Education: PhD
学历：博士
Research areas：Bioinformatics
研究领域：生物信息学
Research focus：Metagenomic methodology; Disease microbiome; Development of Web Server
研究方向：宏基因组方法学、疾病微生物组、Web Server开发
Current position：Distinguished research fellow (Professor), Children's Hospital of Zhejiang University School of Medicine
当前单位：特聘研究员（正高），浙江大学医学院附属儿童医院
More about me: https://dfwlab.github.io/ https://person.zju.edu.cn/6521170
Work Experience 工作经历
· Sep. 2021-Present: Distinguished research fellow (Professor), National Clinical Research Center for Child Health, Children's Hospital of Zhejiang University School of Medicine
2021年9月至今：浙江大学附属儿童医院国家中心 特聘研究员（正高）
· Sep. 2018-Aug. 2021: Postdoctoral fellow, Biomedical Engineering, Tongji University, Shanghai, China
2018年9月——2021年8月：同济大学 生物信息系 博士后
Education 教育背景
· PhD: Jun. 2018, Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
2013年9月——2018年6月：同济大学 生物信息系 直博
· BS: Jun. 2013, Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
2009年9月——2013年6月：同济大学 生物信息系 本科
Research Project 科研项目
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
国家自然科学基金委员会, 青年科学基金项目，32200529，基于因果理论的疾病肠道微生态系统建模方法研究，2023-01至2025-12，30万，在研，主持
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
中国博士后科学基金会, 2019M651568，基于因果推理的NAFLD基石菌种鉴定和个性化干预，2019-01至2021-12，8万，完成，主持
Publications (SCI paper: 23; first-author SCI paper: 12)
同行评议论文（发表SCI论文23篇（其中12为第一/通讯作者））
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
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
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
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
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
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*. (2020). Risk factors for the critical illness in SARS-CoV-2 infection: a multicenter retrospective cohort study. Respiratory Research, 21(1), 277. DOI: https://doi.org/10.1186/s12931-020-01492-z
Fan†,*, Dingfeng Wu†, Vadim Goremykin_, Jing Xiao, YanbingXu, Sriram Garg, Chuanlun Zhang, William F. Martin*, RuixinZhu*. (2020). Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria. Nature Ecology & Evolution, 4(9), 1213–1219. DOI: https://doi.org/10.1038/s41559-020-1239-x.
Dingfeng Wu†, WenxingGao†, Xiaoyi Li†, Chuan Tian, Na Jiao, Sa Fang, Jing Xiao, Zhifeng Xu, Lixin Zhu*, Guoqing Zhang* and Ruixin Zhu*. (2020). Dr AFC: Drug Repositioning Through Anti-Fibrosis Characteristic. Briefings in Bioinformatics, 22(3). DOI: https://doi.org/10.1093/bib/bbaa115.
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*, Ping Lan*. (2020). Enteric involvement in hospitalised patients with COVID-19 outside Wuhan. The Lancet Gastroenterology & Hepatology, 5(6), 534–535. DOI: https://doi.org/10.1016/S2468-1253(20)30118-7.
Tianyi Qiu†,Yiyan Yang†, JingxuanQiu, Yang Huang, Tianlei Xu, Han Xiao, Dingfeng Wu, QingchenZhang, Chen Zhou, Xiaoyan Zhang, KailinTang, Jianqing Xu, ZhiweiCao. (2018). CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens. Nature communications, 9(1), 1772. DOI: https://doi.org/10.1038/s41467-018-04171-2.
Tianyi Qiu†,Dingfeng Wu†, JingxuanQiu, Zhiwei Cao. (2018). Finding the molecular scaffold of nuclear receptor inhibitors through high-throughput screening based on Proteochemometric modelling. Journal of cheminformatics, 10(1), 21. https://doi.org/10.1186/s13321-018-0275-x.
Qiu T#, Wu D#, Yang L, Ye H, Wang Q, Cao Z*, and Tang K*, Exploring the mechanism of flavonoids through systematic bioinformatics analysis. Frontiers in pharmacology 2018;9:918.
Tianyi Qiu†,Jingxuan Qiu, Jun Feng, Dingfeng Wu, YiyanYang, Kailin Tang, ZhiweiCao, Ruixin Zhu. (2016). The recent progress in proteochemometricmodelling: focusing on target descriptors, cross-term descriptors and application scope. Briefings in bioinformatics, 18(1), 125–136. https://doi.org/10.1093/bib/bbw004.
Jingxuan Qiu†,Tianyi Qiu, Yiyan Yang, Dingfeng Wu, Zhiwei Cao. (2016) Incorporating structure context of HA protein to improve antigenicity calculation for influenza virus A/H3N2. Scientific reports, 6, 31156. https://doi.org/10.1038/srep31156.
Jun Gao†, QingchenZhang, Min Liu, Lixin Zhu, Dingfeng Wu, Zhiwei Cao, RuixinZhu. (2016). bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming. Journal of cheminformatics, 8, 38. https://doi.org/10.1186/s13321-016-0149-z.
Lei Liu†, Maria Tsompana, Yong Wang, Dingfeng Wu, Lixin Zhu, RuixinZhu. (2016). Connection map for compounds (CMC): a server for combinatorial drug toxicity and efficacy analysis. Journal of chemical information and modeling, 56(9), 1615–1621. https://doi.org/10.1021/acs.jcim.6b00397.
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, Lixin Zhu. (2016). Systematic transcriptome analysis reveals elevated expression of alcohol-metabolizing genes in NAFLD livers. The Journal of pathology, 238(4), 531–542. https://doi.org/10.1002/path.4650.
Yi Sun†, Zhen Sheng†, Chao Ma, Kailin Tang, RuixinZhu, Zhuanbin Wu, Ruling Shen, Jun Feng, Dingfeng Wu, DanyiHuang, Dandan Huang, Jian Fei, Qi Liu, Zhiwei Cao. (2015). Combining genomic and network characteristics for extended capability in predicting synergistic drugs for cancer. Nature communications, 6, 8481. https://doi.org/10.1038/ncomms9481.
Dingfeng Wu†, TianyiQiu†, QingchenZhang, Hong Kang, Shaohua Yuan, LixinZhu, Ruixin Zhu. (2015). Systematic toxicity mechanism analysis of proton pump inhibitors: an in silico study. Chemical research in toxicology, 28(3), 419–430. https://doi.org/10.1021/tx5003782.
Tianyi Qiu†, Han Xiao, Qingchen Zhang, JingxuanQiu, Yiyan Yang, Dingfeng Wu, ZhiweiCao, Ruixin Zhu. (2015). Proteochemometric modeling of the antigen-antibody interaction: new fingerprints for antigen, antibody and epitope-paratope interaction. PloS one, 10(4), e0122416. https://doi.org/10.1371/journal.pone.0122416.
Tao Qi†, TianyiQiu†, QingchenZhang, Kailin Tang, Yangyang Fan, Jingxuan Qiu, Dingfeng Wu, Wei Zhang, Yanan Chen, Jun Gao, Ruixin Zhu, Zhiwei Cao. (2014). SEPPA 2.0--more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen. Nucleic acids research, 42(Web Server issue), W59–W63. https://doi.org/10.1093/nar/gku395.
Jun Gao†, Qi Huang, Dingfeng Wu, QingchenZhang, Yida Zhang, Tian Chen, Qi Liu, Ruixin Zhu, Zhiwei Cao, Yuan He. (2013). Study on human GPCR-inhibitor interactions by proteochemometric modeling. Gene, 518(1), 124–131. https://doi.org/10.1016/j.gene.2012.11.061.
Dingfeng Wu†, Qi Huang, Yida Zhang, Qingchen Zhang, Qi Liu, Jun Gao, Zhiwei Cao, RuixinZhu. (2012). Screening of selective histone deacetylase inhibitors by proteochemometricmodeling. BMC bioinformatics, 13, 212. https://doi.org/10.1186/1471-2105-13-212.
Academic Conference 会议交流
1.Wu D. miMatch: A microbial metabolic background matching tool bolstering the causal link between microbiota and human disease in metagenomics. ChinaGut Conference Series, 2023. Oral presentation. Beijing, China.
吴顶峰，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，口头报告，肠道大会，2023，中国北京
2. Wu D. 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.
吴顶峰，基于因果推理和动态干预模拟的非酒精性脂肪肝关键菌种鉴定，口头报告，中国微生物学会学术年会, 2020，中国成都。
3. Wu D. 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.
吴顶峰，不良膳食模式引起肠道菌群紊乱和代谢失调导致儿童性早熟，墙报，中国微生物学会学术年会, 2020，中国成都。
4. Wu D. Microbiome analysis cloud iMAC (integrated Microbiome Analysis Cloud). Chinese Society for Microbiology Annual Conference 2020. Poster. Chengdu, China.
吴顶峰，微生物组分析云iMAC (integrated Microbiome Analysis Cloud)，墙报，中国微生物学会学术年会, 2020，中国成都。
5. Wu D#, Fang S#, Yang Z, Jiao N, Gao W, Lan P, Zhu R*, Loomba R*, Zhu L*. 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. Wu D. 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
吴顶峰，Rate-limiting enzymes in the THF-WL pathway of planktonic SAR324 perform keystone functions in ocean carbon cycling，口头报告，中国微生物学会第八届地质微生物学学术研讨会，2019，中国青岛。
7. Wu D#, Fang S#, Yang Z, Jiao N, Lin Y, Li X, Xiao J, Yuan M, Zhu R*, Zhu L*. Causal inference reveals that Clostridiales species are keystone species in NAFLD pathogenesis. Digestive Diseases Week 2019. Poster. San Diego, CA.
8. Wu D. Amplicon analysis and its application in disease. Symposium on Flora Analysis 2019. Oral presentation. Guangzhou, China.
吴顶峰，扩增子分析以及在疾病中的应用，主讲，菌群分析研讨会，2019，中国广州。
Honors and Awards 获得荣誉
1. 2016, The First “Academic Pioneer” Forum, School of Life Sciences and Technology, Tongji University (Star Pioneer Award)
2016年，同济大学生命科学与技术学院第一届博士生学术文化节“学术先锋”论坛星空先锋奖
2. 2012, Tongji University Scholarship (3rd place)
2012年，同济大学学习奖学金三等奖
3. 2011, Tongji University Scholarship (2nd place)
2011年，同济大学学习奖学金二等奖
Community Involvement 社会服务
1. Frontiers in Microbiology (IF=5.64). Review editor (2019-)
2. Frontiers in Pharmacology (IF=5.81). Review editor (2019-)
