Next-Generation Sequencing

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.

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

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.

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.

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.

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

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.

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

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.