【科研项目/Funding】

1. 国家自然科学基金（National Natural Science Foundation of China），82072236，2021/01-2024/12，主持

2. 国家自然科学基金（National Natural Science Foundation of China），81702037，2018/01-2020/12，主持

3. 上海市“医苑新星”青年医学人才培养资助计划（Shanghai “Rising Stars of Medical Talent” Youth Development Program），2020

4. 同济大学附属第十人民医院攀登人才计划（Pandeng Research Foundation of Shanghai Tenth People’s Hospital），2018SYPDRC015，2018/09-2020/08

【发表论文/Publication】

1. Bi D*, Zhu Y, Gao Y, Li H, Zhu X, Wei R, Xie R, Cai C, Wei Q, Qin H. Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer. Nature Communications. 2022, 13:3336

2. Zhu H#, Bi D#, Zhang Y#, Kong C#, Du J, Wu X, Wei Q, Qin H. Ketogenic diet for human diseases: the underlying mechanisms and potential for clinical implementations. Signal Transduction and Targeted Therapy, 2022, 7:11. (Review; # joint-first author)

3. Bi D, Zhu Y, Gao Y, Li H, Zhu X, Wei R, Xie R, Wei Q, Qin H. A newly developed PCR-based method revealed distinct Fusobacterium nucleatum subspecies infection patterns in colorectal cancer. Microbial Biotechnology, 2021, 14, 2176-2186.

4. Gao Y#, Bi D#, Xie R#, Li M, Guo J, Liu H, Guo X, Fang J, Ding T, Zhu H, Cao Y, Xing M, Zheng J, Xu Qing, Xu Qian, Wei Q, Qin H. Fusobacterium nucleatum enhances the efficacy of PD-L1 blockade in colorectal cancer. Signal Transduction and Targeted Therapy, 2021, 6:398. (# joint-first author)

5. Cai C#, Bi D#, Bick G#, Wei Q, Liu H, Lu L, Zhang X, Qin H. HNF1A serves as a potential regulator in shaping super-enhancer landscape in colorectal cancer liver metastasis. FEBS Letters, 2021, 595:3056–3071. (# joint-first author)

6. Bi D, Zheng J, Xie R, Zhu Y, Wei R, Ou HY, Wei Q, Qin H. Comparative analysis of AbaR-type genomic islands reveals distinct patterns of genetic features in elements with different backbones. mSphere, 2020, 5:e00349-20.

7. Mao S, Wu Y, Wang R, Guo Y, Bi D, Ma W, Zhang W, Zhang J, Yan Y, Yao X. Overexpression of GAS6 promotes cell proliferation and invasion in bladder cancer by activation of the PI3K/AKT pathway. OncoTargets and Therapy, 2020, 13:4813-4824.

8. Huang X, Yan Y, Wei Rong, Liu Hu, Zhu X, Bi D, Wei Q, Yao X. Centrosome protein 78 is overexpressed in muscle-invasive bladder cancer and associated with tumour molecular subtypes and mutation signatures. 2020, Medical Science Monitor, 2020, 26:e925197.

9. Bi D, Xie R, Zheng J, Yang H, Ou HY, Wei Q. Large-scale identification of AbaR-type genomic islands in Acinetobacter baumannii reveals diverse insertion sites and clonal lineage-specific antimicrobial resistance gene profiles. Antimicrobial Agents and Chemotherapy, 2019, 63:e02526-18.

10. Lu L, Xie R, Wei R, Cai C, Bi D, Yin D, Zheng J, Song F, Gao Y, Zhang Y, Tan L, Liu H, Wei Q, Qin H. Integrin α5 subunit is required for tumor supportive role of fibroblasts in colorectal adenocarcinoma and serves as a potential stroma prognostic marker. Molecular Oncology, 2019, 13: 2697-2714. (Cover article)

11. Yang Y, Misra BB, Liang L, Bi D, Weng W, Wu W, Cai S, Qin H, Goel A, Li X, Ma Y. Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer. Theranostics, 2019; 9:4101-4114.

12. Zhao W, Yang J, Ni B, Bi D, Sun Y, Xu M, Zhu X, Li C, Jin L, Gao P, Wang P, Hua Y, Li M. Towards automatic prediction of EGFR mutation status in pulmonary adenocarcinoma with 3D deep learning. Cancer Medicine, 2019, 8:3532–3543. (Cover article)

13. Gao Y, Yan Y, Guo J, Zhang Q, Bi D, Wang F, Chang Z, Lu Ling, Yao X, Wei Q. HNF-4α downregulation promotes tumor migration and invasion via regulating E-cadherin in renal cell carcinoma. Oncology Reports, 2019, 42: 1066-1074.

14. Liu M, Li X, Xie Y, Bi D, Sun J, Li J, Tai C, Deng Z, Ou HY. ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Research, 2019, 47: D660-D665.

15. Wu X, Tan G, Gao R, Yao L, Bi D, Guo Y, Yu F, Fan L. Assessment of the Xpert MTB/RIF Ultra assay on rapid diagnosis of extrapulmonary tuberculosis. International Journal of Infectious Diseases, 2019, 81:91-96.

16. Dong X, Song J, Chen J, Bi D, Wang W, Ren Y, Wang H, Tang KFJ, Wang X, Huang J. Conjugative transfer of the pVA1-type plasmid carrying the pirABvp genes results in the formation of new AHPND-causing Vibrio. Frontiers in Cellular and Infection Microbiology, 2019, 9:195.

17. Bi D, Zheng J, Li JJ, Sheng ZK, Zhu X, Ou HY, Li Q, Wei Q. In silico typing and comparative genomic analysis of IncFIIK plasmids and insights into the evolution of replicons, plasmid backbones and resistance determinant profiles. Antimicrobial Agents and Chemotherapy, 2018, 62:e00764-18.

18. Bai F, Wei C, Zhang P, Bi D, Ge M, Chen Q, Jia Y, Lu Y, Wu K. Use of peripheral lymphocytes and support vector machine for survival prediction in breast cancer patients. Translational Cancer Research, 2018, 7:978-87.

19. Dong X#, Bi D#, Wang H, Zou P, Xie G, Wan X, Yang Q, Zhu Y, Chen M, Guo C, Liu Z, Wang W, Huang J. pirABvp-Bearing Vibrio parahaemolyticus and Vibrio campbellii pathogens isolated from the same AHPND-affected pond possess highly similar pathogenic plasmids. Frontiers in Microbiology, 2017, 8:1859. (# joint-first author)

20. Wei Y, Bi D, Wei D, Ou HY. Prediction of type II toxin-antitoxin loci in Klebsiella pneumoniae genome sequences. Interdisciplinary Sciences: Computational Life Sciences, 2016, 8:143-9.

21. Bi D, Jiang X, Sheng ZK, Tai C, Wang M, Deng Z, Rajakumar K, Ou HY. Mapping the resistance-associated mobilome of a carbapenem-resistant Klebsiella pneumoniae strain reveals insights into factors shaping these regions and facilitates generation of a ‘resistance-disarmed’ model organism. Journal of Antimicrobial Chemotherapy, 2015, 70: 2770-4.

22. Li G#, Zhang Y#, Bi D#, Shen P, Ai F, Liu H, Tian Y, Ma Y, Wang B, Rajakumar K, Ou HY, Jiang X. First report of a clinical, multidrug-resistant Enterobacteriaceae isolate coharboring fosfomycin resistance gene fosA3 and cabarpenemase gene blaKPC-2 on the same transposon, Tn1721. Antimicrobial Agents and Chemotherapy, 2015, 59:338-343. (# joint-first author)

23. Bi D, Liu L; Tai C, Deng Z, Rajakumar K, Ou HY. SecReT4: a web-based bacterial type IV secretion system resource. Nucleic Acids Research, 2013, 41: D660-5.

24. Bi D, Xu Z, Harrison EM, Tai C, Wei Y, He X, Jia S, Deng Z, Rajakumar K, Ou HY. ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Research, 2012, 40: D621-6.

25. Liu P, Li P, Jiang X, Bi D, Xie Y, Tai C, Deng Z, Rajakumar K, Ou HY. Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. Journal of Bacteriology, 2012, 194: 1841-1842.

26. Shao Y, Harrison EM, Bi D, Tai C, He X, Ou HY, Rajakumar K, Deng Z. TADB: a web-based resource for Type 2 toxin-antitoxin loci in Bacteria and Archaea. Nucleic Acids Research, 2011, 39: D606-D611.

27. Bi D, Chu D, Zhu P, Lu C, Fan C, Zhang J, Bao J. Utilization of dry distiller