Publication.

EditedBook

  • Wu J, Zhou Z*. TSNAD and TSNAdb: The Useful Toolkit for Clinical Application of Tumor-Specific Neoantigens. In: Reche, P.A. (eds) Computational Vaccine Design. Methods in Molecular Biology, 2023, 2673: 167-174. Humana, New York, NY. doi:10.1007/978-1-0716-3239-0_11

Refereed Publications

#: Equal contributor; *: Corresponding author

2023

  • Wu J, Chen W, Zhou Y, Chi Y, Hua X, Wu J, Gu X, Chen S, Zhou Z*. TSNAdb v2.0: the Updated Version of Tumor-specific Neoantigen Database. Genomics Proteomics Bioinformatics, 2023, in press. doi:10.1016/j.gpb.2022.09.012
  • Zhou B, Zhou H, Zhang X, Xu X, Chai Y, Zheng Z, Kot AC, Zhou Z*. TEMPO: A transformer-based mutation prediction framework for SARS-CoV-2 evolution. Comput Biol Med, 2023, 152:106264. doi: 10.1016/j.compbiomed.2022.106264
  • Zhou Z*, Gu J*, Wang Y*. Editorial: Evolutionary Mechanisms of Infectious Diseases, Volume II, Front Microbiol, 2023, 14:1192566. doi:10.3389/fmicb.2023.1192566
  • Chen Y#, Cai G#, Jiang J#, He C, Chen Y, Ding Y, Lu J, Zhao W, Yang Y, Zhang Y, Wu G, Wang H, Zhou Z, Teng L*. Proteomic profiling of gastric cancer with peritoneal metastasis identifies a protein signature associated with immune microenvironment and patient outcome. Gastric Cancer. 2023, 26:504-516. doi:10.1007/s10120-023-01379-0
  • Cai G, Zhao W, Zhou Z*, Gu X*. MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis. Brief Bioinform, 2023 24(4): bbad207. doi: 10.1093/bib/bbad207
  • Zhu X, Zhao W, Zhou Z*, Gu X*. Unraveling the Drivers of Tumorigenesis in the Context of Evolution: Theoretical Models and Bioinformatics Tools. J Mol Evol, 2023, 91:405-423.  doi:10.1007/s00239-023-10117-0
  • Zhang X, Wu J, Baeza J, Gu K, Zheng Y*, Chen S*, Zhou Z*. DeepTAP: an RNN-based method of TAP-binding peptide prediction in the selection of tumor neoantigens. Comput Biol Med, 2023, 164:107247. doi:10.1016/j.compbiomed.2023.107247
  • Zhou Y#, Wu J#, Yao S, Xu Y, Zhao W, Tong Y*, Zhou Z*. DeepCIP: a multimodal deep learning method for the prediction of internal ribosome entry sites of circRNAs. Comput Biol Med, 2023, 164:107288. doi:10.1016/j.compbiomed.2023.107288
  • Zhao Z, Zhao G, Chai Y, Li W, Song K, Zhao W, Li H, Wu M, Zhou Z*, Du Y*. Targeted genome mining for microbial antitumor agents acting through DNA intercalation. Synth Syst Biotechnol, 2023, 8(3): 520-526. doi:10.1016/j.synbio.2023.07.003

2021-2022

  • Chen XK#, Zhao WB#,*, Zhou Z*, Cao J*. Tumor immunity: a novel dimension for PROTACs to conquer cancer? Acta Pharmacol Sin, 2022, 43: 2171-2172. doi:10.1038/s41401-021-00829-8
  • Jiang TH, Zhou QF, Yan ZQ, Zhou Z*, Optimization of procedure for preparation of attenuated vaccine by suspension culture of avian metapneumovirus in bioreactor. Chin J Biologicals, 2022, 35(3):316-320. doi:10.13200/j.cnki.cjb.003563
  • Jiang J#, Ding Y#, Lu J#, Chen Y, Chen Y, Zhao W, Chen W, Kong M, Li C, Teng X, Zhou Q, Xu N, Zhou D, Zhou Z*, Wang H*, Teng L*. Integrative analysis reveals a clinicogenomic landscape associated with liver metastasis and poor prognosis in hepatoid adenocarcinoma of the stomach. Int J Biol Sci 2022, 18(14):5554-5574. doi:10.7150/ijbs.71449
  • Zhao W, Gu X, Chen S, Wu J*, Zhou Z*. MODIG: Integrating Multi-Omics and Multi-Dimensional Gene Network for Cancer Driver Gene Identification based on Graph Attention Network Model. Bioinformatics, 2022, 38(21):4901-4907. doi:10.1093/bioinformatics/btac622
  • Wu J, Chen S*, Zhou Z*. Advances in Tumor Neoantigen Prediction Methods. Chin J Mod Appl Pharm, 2022, 39(21): 2879-2886. doi: 10.13748/j.cnki.issn1007-7693.2022.21.026
  • 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 22(5): bbab131.  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, 24(6):1227-1241,   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.
  • Sun YS#, Zhou JJ#, Zhu HP, Xu F, Zhao WB, Lu HJ, Wang Z, Chen SQ, Yao PP*, Jiang JM*, Zhou Z*. Development of a Recombinant RBD Subunit Vaccine for SARS-CoV-2. Viruses, 2021, 13(10): 1936. doi:10.3390/v13101936

2019-2020

  • 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

2017-2018

  • 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

2015-2016

2013-2014

  • 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. doi:10.1504/IJCBDD.2014.066554
  • 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. doi:10.1109/bibm.2013.6732711

Before

  • 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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