* represents first authorship.
# represents corresponding authorship.
1. Wang D*, Li S*, Yang Z*, Yu C*, Wu P, Yang Y, Zhang R, Li Q, Yang J, Li H, Ji G, Wang Y, Xie K, Liu Y, Wang K, Zhu D, Zhang W, Liu D, Chen B, Li W, Single-cell transcriptome analysis deciphers the CD74-mediated immune evasion and tumour growth in lung squamous cell carcinoma with chronic obstructive pulmonary disease, Clin Transl Med,2024 Aug;14(8):e1786. [Abstract] [Full Paper]
2. Lang X*, Yu C*, Shen M*, Gu L, Qian Q, Zhou D, Tan J, Li Y, Peng X, Diao S, Deng Z, Ruan Z, Xu Z, Xing J, Li C, Wang R, Ding C, Cao Y, Liu Q, PRMD: an integrated database for plant RNA modifications, Nucleic Acids Res, 2024 Jan 5;52(D1):D1597-D1613. [Abstract] [Full Paper]
3. Lu C*, Pi X*, Xu W, Qing P, Tang H, Li Y, Zhao Y, Liu X, Tang H, Liu Y, Clinical significance of T cell receptor repertoire in primary Sjogren's syndrome, EBioMedicine, 2022 Oct;84:104252. [Abstract] [Full Paper]
4. Luo C*, Pi X*, Zhang Q, Hu N, Xiao Y, Sweeney JA, Bishop JR, Gong Q, Xie D#, Lui S#, A subtype of schizophrenia patients with altered methylation level of genes related to immune cell activity, Psychol Med, 2024 Jul;54(10):2538-2546. [Abstract] [Full Paper]
5. Kailing Tu*, Xuemei Li, Qilin Zhang, Wei Huang#, Dan Xie#, A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing, Bioinformatics, Volume 40, Issue 5, May 2024, btae206. [Abstract] [Full Paper]
6. Wang X, Luo Y, He S, Lu Y, Gong Y, Gao L, Mao S, Liu X, Jiang N, Pu Q, Du D, Shu Y, Hai S, Li S, Chen HN, Zhao Y, Xie D, Qi S, Lei P, Hu H, Xu H, Zhou ZG, Dong B, Zhang H, Zhang Y, Dai L. ,Age-, sex- and proximal-distal-resolved multi-omics identifies regulators of intestinal aging in non-human primates. Nat Aging, 2024 Feb 6. doi: 10.1038/s43587-024-00572-9 IF: 17.0 Q1 [Abstract] [Full Paper]
7. Xuemei Li*, Keying Lu*,Xiao Chen*, Kailing Tu, Dan Xie#,capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements. Communications Biology, 2023, 6(1): 974.doi: 10.1038/s42003-023-05349-1 IF: 5.2 Q1 [Abstract] [Full Paper]
8. Zhidong Zhang*, Xuenan Pi*,Chang Gao, Jun Zhang, Lin Xia, Xiaoqin Yan, Xinlei Hu, Ziyue Yan, Shuxin Zhang, Ailin Wei, Yuer Guo, Jingfeng Liu, Ang Li, Xiaolong Liu, Wei Zhang, Yanhui Liu, Dan Xie#,Integrated fragmentomic profile and 5-Hydroxymethylcytosine of capture-based low-pass sequencing data enables pan-cancer detection via cfDNA. Translational Oncology, Volume 34,2023,101694. https://doi.org/10.1016/j.tranon.2023.101694.IF: 4.5 Q1 [Abstract] [Full Paper]
9. Shuxin Zhang*, Jun Zhang*, Xinlei Hu, Senlin Yin, Yunbo Yuan, Lin Xia, Feng Cao, Xiaoqin Yan, Ziyue Yan, Qing Mao, Dan Xie#, Yanhui Liu#,Non-invasive Detection of Brain Gliomas Using Plasma Cell-free DNA 5-Hydroxymethylcytosine Sequencing. Int J Cancer, 2022 Dec 15. doi: 10.1002/ijc.34401.IF: 5.7 Q1 [Abstract] [Full Paper]
10. Haoyu Wang, Shuxin Zhang, Xiang Xing, Qiang Yue, Wentao Feng, Siliang Chen, Jun Zhang, Dan Xie, Ni Chen, Yanhui Liu#,Radiomic study on preoperative multi-modal magnetic resonance images identifies IDH-mutant TERT promoter-mutant gliomas. Cancer Med , 2022 Sep 29.doi: 10.1002/cam4.5097.IF: 2.9 Q2 [Abstract] [Full Paper]
11. Ying Zhao*, Qilin Zhang*, Kailin Tu, Yanmei Chen, Yuxuan Peng, Yinyun Ni, Guonian Zhu, Cheng Cheng, Yangqian Li, Xue Xiao, Chunyan Yu, Keying Lu, Yaxin Chen, Chengpin Li, Jun Tang, Gang Wang, Wenxin Luo，Wengeng Zhang, Guowei Che, Weimin Li, Zhoufeng Wang#, Dan Xie#,Single-cell transcriptomics of immune cells reveal diversity and exhaustion signatures in non-small-cell lung cancer. Front Immunol, 2022 Jul 6;13:854724. [Abstract] [Full Paper]
12. Na F*, Pan X*, Chen J*, Chen X*, Wang M, Chi P, You L, Zhang L, Zhong A, Zhao L, Dai S, Zhang M, Wang Y, Wang B, Zheng J, Wang Y, Xu J, Wang J, Wu B, Chen M, Liu H, Xue J, Huang M, Gong Y, Zhu J, Zhou L, Zhang Y, Yu M, Tian P, Fan M, Lu Z, Xue Z, Zhao Y, Yang H, Zhao C, Wang Y, Han J, Yang S, Xie D, Chen L, Zhong Q, Zeng M, Lowe SW, Lu Y, Liu Y, Wei Y, Chen C#. KMT2C deficiency promotes small cell lung cancer metastasis through DNMT3A-mediated epigenetic reprogramming. Nat Cancer, 2022 Jun;3(6):753-767. [Abstract] [Full Paper]
13. Xinlei Hu*, Kai Luo*, Hui Shi*, Xiaoqin Yan*, Ruichen Huang, Bi Zhao, Jun Zhang, Dan Xie#,Wei Zhang#,Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer. Clinical Epigenetics,14,15(2022). [Abstract] [Full Paper]
14. Lin Xia*, Zhoufeng Wang*, XinYue Wu*, Tianfu Zeng*, Wenxin Luo, Xinlei Hu, Yinyun Ni, Guowei Che, Lunxu Liu, Wei Zhang, Dan Xie#,Weimin Li#, Multi-platform Discovery and Regulatory Function Analysis of Structural Variations in Non-small Cell Lung Carcinoma .Cell Reports, 2021, 36(10). [Abstract] [Full Paper]
15. Chunyan Luo, XueNan Pi, Na Hu, Xiao Wang, Yuan Xiao, Siyi Li, John A. Sweeney, Jeffrey R. Bishop, Qiyong Gong#, Dan Xie#,Su Lui#, Subtypes of schizophrenia identified by multi-omic measures associated with dysregulated immune function.Molecular Psychiatry(2021). https://doi.org/10.1038/s41380-021-01308-6.IF: 9.6 Q1 [Abstract] [Full Paper]
16. Jie Deng*, Kai Luo*,Pengchao Xu*, Qingyuan Jiang, Yuan Wang, Yunqi Yao, Xiaolei Cheng, Fuyi Cheng, Dan Xie#, Hongxin Deng#, High-efficiency cMYC-mediated Induction of Fuctional Hepatoblasts from Human Umbilical Cord Mesenchymal Stem Cells.Stem Cell Research and therapy,12, 375 (2021). [Abstract] [Full Paper]
17. Jie Tang*,Kailing Tu*, Keying Lu*, Jiaxun Zhang*, Kai Luo, Haoxuan Jin, Lei Wang, Lie Yang, Weiran Xiao, Qilin Zhang, Xiaoling Liu, Xinyi Ge, Guibo Li#, Zongguang Zhou#, Dan Xie#, Single-cell exome sequencing reveals multiple subclones in metastatic colorectal carcinoma. Genome Medicine, Genome Med 13, 148 (2021). [Abstract] [Full Paper]
18. Kailing Tu*, Keying Lu*, Qilin Zhang, Wei Huang#, Dan Xie#, Accurate single-cell genotyping utilizing information from the local genome territory. Nucleic Acids Research, Volume 49, Issue 10, 4 June 2021, Page e57. [Abstract] [Full Paper]
19. Z. Cai*, J. Zhang*, Y. He*, L. Xia*, X. Dong, G. Chen, Y. Zhou, X. Hu, S. Zhong, Y. Wang, H. Chen, D. Xie#, X. Liu#, J. Liu#, Liquid biopsy by combining 5-hydroxymethylcytosine signatures of plasma cell-free DNA and protein biomarkers for diagnosis and prognosis of hepatocellular carcinoma. ESMO Open, 2021, 6(1): 100021. [Abstract] [Full Paper]
20. Feng Cao*, Ailin Wei*, Xinlei Hu, Yijing He, Jun Zhang, Lin Xia, Kailing Tu, Jue Yuan, Ziheng Guo, Hongying Liu, Dan Xie#, Ang Li#, Integrated Epigenetic Biomarkers in Circulating Cell-free DNA as a Robust Classifier for Pancreatic Cancer.Clinical Epigenetics, 2020, 12: 112. [Abstract] [Full Paper]
21. Senlin Yin*, Keying Lu*, Tao Tan*, Jie Tang*, Jingkuan Wei, Xu Liu, Xinlei Hu, Haisu Wan, Wei Huang, Yong Fan#, Dan Xie#, Yang Yu#, Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain. Nature Communications, 2020, 11(1):474. [Abstract] [Full Paper]
22. Zhoufeng Wang*; Kailing Tu*; Lin Xia*; Kai Luo*; Wenxin Luo; Jie Tang; Keying Lu; Xinlei Hu; Yijing He; Wenliang Qiao; Yongzhao Zhou; Jun Zhang; Feng Cao; Shuiping Dai; Panwen Tian; Ye Wang; Lunxu Liu; Guowei Che; Qinghua Zhou; Dan Xie#; Weimin Li#, The Open Chromatin Landscape of Non-small Cell Lung Carcinoma. Cancer Research, 2019, 79(19):4840-4854. [Abstract] [Full Paper]
23. Rui Chen*; Lin Xia*; Kailing Tu*; Meixue Duan; Kimberly Kukurba; Jennifer Li-Pook-Than; Dan Xie#; Michael Snyder#, Longitudinal Personal DNA Methylome Dynamics Associate with a Chronic Condition. Nature Medicine, 2018, 24(12): 1930-1939 (This paper is a cover story). [Abstract] [Full Paper]
24. Tao Tan*; Lin Xia*; Kailing Tu*; Jie Tang*; Senlin Yin; Lunzhi Dai; Peng Lei; Biao Dong; Hongbo Hu; Yong Fan; Yang Yu#; Dan Xie#, Improved Macaca fascicularis gene annotation reveals evolution of gene expression profiles in multiple tissues.BMC Genomics, 2018, 19(1):787. [Abstract] [Full Paper]
25. Chun-Xiao Song*; Senlin Yin*; Li Ma; Amanda Wheeler; Yu Chen; Yan Zhang; Bin Liu; Junjie Xiong; Weihan, Zhang; Jiankun Hu; Zongguang Zhou; Biao Dong; Zhiqi Tian; Stefanie S. Jeffrey; Mei-Sze Chua; Samuel So; Weimin Li; Yuquan Wei; Jiajie Diao; Dan Xie#; Stephen R Quake#, 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages. Cell Research, 2017, 27(10):1231-1242. [Abstract] [Full Paper]
26. Volodymyr Kuleshov*, Dan Xie*, Rui Chen*, Dmitry Pushkarev, Zhihai Ma, Tim Blauwkamp, Michael Kertesz, Michael Snyder. Whole genome haplotyping using a combination of dilution and statistical methods.Nature Biotechnology, 2014, 32, 261-266. [Abstract] [Full Paper]
27.The modENCODE Consortia. Comparative analysis of regulatory information and circuits across diverse species. Nature, 2014, 512(7515):453-6. [Abstract] [Full Paper]
28.Carlos Araya, Trupti Kawli, Anshul Kundaje, Lixia Jiang, Beijing Wu, Dionne Vafreados, Robert Terrell, Peter Weissdepp, Louis Gevirtzman, Daniel Mace, Wei Niu, Alan Boyle, Dan Xie, Lijia Ma, John Murray, Valerie Reinke, Robert Waterston, Michael Snyder. A cis-regulatory analysis of the c. elegans genome with temporal and spatial resolution. Nature, 2014, 512(7515):400-5. [Abstract] [Full Paper]
29. Dan Xie*, Alan Boyle*, Linfeng Wu*, Jie Zhai, Trupti Kwali, Michael Snyder. Dynamic Trans-Acting Factor Co-localization in Human Cells. Cell, 2013, 155(3):713-724. [Abstract] [Full Paper]
30. Maya Kasowski*, Sofia Kyriazopoulou-Panagiotopoulou*, Fabian Grubert*, Judith B Zaugg*, Anshul Kundaje*, Yuling Liu, Alan P Boyle, Qiangfeng Cliff Zhang, Fouad Zakharia, Damek V Spacek, Jingjing Li, Dan Xie, Lars M Steinmetz, John B. Hogenesch, Manolis Kellis, Serafim Batzoglou, Michael Snyder. Extensive variation in chromatin states across humans. Science, 2013, 342(6159):750-2. [Abstract] [Full Paper]
31. Linfeng Wu*, Sophie Candille*, Yoonha Choi, Dan Xie, Lihua Jiang, Jennifer Li-Pook-Than, Hua Tang, Michael Snyder. Variation and genetic control of protein abundance in humans.Nature, 2013, 499:79-82. [Abstract] [Full Paper]
32. Chieh-Chun Chen, Shu Xiao, Dan Xie, Xiaoyi Cao, Chun-Xiao Song, Ting Wang, Chuan He, Sheng Zhong. Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PLoS Computational Biology, 2013, 9(12):e1003367. [Abstract] [Full Paper]
33. Shu Xiao*, Dan Xie*, Xiaoyi Cao*, Pengfei Yu*, Xiaoyun Xing, Chieh-Chun Chen, Meagan Musselman, Mingchao Xie, Franklin D. West, Harris A. Lewin, Ting Wang, Sheng Zhong. Comparative epigenomic annotation of regulatory DNA.Cell, 2012, 149:1381-1391. [Abstract] [Full Paper]
34. Dan Xie*, Chieh-Chun Chen*, Xin He, Sheng Zhong. Towards an evolutionary model of transcription network. PLoS Computational Biology, 2011, 7(6):e1002064. [Abstract] [Full Paper]
35. Marcelo Rivas-Astroza, Dan Xie, Xiaoyi Cao, Sheng Zhong. Mapping personal functional data to personal genome.Bioinformiatics, 2011, 27(24):3427-3429. [Abstract] [Full Paper]
36. Dan Xie*, Chieh-Chun Chen*, Leon Ptaszek, Shu Xiao, Xiaoyi Cao, Yanen Li, Douglas A. Melton, Harris A Lewin, Chad Cowan, Sheng Zhong. Rewireable gene regulatory networks in the preimplantation development of three mammalian species. Genome Research, 2010, 20:804-815(This paper is a cover story and has been highlighted on Nature). [Abstract] [Full Paper]
37. Jun Cai, Dan Xie, Zhewen Fan, John Marden, Wing H. Wong, Sheng Zhong. Modeling Co-expression Across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem C.PLoS Computational Biology, 2010, 6(3):e1000707 [Abstract] [Full Paper]
38. Feng Hong, Fang Fang, Xuming He, Xiaoyi Cao, Hiram Chipperfield, Dan Xie, NG Huck Hui, Wing H. Wong, Sheng Z Detecting early differentially expressed genes in a mixture of differentiating embryonic stem cells. PLoS Computational Biology, 2009, 5(12):e1000607 [Abstract] [Full Paper]
39. Dan Xie, Jun Cai, Na-Yu Chia, Huck H. Ng and Sheng Zhong. Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells. Genome Research, 2008, 18:1325-1335. [Abstract] [Full Paper]
40. Sheng Zhong and Dan Xie. Gene Ontology analysis in multiple gene clusters under multiple hypothesis testing framework. Artificial Intelligence in Medicine, 2007, 41:105-115 (This paper is reviewed by Editorial on Artificial Intelligence in Medicine 41:83-86). [Abstract] [Full Paper]
41. Chulyun Kim, Sangkyum Kim, Russell Dorer, Dan Xie, Jiawei Han, Sheng Zhong. TagSmart: Software for Analysis and Visualization of Yeast Mutant Fitness Data Measured by TAG Microarrays. BMC Bioinformatics., 2007, 8:128. [Abstract] [Full Paper]
42. Dan Xie*; Li, Ao; Wang, Minghui; Fan, Zhewen; Feng, Huanqing. LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST. Nucleic Acids Research., 2005.7.1, 33: W105-W110. [Abstract] [Full Paper]