Dingfeng Wu Professor

Education: Ph.D.

Research areas: Bioinformatics

Research focus: Metagenomics, Big data and Artificial intelligence

dingfengwu

Current position：Distinguished research fellow (Professor), Children’s Hospital of Zhejiang University School of Medicine

More about me：吴顶峰-浙江大学个人主页、吴顶峰-同济CADD课题组个人主页

Work Experience

  • Sep. 2021-Present: Distinguished research fellow (Professor), National Clinical Research Center for Child Health, Children’s Hospital of Zhejiang University School of Medicine

  • Sep. 2018-Aug. 2021: Postdoctoral fellow, Biomedical Engineering, Tongji University, Shanghai, China

Education

  • Ph.D.: Jun. 2018, Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China

  • B.S.: Jun. 2013, Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China

Research Project

  1. National Natural Science Foundation of China, Young Scientists Fund,32200529, Research on modeling method of disease gut microbial ecosystem based on causal theory, 2023-01 to 2025-12, RMB 300000, in research，PI

  2. China Postdoctoral Science Foundation, 2019M651568, Research on NAFLD key bacteria identification and personalized intervention based on causal inference, 2019-01 to 2021-12, RMB 80000, completed, PI

Publications

  1. Xiaoyi Li†, Dingfeng Wu†, Qiuyu Li, Jinglan Gu, Wenxing Gao, Xinyue Zhu, Wenjing Yin, Ruixin Zhu*, Lixin Zhu*, and Na Jiao*. Host-microbiota interactions contributing to the heterogeneous tumor microenvironment in colorectal cancer. Physiol Genomics. 2024 Feb 1;56(2):221-234. doi: 10.1152/physiolgenomics.00103.2023. Epub 2023 Dec 11. PMID: 38073489.

  2. Suqi Cao†, Zicheng Zhang†, Lei Liu, Yin Li, Wei Li, Yunling Li* and DDingfeng Wu*. Causal relationships between atopic dermatitis and psychiatric disorders: a bidirectional two-sample Mendelian randomization study. BMC psychiatry; 2024, 24(1), 16. https://doi.org/10.1186/s12888-023-05478-1.

  3. Tingjun Xu†, Wenxing Gao†, Lixin Zhu*, Wanning Chen, Chaoqun Niu, Wenjing Yin, Liangxiao Ma, Xinyue Zhu, Yunchao Ling, Sheng Gao, Lei Liu, Na Jiao, Weiming Chen, Guoqing Zhang*, Ruixin Zhu*, and Dingfeng Wu*. NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease. J. Chem. Inf. Model. 2023; https://pubs.acs.org/doi/10.1021/acs.jcim.3c00395.

  4. Wenjun Gu†, LuChengChen Shu, WanNing Chen, Jinhua Wang, Dingfeng Wu*, ZiSheng Ai*, and Jiyu Li*. Evaluation of Chinese Healthcare Organizations Innovative Performance in the Digital Health Era. Front. Public Health. 2023; https://www.frontiersin.org/articles/10.3389/fpubh.2023.1141757.

  5. Lei Liu†, Ruixin Zhu,and Dingfeng Wu*. Misuse of reporter score in microbial enrichment analysis. iMeta. 2023; e95.https://doi.org/10.1002/imt2.95.

  6. Dingfeng Wu†, Lei Liu†, Na Jiao†, Yida Zhang, Li Yang, Chuan Tian, Ping Lan, Lixin Zhu*, Rohit Loomba*, and Ruixin Zhu*. Targeting Keystone Species Helps Restore the Dysbiosis of Butyrate-Producing Bacteria in Nonalcoholic Fatty Liver Disease. iMeta, 2022; e61. https://doi.org/10.1002/imt2.61.

  7. Jing Zhong†, Dingfeng Wu†, Yuanyuan Zeng†, Gaosong Wu†, Ningning Zheng, Wenjin Huang, Yan Li, Xin Tao, Weize Zhu, Lili Sheng, Xiaoxu Shen, Weidong Zhang*, Ruixin Zhu*, and Houkai Li*. The Microbial and Metabolic Signatures of Patients with Stable Coronary Artery Disease. Microbiology spectrum, 2022; 10(6):e0246722. doi:10.1128/spectrum.02467-22.

  8. Sijing Cheng†, Dingfeng Wu†, Jie Li, Yifeng Zou, Yunle Wan, Lihan Shen, Lixin Zhu*, Mang Shi, Linlin Hou, Tao Xu, Na Jiao, Yichen Li, Yibo Huang, Zhipeng Tang, Mingwei Xu, Shusong Jiang, Maokun Li*, Guangjun Yan*, Ping Lan*, and Ruixin Zhu*. Risk factors for the critical illness in SARS-CoV-2 infection: a multicenter retrospective cohort study. Respiratory Research, 2020; 21(1), 277. DOI: https://doi.org/10.1186/s12931-020-01492-zLu.

  9. Fan†,*, Dingfeng Wu†, Vadim Goremykin, Jing Xiao, YanbingXu, Sriram Garg, Chuanlun Zhang, William F. Martin*, RuixinZhu*. Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria. Nature Ecology & Evolution, 2020; 4(9), 1213–1219. DOI: https://doi.org/10.1038/s41559-020-1239-x.

  10. Dingfeng Wu†, WenxingGao†, Xiaoyi Li†, Chuan Tian, Na Jiao, Sa Fang, Jing Xiao, Zhifeng Xu, Lixin Zhu*, Guoqing Zhang* and Ruixin Zhu*. Dr AFC: Drug Repositioning Through Anti-Fibrosis Characteristic. Briefings in Bioinformatics, 2020; 22(3). DOI: https://doi.org/10.1093/bib/bbaa115.

  11. Yunle Wan†, Jie Li†, Lihan Shen†,Yifeng Zou†, Linlin Hou†, Lixin Zhu†,*, Howard S.Faden, Zhipeng Tang, Mang Shi, Na Jiao, Yichen Li, Sijing Cheng, Yibo Huang, Dingfeng Wu, ZhifengXu, Linnuo Pan, Jun Zhu, GuangjunYan*, Ruixin Zhu*, and Ping Lan*. Enteric involvement in hospitalised patients with COVID-19 outside Wuhan. The Lancet Gastroenterology & Hepatology, 2020; 5(6), 534–535. DOI: https://doi.org/10.1016/S2468-1253(20)30118-7.

  12. Tianyi Qiu†, Yiyan Yang†, JingxuanQiu, Yang Huang, Tianlei Xu, Han Xiao, Dingfeng Wu, QingchenZhang, Chen Zhou, Xiaoyan Zhang, KailinTang, Jianqing Xu*, and ZhiweiCao*. CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens. Nature communications, 2018; 9(1), 1772. DOI: https://doi.org/10.1038/s41467-018-04171-2.

  13. Tianyi Qiu†, Dingfeng Wu†, JingxuanQiu, and Zhiwei Cao*. Finding the molecular scaffold of nuclear receptor inhibitors through high-throughput screening based on Proteochemometric modelling. Journal of cheminformatics, 2018; 10(1), 21. DOI: https://doi.org/10.1186/s13321-018-0275-x.

  14. Tianyi Qiu†, Dingfeng Wu†, LinLin Yang, Hao Ye, Qiming Wang, Zhiwei Cao*, and Kailin Tang*. Exploring the mechanism of flavonoids through systematic bioinformatics analysis. Frontiers in pharmacology, 2018; 9:918. DOI: https://doi.org/10.3389/fphar.2018.00918.

  15. Tianyi Qiu†, Jingxuan Qiu, Jun Feng, Dingfeng Wu, YiyanYang, Kailin Tang, ZhiweiCao, and Ruixin Zhu*. The recent progress in proteochemometricmodelling: focusing on target descriptors, cross-term descriptors and application scope. Briefings in bioinformatics, 2016. 18(1), 125–136. DOI: https://doi.org/10.1093/bib/bbw004.

  16. Jingxuan Qiu†,Tianyi Qiu, Yiyan Yang, Dingfeng Wu, and Zhiwei Cao*. Incorporating structure context of HA protein to improve antigenicity calculation for influenza virus A/H3N2. Scientific reports, 2016; 6, 31156. DOI: https://doi.org/10.1038/srep31156.

  17. Jun Gao†, QingchenZhang†, Min Liu, Lixin Zhu, Dingfeng Wu, Zhiwei Cao, and RuixinZhu*. bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming. Journal of cheminformatics, 2016; 8, 38. DOI: https://doi.org/10.1186/s13321-016-0149-z.

  18. Lei Liu†, Maria Tsompana, Yong Wang, Dingfeng Wu, Lixin Zhu, and RuixinZhu*. Connection map for compounds (CMC): a server for combinatorial drug toxicity and efficacy analysis. Journal of chemical information and modeling, 2016; 56(9), 1615–1621. DOI: https://doi.org/10.1021/acs.jcim.6b00397.

  19. Ruixin Zhu†, Susan S Baker, Cynthia A Moylan, Manal F Abdelmalek, Cynthia D Guy, Fausto Zamboni, Dingfeng Wu, Weili Lin, WenshengLiu, Robert D Baker, Sugantha Govindarajan,Zhiwei Cao, Patrizia Farci, Anna Mae Diehl, and Lixin Zhu*. Systematic transcriptome analysis reveals elevated expression of alcohol-metabolizing genes in NAFLD livers. The Journal of pathology, 2016; 238(4), 531–542. DOI: https://doi.org/10.1002/path.4650.

  20. Yi Sun†, Zhen Sheng†, Chao Ma, Kailin Tang, RuixinZhu, Zhuanbin Wu, Ruling Shen, Jun Feng, Dingfeng Wu, DanyiHuang, Dandan Huang, Jian Fei*, Qi Liu*, and Zhiwei Cao*. Combining genomic and network characteristics for extended capability in predicting synergistic drugs for cancer. Nature communications, 2015; 6, 8481. DOI: https://doi.org/10.1038/ncomms9481.

  21. Dingfeng Wu†, Tianyi Qiu†, Qingchen Zhang, Hong Kang, Shaohua Yuan, Lixin Zhu*, and Ruixin Zhu*. Systematic toxicity mechanism analysis of proton pump inhibitors: an in silico study. Chemical research in toxicology, 2015; 28(3), 419–430. DOI: https://doi.org/10.1021/tx5003782.

  22. Tianyi Qiu†, Han Xiao, Qingchen Zhang, Jingxuan Qiu, Yiyan Yang, Dingfeng Wu, Zhiwei Cao*, and Ruixin Zhu*. Proteochemometric modeling of the antigen-antibody interaction: new fingerprints for antigen, antibody and epitope-paratope interaction. PloS one, 2015; 10(4), e0122416. DOI: https://doi.org/10.1371/journal.pone.0122416.

  23. Tao Qi†, Tianyi Qiu†, Qingchen Zhang, Kailin Tang, Yangyang Fan, Jingxuan Qiu, Dingfeng Wu, Wei Zhang, Yanan Chen, Jun Gao, Ruixin Zhu*, and Zhiwei Cao*. SEPPA 2.0–more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen. Nucleic acids research, 2014; 42(Web Server issue), W59–W63. DOI: https://doi.org/10.1093/nar/gku395.

  24. Jun Gao†, Qi Huang†, Dingfeng Wu, Qingchen Zhang, Yida Zhang, Tian Chen, Qi Liu, Ruixin Zhu, Zhiwei Cao*, and Yuan He*. Study on human GPCR-inhibitor interactions by proteochemometric modeling. Gene, 2013; 518(1), 124–131. DOI: https://doi.org/10.1016/j.gene.2012.11.061.

  25. Dingfeng Wu†, Qi Huang†, Yida Zhang, Qingchen Zhang, Qi Liu, Jun Gao, Zhiwei Cao*, and RuixinZhu*. Screening of selective histone deacetylase inhibitors by proteochemometricmodeling. BMC bioinformatics, 2012; 13, 212. DOI: https://doi.org/10.1186/1471-2105-13-212.

Academic Conference

  1. Dingfeng Wu. miMatch:一种微生物代谢背景匹配工具能够加强宏基因组研究中微生物与人类疾病之间的因果关系. 中国肠道大会(CHINAGUT), 2023. Oral presentation. Beijing, China.

  2. Dingfeng Wu. Identification of the keystone species in non-alcoholic fatty liver disease by causal inference and dynamic intervention modeling. Chinese Society for Microbiology Annual Conference, 2020. Oral presentation. Chengdu, China.

  3. Dingfeng Wu. Unbalanced dietary patterns contribute to the pathogenesis of precocious puberty by affecting gut microbiota and host metabolites.Chinese Society for Microbiology Annual Conference, 2020. Poster. Chengdu, China.

  4. Dingfeng Wu. Microbiome analysis cloud iMAC (integrated Microbiome Analysis Cloud). Chinese Society for Microbiology Annual Conference, 2020. Poster. Chengdu, China.

  5. Dingfeng Wu. Analysis and application of keystone species in nonalcoholic fatty liver disease based on causal inference and dynamic intervention modeling. Digestive Diseases Week, 2020. Poster. Chicago, IL.

  6. Dingfeng Wu. Rate-limiting enzymes in the THF-WL pathway of planktonic SAR324 perform keystone functions in ocean carbon cycling. The 8th Symposium on Geological Microbiology, 2019, Chinese Society for Microbiology. Oral presentation. Qingdao, China

  7. Dingfeng Wu. Causal inference reveals that Clostridiales species are keystone species in NAFLD pathogenesis. Digestive Diseases Week, 2019. Poster. San Diego, CA.

  8. Dingfeng Wu. Amplicon analysis and its application in disease. Symposium on Flora Analysis, 2019. Oral presentation. Guangzhou, China.

Community Involvement

  1. iMeta (IF>10). Youth editor (2023-)

  2. Frontiers in Microbiology (IF=6.06). Review editor (2019-)

  3. Frontiers in Pharmacology (IF=5.98). Review editor (2019-)