电子邮件： xpliu@ucas.ac.cn
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研究领域
招生信息
招生专业
招生方向
教育背景
学位
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
工作经历
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
专利与奖励
1. 陈洛南，刘小平，合原一幸，基于单样本数据的个体特异性网络构建方法和装置，2019.6.18，中国，ZL201510058477.X
2. 林旭，陈洛南，刘小平，张昕妍，张旭光，吴延普，孙亮，李忠霞，邓超明，表型状态模型及其使用方法，2023.7.14，中国，ZL202310862476.5
3. 张旭光，吴延普，李忠霞，林旭，陈洛南，刘小平，张昕妍，孙亮，邓超明，弹性稳态模型及其使用方法，2023.7.14，中国，ZL202310862474.6
4. 刘小平，吕承尚，一种基于网络信息熵的关键基因预测方法，2025.1.24，中国，ZL202411517889.0
论文列表
1. Xinzhe Huang, Luonan Chen*, Xiaoping Liu*, "Constructing Cell-Specific CausalNetworks of Individual Cells for Depicting Dynamical Biological Processes", Research, 8: 0743, 2025.
2. Yuelei Zhang, Qingcui Li, Jiachen Wang, Xiao Chang* , Luonan Chen*, Xiaoping Liu*, "Causal network inference based on cross-validation predictability", Communications Physics, 8: 173, 2025.
3. Xinyu Bao, Xiaosheng Bai, Xiaoping Liu*, Qianqian Shi*, ChuanchaoZhang*, "Spatially informed graph transformers for spatially resolved transcriptomics", Communications biology, 8: 574, 2025.
4. Ze Zhang, Yang Li, Di Zhang, Shuai Chen*, Sien Lu, Kang Wang, Miao Zhou, Zehe Song, Qingcui Li*, Jie Yin*, Xiaoping Liu*, "FACdb: a comprehensive resource for genes, gut Microbiota, and metabolites in farm animals", Frontiers in Microbiology, 16:1557285, 2025.
5. Zedong Wang, Yi Liu, Xiao Chang*, Xiaoping Liu*, "Deconvolution and inference of spatial communication through optimization algorithm for spatial transcriptomics", Communications biology, 8: 235, 2025.
6. Yanpu Wu, Xinyan Zhang, Liang Sun, Qingqing Wu, Xiaoping Liu, Yueyi Deng, Zhenzhen Lu, Zhongxia Li, Chaoming Deng, Ruikun He, Luyun Zhang, Rong Zeng, Xuguang Zhang, Luonan Chen, Xu Lin, "Two-dimensional Health State Map to define metabolic health using separated static and dynamic homeostasis features: a proof-of-concept study",12: nwae425, 2025.
7. Jiachen Wang, Yuelei Zhang, Luonan Chen*, Xiaoping Liu*, "Reconstructing Molecular Networks by Causal Diffusion Do-Calculus Analysis with Deep Learning", Advanced Science, 11(46): 2409170, 2024.
8. Xinlei Cai, Yi Ye, Xiaoping Liu, Zhaoyuan Fang, Luonan Chen, Fei Li, Hongbin Ji, "Multi-gradient Permutation Survival Analysis Identifies Mitosis and Immune Signatures Steadily Associated with Cancer Patient Prognosis", eLife, 13:RP101619, 2024.
9. Chengshang Lyu, Lingxi Chen, Xiaoping Liu*, "Detecting tipping points of complex diseases by network information entropy", Briefings in Bioinformatics, 25(4): bbae311, 2024.
10. Xingyu Liao, Xiaoping Liu*, "Hidden Variable Discovery Based on Regression and Entropy", Mathematics, 12:1375, 2024
11. Yi Liu, Xiao Chang*, Xiaoping Liu*, "Protocol for unsupervised inference of cell-cell communication using matrix decomposition", STAR Protocols, 5(2): 103006, 2024
12. 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.
13. Yi Liu, Yuelei Zhang, Xiao Chang*, Xiaoping Liu*, "MDIC3: Matrix decomposition to infer cell-cell communication", Patterns, 5(2): 100911, 2024.
14. 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)
15. 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.
16. 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.
17. Kazuyuki Aihara*, Rui Liu, Keiichi Koizumi, Xiaoping Liu, Luonan Chen*, "Dynamical network biomarkers: Theory and applications", Gene, 808: 145997, 2022.
18. 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.
19. 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)
20. Yuelei Zhang, Xiao Chang*, Xiaoping Liu*, "Inference of gene regulatory networks using pseudo-time series data", Bioinformatics, 37(16): 2423-2431, 2021.
21. 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.
22. 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.
23. 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.
24. Fuyan Hu, Qing Wang, Zhiyuan Yang, Zeng Zhang, Xiaoping Liu*, "Network-based identification of biomarkers for colon adenocarcinoma", BMC Cancer, 20: 668, 2020.
25. 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.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. 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.
37. Xiaoping Liu, Xiao Chang*, "Identifying module biomarkers from gastric cancer by differential correlation network", OncoTargets and Therapy, 2016(9): 5701-5711, 2016.
38. 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.
39. 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.
40. 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)
41. 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.
42. Duojiao Wu#, Xiaoping Liu#, 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)
43. 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.
44. 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.
45. 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.
46. Xiaoping Liu, Jiguang Wang, Luonan Chen*, "Whole-exome sequencing reveals recurrent somatic mutation networks in cancer", Cancer Letters, 340: 270-276, 2013.
47. 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.
48. 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.
49. 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.
50. 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.
51. 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.
52. 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.