2024

1. Lei Liu^†, Liu Yang^†, Suqi Cao, Zhigang Gao, Bin Yang, Guoqing Zhang^*, Ruixin Zhu^* and Dingfeng Wu^*. CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides. Briefings in bioinformatics. 2024; 25(3), bbae190. https://doi.org/10.1093/bib/bbae190. PMID: 38678388.

2. 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.

3. 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.

2023

1. 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.

2. 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.

3. 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.

2022

1. 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.

2. 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.

2020

1. 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.

2. 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.

3. 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.

4. 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.

Before 2020

1. 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.

2. 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.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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.

13. 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.

14. 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.