Tian-Hao Zhang

Research project:

Virus fitness landscape

Publications:

Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease – Zhang, T.H., Dai, L., Barton, J.P., Du, Y., Tan, Y., Pang, W., Chakraborty, A.K., Lloyd-Smith, J.O. and Sun, R., 2019. PLoS Genetics, doi:10.1371/journal.pgen.1009009.

High-throughput fitness profiling of Zika virus E protein reveals different roles for glycosylation during infection of mammalian and mosquito cells – Gong, D., Zhang, T.H., Zhao, D., Du, Y., Chapa, T.J., Shi, Y., Wang, L., Contreras, D., Zeng, G., Shi, P.Y. and Wu, T.T., 2018. iScience, 1, pp.97-111.

A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing – Zhang TH*, Wu NC*, and Sun R. A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing. BMC Genomics. 2016; 17: 108. doi: 10.1186/s12864-016-2388-9

Effects of Mutations on Replicative Fitness and Major Histocompatibility Complex Class I Binding Affinity Are Among the Determinants Underlying Cytotoxic-T-Lymphocyte Escape of HIV-1 Gag Epitopes – Du Y*, Zhang TH*, Dai L*, Zheng X*, Gorim AM, Oishi J, Wu TT, Yoshizawa JM, Li X, Yang OO, and Martinez-Maza O. Effects of Mutations on Replicative Fitness and Major Histocompatibility Complex Class I Binding Affinity Are Among the Determinants Underlying Cytotoxic-T-Lymphocyte Escape of HIV-1 Gag Epitopes. MBio. 2017; 8(6): 1-12. doi: 10.1128/mBio.01050-17

Emergence of integrase resistance mutations during initial therapy containing dolutegravir – Fulcher JA, Du Y, Zhang TH, Sun R, and Landovitz RJ. Emergence of integrase resistance mutations during initial therapy containing dolutegravir. Clinical Infectious Diseases. 2018; 67(5): 791-794. doi: 10.1093/cid/ciy228

Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design – Du Y, Xin L, Shi Y, Zhang TH, Wu NC, Dai L, Gong D, Brar G, Shu S, Luo J, Reiley W. Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design. Science. 201; 359(6373): 290-296. doi :10.1126/science.aan8806

Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing – Du Y, Chi X, Wang C, Jiang J, Kong F, Yan H, Wang X, Li J, Wu NC, Dai L, and Zhang TH. Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing. Scientific Reports. 2017; 7(1): 10168

HIV-1 epitopes presented by MHC class I types associated with superior immune containment of viremia have highly constrained fitness landscapes – Gorin AM, Du Y, Liu FY, Zhang TH, Ng HL, Hofmann C, Cumberland WG, Sun R, and Yang OO. HIV-1 epitopes presented by MHC class I types associated with superior immune containment of viremia have highly constrained fitness landscapes. PLoS Pathogens. 2017; 13(8): p.e1006541

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis – Du Y, Wu NC, Jiang L, Zhang T, Gong D, Shu S, Wu TT, Sun R. MBio. 2016; 7(6). pii: e01801-16. doi: 10.1128/mBio.01801-16

A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing – Zhang TH, Wu NC, Sun R. BMC Genomics. 2016; 17:108. doi: 10.1186/s12864-016-2388-9

Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment – Wu NC, Du Y, Le S, Young AP, Zhang TH, Wang Y, Zhou J, Yoshizawa JM, Dong L, Li X, Wu TT, Sun R. BMC Genomics. 2016; 17:46. doi: 10.1186/s12864-015-2358-7