生物信息辅助药物设计课题组

1. 恶性肿瘤治疗性疫苗的生物信息学设计研究（科技部重点研发计划）参与 在研

2. 肿瘤基因突变产生的新抗原负荷与疫苗研究策略 (自然基金重点项目) 参与 在研

3. 慢性肝病湿热证诊断的生物标志物研究（上海申康医院发展中心，三年行动计划项目）参与 在研

4. 中药复方配伍理论的计算模拟与系统分析（科技部重点研发计划）参与 结题

5. 基于临床代谢组学推断代谢功能异常的生物信息学方法（自然基金面上项目）主持 结题

6. 口腔鳞癌全基因组与miRNA表达谱及通路网络的研究 （中央高校交叉项目） 主持 结题

7. 转化医学生物信息技术及产品研发（科技部863） 参与 结题

8. 基于转化医学的慢性乙型病毒性肝炎中医证候生物学研究（科技部传染病重大专项）参与 结题

9. 基于反向对接和网络分析的中药协同机制研究（自然基金青年项目）主持 结题

近5年论文

1. Gao J, Mo S, Wang J, Zhang M, Shi Y, Zhu C, Shang Y, Tang X, Zhang S, Wu X, Xu X, Wang Y, Li Z, Zheng G, Chen Z, Wang Q, Tang K*, Cao Z*. MACC: a visual interactive knowledgebase of metabolite-associated cell communications. Nucleic Acids Res. 2024 Jan 5;52(D1):D633-D639. doi: 10.1093/nar/gkad914. PMID: 37897362; PMCID: PMC10767829.

2. Qiu T, Zhang L, Chen Z, Wang Y, Mao T, Wang C, Cun Y, Zheng G, Yan D, Zhou M, Tang K*, Cao Z*. SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs. Nucleic Acids Res. 2023 Jul 5;51(W1):W528-W534. doi: 10.1093/nar/gkad427. PMID: 37216611; PMCID: PMC10320061.

3. Zhao R, Han W, Tang K, Shao R, Zhu P, Zhang S, Xu P, He Y. Function of normal oral mucosa revealed by single-cell RNA sequencing. J Cell Biochem. 2022 Sep;123(9):1481-1494. doi: 10.1002/jcb.30307. Epub 2022 Jul 27. PMID: 35894175.

4. Chen Z, Yan D, Zhang M, Han W, Wang Y, Xu S, Tang K, Gao J, Cao Z. MetNC: Predicting Metabolites in vivo for Natural Compounds. Front Chem. 2022 May 12;10:881975. doi: 10.3389/fchem.2022.881975. PMID: 35646826; PMCID: PMC9135178.

5. Yan D, Zheng G, Wang C, Chen Z, Mao T, Gao J, Yan Y, Chen X, Ji X, Yu J, Mo S, Wen H, Han W, Zhou M, Wang Y, Wang J, Tang K*, Cao Z*. HIT 2.0: an enhanced platform for Herbal Ingredients' Targets. Nucleic Acids Res. 2022 Jan 7;50(D1):D1238-D1243. doi: 10.1093/nar/gkab1011. PMID: 34986599; PMCID: PMC8728248.

6. Tang K, Ji X, Zhou M, Deng Z, Huang Y, Zheng G, Cao Z*. Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer. Nucleic Acids Res. 2021 Sep 27;49(17):e99. doi: 10.1093/nar/gkab554. PMID: 34214174; PMCID: PMC8464058.

7. Gao J, Yin Z, Wu Z, Sheng Z, Ma C, Chen R, Zhang X, Tang K*, Fei J*, Cao Z*. Probing Synergistic Targets by Natural Compounds for Hepatocellular Carcinoma. Front Cell Dev Biol. 2021 Jul 28;9:715762. doi: 10.3389/fcell.2021.715762. PMID: 34395446; PMCID: PMC8355820.

8. Yan X, Yang Y, Chen Z, Yin Z, Deng Z, Qiu T, Tang K, Cao Z. H-RACS: a handy tool to rank anti-cancer synergistic drugs. Aging (Albany NY). 2020 Nov 10;12(21):21504-21517. doi: 10.18632/aging.103925. Epub 2020 Nov 10. PMID: 33173014; PMCID: PMC7695372.

9. Chen Z, Wang X, Li Y, Wang Y, Tang K, Wu D, Zhao W, Ma Y, Liu P, Cao Z. Comparative Network Pharmacology Analysis of Classical TCM Prescriptions for Chronic Liver Disease. Front Pharmacol. 2019 Nov 22;10:1353. doi: 10.3389/fphar.2019.01353. PMID: 31824313; PMCID: PMC6884058.

10. Zhou C, Chen Z, Zhang L, Yan D, Mao T, Tang K, Qiu T, Cao Z. SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens. Nucleic Acids Res. 2019 Jul 2;47(W1):W388-W394. doi: 10.1093/nar/gkz413. PMID: 31114919; PMCID: PMC6602482.

11. Gao J, Wang Q, Huang Y, Tang K, Yang X, Cao Z. In Silico Study of Anti-Insomnia Mechanism for Suanzaoren Prescription. Front Pharmacol. 2019 Aug 22;10:925. doi: 10.3389/fphar.2019.00925. PMID: 31507421; PMCID: PMC6713715.

12. Sheng Z, Sun Y, Yin Z, Tang K, Cao Z. Advances in computational approaches in identifying synergistic drug combinations. Brief Bioinform. 2018 Nov 27;19(6):1172-1182. doi: 10.1093/bib/bbx047. PMID: 28475767.

13. Qiu T, Wu D, Yang L, Ye H, Wang Q, Cao Z, Tang K*. Exploring the Mechanism of Flavonoids Through Systematic Bioinformatics Analysis. Front Pharmacol. 2018 Aug 15;9:918. doi: 10.3389/fphar.2018.00918. PMID: 30158870; PMCID: PMC6104453.