2009,9–2012,7 上海大学系统生物技术研究所 信息学与系统生物学 工学博士

2005,9–2008,6 新疆大学生命科学和技术学院 生物化学与分子生物学 理学硕士

2000,9–2004,7 烟台大学化学生物理工学院 生物科学 理学学士

2020.10–至今 国科大杭州高等研究院生命与健康学院 研究员

2017. 06 –2020.10 山东大学（威海）数学与统计学院 研究员

1. Yi Liu, Xiao Chang*, Xiaoping Liu*, "Protocol for unsupervised inference of cell-cell communication using matrix decomposition", STAR Protocols, 5(2): 103006, 2024

2. Yaofeng Hu, Kai Xiao, Hengyu Yang, Xiaoping Liu*, Chuanchao Zhang*, Qianqian Shi*, "Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics", Briefings in Bioinformatics, 25(2): bbae016, 2024.

3. Yi Liu, Yuelei Zhang, Xiao Chang*, Xiaoping Liu*, "MDIC3: Matrix decomposition to infer cell-cell communication", Patterns, 5:100911, 2024.

4. Jing Guo, Ze Zhang, Qingcui Li, Xiao Chang*, Xiaoping Liu*, "TeCD: The eccDNA Collection Database for extrachromosomal circular DNA", BMC Genomics, 24(1):47, 2023. (IF 4.547)

5. Yu Zhang#, Xiao Chang#,*, Jie Xia#, Yanhong Huang, Shaoyan Sun, Luonan Chen*, Xiaoping Liu*, "Identifying network biomarkers of cancer by sample-specific differential network", BMC Bioinformatics, 23:230, 2022.

6. Yiwei Meng#, Yanhong Huang#, Xiao Chang*, Xiaoping Liu*, Luonan Chen*, "Transcriptome analysis method based on differential distribution evaluation", Briefings in Bioinformatics,  23(2): bbab608, 2022. 

7. Kazuyuki Aihara*, Rui Liu, Keiichi Koizumi, Xiaoping Liu, Luonan Chen*, "Dynamical network biomarkers: Theory and applications", Gene, 808: 145997, 2022.

8. Yuyao Gao, Xiao Chang*, Jie Xia, Shaoyan Sun, Zengchao Mu*, Xiaoping Liu*, "Identification of HCC-Related Genes Based on Differential Partial Correlation Network", frontiers in Genetics, 12: 672117, 2021.

9. Zengchao Mu#, Ting Yu#, Xiaoping Liu#, Hongyu Zheng, Leyi Wei* and Juntao Liu*, "FEGS: a novel feature extraction model for protein sequences and its applications", BMC Bioinformatics, 22: 297, 2021. (#Co-first authors)

10. Yuelei Zhang, Xiao Chang*, Xiaoping Liu*, "Inference of gene regulatory networks using pseudo-time series data", Bioinformatics, 37(16): 2423-2431, 2021. 

11. Yanhong Huang, Xiao Chang, Yu Zhang, Luonan Chen*, Xiaoping Liu*, "Disease characterization using a partial correlation-based sample-specific network", Briefings in Bioinformatics, 22(3): bbaa062, 2021.

12. Jing Ge, Chenxi Song, Chengming Zhang, Xiaoping Liu, Jingzhou Chen, Kefei Dou, Luonan Chen, "Personalized Early-Warning Signals during Progression of Human Coronary Atherosclerosis by Landscape Dynamic Network Biomarker", Genes, 11: 676, 2020.   

13. Ting Yu, Zengchao Mu, Zhaoyuan Fang, Xiaoping Liu, Xin Gao, Juntao Liu, "TransBorrow: Genome-guided transcriptome assembly by borrowing assemblies from different assemblers", Genome Research, 30(8): 1181-1190, 2020. 

14. Fuyan Hu, Qing Wang, Zhiyuan Yang, Zeng Zhang, Xiaoping Liu*, "Network-based identification of biomarkers for colon adenocarcinoma", BMC Cancer, 20: 668, 2020. 

15. Yichong Wu, Tiejun Li, Xiaoping Liu, Luonan Chen, "Differential network inference via the fused D-trace loss with cross variables", Electronic Journal of Statistics, 14: 1269-1301, 2020. 

16. Jifan Shi, Juan Zhao, Xiaoping Liu, Luonan Chen*, Tiejun Li*, "Quantifying direct dependencies in biological networks by multiscale association analysis", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(2): 449-458, 2020. 

17. Fuyan Hu, Wenying Zeng, Xiaoping Liu*, "A Gene Signature of Survival Prediction for Kidney Renal Cell Carcinoma by Multi-Omic Data Analysis", International Journal of Molecular Sciences, 20(22): 5720, 2019. 

18. Xiaoping Liu, Xiao Chang, Siyang Leng, Hui Tang, Kazuyuki Aihara^*, Luonan Chen^*, "Detection for disease tipping points by landscape dynamic network biomarkers", National Science Review, 6(4): 775-785, 2019. 

19. Xiaoqiang Sun^*, Xiaoping Liu, Mengxue Xia, Yongzhao Shao^*, Xiaohua Douglas Zhang^*, "Multicellular gene network analysis identifies a macrophage‑related gene signature predictive of therapeutic response and prognosis of gliomas", Journal of Translational Medicine, 17: 159, 2019.

20. Fuping Zhang, Xiaoping Liu, Aidi Zhang, Zhonglin Jiang, Luonan Chen^*, Xiujun Zhang^*, "Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis", BMC Plant Biology, 19: 11, 2019. 

21. Bo Hu, Xiao Chang, Xiaoping Liu*, "Predicting Functional Modules of Liver Cancer Based on Differential Network Analysis", Interdisciplinary Sciences-Computational Life Sciences, 11(4): 636-644, 2019. 

22. Shenghui Liu, Chunrui Xu, Yusen Zhang*, Jiaguo Liu, Bin Yu, Xiaoping Liu*, Matthias Dehmer, "Feature selection of gene expression data for Cancer classification using double RBF-kernels", BMC Bioinformatics, 19: 396, 2018. 

23. Ben-gong Zhang, Weibo Li, Yazhou Shi, Xiaoping Liu, Luonan Chen^*, "Detecting causality from short time-series data based on prediction of topologically equivalent attractors", BMC Syst Biol, 11(Suppl 7): 128, 2017. 

24. Pei Chen, Yongjun Li, Xiaoping Liu, Rui Liu^*, Luonan Chen^*, "Detecting the tipping points in a three-state model of complex diseases by temporal differential networks", Journal of Translational Medicine, 15: 217, 2017. 

25. Xiaoping Liu, Xiao Chang, Rui Liu, Xiangtian Yu, Luonan Chen^*, Kazuyuki Aihara^*, "Quantifying critical states of complex diseases using single-sample dynamic network biomarkers", PLoS Computational Biology, 13(7): e1005633, 2017. 

26. Xiaoping Liu, Yuetong Wang, Hongbin Ji^*, Kazuyuki Aihara^*, Luonan Chen^*, "Personalized characterization of diseases using sample-specific networks", Nucleic Acids Research, 44(22): e164, 2016.

27. Xiaoping Liu, Xiao Chang^*, "Identifying module biomarkers from gastric cancer by differential correlation network", OncoTargets and Therapy, 2016(9): 5701-5711, 2016.

28. Tao Zeng, Wanwei Zhang, Xiangtian Yu, Xiaoping Liu, Meiyi Li and Luonan Chen^*, "Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals", Briefings in Bioinformatics, 17(4): 576-592, 2016. 

29. Jiye Wang, Mi Li, Yun Wang, Xiaoping Liu, "Integrating subpathway analysis to identify candidate agents for hepatocellular carcinoma", OncoTargets and Therapy, 2016(9): 1221-1230, 2016. 

30. Qianqian Shi^#, Xiaoping Liu^#, Tao Zeng, William Wang, Luonan Chen^*, "Detecting disease genes of non-small lung cancer based on consistently differential interactions", Cancer and Metastasis Reviews, 34(2): 195-208, 2015. (#Co-first authors)

31. Wanwei Zhang, Tao Zeng, Xiaoping Liu, Luonan Chen^*, "Diagnosing phenotypes of single-sample individuals by edge biomarkers", Journal of Molecular Cell Biology, 7(3): 231-241, 2015. 

32. Duojiao Wu^#, Xiaoping Li^u#, Chen Liu, Zhiping Liu, Ming Xu, Ruiming Rong, Mengjia Qian, Luonan Chen^*, Tongyu Zhu^*, "Network analysis reveals roles of inflammatory factors in different phenotypes of kidney transplant patients", Journal of Theoretical Biology, 362: 62-68, 2014. (#Co-first authors)

33. Andrew E. Teschendorff^*, Xiaoping Liu, Helena Caren, Steve M. Pollard, Stephan Beck, Martin Widschwendter, Luonan Chen, “The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis”, PLoS Computational Biology, 10(7): e1003709, 2014. 

34. Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara^*, and Luonan Chen^*, "Identifying critical transitions of complex diseases based on a single sample", Bioinformatics, 30(1): 1579-1586, 2014. 

35. ZENG Tao, ZHANG WanWei, YU XiangTian, LIU XiaoPing, LI MeiYi, LIU Rui & CHEN LuoNan^*, “Edge biomarkers for classification and prediction of phenotypes”, Science China-Life Sciences, 57: 1103–1114, 2014. 

36. Xiaoping Liu, Jiguang Wang, Luonan Chen^*, "Whole-exome sequencing reveals recurrent somatic mutation networks in cancer", Cancer Letters, 340: 270-276, 2013. 

37. Xiaoping Liu, Xiaodong Zhang, Wei-Hua Tang, Luonan Chen^* and Xing-Ming Zhao^*, "eFG: an electronic resource for Fusarium graminearum", DATABASE-OXFORD, Vol. 2013: bat042, 2013, doi:10.1093/database/bat042.

38. Xiaoping Liu, Rui Liu, Xing-Ming Zhao^*, Luonan Chen^*, "Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers", BMC Medical Genomics, 6(Suppl 2): S8, 2013. 

39. Xiaoping Liu, Zhi-Ping Liu, Xing-Ming Zhao^*, Luonan Chen^*, "Identifying disease genes and module biomarkers by differential interactions", Journal of the American Medical Informatics Association, 19: 241-248, 2012. 

40. Achyut Sapkota, Xiaoping Liu, Xing-Ming Zhao, Yongwei Cao, Jingdong Liu, Zhi-Ping Liu and Luonan Chen^*, "DIPOS: database of interacting proteins in Oryza sativa", Molecular BioSystems, 7: 2615-2621, 2011. 

41. Xiaoping Liu, Wei-Hua Tang, Xing-Ming Zhao^*, Luonan Chen^*, "A network approach to predict pathogenic genes for Fusarium graminearum", PLOS ONE, 5(10): e13021, 2010. 

42. Xiaoping Liu, Jiye Wang, Ping Gou, Cungui Mao^*, Zeng-Rong Zhu^*, Hongye Li^*, "In vitro inhibition of postharvest pathogens of fruit and control of gray mold of strawberry and green mold of citrus by aureobasidin A", International Journal of Food Microbiology, 119: 223–229, 2007.