Publications

Peer-reveiwed Papers

May, A. J., Lella, M., Lindenberger, J., Berkman, A., Kumar, U., Liu, K., Dutta, M., Barr, M., Parks, R., Lu, X., Berry, M., Powell, A., Thompson, A. G., Sowdamini Nakka, S., França, C. T., Huang, X., Mrigwani, A., Song, K., Ilevbare, V., Sammour, S., Park, C. S., Devkota Adhikari, R., Devkota, P., Janowska, K., Liu, Y., Scapellato, G., Spence, T. N., Mansouri, K., Wiehe, K., Sullivan, N. J., Mason, R., Edwards, R. J., Saunders, K. O., Haynes, B. F., Acharya, P. (2026). Mechanistic and antigenic boundaries of Henipavirus and Parahenipavirus glycoproteins. Nat Commun, 17(1). https://doi.org/10.1038/s41467-026-74212-8

Do, H. N., McKenzie, J., & Gnanakaran, S. (2026). Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics. Scientific Reports. https://doi.org/10.1038/s41598-026-50650-8

Liu Q, Parsons RJ, Wiehe K, Edwards RJ, Saunders KO, Zhang P, Miao H, Tilahun K, Jones J, Chen Y, Hora B, Williams WB, Easterhoff D, Huang X, Janowska K, Mansouri K, Haynes BF, Acharya P, Lusso P. Acquisition of quaternary trimer interaction as a key step in the lineage maturation of a broad and potent HIV-1 neutralizing antibody. Structure. 2025 May 23:S0969-2126(25)00176-5. doi: 10.1016/j.str.2025.04.020. Epub ahead of print. PMID: 40412376.

 
Thakur B, Katte RH, Xu W, Janowska K, Sammour S, Henderson R, Lu M, Kwong PD, Acharya P. Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening. Nat Commun. 2025 May 17;16(1):4595. doi: 10.1038/s41467-025-59721-2. PMID: 40382314; PMCID: PMC12085566.
 
Do HN, Zhao M, Alam SM, Gnanakaran S. Dynamics and activation of membrane-bound B cell receptor assembly. Commun Biol. 2025 Feb 13;8(1):226. doi: 10.1038/s42003-025-07478-1. PMID: 39948415; PMCID: PMC11825855.
 

Katte RH, Xu W, Han Y, Hong X, Lu M. (2025) Inter-protomer opening cooperativity of envelope trimers positively correlates with HIV-1 entry stoichiometry. mBio. 2025 Apr 9;16(4):e0275424. doi: 10.1128/mbio.02754-24. Epub 2025 Feb 25. PMID: 39998217; PMCID: PMC11980385.https://journals.asm.org/doi/10.1128/mbio.02754-24

Watson, A. J. I., & Bartesaghi, A. (2024). Advances in cryo-ET data processing: meeting the demands of visual proteomics. Current Opinion in Structural Biology, 87, 102861. https://doi.org/10.1016/j.sbi.2024.102861

Vukovich, M. J., Shiakolas, A. R., Lindenberger, J., Richardson, R. A., Bass, L. E., Barr, M., Liu, Y., Go, E. P., Park, C. S., May, A. J., Sammour, S., Kambarami, C., Huang, X., Janowska, K., Edwards, R. J., Mansouri, K., Spence, T. N., Abu-Shmais, A. A., Manamela, N. P., Georgiev, I. S. (2024). Isolation and characterization of IgG3 glycan-targeting antibodies with exceptional cross-reactivity for diverse viral families. PLoS Pathogens, 20(9), e1012499. https://doi.org/10.1371/journal.ppat.1012499

Saunders, K. O., Counts, J., Thakur, B., Stalls, V., Edwards, R., Manne, K., Lu, X., Mansouri, K., Chen, Y., Parks, R., Barr, M., Sutherland, L., Bal, J., Havill, N., Chen, H., Machiele, E., Jamieson, N., Hora, B., Kopp, M., . . . Haynes, B. F. (2024). Vaccine induction of CD4-mimicking HIV-1 broadly neutralizing antibody precursors in macaques. Cell, 187(1), 79-94.e24. https://doi.org/10.1016/j.cell.2023.12.002

Parthasarathy, D., Pothula, K. R., Ratnapriya, S., Cervera Benet, H., Parsons, R., Huang, X., Sammour, S., Janowska, K., Harris, M., Sodroski, J., Acharya, P., & Herschhorn, A. (2024). Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted/founder sensitivity to broadly neutralizing antibodies. Nat Commun, 15(1), 7334. https://doi.org/10.1038/s41467-024-51656-4

López, C. A., Alam, S. M., Derdeyn, C. A., Haynes, B. F., & Gnanakaran, S. (2024). Influence of membrane on the antigen presentation of the HIV-1 envelope membrane proximal external region (MPER). Current Opinion in Structural Biology, 88, 102897. https://doi.org/https://doi.org/10.1016/j.sbi.2024.102897

Henderson R, Anasti K, Manne K, Stalls V, Saunders C, Bililign Y, Williams A, Bubphamala P, Montani M, Kachhap S, Li J, Jaing C, Newman A, Cain DW, Lu X, Venkatayogi S, Berry M, Wagh K, Korber B, Saunders KO, Tian M, Alt F, Wiehe K, Acharya P, Alam SM, Haynes BF. Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies. Nat Commun. 2024 Nov 3;15(1):9503. doi: 10.1038/s41467-024-53120-9. PMID: 39489734; PMCID: PMC11532496.
 
Lee M, Lu M, Zhang B, Zhou T, Katte R, Han Y, Rawi R, Kwong PD. HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state. Comput Struct Biotechnol J. 2024 Nov 12;23:4192-4204. doi: 10.1016/j.csbj.2024.11.020. PMID: 39640534; PMCID: PMC11617889.
 
Zhao M, Lopes LJS, Sahni H, Yadav A, Do HN, Reddy T, López CA, Neale C, Gnanakaran S. Insertion and Anchoring of the HIV-1 Fusion Peptide into a Complex Membrane Mimicking the Human T-Cell. J Phys Chem B. 2024 Dec 26;128(51):12710-12727. doi: 10.1021/acs.jpcb.4c05018. Epub 2024 Dec 13. PMID: 39670799.
 
Jin W, Zhou Y, Bartesaghi A. Accurate size-based protein localization from cryo-ET tomograms. J Struct Biol X. 2024 Jun 26;10:100104. doi: 10.1016/j.yjsbx.2024.100104. PMID: 39044770; PMCID: PMC11263962.

Huang, Q., Zhou, Y., Liu, H. F., & Bartesaghi, A. (2023). Multiple-image super-resolution of cryo-electron micrographs based on deep internal learning. Biol Imaging, 3, e3. https://doi.org/10.1017/S2633903X2300003X

Bennett, A. L., Edwards, R., Kosheleva, I., Saunders, C., Bililign, Y., Williams, A., Bubphamala, P., Manosouri, K., Anasti, K., Saunders, K. O., Alam, S. M., Haynes, B. F., Acharya, P., & Henderson, R. (2024). Microsecond dynamics control the HIV-1 Envelope conformation. Sci Adv, 10(5), eadj0396. https://doi.org/10.1126/sciadv.adj0396

Ao, Y., Grover, J. R., Gifford, L., Han, Y., Zhong, G., Katte, R., Li, W., Bhattacharjee, R., Zhang, B., Sauve, S., Qin, W., Ghimire, D., Haque, M. A., Arthos, J., Moradi, M., Mothes, W., Lemke, E. A., Kwong, P. D., Melikyan, G. B., & Lu, M. (2024). Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging. Cell Chem Biol, 31(3), 487-501.e487. https://doi.org/10.1016/j.chembiol.2023.12.017

Williams, W. B., Alam, S. M., Ofek, G., Erdmann, N., Montefiori, D. C., Seaman, M. S., Wagh, K., Korber, B., Edwards, R. J., Mansouri, K., Eaton, A., Cain, D. W., Martin, M., Hwang, J., Arus-Altuz, A., Lu, X., Cai, F., Jamieson, N., Parks, R., . . . Haynes, B. F. (2024). Vaccine induction of heterologous HIV-1-neutralizing antibody B cell lineages in humans. Cell, 187(12), 2919-2934.e2920. https://doi.org/10.1016/j.cell.2024.04.033

Weber, N., Hinks, B., Jensen, J., Lidahl, T., & Mendonça, L. (2023). Sample Preparation for In Situ Cryotomography of Mammalian Cells. J Vis Exp(202). https://doi.org/10.3791/65697

May, A. J., Pothula, K. R., Janowska, K., & Acharya, P. (2023). Structures of Langya Virus Fusion Protein Ectodomain in Pre- and Postfusion Conformation. Journal of Virology, 97(6), e0043323. https://doi.org/10.1128/jvi.00433-23

Liu, H. F., Zhou, Y., Huang, Q., Piland, J., Jin, W., Mandel, J., Du, X., Martin, J., & Bartesaghi, A. (2023). nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography. Nat Methods. https://doi.org/10.1038/s41592-023-02045-0

Huang, Q., Zhou, Y., & Bartesaghi, A. (2024). MiLoPYP: self-supervised molecular pattern mining and particle localization in situ. Nature Methods. https://doi.org/10.1038/s41592-024-02403-6

Henderson, R., Zhou, Y., Stalls, V., Wiehe, K., Saunders, K. O., Wagh, K., Anasti, K., Barr, M., Parks, R., Alam, S. M., Korber, B., Haynes, B. F., Bartesaghi, A., & Acharya, P. (2023). Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage. Nat Commun, 14(1), 2782. https://doi.org/10.1038/s41467-023-38108-1

Reviews

Dutta, M., & Acharya, P. (2024). Cryo-electron microscopy in the study of virus entry and infection [Review]. Frontiers in Molecular Biosciences, 11. https://doi.org/10.3389/fmolb.2024.1429180

Pre-publications

Revansiddha H. Katte, Junyu Liu, Yufan He, Bhishem Thakur, Xiao Huang, Jared J.Lindenberger, Wang Xu, Narendra Kumar Gonepudi, Yang Han, Katarzyna Janowska, Robert J. Edwards, Priyamvada Acharya, and Maolin Lu* (2026). Peptide inhibitors recognize prefusion viral fusion proteins with heterogeneous stoichiometry and rapid kinetics.bioRxiv 2026 Pages 2026.09.14.750718. https://doi.org/10.64898/2026.09.14.750718

Chen-Hao Yeh*, Stephen R. Walsh*, Ruth J. Parsons, Qianyi E. Zhang, Bhishem Thakur, Kijun Song, Kejun Liu, Hélène Fradin Kirshner, Elizabeth Van ltallie, Matthew Clark, William O. Hahn,0, Shengli Song, Liwen Lin, Hsin-I Huang, Jade Lugo, Alex Quan, Yue Xue, Yue Chen, Ryan Tuck, Katayoun Mansouri, Taylor N. Spence, Helena A. Laukaitis, Rob Parks, Margaret Barr, Elise Schweer, Nicholas Levering, Amanda Eaton, Shaunna Shen, Katarzyna Janowska, Victor Ilevbare, Graham Johnson, Peng Wang, Derek Cain, Aria Arus-Altuz, Elizabeth Donahue, Ilya Zhbannikov, Madison Berry, Sravani Venkatayogi, Joshua S. Martin Beem, Ollivier Hyrien, Pei-Chun Yu, Laura L. Polakowski, India Tindale, Claudio Yurdadon, Randy Burnham, Jessica Andriesen, Kshitij Wagh, Michael S. Seaman, Emmanuel B. Walter, Garnett Kelsoe, M. Juliana McElrath,Lawrence Corey, Kenneth Mayer, Persephone Borrow, Wilton Williams, Kevin O.Saunders, Kevin Wiehe, David Montefiori, Robert J. Edwards, Priyamvada Acharya*, Lindsey Baden* and Barton F. Haynes*. Priming of Multiple HIV Neutralizing B Cell Precursors in Humans. medRxiv. pages 2026.05.02.26352058 (2026) https://doi.org/10.64898/2026.05.02.26352058 

Do, H., Lella, M., Fulmali, D., Rajpara, N., Unarta, I., Johnson, A., Janowska, K., Laukaitis, H., Saunders, C., Edwards, R. J., Acharya, P., Sharma, A., Gnanakaran, S., & Henderson, R. Sequential HIV-1 fusion protein gates control the initiation of host cell entry. bioRxiv, 2026.2008.2006.743292. https://doi.org/10.64898/2026.08.06.743292

R. Pathirage, M. Dutta, R. J. Parsons, M. Lella, E. Atwood, Q.E. Zhang, A. May, A. Johnson, X. Huang, J. Flemming, U. Kumar, B.F. Marayati, M. Ariel Spurrier, C. Liu, J. Zhuo, K. Song, R. Devkota Adhikari, S. Sammour, V. Ilevbare, C. Abram, M. Diaz, A. Guzman, J. Rai, A.N. Skelly, M. P. Hogarty, K. Anasti, M. Purro, M. Lindsay, M. Alam, D. Weissman, A. Herschchorn, B. H. Hahn, G.M. Shaw, A. Sharma, N.S. Heaton, R.J Edwards, R. Henderson, T. Denny, K.O. Saunders, J. Siliciano, R. Siliciano, B.F. Haynes, K. Janowska, P. Acharya., An integrated workflow for structural virology with a 100 keV electron microscope. bioRxiv, 2025.2012.2008.693081 (2025).https://oi.org/10.64898/2025.12.08.693081

Harry M Williams, Wyatt A Curtis, Michal Haubner, Jakub Hruby, Marcel Drabbels, Ulrich J Lorenz. Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification. bioRxiv 2025.09.14.676144; https://doi.org/10.1101/2025.09.14.676144

Jamieson, P. J., Shen, X., Abu-Shmais, A. A., Wasdin, P. T., Janowska, K., Edwards, R. J., Scapellato, G., Richardson, S. I., Manamela, N. P., Liu, S., Barr, M., Gillespie, R. A., Mimms, J., Suryadevara, N., Sornberger, T. A., Zost, S., Parks, R., Flaherty, S., Janke, A. K., . . . Georgiev, I. S. (2025). Glycan-reactive antibodies isolated from human HIV-1 vaccine trial participants show broad pathogen cross-reactivity. bioRxiv, 2025.2001.2017.633475. https://doi.org/10.1101/2025.01.17.633475

Thakur, B., Alam, J., Cronin, K., Patel, P., Anasti, K., Kane, A. P., Hossain, A., Do, H., Mansouri, K., Spence, T. N., Edwards, R. J., Janowska, K., Lella, M., Cook, A., Saunders, K., Gnanakaran, S., Haynes, B. F., Acharya, P., & Alam, S. M. (2024). Anti-HIV-1 B cell antigen receptor signaling and structure. bioRxiv, 2024.2011.2015.623645. https://doi.org/10.1101/2024.11.15.623645

Editorials (affiliated PIs)

Gorfe AA, Gnanakaran S. Editorial. Curr Opin Struct Biol. 2024 Dec;89:102938. doi: 10.1016/j.sbi.2024.102938. Epub 2024 Oct 4. PMID: 39368258.