† Equal contribution. * Corresponding author.

Bing Han, Shunheng Zhou, Yuan Zhang, Sina Chen, Wen Xi, Chenchen Liu, Xu Zhou, Mengqin Yuan, Xiaoyu Yu, Lu Li, Yu Wang, Hui Ren, Jian Xie, Bin Li, Minzi Ju, You Zhou, Ziqi Liu, Zhongli Xiong, Ling Shen, Yuan Zhang, Ying Bai, Jun Chen, Wei Jiang*, Honghong Yao*. Integrating spatial and single-cell transcriptomics to characterize the molecular and cellular architecture of the ischemic mouse brain. Science Translational Medicine. 2024 Feb 7;16(733):eadg1323. PubMed

Xinyu Cao, Xu Zhou, Fei Hou, Yu-e Huang, Mengqin Yuan, Min Long, Sina Chen, Wanyue Lei, Jicun Zhu, Jiahao Chen, Tao Zhang, An-Yuan Guo*, Wei Jiang*. ncRNADrug: a database for validated and predicted ncRNAs associated with drug resistance and targeted by drugs. Nucleic Acids Research. 2024 Jan 5. 52(D1):D1393-D1399. PubMed

Shaoqi Yang, Yuheng Sun, Min Long, Xinbei Zhou, Mengqin Yuan, Liliang Yang, Wei Luo, Yusi Cheng, Xinxin Zhang, Wei Jiang*, Jie Chao*. Single-cell transcriptome sequencing-based analysis: probing the mechanisms of glycoprotein NMB regulation of epithelial cells involved in silicosis. Particle and Fibre Toxicology. 2023 Jul 19. 20(1):29. PubMed

Mengling Chen, Jing Wang, Mengqin Yuan, Min Long, Yuheng Sun, Sha Wang, Wei Luo, Yun Zhou, Wei Zhang, Wei Jiang*, Jie Chao*. AT2 cell-derived IgA trapped by the extracellular matrix in silica-induced pulmonary fibrosis. International Immunopharmacology. 2023 Jun 28. 122:110545. PubMed

Xu Zhou, Ramkrishna Mitra, Fei Hou, Shunheng Zhou, Lihong Wang*, Wei Jiang*. Genomic Landscape and Potential Regulation of RNA Editing in Drug Resistance. Advanced Science. 2023 Mar 13. e2207357. PubMed

Yu-e Huang, Shunheng Zhou, Haizhou Liu, Xu Zhou, Mengqin Yuan, Fei Hou, Sina Chen, Jiahao Chen, Lihong Wang*, Wei Jiang*. DRdriver: identifying drug resistance driver genes using individual-specific gene regulatory network. Briefings in Bioinformatics. 2023 Mar 3. bbad066. PubMed

Wanyue Lei, Mengqin Yuan, Min Long, Tao Zhang, Yu-e Huang, Haizhou Liu*, Wei Jiang*. scDR: Predicting Drug Response at Single-Cell Resolution. Genes. 2023 Jan 19. 14(2):268. PubMed


Jing Wang, Xinxin Zhang, Min Long, Mengqin Yuan, Juan Yin, Wei Luo, Sha Wang, Yu Cai, Wei Jiang*, Jie Chao*. Macrophage-derived GPNMB trapped by fibrotic extracellular matrix promotes pulmonary fibrosis. Communications Biology. 2023 Feb 2. 6(1):136. PubMed

Sina Chen, Shunheng Zhou, Yu-e Huang, Mengqin Yuan, Wanyue Lei, Jiahao Chen, Kongxuan Lin, Wei Jiang*. Estimating Metastatic Risk of Pancreatic Ductal Adenocarcinoma at Single-Cell Resolution. International Journal of Molecular Sciences. 2022 Nov 30. 23(23):15020. PubMed

Haizhou Liu, Mengqin Yuan, Ramkrishna Mitra, Xu Zhou, Min Long, Wanyue Lei, Shunheng Zhou, Yu-e Huang, Fei Hou, Christine M Eischen*, Wei Jiang*. CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research. Genome Medicine. 2022 Oct 13. 14(1):118. PubMed

Shunheng Zhou, Yu-e Huang, Jiani Xing, Xu Zhou, Sina Chen, Jiahao Chen, Lihong Wang*, Wei Jiang*. ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis. Genomics Proteomics Bioinformatics. 2022 Sep 23. S1672-0229(22)00120-6. PubMed

Fei Hou, Xu Zhou, Shunheng Zhou, Haizhou Liu, Yu-e Huang, Mengqin Yuan, Jicun Zhu, Xinyu Cao, Wei Jiang*. DNA Methylation Dynamics Associated with Long-term Isolation of Simulated Space Travel. iScience. 2022 May 29. 25(6):104493. PubMed

Jiani Xing, Haizhou Liu, Wei Jiang*, Lihong Wang*. LncRNA-Encoded Peptide: Functions and Predicting Methods. Frontiers in Oncology. 2021 Jan 14. 10:622294. PubMed

Shunheng Zhou, Yu-e Huang, Haizhou Liu, Xu Zhou, Mengqin Yuan, Fei Hou, Lihong Wang*, Wei Jiang*. Single-cell RNA-seq dissects the intratumoral heterogeneity of triple-negative breast cancer based on gene regulatory networks. Molecular Therapy Nucleic Acids. 2021 Jan 1. 23:682-690. PubMed

Mengqin Yuan, Haizhou Liu, Shunheng Zhou, Xu Zhou, Yu-e Huang, Fei Hou, Wei Jiang*. Integrative Analysis of Regulatory Module Reveals Associations of Microgravity with Dysfunctions of Multi-body Systems and Tumorigenesis. International Journal of Molecular Sciences. 2020 Oct 14. 21(20):7585. PubMed

Sabrina Fritah, Arnaud Muller, Wei Jiang, Ramkrishna Mitra, Mohamad Sarmini, Monika Dieterle, Anna Golebiewska, Tao Ye, Eric Van Dyck, Christel Herold-Mende, Zhongming Zhao, Francisco Azuaje, Simone P Niclou*. Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma. Cancers (Basel). 2020 Sep 10. 12(9):2583. PubMed

Shuyuan Wang, Shunheng Zhou, Haizhou Liu, Qianqian Meng, Xueyan Ma, Hui Liu, Lihong Wang*, Wei Jiang*. ncRI: a manually curated database for experimentally validated non-coding RNAs in inflammation. BMC Genomics. 2020 Jun 1. 21(1):380. PubMed

Li Yang, Bing Han, Zhiting Zhang, Shuguo Wang, Ying Bai, Yuan Zhang, Ying Tang, Lingli Du, Ling Xu, Fangfang Wu, Lei Zuo, Xufeng Chen, Yu Lin, Kezhong Liu, Qingqing Ye, Biling Chen, Bin Li, Tianci Tang, Yu Wang, Ling Shen, Guangtian Wang, Minzi Ju, Mengqin Yuan, Wei Jiang, John H. Zhang, Gang Hu, JianHong Wang*, Honghong Yao*. Extracellular Vesicle-Mediated Delivery of CircSCMH1 Promotes Functional Recovery in Rodent and Nonhuman Primate Ischemic Stroke Models. Circulation. 2020 May 22. doi: 10.1161/CIRCULATIONAHA.120.045765. PubMed

Haizhou Liu, Xu Zhou, MengqinYuan, Shunheng Zhou, Yu-e Huang, Fei Hou, Xiaofeng Song*, Lihong Wang*, Wei Jiang*. ncEP: A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides. Journal of Molecular Biology. 2020 Feb 24. pii: S0022-2836(20)30195-9. PubMed

Ramkrishna Mitra, Clare M. Adams, Wei Jiang, Evan Greenawalt, Christine M. Eischen*. Pan-cancer analysis reveals cooperativity of both strands of microRNA that regulate tumorigenesis and patient survival. Nature Communications. 2020 Feb 20. 11(1):968. PubMed

Yu-e Huang, Shunheng Zhou, Haizhou Liu, Xu Zhou, Mengqin Yuan, Fei Hou, Lihong Wang*, Wei Jiang*. Identification of drug resistance associated ncRNAs based on comprehensive heterogeneous network. Life Sciences. 2020 Feb 15. 243:117256. PubMed

Lei Zuo, Lin Zhang, Juan Zu, Zan Wang, Bing Han, Biling Chen, Mengjing Cheng, Minzi Ju, Mingyue Li, Guofang Shu, Mengqin Yuan, Wei Jiang, Xufeng Chen, Fuling Yan, Zhijun Zhang*, Honghong Yao*. Circulating Circular RNAs as Biomarkers for the Diagnosis and Prediction of Outcomes in Acute Ischemic Stroke. Stroke. 2019 Nov 6:STROKEAHA119027348. PubMed

Qianqian Meng, Shuyuan Wang, Shunheng Zhou, Haizhou Liu, Xueyan Ma, Xu Zhou, Hui Liu, Chaohan Xu*, Wei Jiang*. Dissecting the m6A methylation affection on afatinib resistance in non-small cell lung cancer. The Pharmacogenomics Journal. 2019 Oct 17. doi: 10.1038/s41397-019-0110-4. PubMed

Wei Jiang*, Yinwei Qu, Qian Yang, Xueyan Ma, Qianqian Meng, Juan Xu*, Xinyi Liu*, Shuyuan Wang*. D-lnc: a comprehensive database and analytical platform to dissect the modification of drugs on lncRNA expression. RNA Biology. 2019 Aug 7. 16(11):1586-1591. PubMed

Enyu Dai, Hao Zhang, Xu Zhou, Qian Song, Di Li, Lei Luo, Xinyu Xu, Wei Jiang*, Hong Ling*. MycoResistance: a curated resource of drug resistance molecules in Mycobacteria. Database (Oxford). 2019 Jan 1. pii: baz074. PubMed

Lihong Wang*, Tian Luan, Shunheng Zhou, Jing Lin, Yue Yang, Wei Liu, Xiao Tong, Wei Jiang*. LncRNA HCP5 promotes triple negative breast cancer progression as a ceRNA to regulate BIRC3 by sponging miR-219a-5p. Cancer Medicine. 2019 Jun 18. 8(9):4389-4403. PubMed

Haizhou Liu, Shuyuan Wang, Shunheng Zhou, Qianqian Meng, Xueyan Ma, Xiaofeng Song*, Lihong Wang*, Wei Jiang*. Drug Resistance-Related Competing Interactions of lncRNA and mRNA across 19 Cancer Types. Molecular Therapy Nucleic Acids. 2019 Apr 11. 16:442-451. PubMed

Xu Zhou, Enyu Dai, Qian Song, Xueyan Ma, Qianqian Meng, Yongshuai Jiang*, Wei Jiang*. In silico drug repositioning based on drug-miRNA associations. Briefings in Bioinformatics. 2019 Feb 11. doi: 10.1093/bib/bbz012. PubMed

Leiming Jiang, Xuexin Yu, Xueyan Ma, Haizhou Liu, Shunheng Zhou, Xu Zhou, Qianqian Meng, Lihong Wang*, Wei Jiang*. Identification of transcription factor-miRNA-lncRNA feed-forward loops in breast cancer subtypes. Computational Biology and Chemistry. 2018 Nov 16. 78:1-7. PubMed

Shuyuan Wang, Wencan Wang, Qianqian Meng, Shunheng Zhou, Haizhou Liu, Xueyan Ma, Xu Zhou, Hui Liu, Xiaowen Chen*, Wei Jiang*. Inferring novel autophagy regulators based on transcription factors and non-Coding RNAs coordinated regulatory network. CELLS-BASEL. 2018 Nov 2. 7(11). pii: E194. PubMed

Shunheng Zhou, Lihong Wang, Qian Yang, Haizhou Liu, Qianqian Meng, Leiming Jiang, Shuyuan Wang*, Wei Jiang*. Systematical analysis of lncRNA–mRNA competing endogenous RNA network in breast cancer subtypes. Breast Cancer Research and Treatment. 2018 Feb 1. 169(2):267-275. PubMed

Enyu Dai, Jing Wang, Feng Yang, Xu Zhou, Qian Song, Shuyuan Wang, Xuexin Yu, Dianming Liu, Qian Yang, Hong Dai, Wei jiang*, Hong Ling*. Accurate prediction and elucidation of drug resistance based on the robust and reproducible chemoresponse communities. International Journal of Cancer. 2018 Apr 1. 142(7):1427-1439. PubMed

Jing Lin, Wei Liu, Tian Luan, Lili Yuan, Wei Jiang, Huilong Cai, Weiguang Yuan, Yuwen Wang, Qingyuan Zhang*, Lihong Wang*. High expression of PU.1 is associated with Her-2 and shorter survival in patients with breast cancer. Oncology Letters. 2017 Dec. 14(6):8220-8226. PubMed

Ramkrishna Mitra, Xi Chen, Evan J. Greenawalt, Ujjwal Maulik, Wei Jiang, Zhongming Zhao, Christine M. Eischen*. Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition. Nature Communications. 2017 Nov 17. 8(1):1604. PubMed

Weisha Liu, Shuyuan Wang, Shunheng Zhou, Feng Yang, Wei Jiang, Qingyuan Zhang*, Lihong Wang*. A systems biology approach to identify microRNAs contributing to cisplatin resistance in human ovarian cancer cells. Molecular BioSystems. 2017 Sep 1. 13(11):2268-2276. PubMed

Enyu Dai, Feng Yang, Jing Wang, Xu Zhou, Qian Song, Weiwei An, Lihong Wang*, Wei Jiang*. ncDR: a comprehensive resource of non-coding RNAs involved in drug resistance. Bioinformatics. 2017 Dec 15. 33(24):4010-4011. PubMed

Qian Yang, Shuyuan Wang, Enyu Dai, Shunheng Zhou, Dianming Liu, Haizhou Liu, Qianqian Meng, Bin Jiang*, Wei Jiang*. Pathway enrichment analysis approach based on topological structure and updated annotation of pathway. Briefings in Bioinformatics. 2017 Aug 16. 20(1):168-177. PubMed

Xinyi Liu, Dongfei Feng, Dianming Liu, Shuyuan Wang, Xuexin Yu, Enyu Dai, Jing Wang, Lihong Wang*, Wei Jiang*. Dissecting the Origin of Breast Cancer Subtype Stem Cell and the Potential Mechanism of Malignant Transformation. PloS ONE. 2016 Oct 21. 11(10):e0165001. PubMed

Xiaowen Chen, Hongbo Shi, Feng Yang, Lei Yang, Yingli Lv, Shuyuan Wang, Enyu Dai, Dianjun Sun*, Wei Jiang*. Large-scale identification of adverse drug reaction-related proteins through a random walk model. Scientific Reports. 2016 Nov 2. 6:36325. PubMed

Dianming Liu, Xuexin Yu, Shuyuan Wang, Enyu Dai, Leiming Jiang, Jing Wang, Qian Yang, Feng Yang, Shunheng Zhou, Wei Jiang*. The gain and loss of long noncoding RNA associated-competing endogenous RNAs in prostate cancer. Oncotarget. 2016 Aug 9. 7(35):57228-57238. PubMed

Jing Wang, Fanlin Meng, Enyu Dai, Feng Yang, Shuyuan Wang, Xiaowen Chen, Lei Yang, Yuwen Wang, Wei Jiang*. Identification of associations between small molecule drugs and miRNAs based on functional similarity. Oncotarget. 2016 Jun 21. 7(25):38658-38669. PubMed

Xuexin Yu, Lin Feng, Zujing Han, Bo Wu, Shuyuan Wang, Yun Xiao, Feng Li, Lianfeng Zhang, Bangrong Cao, Xuebing Di, Dan Lu, Xia Li, Wei Jiang*, Kaitai Zhang*, Shujun Cheng*. Crosstalk of dynamic functional modules in lung development of rhesus macaques. Molecular Biosystems. 2016 Apr. 12(4):1342-1349. PubMed

Xuexin Yu, Lin Feng, Dianming Liu, Lianfeng Zhang, Bo Wu, Wei Jiang*, Zujing Han*, Shujun Cheng*. Quantitative proteomics reveals the novel co-expression signatures in early brain development for prognosis of glioblastoma multiforme. Oncotarget. 2016 Mar 22. 7(12):14161-14171. PubMed

Fanlin Meng, Jing Wang, Engyu Dai, Feng Yang, Xiaowen Chen, Shuyuan Wang, Xuexin Yu, Dianming Liu, Wei Jiang*. Psmir: a database of potential associations between small molecules and miRNAs. Scientific Reports. 2016 Jan 13. 6:19264. PubMed

Wei Jiang, Ramkrishna Mitra, Chen-Ching Lin, Quan Wang, Feixiong Cheng, Zhongming Zhao*. Systematic dissection of dysregulated transcription factor–miRNA feed-forward loops across tumor types. Briefings in Bioinformatics. 2015 Dec 9. 17(6):996-1008. PubMed

Feng Li, Yun Xiao, Fei Huang, Wei Deng, Hongying Zhao, Xinrui Shi, Shuyuan Wang, Xuexin Yu, Lianfeng Zhang, Zujing Han, Longhai Luo, Qianhua Zhu, Wei Jiang, Shujun Cheng*, Xia Li*, Kaitai Zhang*. Spatiotemporal-specific lncRNAs in the brain, colon, liver and lung of macaque during development. Molecular Biosystems. 2015 Dec. 11(12):3253-3263. PubMed

Yan Zhang, Dianming Liu, Lihong Wang, Shuyuan Wang, Xuexin Yu, Enyu Dai, Xinyi Liu, Shanshun Luo*, Wei Jiang*. Integrated systems approach identifies risk regulatory pathways and key regulators in coronary artery disease. Journal of Molecular Medicine. 2015 Dec. 93(12):1381-1390. PubMed

Yingli Lv, Shuyuan Wang, Fanlin Meng, Lei Yang, Zhifeng Wang, Jing Wang, Xiaowen Chen, Wei Jiang*, Yixue Li*, Xia Li*. Identifying novel associations between small molecules and miRNAs based on integrated molecular networks. Bioinformatics. 2015 Nov 15. 31(22):3638-3644. PubMed

Chen-Ching Lin, Wei Jiang, Ramkrishna Mitra, Feixiong Cheng, Hui Yu, Zhongming Zhao*. Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers. Scientific Reports. 2015 Jul 9. 5:12063. PubMed

Xiaowen Chen, Yanqiu Wang, Pingping Wang, Baofeng Lian, Chunquan Li, Jing Wang, Xia Li*, and Wei Jiang*. Systematic Analysis of the Associations between Adverse Drug Reactions and Pathways. BioMed Research International. 2015 May. 2015:670949. PubMed

Shuyuan Wang, Wei Li, Baofeng Lian, Xinyi Liu, Yan Zhang, Enyu Dai, Xuexin Yu, Fanlin Meng, Wei Jiang*, Xia Li*. TMREC: a database of transcription factor and miRNA regulatory cascades in human diseases. PLoS ONE. 2015 May 1. 10(5):e0125222. PubMed

Lei Yang, Dapeng Hao, Jizhe Wang, Xudong Xing, Yingli Lv, Yongchun Zuo*, Wei Jiang*. Characterization of proteins in S. cerevisiae with subcellular localizations. Molecular Biosystems. 2015 May. 11(5):1360-1369. PubMed

Wei Jiang, Peilin Jia, Katherine E Hutchinson, Douglas B Johnson, Jeffrey A Sosman, Zhongming Zhao*. Clinically relevant genes and regulatory pathways associated with NRASQ61 mutations in melanoma through an integrative genomics approach. Oncotarget. 2015 Feb 10. 6(4):2496-2508. PubMed

Lei Yang, Dapeng Hao, Yingli Lv, Yongchun Zuo*, Wei Jiang*. Genome-wide characterization of essential, toxicity-modulating and no-phenotype genes in S. cerevisiae. Gene. 2015 Mar 15. 559(1):1-8. PubMed

Xuexin Yu, Baofeng Lian, Lihong Wang, Yan Zhang, Enyu Dai, Fanlin Meng, Dianming Liu, Shuyuan Wang, Xinyi Liu, Jing Wang, Xia Li*, Wei Jiang*. The pan-cancer analysis of gene expression patterns in the context of inflammation. Molecular Biosystems. 2014 Jul 29. 10(9):2270-2276. PubMed Front cover

Lei Yang, Jizhe Wang, Huiping Wang, Yingli Lv, Yongchun Zuo, Xiang Li*, Wei Jiang*. Analysis and identification of essential genes in humans using topological properties and biological information. Gene. 2014 Nov 10. 551(2):138-151. PubMed

Lei Yang, Jizhe Wang, Huiping Wang, Yingli Lv, Yongchun Zuo*, Wei Jiang*. Analysis and identification of toxin targets by topological properties in protein-protein interaction network. Journal of Theoretical Biology. 2014 May 21. 349:82-91. PubMed

Yanqiu Wang, Yang Li, Qi Wang, Yingli Lv, Shiyuan Wang, Xi Chen, Xuexin Yu, Wei Jiang*, Xia Li*. Computational identification of human long intergenic non-coding RNAs using a GA-SVM algorithm. Gene. 2014 Jan 1. 533(1):94-99. PubMed

Lei Yang, Jizhe Wang, Huiping Wang, Yingli Lv, Yongchun Zuo*, Wei Jiang*. Characterization of essential genes by topological properties in the perturbation sensitivity network. Biochemical and Biophysical Research Communications. 2014 Jun 13. 448(4):473-479. PubMed

Lin Feng, Jiamei Wang, Bangrong Cao, Yi Zhang, Bo Wu, Xuebing Di, Wei Jiang, Ning An, Dan Lu, Suhong Gao, Yuda Zhao, Zhaoli Chen, Yousheng Mao, Yanning Gao, Deshan Zhou, Jin Jen, Xiaohong Liu, Yunping Zhang, Xia Li, Kaitai Zhang*, Jie He*, Shujun Cheng*. Gene expression profiling in human lung development: an abundant resource for lung adenocarcinoma prognosis. PLoS ONE. 2014 Aug 20. 9(8):e105639. PubMed

Lei Yang, Jizhe Wang, Yingli Lv, Dapeng Hao, Yongchun Zuo, Xiang Li*, Wei Jiang*. Characterization of TATA-containing genes and TATA-less genes in S. cerevisiae by network topologies and biological properties. Genomics. 2014 Dec. 104(6 Pt B). PubMed

Enyu Dai, Yingli Lv, Fanlin Meng, Xuexin Yu, Yan Zhang, Shuyuan Wang, Xinyi Liu, Dianming Liu, Jing Wang, Xia Li*, Wei Jiang*. CREAM: a database for chemotherapy resistance-associated miRSNP. CELL DEATH and DISEASE. 2014 May 29. 5:e1272. PubMed

Lei Yang, Yingli Lv, Tao Li, Yongchun Zuo*, Wei Jiang*. Human proteins characterization with subcellular localizations. Journal of Theoretical Biology. 2014 Oct 7. 358:61-73. PubMed

Enyu Dai, Xuexin Yu, Yan Zhang, Fanlin Meng, Shuyuan Wang, Xinyi Liu, Dianming Liu, Jing Wang, Xia Li*, Wei Jiang*. EpimiR: a database of curated mutual regulation between miRNAs and epigenetic modifications. Database (Oxford). 2014 Mar 28. 2014:bau023. PubMed

Fanlin Meng, Enyu Dai, Xuexin Yu, Yan Zhang, Xiaowen Chen, Xinyi Liu, Shuyuan Wang, Lihua Wang*, Wei Jiang*. Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease. Journal of The Royal Society Interface. 2013 Dec 18. 11(92):20131057. PubMed

Hongbo Shi, Juan Xu, Guangde Zhang, Liangde Xu, Chunquan Li, Li Wang, Zheng Zhao, Wei Jiang, Zheng Guo*, Xia Li*. Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes. BMC System Biology. 2013 Oct 8. 7:101. PubMed

Xinyi Liu, Shuyuan Wang, Fanlin Meng, Jizhe Wang, Yan Zhang, Enyu Dai, Xuexin Yu, Xia Li*, Wei Jiang*. SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression. Bioinformatics. 2013 Feb 1. 29(3):409-411. PubMed

Wei Jiang, Yan Zhang, Fanlin Meng, Baofeng Lian, Xiaowen Chen, Xuexin Yu, Enyu Dai, Shuyuan Wang, Xinyi Liu, Xiang Li, Lihong Wang*, Xia Li*. Identification of active transcription factor and miRNA regulatory pathways in Alzheimer's disease. Bioinformatics. 2013 Oct 15. 29(20):2596-2602. PubMed

Hui Han, Yu-Hong Wang, Guang-Jin Qu, Ting-Ting Sun, Feng-Qing Li, Wei Jiang*, Shan-Shun Luo*. Differentiated miRNA expression and validation of signaling pathways in apoE gene knockout mice by cross-verification microarray platform. Experimental and Molecular Medicine. 2013 Mar 8. 45:e13. PubMed

Lihong Wang, Wei Liu, Wei Jiang, Jing Lin, Yongdong Jiang, Bo Li*, Da Pang*. A miRNA binding site single-nucleotide polymorphism in the 3'-UTR region of the IL23R gene is associated with breast cancer. PLoS ONE. 2012 Dec 11. 7(12):e49823. PubMed

Lihong Wang, Yongdong Jiang, Youxue Zhang, Yuwen Wang, Sunhui Huang, Zhihua Wang, Baoling Tian, Yue Yang, Wei Jiang*, Da Pang*. Association analysis of IL-17A and IL-17F polymorphisms in Chinese Han women with breast cancer. PLoS ONE. 2012 Mar 26. 7(3): e34400. PubMed

Xia Li*,†, Wei Jiang, Wei Li, Baofeng Lian, Shuyuan Wang, Mingzhi Liao, Xiaowen Chen, Yanqiu Wang, Yingli Lv, Shiyuan Wang, Lei Yang. Dissection of human MiRNA regulatory influence to subpathway. Briefings in Bioinformatics. 2012 Mar. 13(2):175-186. PubMed

Chunquan Li, Desi Shang, Yan Wang, Jing Li, Junwei Han, Shuyuan Wang, Qianlan Yao, Yingying Wang, Yunpeng Zhang, Chunlong Zhang, Yanjun Xu, Wei Jiang, Xia Li*. Characterizing the network of drugs and their affected metabolic subpathways. PLoS ONE. 2012 Oct. 7(10):e47326. PubMed

Wei Jiang, Xiaowen Chen, Mingzhi Liao, Wei Li, Baofeng Lian, Lihong Wang, Fanlin Meng, Xinyi Liu, Xiujie Chen, Yan Jin, Xia Li*. Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses. Scientific Reports. 2012 Feb. 2:282. PubMed

Xin Chen, Wei Jiang, Qianghu Wang, Teng Huang, Peng Wang, Yan Li, Xiaowen Chen, Yingli Lv, Xia Li*. Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network. BMC Medical Genomics. 2012 Oct 2. 5:43. PubMed

Juan Xu, Chuan-Xing Li, Yong-Sheng Li, Jun-Ying Lv, Ye Ma, Ting-Ting Shao, Liang-De Xu, Ying-Ying Wang, Lei Du, Yun-Peng Zhang, Wei Jiang, Chun-Quan Li, Yun Xiao, Xia Li*. MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Research. 2011 Feb. 39(3):825-836. PubMed

Jian Wu, Maomao Zhang, Fang Liu, Wei Jiang, Li Yin, Haibo Jia, Meng Sun, Xiaoli Han, Huimin Liu, Xingtao Huang, Bo Yu. Differential expression profile of circulating microRNAs in patients with in-stent stenosis. Heart. 2011 Oct. 97:A68-A68.

Yanqiu Wang, Xiaowen Chen, Wei Jiang, Li Li, Wei Li, Lei Yang, Mingzhi Liao, Baofeng Lian, Yingli Lv, Shiyuan Wang, Shuyuan Wang, Xia Li*. Predicting human microRNA precursors based on an optimized feature subset generated by GA-SVM. Genomics. 2011 Aug. 98(2):73-78. PubMed

Chenqu Wang, Wei Jiang, Wei Li, Baofeng Lian, Xiaowen Chen, Lin Hua, Hui Lin, Dongguo Li, Xia Li*, Zhicheng Liu*. Topological properties of the drug targets regulated by microRNA in human protein-protein interaction network. Journal of Drug Targeting. 2011 Jun. 19(5):354-364. PubMed

Shihua Zhang, Chao Wu, Xia Li*,†, Xi Chen, Wei Jiang, Bin-Sheng Gong, Jiang Li, Yu-Qing Yan. From phenotype to gene: detecting disease-specific gene functional modules via a text-based human disease phenotype network construction. FEBS Letters. 2010 Aug 20. 584(16):3635-3643. PubMed

Gao Xiang, Fu Zhenkun, Chen Shuang, Zhang Jie, Zhang Hua, Jiang Wei, Pang Da*, Li Dianjun*. Association of DNMT1 gene polymorphisms in exons with sporadic infiltrating ductal breast carcinoma among Chinese Han women in the Heilongjiang Province. Clinical Breast Cancer. 2010 Oct 1. 10(5):373-377. PubMed

Mingzhi Liao, Wei Jiang, Xiaowen Chen, Baofeng Lian, Wei Li, Yingli Lv, Yanqiu Wang, Shiyuan Wang, Xia Li*. Systematic analysis of regulation and functions of co-expressed microRNAs in humans. Molecular Biosystems. 2010 Oct. 6(10):1863-1872. PubMed

Zhenkun Fu, Dalin Li, Wei Jiang, Lihong Wang, Jie Zhang, Fengyan Xu, Da Pang*, Dianjun Li*. Association of BTLA gene polymorphisms with the risk of malignant breast cancer in Chinese women of Heilongjiang Province. Breast Cancer Research and Treatment. 2010 Feb. 120(1):195-202. PubMed

Mingzhu Zhu, Lei Gao, Xia Li*, Zhicheng Liu, Chun Xu, Yuqing Yan, Erin Walker, Wei Jiang, Bin Su, Xiujie Chen, Hui Lin. The analysis of the drug-targets based on the topological properties in the human protein-protein interaction network. Journal of Drug Targeting. 2009 Aug. 17(7):524-532. PubMed

Jie Zhang, Mingyan Zhang, Wei Jiang, Lihong Wang, Zhenkun Fu, Dalin Li, Da Pang*, Dianjun Li*. B7-H4 gene polymorphisms are associated with sporadic breast cancer in a Chinese Han population. BMC Cancer. 2009 Nov 11. 9:394. PubMed

Chunquan Li, Xia Li*,†, Yingbo Miao, Qianghu Wang, Wei Jiang, Chun Xu, Jing Li, Junwei Han, Fan Zhang, Binsheng Gong, Liangde Xu. SubpathwayMiner: a software package for flexible identification of pathways. Nucleic Acids Research. 2009 Oct. 37(19):e131. PubMed

Wei Jiang, Lijie Zhang, Bo Na, Lihong Wang, Jiankai Xu, Xia Li*, Yadong Wang, Shaoqi Rao. Mapping and characterization of two relevance networks from SNP and gene levels. Progress in Natural Science. 2009 May. 19:653-657.

Chuanxing Li, Guangmei Zhang, Xia Li*, Shaoqi Rao, Binsheng Gong, Wei Jiang, Dapeng Hao, Peng Wu, Chao Wu, Lei Du, Yun Xiao, Yingying Wang. A systematic method for mapping multiple loci: an application to construct a genetic network for rheumatoid arthritis. Gene. Jan 31. 408(1-2):104-111. PubMed

Wei Jiang, Xia Li, Shaoqi Rao, Lihong Wang, Lei Du, Chuanxing Li, Chao Wu, Hongzhi Wang, Yadong Wang, Baofeng Yang*. Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. BMC Systems Biology. 2008 Aug 10. 2:72. PubMed

Wei Zhang, Li Li, Xia Li*, Wei Jiang, Jianmin Huo, Yadong Wang, Meihua Lin, Shaoqi Rao. Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering. BMC Genomics. 2007 Sep 22. 8:332. PubMed

Lihong Wang, Dalin Li, Zhenkun Fu, Heng Li, Wei Jiang, Dianjun Li*. Association of CTLA-4 gene polymorphisms with sporadic breast cancer in Chinese Han population. BMC Cancer. 2007 Sep 10. 7:173. PubMed

Shao-Qi Rao*,†, Liang-De Xu, Guang-Mei Zhang, Xia Li*, Lin Li, Gong-Qing Shen, Yang Jiang, Yue-Ying Yang, Bin-Sheng Gong, Wei Jiang, Fan Zhang, Yun Xiao, Qing K Wang. Familial aggregation analysis of gene expressions. BMC Proc. 2007 Dec 18. 1 Suppl 1:S49. PubMed

Xia Li*, Shao-qi Rao*, Wei Zhang, Zheng Guo, Wei Jiang, Lei Du. Decision forest analysis of large-scale sib-pair identical-by-decent profiles for locating the underlying disease genes for alcoholism in human. Beijing Da Xue Xue Bao. 2006 Feb 18. 38(1):71-73. PubMed

Xia Li*,†, Shaoqi Rao*,†, Wei Jiang, Chuanxing Li, Yun Xiao, Zheng Guo, Qingpu Zhang, Lihong Wang, Lei Du, Jing Li, Li Li, Tianwen Zhang, Qing K Wang. Discovery of Time-Delayed Gene Regulatory Networks based on temporal gene expression profiling. BMC Bioinformatics. 2006 Jan 18. 7:26. PubMed

Li Li, Xia Li, Yi-Han Chen, Zheng Guo, Wei Jiang, Rui-Jie Zhang, Shao-Qi Rao*. Analysis of diffuse large B-cell lymphoma heterogeneity based on coupled two-way clustering. Yi Chuan. 2006 Sep. 28(9):1129-1134. PubMed

Wei Jiang, Xia Li*,†, Zheng Guo, Chuanxing Li, Lihong Wang, Shaoqi Rao*. A novel model-free approach for reconstruction of time-delayed gene regulatory networks. Science in China Series C Life Sciences. 2006 Apr. 49(2):190-200. PubMed

Li Li, Wei Jiang, Xia Li*,†, Kathy L Moser, Zheng Guo, Lei Du, Qiuju Wang, Eric J Topol, Qing Wang, Shaoqi Rao*,†. A robust hybrid between genetic algorithm and support vector machine for extracting an optimal feature gene subset. Genomics. 2005 Jan. 85(1):16-23. PubMed