Pharmacogenomics Group

Zhou Z^#,*, Wu J^#, Ren J, Chen W, Zhao W, Gu X, Chi Y, He Q, Yang B, Wu J*, Chen S*. TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection, Comput Struct Biotechnol J, 2021, 19:4510-4516. doi:10.1016/j.csbj.2021.08.016.
Zhao W^#, Yang J^#, Wu J, Cai G, Zhang Y, Haltom J, Su W, Dong M. Chen S, Wu J, Zhou Z*, Gu X*, CanDriS: posterior profiling of cancer-driving sites based on two-component evolutionary model, Brief Bioinform, 2021, In Press. doi:10.1093/bib/bbab131
Wu S^#, Haltom J^#, Zhao W, Yang J, Zhou Z*, Gu X*. Evolution and functional divergence of the ERBB receptor family, Pharmacogenomics, 2021, 22(8): 473-484. doi:10.2217/pgs-2020-0158
Gu J*, Zhou Z*, Wang Y*. Editorial: Evolutionary Mechanisms of Infectious Diseases, Front Microbiol, 2021, 12:667561. doi:10.3389/fmicb.2021.667561
Wang H^#, Ding Y^#, Chen Y^#, Jiang J, Chen Y, Lu J, Kong M, Mo F, Huang Y, Zhao W, Fang P, Chen X, Teng X, Xu N, Lu Y, Yu X, Li Z, Zhang J, Wang H, Bao X, Zhou D, Chi Y, Zhou T, Zhou Z*, Chen S*, Teng L*. A novel genomic classification system of gastric cancer via integrating multidimensional genomic characteristics, Gastric Cancer, 2021, In Press, doi:10.1007/s10120-021-01201-9
Lu J^#, Ding Y^#, Chen Y^#, Jiang J, Chen Y, Huang Y, Wu M, Li C, Kong M, Zhao W, Wang H, Zhang J, Li Z, Lu Y, Yu X, Jin K, Zhou D, Zhou T, Zhou Z*, Wang H*, Teng L*, Whole-exome sequencing of alpha-fetoprotein producing gastric carcinoma (AFPGC) reveals genomic profile and therapeutic targets, Nat Commun, 2021, 12:3946. doi:10.1038/s41467-021-24170-0
Zhao WB, Shen Y, Liu WH, Li YM, Jin SJ, Xu YC, Pan LQ, Zhou Z*, Chen SQ*, Soluble Expression of Fc-Fused T Cell Receptors Allows Yielding Novel Bispecific T Cell Engagers, Biomedicines, 2021, 9(7):790. doi:10.3390/biomedicines9070790
Wei R, Li P, He F, Wei G, Zhou Z, Su Z*, Ni T*, Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers, Brief Bioinform, 2021, 22(3): bbaa066. doi:10.1093/bib/bbaa066
Qi M^#, Zhang B^#, Jiang L, Xu S, Dong C, Du YL, Zhou Z, Huang L, Xu Z, Lian J*, PCR & Go: A Pre-installed Expression Chassis for Facile Integration of Multi-Gene Biosynthetic Pathways, Front Bioeng Biotechnol, 2021, 8:613771. doi:10.3389/fbioe.2020.613771
Yang X^#, Fan J^#, Wu Y^#, Ma Z, Huang J, Zhang Y, Zhou Z, Mo F, Liu X, Yuan H, Xu Y, Pan L*, Chen S*. Synthetic multiepitope neoantigen DNA vaccine for personalized cancer immunotherapy. Nanomedicine, 2021, 37:102443. doi:10.1016/j.nano.2021.102443
Fan J, Zhuang X, Yang X, Xu Y, Zhou Z, Pan L*, Chen S*. A multivalent biparatopic EGFR-targeting nanobody drug conjugate displays potent anticancer activity in solid tumor models. Signal Transduct Target Ther, 2021, 6(1):320. doi:10.1038/s41392-021-00666-5.
Bai X, Liu W, Jin S, Zhao W, Xu Y, Zhou Z, Chen S*, Pan L*. Facile Generation of Potent Bispecific Fab via Sortase A and Click Chemistry for Cancer Immunotherapy. Cancers, 2021, 13:4540. doi:10.3390/cancers13184540.

Wu J, Chen W, Zhou J, Zhao W, Sun Y, Zhu H, Yao P, Chen S, Jiang J*, Zhou Z*, COVIEdb: A database for potential immune epitopes of coronaviruses, Front Pharmacol, 2020, 11:572249 doi:10.3389/fphar.2020.572249
Yang X, Ma Z, Zhang Y, Wu J, Huang J, Zhao W, Mo F, Lin Z, Xu Y, Zhou Z*, Chen S*. Anti-tumor immune response varies among individuals: A gene expression profiling of mouse melanoma. Int Immunopharmacol, 2020, 80:106211. doi:10.1016/j.intimp.2020.106211
Zhao W, Wu J, Chen S, Zhou Z*, Shared neoantigens: ideal targets for off-the-shelf cancer immunotherapy. Pharmacogenomics, 2020, 21(9): 637-645. doi:10.2217/pgs-2019-0184
Zhang Y, Wu S, Zhuang X, Weng G, Fan J, Yang X, Xu Y, Pan L, Hou T, Zhou Z*, Chen S*. Identification of an Activating Mutation in the Extracellular Domain of HER2 Conferring Resistance to Pertuzumab. Onco Targets Ther, 2019, 12:11597-11608. doi:10.2147/OTT.S232912
Liu W^#, Zhao W^#, Bai X, Jin S, Li Y, Qiu C, Pan L, Ding D, Xu Y, Zhou Z*, Chen SQ*. High antitumor activity of Sortase A-generated anti-CD20 antibody fragment drug conjugates. Eur J Pharm Sci, 2019, 134:81-92. doi:10.1016/j.ejps.2019.04.015
Wu J, Wang W, Zhang J, Zhou B, Zhao W, Su Z, Gu X, Wu J, Zhou Z*, Chen S*. DeepHLApan: A deep learning approach for neoantigen prediction considering both HLA-peptide binding and immunogenicity. Front Immunol, 2019, 10: 2559. doi:10.3389/fimmu.2019.02559
Shen Y, Wei X, Jin S, Wu Y, Zhao W, Xu Y, Pan L, Zhou Z, Chen S*, TCR-Mimic Antibody-Drug Conjugates Targeting Intracellular Tumor-Specific Mutant Antigen KRAS G12V Mutation, Asian J Pharm Sci, 2020, 15(6): 777-785. doi:10.1016/j.ajps.2020.01.002
Fang Y^#, Mo F^#, Shou J^#, Wang H, Luo K, Zhang S, Han N, Li H, Ye S, Zhou Z, Chen R, Chen L, Liu L, Wang H, Pan H*, Chen S*, A pan-cancer clinical study of personalized neoantigen vaccine monotherapy in treating patients with various types of advanced solid tumors, Clin Cancer Res, 2020, 26(17):4511-4520. doi:10.1158/1078-0432.CCR-19-2881
Qiu CX, Bai XF, Shen Y, Zhou Z, Pan LQ, Xu YC, Zhao WB*, Chen SQ*, Specific Inhibition of Tumor Growth by T Cell Receptor-Drug Conjugates Targeting Intracellular Cancer-Testis Antigen NY-ESO-1/LAGE-1, Bioconjug Chem, 2020, 31(12):2767-2778. doi:10.1021/acs.bioconjchem.0c00548
He F, Wei R, Zhou Z, Huang L, Wang Y, Tang J, Zou Y, Shi L, Gu X, Davis MJ, Su Z*. Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes. Sci Rep, 2019, 9:8205. doi:10.1038/s41598-019-44489-5
Zhou J^#, Zhao WY^#, Wu JC, Lu J, Ding YF, Wu SS, Wang HY, Ding D, Mo F, Zhou Z, Teng LS*, Chen SQ*. Neoantigens Derived from Recurrently Mutated Genes as Potential Immunotherapy Targets for Gastric Cancer. Biomed Res Int, 2019, 2019: 8103142. doi:10.1155/2019/8103142
Shen Y, Li YM, Zhou JJ, Zhou Z, Xu YC, Zhao WB*, Chen SQ*. The Antitumor Activity of TCR-Mimic Antibody-Drug Conjugates (TCRm-ADCs) Targeting the Intracellular Wilms Tumor 1 (WT1) Oncoprotein. Int J Mol Sci, 2019, 20(16): 3912. doi:10.3390/ijms20163912
Sharma A, Merritt E, Hu X, Cruz A, Jiang C, Sarkodie H, Zhou Z, Malhotra J, Riedlinger GM, De S*. Non-Genetic Intra-Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics in Lung Tumors. Cell Rep, 2019, 29:2164-2174 e2165. doi:10.1016/j.celrep.2019.10.045

Zhao WB^#, Qiu CX^#, Shen Y, Liu WH, Zhou J, Xu YC, Zhou Z*, Chen SQ*. In situ quantitative bioanalysis of monomethyl auristatin E-conjugated antibody-drug conjugates by flow cytometry. Eur J Pharm Sci, 2018, 120:89-95. doi:10.1016/j.ejps.2018.04.046
Wu J, Zhao W, Zhou B, Su Z, Gu X, Zhou Z*, Chen SQ*. TSNAdb: a database for tumor-specific neoantigens from immunogenomics data analysis. Genomics Proteomics Bioinformatics. 2018, 16(4):276-282. doi:10.1016/j.gpb.2018.06.003
Ahmed S, Zhou J, Zhou Z*, Chen SQ*. Genetic Polymorphisms and in silico Mutagenesis analyses of CYP2C9, CYP2D6 and CYPOR Genes in Pakistani Population. Genes. 2018, 9(10):514. doi:10.3390/genes9100514
Zhou Z^#, Lyu X^#, Wu J, Yang X, Wu S, Zhou J, Gu X, Su Z*, Chen SQ*. TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection. R Soc Open Sci. 2017, 4: 170050. doi:10.1098/rsos.170050
Zhou Z^#, Wu S^#, Lai J, Shi Y, Qiu C, Chen Z, Wang Y, Gu X, Zhou J*, Chen SQ*: Identification of trunk mutations in gastric carcinoma: a case study. BMC Med Genomics, 2017, 10(1):49. doi:10.1186/s12920-017-0285-y
Zhou Z^#, Zou Y^#, Liu G, Zhou J, Wu J, Zhao S, Su Z*, Gu X*. Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis. Oncotarget, 2017, 8(35):58835-58846. doi:10.18632/oncotarget.19371
Wu JC, Lv XZ, Lei YJ, Zhou J, Zhou Z*, Chen SQ*. Analysis of online Mendelian inheritance in man. Chinese Journal of Biochemical Pharmaceutics, 2017, 37(3):1-4.
Lai J, Wang Y, Wu SS, Ding D, Sun ZY, Zhang Y, Zhou J, Zhou Z, Xu YC, Pan LQ* and Chen SQ*. Elimination of melanoma by sortase A-generated TCR-like antibody-drug conjugates (TL-ADCs) targeting intracellular melanoma antigen MART-1. Biomaterials. 2018, 178:158-169. doi:10.1016/j.biomaterials.2018.06.017
Zhang D, Zhou LF, Lei YJ, Zhou Z, Zhou J*, Chen SQ*. Investigation of diethylstilbestrol residue level in human urine samples by a specific monoclonal antibody. Environ Sci Pollut Res Int, 2017, 24(8):7042-7050. doi:10.1007/s11356-017-8405-y
Lv LX^#, Zhou ZX^#, Zhou Z, Zhang LJ, Yan R, Zhao Z, Yang LY, Bian XY, Jiang HY, Li YD, Sun YS, Xu QQ, Hu GL, Guan WJ*, Li YQ*, Hispidin induces autophagic and necrotic death in SGC-7901 gastric cancer cells through lysosomal membrane permeabilization by inhibiting tubulin polymerization, Oncotarget, 2017, 8(16): 26992-27006. doi:10.18632/oncotarget.15935

Zhou Z, Sun N, Wu S, Li YQ*, Wang Y*. Genomic data mining reveals a rich repertoire of transport proteins in Streptomyces. BMC Genomics, 2016, 17(Suppl 7):510. doi:10.1186/s12864-016-2899-4
Wu SS, Zhou Z*, Chen SQ*, Analysis of Somatic Mutations in Membrane Proteins of Tumor Cells. Chinese Journal of Biochemical Pharmaceutics, 2015, 35(11):1-4.
Wei XY, Zhou Z, Chen SQ*, Personalized antibody-drug conjugates: a means of tumor precision medicine. Chinese Journal of Biochemical Pharmaceutics, 2016, 36(1): 1-6.
Lai J, Zhou Z, Tang XJ, Gao ZB, Zhou J*, Chen SQ*. A Tumor-Specific Neo-Antigen Caused by a Frameshift Mutation in BAP1 Is a Potential Personalized Biomarker in Malignant Peritoneal Mesothelioma. Int J Mol Sci 2016, 17(5):739. doi:10.3390/ijms17050739
Xu Y, Zhou J, Zhou Z, Chen SQ*, Bibliometric analysis of antibody-drug conjugates. Chinese Journal of Biochemical Pharmaceutics, 2016, 36(6): 10-14.
Ahmed S, Zhou Z, Zhou J, Chen SQ*, Pharmacogenomics of Drug Metabolizing Enzymes and Transporters: Relevance to Precision Medicine. Genomics Proteomics Bioinformatics, 2016, 14(5): 298–313. doi:10.1016/j.gpb.2016.03.008
Shen L, Liu G, Zou Y, Zhou Z, Su Z, Gu X*. The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species. PLoS One, 2015,10(2): e0116872. doi:10.1371/journal.pone.0116872

Zhou Z, Zhou J, Su Z*, Gu X*. Asymmetric evolution of human transcription factor regulatory networks. Mol Biol Evol, 2014, 31(8):2149-2155. doi:10.1093/molbev/msu163
Zhou Z, Li YD*, Sun N, Sun ZH, Lv LX, Wang Y, Shen L, Li YQ*. Function and Evolution of the two forms of SecDF homologs in Streptomyces. PLoS One, 2014,9(8):e105237. doi:10.1371/journal.pone.0105237
Lilburn TG, Cai H, Gu J, Zhou Z, Wang Y*. Exploring systems affected by the heat shock response in Plasmodium falciparum via protein association networks. Int J Comput Biol Drug Des, 2014, 7(4): 369-383.
Li Y*, Zhang W, Zheng D, Zhou Z, Feng L, Liang X, Yu W, Zhou J, Chen J*, Lin Z*, Genomic Evolution of Saccharomyces cerevisiae under Chinese Rice Wine Fermentation. Genome Biol Evol, 2014, 6(9):2516-2526. doi:10.1093/gbe/evu201
Gu X*, Zou Y, Su Z, Huang W, Zhou Z, Arendsee Z, Zeng Y. An Update of DIVERGE Software for Functional Divergence Analysis of Protein Family. Mol Biol Evol, 2013, 30(7):1713-1719. doi:10.1093/molbev/mst069
Mao XM, Sun N, Wang F, Luo S, Zhou Z, Feng WH, Huang FL, Li YQ*: Dual Positive Feedback Regulation of Protein Degradation of an ECF (extra-cytoplasmic function) Sigma Factor for Cell Differentiation in Streptomyces coelicolor. J Biol Chem, 2013, 288(43):31217-31228. doi:10.1074/jbc.M113.491498
Lilburn TG, Cai H, Gu J, Zhou Z, Wang Y*. Network Analysis Reveals Complex Interactions in Heat Shock Response in the Malaria Parasite. In: 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shanghai, China: IEEE Computer Society, 2013, 11-16.

Zhou Z, Gu J, Li YQ*, Wang Y*. Genome plasticity and systems evolution in Streptomyces. BMC Bioinformatics, 2012, 13(Suppl 10):S8. doi:10.1186/1471-2105-13-S10-S8
Zhou Z, Gu J, Du YL, Li YQ*, Wang Y*. The -omics era- toward a systems-level understanding of Streptomyces. Curr Genomics, 2011, 12(6):404-416. doi:10.2174/138920211797248556
Zhou Z, Li Q, Tudyk J, Li YQ, Wang Y. ECF sigma factor-associated regulatory networks in Streptomyces colicolor A3(2). In: 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), San Antonio, Texas, USA: IEEE Computer Society, 2011, 182-185. doi:10.1109/GENSiPS.2011.6169475
Cai H#, Zhou Z#, Gu J*, Wang Y*. Comparative genomics and systems biology of malaria parasites Plasmodium. Curr Bioinform, 2012, 7(4):478-489. doi:10.2174/157489312803900965
Du YL, Li SZ, Zhou Z, Chen SF, Fan WM, Li YQ*. The pleitropic regulator AdpAch is required for natamycin biosynthesis and morphological differentiation in Streptomyces chattanoogensis. Microbiology, 2011, 157(Pt 5):1300-1311. doi:10.1099/mic.0.046607-0
Lilburn TG, Cai H, Zhou Z, Wang Y*. Protease-associated cellular networks in malaria parasite Plasmodium falciparum. BMC Genomics, 2011, 12(Suppl 5):S9. doi:10.1186/1471-2164-12-S5-S9
Mao XM, Zhou Z, Hou XP, Guan WJ, Li YQ*. Reciprocal regulation between SigK and differentiation programs in Streptomyces coelicolor. J Bacteriol, 2009, 191(21):6473-6481. doi:10.1128/JB.00875-09
Mao XM, Zhou Z, Cheng LY, Hou XP, Guan WJ, Li YQ*. Involvement of SigT and RstA in the differentiation of Streptomyces coelicolor. FEBS Lett, 2009, 583(19):3145-3150. doi:10.1016/j.febslet.2009.09.025
Li YD, Zhou Z, Lv LX, Hou XP, Li YQ*. New approach to achieve high-level secretory expression of heterologous proteins by using Tat signal peptide. Protein Pept Lett, 2009, 16(6):706-710. doi:10.2174/092986609788490096
Li YD, Xie ZY, Du YL, Zhou Z, Mao XM, Lv LX, Li YQ*. The rapid evolution of signal peptides is mainly caused by relaxed selection on non-synonymous and synonymous sites. Gene, 2009, 436(1-2):8-11. doi:10.1016/j.gene.2009.01.015

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