All Publications

An MPER antibody neutralizes HIV-1 using germline features shared among donors

Nat Commun 10, 5389 (2019) doi:10.1038/s41467-019-12973-1
Lei Zhang, Adriana Irimia, Lingling He, Elise Landais, Kimmo Rantalainen, Daniel P. Leaman, Thomas Vollbrecht, Armando Stano, Daniel I. Sands, Arthur S. Kim, IAVI Protocol G Investigators, Pascal Poignard, Dennis R. Burton, Ben Murrell, Andrew B. Ward, Jiang Zhu, Ian A. Wilson & Michael B. Zwick

Development of a Potent and Protective Germline-Like Antibody Lineage Against Zika Virus in a Convalescent Human

Front. Immunol., 24 October 2019 | https://doi.org/10.3389/fimmu.2019.02424
Fei Gao, Xiaohe Lin, Linling He, Ruoke Wang, Han Wang, Xuanling Shi, Fuchun Zhang, Chibiao Yin, Linqi Zhang, Jiang Zhu and Lei Yu

Genetic and structural insights into broad neutralization of hepatitis C virus by human VH1-69 antibodies

Science Advances 02Jan 2019:eaav1882
Netanel Tzarum, Erick Giang, Leopold Kong, Linling He, Jannick Prentoe, Elias Augestad, Yuanzi Hua, Shaun Castillo, Georg M. Lauer, Jens Bukh, Jiang Zhu, Ian A. Wilson and Mansun Law

HIV-1 vaccine design through minimizing envelope metastability

Science Advances21 Nov 2018 : eaau6769
He L, Kumar S, Allen JJ, Huang D, Lin X, Mann CJ, Saye-Francisco KL, Copps J, Sarkar A, Blizard GS, Ozorowski G, Sok D, Crispin M, Ward AB, Burton DR, Wilson IA*, Zhu J* (*Co-corresponding authors)

Hidden lineage complexity of glycan-dependent HIV-1 broadly neutralizing antibodies uncovered by digital panning and native-like gp140 trimer

Frontiers in Immunology  2017 8
He, L., Lin, X., de Val, N., Saye-Francisco, K. L., Mann, C. J., Augst, R., Morris, C. D., Azadnia, P., Zhou, B., Sok, D., Ozorowski, G., Ward, A. B., et al.

Active evolution of memory B-cells specific to viral gH/gL/pUL128/130/131 pentameric complex in healthy subjects with silent human cytomegalovirus infection

Oncotarget  2017 8:73654-73669
Xia, L., Tang, A. M., Meng, W., Freed, D. C., He, L., Wang, D., Li, F., Li, L., Xiong, W., Gui, X., Schultz, R. D., Chen, H., et al.

Differential antibody responses to conserved HIV-1 neutralizing epitopes in the context of multivalent scaffolds and native-like gp140 trimers

mBio 2017 8:e00036-17
Morris, C. D., Azadnia, P., de Val, N., Vora, N., Honda, A., Giang, E., Saye-Francisco, K., Cheng, Y. S., Lin, X., Mann, C. J., Tang, J., Sok, D., et al.

Regulation of B-cell development and tolerance by different members of the miR-17∼92 family microRNAs

Nature Communications  2016 7
Lai, M. Gonzalez-Martin, A. Cooper, A. B. Oda, H. Jin, Hyun-Yong Shepherd, J. He, L. Zhu, Jiang Nemazee, David Xiao, Changchun

A prominent site of antibody vulnerability on HIV envelope incorporates a motif associated with CCR5 binding and its camouflaging glycans Immunity

Immunity  2016 45:31-45
Sok, D., Pauthner, M., Briney, B., Lee, J. H., Saye-Francisco, K. L., Hsueh, J., Ramos, A., Le, K. M., Jones, M., Jardine, J. G., Bastidas, R., Sarkar, A., et al.

Presenting native-like trimeric HIV-1 antigens with self-assembling nanoparticles

Nature Communications 2016 7
He, L. de Val, N. Morris, C. D. Vora, N. Thinnes, T. C. Kong, L. Azadnia, P. Sok, Devin Zhou, Bin Burton, Dennis Wilson, Ian Nemazee, David Ward, Andrew Zhu, Jiang

Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability

Nature Communications 2016 7
Kong, L. He, L. de Val, N. Vora, N. Morris, C. D. Azadnia, P. Sok, Devin Zhou, Bin Burton, Dennis Ward, Andrew Wilson, Ian Zhu, Jiang

Prevention of cell death by antibodies selected from intracellular combinatorial libraries

Nature Communications 2016
He, L. de Val, N. Morris, C. D. Vora, N. Thinnes, T. C. Kong, L. Azadnia, P. Sok, Devin Zhou, Bin Burton, Dennis Wilson, Ian Nemazee, David Ward, Andrew Zhu, Jiang

High-resolution longitudinal study of HIV-1 Env vaccine-elicited B cell responses to the virus primary receptor binding site reveals affinity maturation and clonal persistence

Journal of Immunology  2016 196:3729-3743
Wang, Y. Sundling, C. Wilson, R. O'Dell, S. Chen, Y. Dai, K. Phad, G. E. Zhu, Jiang Xiao, Y. Mascola, J. R. Hedestam, G. B. K. Wyatt, Richard Li, Y.

Key gp120 glycans pose roadblocks to the rapid development of VRC01-class antibodies in an HIV-1-infected Chinese donor

Immunity  2016 44:939-950
Kong, L. Ju, B. Chen, Y. He, L. Ren, L. Liu, J. Hong, K. Su, B. Wang, Z. Ozorowski, G. Ji, X. Hua, Y. Chen, Y. Deller, M. C. Hao, Y. Feng, Y. Garces, F. Wilson, R. Dai, K. O'Dell, S. McKee, K. Mascola, J. R. Ward, Andrew Wyatt, Richard Li, Y. Wilson, Ian Zhu, Jiang Shao, Y.

HIV-1 vaccine-elicited antibodies reverted to their inferred naive germline reveal associations between binding affinity and in vivo activation

Scientific Reports  2016 6
Dai, K., Khan, S. N., Wang, Y., He, L., Guenaga, J., Ingale, J., Sundling, C., O'Dell, S., McKee, K., Phad, G., Corcoran, M., Wilson, R., et al.

Rhesus macaque B-cell responses to an HIV-1 trimer vaccine revealed by unbiased longitudinal repertoire analysis

mBio 2015 6:e01375-15
Dai, K. He, L. Khan, S. N. O'Dell, S. McKee, K. Tran, K. Li, Y. Sundling, C. Morris, C. D. Mascola, J. R. Hedestam, G. B. K. Wyatt, Richard Zhu, Jiang

Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding

Scientific Reports 2015 5:12501
He, L. Cheng, Y. Kong, L. Azadnia, P. Giang, E. Kim, J. Wood, Malcolm R. Wilson, Ian Law, Mansun Zhu, Jiang

Computational tools for epitope vaccine design and evaluation

Current Opinion in Virology 2015 11:103-112
He, L. Zhu, Jiang

Transplanting supersites of HIV-1 vulnerability

PLoS One 2014 9:e99881
Zhou, T. Zhu, Jiang Yang, Y. Gorman, J. Ofek, G. Srivatsan, S. Druz, A. Lees, C. R. Lu, G. Soto, C. Stuckey, J. Burton, Dennis Koff, W. C. Connors, M. Kwon, P. D.

De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts

Proceedings of the National Academy of Sciences of the United States of America 2013 110:E4088-E4097
Zhu, Jiang Wu, X. Zhang, B. McKee, K. O'Dell, S. Soto, C. Zhou, T. Casazza, J. P. NISC Comparative Sequencing Program Mullikin, J. C. Kwong, P. D. Mascola, J. R. Shapiro, L.

Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies

Immunity 2013 39:245-258
Zhou, T. Zhu, Jiang Wu, X. Moquin, S. Zhang, B. Acharya, P. Georgiev, I. S. Altae-Tran, H. R. Chuang, G. Y. Joyce, M. G. Kwon, Y. D. Longo, N. S. Louder, M. K. Luongo, T. McKee, K. Schramm, C. A. Skinner, J. Yang, Y. Yang, Z. Zhang, Z. Zheng, A. Bonsignori, M. Haynes, B. F. Scheid, J. F. Nussenzweig, M. C. Simek, M. Burton, Dennis Koff, W. C. NISC Comparative Sequencing Program Mullikin, J. C. Connors, M. Shapiro, L. Nabel, G. J. Mascola, J. R. Kwong, P. D.

Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains

Proceedings of the National Academy of Sciences of the United States of America 2013 110:6470-6475
Zhu, Jiang Ofek, G. Yang, Y. P. Zhang, B. S. Louder, M. K. Lu, G. McKee, K. Pancera, M. Skinner, J. Zhang, Z. H. Parks, R. Eudailey, J. Lloyd, K. E. Blinn, J. Alam, S. M. Haynes, B. F. Simek, M. Burton, Dennis Koff, W. C. NISC Comparative Sequencing Program Mullikin, J. C. Mascola, J. R. Shapiro, L. Kwong, P. D.

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

Nature 2013 496:469-476
Liao, H. X. Lynch, R. Zhou, T. Gao, F. Alam, S. M. Boyd, S. D. Fire, A. Z. Roskin, K. M. Schramm, C. A. Zhang, Z. Zhu, Jiang Shapiro, L. Mullikin, J. C. Gnanakaran, S. Hraber, P. Wiehe, K. Kelsoe, G. Yang, G. Xia, S. M. Montefiori, D. C. Parks, R. Lloyd, K. E. Scearce, R. M. Soderberg, K. A. Cohen, M. Kamanga, G. Louder, M. K. Tran, L. M. Chen, Y. Cai, F. Chen, S. Moquin, S. Du, X. Joyce, M. G. Srivatsan, S. Zhang, B. Zheng, A. Shaw, G. M. Hahn, B. H. Kepler, T. B. Korber, B. T. M. Kwong, P. D. Mascola, J. R. Haynes, B. F. NISC Comparative Sequencing Program

Somatic populations of PGT135-137 HIV-1-neutralizing antibodies identified by 454 pyrosequencing and bioinformatics

Frontiers in Microbiology 2012 3:315
Zhu, Jiang O'Dell, S. Ofek, G. Pancera, M. Wu, X. Zhang, B. Zhang, Z. NISC Comparative Sequencing Program Mullikin, J. C. Simek, M. Burton, Dennis Koff, W. C. Shapiro, L. Mascola, J. R. Kwong, P. D.

Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing

Science 2011 333:1593-1602
Wu, X. Zhou, T. Q. Zhu, Jiang Zhang, B. S. Georgiev, I. Wang, C. Chen, X. J. Longo, N. S. Louder, M. McKee, K. O'Dell, S. Perfetto, S. Schmidt, S. D. Shi, W. Wu, L. Yang, Y. P. Yang, Z. Y. Yang, Z. J. Zhang, Z. H. Bonsignori, M. Crump, J. A. Kapiga, S. H. Sam, N. E. Haynes, B. F. Simek, M. Burton, Dennis Koff, W. C. Doria-Rose, N. A. Connors, M. Mullikin, J. C. Nabel, G. J. Roederer, M. Shapiro, L. Kwong, P. D. Mascola, J. R. NISC Comparative Sequencing Program

Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach

Proceedings of the National Academy of Sciences of the United States of America 2011 108:10133-10138
Zhu, Jiang Yu, Y. Ulbrich, M. H. Li, M. H. Isacoff, E. Y. Honig, B. Yang, J.

Crystal structure of human antibody 2909 reveals conserved features of quaternary structure-specific antibodies that potently neutralize HIV-1

Journal of Virology 2011 85:2524-2535
Changela, A. Wu, X. Yang, Y. Zhang, B. Zhu, Jiang Nardone, G. A. O'Dell, S. Pancera, M. Gorny, M. K. Phogat, S. Robinson, J. E. Stamatatos, L. Zolla-Pazner, S. Mascola, J. R. Kwong, P. D.

Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement

Journal of Molecular Biology 2010 397:835-851
Zhu, Jiang Cheng, L. Fang, Q. Zhou, Z. H. Honig, B.

Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics

Journal of Molecular Biology 2010 397:852-863
Cheng, L. Zhu, Jiang Hui, W. H. Zhang, X. Honig, B. Fang, Q. Zhou, Z. H.

Local quality assessment in homology models using statistical potentials and support vector machines

Protein Science  2007 16:1557-1568
Fasnacht, M., Zhu, J., Honig, B.

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

Proteins-Structure Function and Bioinformatics 2008 72:1171-1188
Zhu, J., Fan, H., Periole, X., Honig, B., Mark, A. E.

Loop modeling: sampling, filtering, and scoring

Proteins-Structure Function and Bioinformatics  2008 70:834-843
Soto, C. S., Fasnacht, M., Zhu, J., Forrest, L., Honig, B.