Peer-reveiwed Papers

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

Lee, M., Lu, M., Zhang, B., Zhou, T., Katte, R., Han, Y., Rawi, R., & Kwong, P. D. (2024). HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state. bioRxiv, 2024.2007.2015.603531. https://doi.org/10.1101/2024.07.15.603531

Jin, W., Zhou, Y., & Bartesaghi, A. (2024). Accurate size-based protein localization from cryo-ET tomograms. Journal of Structural Biology: X, 100104.

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

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

Do, H. N., Zhao, M., Alam, S. M., & Gnanakaran, S. (2024). Dynamics and Activation of Membrane-Bound B Cell Receptor Assembly. bioRxiv, 2024.2007.2010.602784. https://doi.org/10.1101/2024.07.10.602784

Thakur, B., Katte, R. H., Xu, W., Janowska, K., Sammour, S., Henderson, R., Lu, M., Kwong, P. D., & Acharya, P. (2024). Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening. bioRxiv, 2024.2009.2014.613076. https://doi.org/10.1101/2024.09.14.613076

Williams, W. B., Alam, S. M., Ofek, G., Erdmann, N., Montefiori, D., Seaman, M. S., Wagh, K., Korber, B., Edwards, R. J., Mansouri, K., Eaton, A., Cain, D. W., Martin, M., Parks, R., Barr, M., Foulger, A., Anasti, K., Patel, P., Sammour, S., . . . Haynes, B. F. (2023). Vaccine Induction of Heterologous HIV-1 Neutralizing Antibody B Cell Lineages in Humans. medRxiv, 2023.2003.2009.23286943. https://doi.org/10.1101/2023.03.09.23286943

Ratnapriya, S., Pothula, K. R., Dam, K. A., Parthasarathy, D., Benet, H. C., Parsons, R., Huang, X., Sammour, S., Janowska, K., Harris, M., Ahmed, S., Sacco, S., Sodroski, J., Bridges, M. D., Hubbell, W. L., Acharya, P., & Herschhorn, A. (2023). Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted / founder sensitivity to broadly neutralizing antibodies. bioRxiv. https://doi.org/10.1101/2023.09.13.557082

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, D., Lu, X., Venkatayogi, S., Berry, M., Wagh, K., Korber, B., . . . Haynes, B. F. (2023). Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies. bioRxiv. https://doi.org/10.1101/2023.12.15.571700