Jinek, JA McCammon (2016) ACS Central Science, 2(10): 756-763.
    • UCSD News: “
  10. YM Huang, Y Miao, J Munguia, L Lin, V Nizet, JA McCammon (2016), Protein Science, 25(8): 1430–1437.
  11. Huber, G., Y. Miao, S. Zhou, B. Li and J. A. McCammon (2016), J Chem Phys 144: 164107.
  12. Miao, Y.*, J. Baudry, J. C. Smith and McCammon JA (2015) Proteins-Structure Function and Bioinformatics 84: 501-514.
  13. Miao, Y.*, Feher V. and McCammon JA (2015) J Chemical Theory and Computation, 11(8): 3584-3595.
    • Cover Highlight: J. Andrew McCammon Festschrift special issue, J. Phys. Chem. B (2016) “Benzene ligand binding to T4 lysozyme, and corresponding free energy surface. The newest MD method from the McCammon group is Gaussian Accelerated Molecular Dynamics (GaMD), developed primarily by Dr. Yinglong Miao (Miao, Y.; et al. J. Chem. Theory Comput. 2015, 11,3584–3595). The method draws upon remarkable advances in theory and computers since the first protein MD simulation (McCammon, J.A.; et al. Nature 1977, 267,585–590). That first simulation covered 9 ps for a 58-residue protein with four explicit solvent molecules. GaMD allows simulations of systems containing hundreds of thousands of atoms, sampling configurations that evolve on millisecond timescales; corresponding free energy landscapes can be calculated by careful reweighting …”
    • Lecture, NBCR-TCBG joint workshop “Simulation-Based Drug Discovery” (2015)
    • Invited Talk, Snowmass Free Energy Calculation Workshop (2015)
    • Invited Talk, 2016 American Chemical Society Meeting (2016)
    • Invited Talk,Vertex Workshop on Free Energy Methods in Drug Design: Targeting Cancer” (2016)
  14. Miao, Y.#,*, F. Feixas#,*, C. Eun#,*and J. A. McCammon (2015) J. Comp. Chem., 36(20): 1536-1549.
  15. Kappel, K., Miao, Y.* and J. A. McCammon (2015). Quarterly Reviews of Biophysics, DOI: 10.1017/S0033583515000153.
  16. Miao, Y.*, Caliman A, McCammon JA (2015) Biophysical J., 108(7): 1796–1806.
  17. Caliman AD, Swift S, Wang Y, Miao, Y., McCammon JA (2015) Protein Science, 24(6): 1004-1012.
  18. Ellingson SR, Miao Y, Baudry J, Smith JC (2014) . J. Phys. Chem. B, 119(3): 1026–1034.
  19. Miao Y*, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA (2014) J Chemical Theory and Computation, 10(7): 2677–2689.
  20. Miao Y*, Nichols SE*, McCammon JA (2014) Phys Chem Chem Phys, 16(14): 6398 – 6406.
  21. Miao Y*, Nichols SE, McCammon JA (2014) Chem Bio Drug Des, 83(2): 237-246.
  22. Miao Y*, Nichols SE, Gasper PM, Metzger VT, McCammon JA (2013) Proc Natl Acad Sci U S A 110(27): 10982-10987.
    • Recommended by “Faculty of 1000
    • Invited Talk, 2015 American Chemical Society Meeting (2015)
    • Invited Talk, 95th AAAS Annual Meeting (2014)
    • Invited Talk, CECAM Workshop (2014)
    • Invited Talk, Beijing Computational Science Research Center (2014)
    • Invited Talk, UCSD Mathematics and Biochemistry-Biophysics Seminar (2013)
    • Invited Talk, 57th Annual Biophysical Society Meeting (2013)
  23. Sinko W., Miao Y., de Oliveira CAF, McCammon J. A. (2013) J. Phys. Chem. B, 117(42): 12759–12768. (Peter Wolynes Festschrift issue)
  24. Miao, Y., L. Hong, Z. Yi and J. C. Smith (2012), Eur. Phys. J. E, 36(7): 72.
    • Cover Highlight: “Topical Issue on Neutron Biological Physics”
  25. Miao, Y., Z. Yi, D. Glass, L. Hong, M. Tyagi, J. Baudry, N. Jain and J. C. Smith (2012), J. Am. Chem. Soc., 134(48): 19576-19579.
    • JACS Spotlights:
  26. Miao, Y., Z. Yi, C. Cantrell, D. Glass, J. Baudry, N. Jain and J. C. Smith (2012), Biophysical J., 103(10): 2167-2176.
    • Press release:
  27. Yi, Z., Y. Miao, N. Jain, J. Baudry and J. C. Smith (2012), J. Phys. Chem. B, 116(16):5028-5036.
  28. Singharoy A., H. Joshi, Y. Miao* and P. J. Ortoleva (2012), J. Phys. Chem. B, 116(29):8335-8336.
  29. Miao, Y. and J. Baudry (2011), Biophysical J., 101(6): 1493-1503.
    • Press release: “Supercomputer reveals new details behind drug-processing protein model”
  30. Miao, Y., J. E. Johnson and P. J. Ortoleva (2010), J. Phys. Chem. B, 114(34), 11181–11195.
  31. Miao, Y. and P. J. Ortoleva (2009), Biopoplymers, 93, 61.
    • Cover Highlight
  32. Pankavich, S., Z. Shreif, Y. Miao, P. J. Ortoleva (2009). J. Chem. Phys., 130(19): 194115.
  33. Pankavich, S., Y. Miao, J. Ortoleva, Z. Shreif, P. Ortoleva, J. Chem. Phys., 2008, 128, 234908.
    • Selected by Virtual Journal of Biological Physics Research
  34. Miao, Y. and P. J. Ortoleva, J. Comp. Chem., 2008, 30(3): 423-437.
  35. Sayyed-Ahmad, A., Y. Miao, and P. J. Ortoleva (2007), Communications in Computational Physics, 3(5): 1100.
  36. Huang, J., Q. Li, X. Wu, Y. Miao, J. Yang (2007), International Journal of Nanoscience, 5(6): 841-846.
  37. Y. Miao and P. J. Ortoleva (2006). J. Chem. Phys., 125, 214901.
    • Selected by Virtual Journal of Nanoscale Science & Technology
  38. Y. Miao and P. J. Ortoleva (2006). J. Chem. Phys., 125, 044901.
    • Selected by Virtual Journal of Biological Physics Research

Reviews and Book Chapters

  1. Y. Miao and J. A. McCammon (2017), David Dixon (editor), Annual Reports in Computational Chemistry, 13:231-278.
  2. Miao, Y.* and McCammon, J. A. (2016). Curr Opin Struct Biol 41: 83-89.
  3. Miao, Y.* and McCammon JA (2016) Molecular Simulation, 42: 1046-1055.
    • Cover Highlight
  4. Vural, D., X. Hu, B. Lindner, N. Jain, Y. Miao, X. Cheng, Z. Liu, L. Hong, J. C. Smith (2016), Biochimica et Biophysica Acta (BBA)-General Subjects, 1861 (1), 3638-3650.
  5. Singharoy A., H. Joshi, S. Cheluvaraja, Y. Miao, D. Brown and P. J. Ortoleva (2012), A. Navid (editor), Microbial Systems Biology: Methods and Protocols, Humana Press, USA, 881: 433-467.