Research

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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

Scientific Reports 2015 5:12501
Linling He, Yushao Cheng, Leopold Kong, Parisa Azadnia, Erick Giang, Justin Kim, Malcolm R. Wood, Ian A. Wilson, Mansun Law, Jiang Zhu

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

mBio 2015 6:e01375-15
Kaifan Dai, Linling He, Salar N. Khan, Sijy O'Dell, Krisha McKee, Karen Tran, Yuxing Li, Christopher Sundlilng, Charles D. Morris, John R. Macola, Gunilla B. Karlsson Hdestam, Richard T. Wyatt, Jiang Zhu

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

Scientific Reports  2016 6
Kaifan Dai, Salar N Khan, Yimeng Wang, Linling He, Javier Guenaga, Jidnyasa Ingale, Christopher Sundling, Sijy O'Dell, Krisha McKee, Ganesh Phad, Martin Corcoran, Richard Wilson, John R Mascola, Jiang Zhu, Yuxing Li, Gunilla B Karlsson Hedestam & Richard T Wyatt

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
Leopold Kong, Bin Ju, Yajing Chen, Linling He, Li Ren, Jiandong Liu, Kunxue Hong, Bin Su, Zheng Wang, Gabriel Ozorowski, Xiaolin Ji, Yuanzi Hua, Yanli Chen, Marc C. Deller, Yanling Hao, Yi Feng, Fernando Garces, Richard Wilson, Kaifan Dai, Siji O'Dell, Krishna McKee, John R. Mascola, Andrew B. Ward, Richard T. Wyatt, Yuxing Li, Ian A. Wilson, Jiang Zhu Yiming Shao

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
Yimeng Wang, Christopher Sundling, Richard Wilson, Sijy O-Dell, Yajing Chen, Kaifan Dai, Ganesh E. Phad, Jiang Zhu, Yongli Xiao, John R. Mascola, Ginilla B. Karlsson Hedestam, Richard T. Wyatt and Yuxing Li

Prevention of cell death by antibodies selected from intracellular combinatorial libraries

Chemistry and Biology
Jia Xie, Kyungmoo Yea, Hongkai Zhang, Brian Moldt, Linling He, Jiang Zhu, Richard A. Lerner

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

Nature Communications 2016 7
Leopold Kong, Linling He, Natalia de Val, Nemil Vora, Charles D. Morris, Parisa Azadnia, Devin Sok, Bin Zhou, Dennis R. Burton, Andrew B. Ward, Ian A. Wilson & Jiang Zhu

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

Nature Communications 2016 7
Linling He, Natalia de Val, Charles D. Morris, Nemil Vora, Therese C. Thinnes, Leopold Kong, Parisa Azadnia, Devin Sok, Bin Zhou, Dennis R. Burton, Ian A. Wilson, David Nemazee, Andrew B. Ward & Jiang Zhu

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

Immunity  2016 45:31-45
Devin Sok, Matthias Pauthner, Bryan Briney, Jeong Hyun Lee, Karen L. Saye-Francisco, Jessica Hsueh, Alejjandra Ramos, Khoa M. Le, Meaghan Jones, Joseph G. Jardine, Raiza Bastidas, Anita Sarkar, Chi-Hui Liang, Sachin S. Shivatare, Chung-yi Wu, William R. Schief, Chi-Huey Wong, Ian A. Wilson, Andrew B. Ward, Jiang Zhu, Pascal Poignard, Dennis R. Burton

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

Nature Communications  2016 7
Maoyi Lai, Alicia Gonzalez-Martin, Anthony B. Cooper, Hiroyo Oda, Huyn Yong Jin, Jovan Shepherd, Linling He, Jiang Zhu, David Nemazee & Changchun Xiao

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
Charles D. Morris, Parisa Azadnia, Natalia de Val, Nemil Vora, Andrew Honda, Erick Giang, Karen Saye-Francisco, Yushao Cheng, Xiaohe Lin, Colin J. Mann, Jeffrey Tang, Devin Sok, Dennis R. Burton, Mansun Law, Andrew B. Ward, Linling He, Jiang Zhu

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
Lin Xia, Aimin Tang, Weixu Meng, Daniel C. Freed. Linling He, Dai Wang, Fengsheng Li, Xun Gui, Robbie D. Schultz, Haotai Chen, Xi He, Ryan Swoyer, Sha Ha, Yaping Liu, Charles D. Morris, Ming Wang, Qinjian Zhao, Wenxin Luo, Ningshao Xia, Amy S. Espeseth, Daria J. Hazuda, Richard E. Barrett, Ningyan Zhang, Jiang Zhu, Tong-Ming Fu and Zhiquiang An

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
Linling He, Xiaohe Lin, Natalia deVal, Karen L. Saye-Francisco, Colin J. Mann, Ryan Augst, Charles D. Morris, Parisa Azadnia, Bin Zhou, Devin Sok, Gabriel Ozorowski, Andrew B. Ward, Dennis R. Burton and Jiang Zhu

HIV-1 vaccine design through minimizing envelope metastability

Science Advances21 Nov 2018 : eaau6769
Linling He, Sonu Kumar, Joel D. Allen, Deli Huang, Xiaohe Lin, Colin J. Mann, Karen L. Saye-Francisco, Jeffrey Copps, Anita Sarkar, Gabrielle S. Blizard, Gabriel Ozorowski, Devin Sok, Max Crispin, Andrew B. Ward, David Nemazee, Dennis R. Burton, Ian A. Wilson and Jiang Zhu

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

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

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, Linling 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

Proof of concept for rational design of hepatitis C virus E2 core nanoparticle vaccines

Science Advances 15 April 2020; Vol 6 No. 16, eaaz6225; DOI 10 1126/sciadv aaz6225
Linling He, Netanel Tzarum, Xiaohe Lin, Benjamin Shapero, Cindy Sou, Colin J. Mann, Armando Stano, Lei Zhang, Kenna Nagy, Erick Giang, Mansun Law, Ian A Wilson, and Jiang Zhu

Functional convergence of a germline-encoded neutralizing antibody response in rhesus macaques immunized with HCV envelope glycoproteins

Chen et al., 2021, Immunity 54, 1-16; https://doi.org/10.1016/j.immuni.2021.02.013
Fang Chen, Netanel Tzarum, Xiaohe Lin, Erick Giang, Rodrigo Velazquez-Moctezume, Elias H. Augestad, Kenna Nagy, Linling He, Mayda Hernandez, Mallorie E. Fouch, Ariadna Grinyo, Deborah Chavez, Benjamin J. Doranz, Jannick Prentoe, Robyn L. Stanfield, Robert Lanford, Ian A. Wilson, Jiang Zhu, Mansun Law

Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimers as HIV-1 vaccine candidates

Nature Communications Volume 14, Article number: 1985 (2023)
Yi-Nan Zhang, Jennifer Paynter, Aleksandar Antanasijevic, Joel D. Allen, Mor Eldad, Yi-Zong Lee, Jeffrey Copps, Maddy L. Newby, Linling He, Deborah Chavez, Pat Frost, Anna Goodroe, John Dutton, Robert Lanford, Christopher Chen, Ian A. Wilson, Max Crispin, Andrew B. Ward & Jiang Zhu