2026

1. Peiyu Chen^†, Jianbo Wei^†, Shuangshuang Guo, Yuhao Jiang, Xiaofei Li, Luojiao Liang, Yunqiu Zhang, Fanke Zeng, Dingfeng Wu^*, Wei Wang^*, Liangsheng Fan^*. Global, Regional, and National Impact of Pelvic Inflammatory Disease: Changing Landscape from 1990 to 2021. International journal of women’s health, 2026; 18, 597831. https://doi.org/10.2147/IJWH.S597831

2. Suqi Cao^†, Duote Cai^†, Shuhao Zhang^†, Yuchen He, Xiaojian Yuan, Zhiqiang Zhu, Xuefeng Miao, Shannan Wu, Yongxing Zhong, Fangyan Yang, Guofeng Yin, Juying Yan, Junjie Chen, Donglai Hu, Menglu Yu, Zhijian Zhou, Qiongjie Ruan, Boyun Xuan, Yihao Cai, Liangting Tao, Weiwei Zhang, Ting Yu, Junfen Zhou, Wei Song, Yanwei Tong, Yanhui Tian, Chunting Zhou, Dingfeng Wu^*, Daqing Ma^* and Zhigang Gao^*. Development and multicenter validation of an explainable machine learning diagnostic criteria for pediatric abdominal sepsis. NPJ digital medicine, 2026; 9(1), 312. https://doi.org/10.1038/s41746-026-02500-0

3. CNCB–NGDC Members and Partners. Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2026. Nucleic acids research, 2026; 54(D1), D28–D47. https://doi.org/10.1093/nar/gkaf1172

4. Jingyu Zhu^†, Suqi Cao, Tan Wang, Nannan Wang, Liu Yang, Xuanli Tang, Mengya Jiang, Qin Zhu, Hong Yu^*, Dingfeng Wu^* and Wan-Xin Peng^*. Guiqi Yishen granule alleviates obstructive nephropathy-induced renal fibrosis by targeting PI3K/AKT signaling pathway. Journal of Ethnopharmacology. 2026;10, 354:120490. https://doi.org/10.1016/j.jep.2025.120490. PMID: 40865661.

2025

1. CNCB-NGDC Members and Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025. Nucleic acids research. 2025; 53(D1), D30–D44. https://doi.org/10.1093/nar/gkae978.

2. Suqi Cao^†, Lei Liu^†, Liu Yang, Haomin Li, Ruixin Zhu, Gang Yu, Na Jiao^* and Dingfeng Wu^*. Assessing severe pneumonia risk in children via clinical prognostic model based on laboratory markers. International Immunopharmacology 2025;151, 114317. https://doi.org/0.1016/j.intimp.2025.114317. PMID: 39983420.

3. Liu Yang^†, Suqi Cao^†, Lei Liu, Ruixin Zhu^* and Dingfeng Wu^*. cyclicpeptide: a Python package for cyclic peptide drug design. Briefings in bioinformatics. 2024;26(1), bbae714. https://doi.org/10.1093/bib/bbae714. PMID: 39783893.

4. Genhui Zheng^†, Dingfeng Wu^†, Xiuxia Wei, Dongpo Xu, Tiantian Mao, Deyu Yan, Wenhao Han, Xiaoxiao Shang, Zikun Chen, Jingxuan Qiu, Kailin Tang, Zhiwei Cao^* and Tianyi Qiu^*. PbsNRs: predict the potential binders and scaffolds for nuclear receptors. Briefings in bioinformatics. 2024;26(1), bbae710. https://doi.org/10.1093/bib/bbae710.

2024

1. Lei Liu^†, Suqi Cao^†, Weili Lin^†, Zhigang Gao, Liu Yang, Lixin Zhu, Bin Yang, Guoqing Zhang^*, Ruixin Zhu^* and Dingfeng Wu^*. miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research. Gut Microbes. 2024; 16(1), 2434029. https://doi.org/10.1080/19490976.2024.2434029. PMID: 39601293.

2. 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.

3. 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. https://doi.org/10.1152/physiolgenomics.00103.2023. Epub 2023 Dec 11. PMID: 38073489.

4. Suqi Cao^†, Zicheng Zhang^†, Lei Liu, Yin Li, Wei Li, Yunling Li^* and Dingfeng 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.