2024
2023
2022
2021
2020
2019
2018
2017
2016
Before2016
2024
- Haiyan Gong#, Sichen Zhang, Xiaotong Zhang* and Yang Chen*. A Method for chromatin domain partitioning based on hypergraph clustering. Computational and Structural Biotechnology Journal, 10 April 2024. PDF
- Longjiang Xu#, Zan Yuan#, Jiafeng Zhou#, Yuan Zhao#, Wei Liu, Shuaiyao Lu1, Zhanlong He, Boqin Qiang, Pengcheng Shu*, Yang Chen*, Xiaozhong Peng*.Temporal transcriptomic dynamics in developing macaque neocortex. eLife, 28 February 2024. PDF
- Xinyuan Tong#, Ayushi S Patel, Eejung Kim, Hongjun Li, Yueqing Chen, Shuai Li, Shengwu Liu, Julien Dilly, Kevin S Kapner, Ningxia Zhang, Yun Xue, Laura Hover, Suman Mukhopadhyay, Fiona Sherman, Khrystyna Myndzar, Priyanka Sahu, Yijun Gao, Fei Li, Fuming Li, Zhaoyuan Fang, Yujuan Jin, Juntao Gao, Minglei Shi, Satrajit Sinha, Luonan Chen, Yang Chen, Thian Kheoh, Wenjing Yang, Itai Yanai, Andre L Moreira, Vamsidhar Velcheti, Benjamin G Neel, Liang Hu, James G Christensen, Peter Olson, Dong Gao, Michael Q Zhang*, Andrew J Aguirre*, Kwok-Kin Wong*, Hongbin Ji*. Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer. Cancer Cell, 11 March 2024, 42, 1–16. PDF
2023
- Haiyan Gong#, Minghong Li#, Mengdie Ji, Xiaotong Zhang*, Zan Yuan, Sichen Zhang, Yi Yang, Chun Li, Yang Chen*. MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network. Cell Reports Methods, 12 January 2023, 100386. PDF
- Shiwei Qumu#, Weiliang Sun#, Jing Guo, Yuting Zhang, Lesi Cai , Chaozeng Si, Xia Xu, Lulu Yang, Xuanming Situ, Tianyi Yang, Jiaze He, Minghui Shi, Dongyan Liu, Xiaoxia Ren, Ke Huang, Hongtao Niu, Hong Li, Chang’An Yu, Yang Chen*, Ting Yang*. Pulmonary rehabilitation restores limb muscle mitochondria and improves the intramuscular metabolic profile. Chinese Medical Journal, 9 February 2023. PDF
- Haiyan Gong#, Minghong Li#, Mengdie Ji, Xiaotong Zhang*, Zan Yuan, Sichen Zhang, Yi Yang, Chun Li, and Yang Chen*. Calculating the spatial density of regulatory chromatin interactions using multi-modal datasets from the same cell line. STAR Protocols, 31 March 2023. PDF
- Haiyan Gong#, Zhengyuan Chen, Yuxin Tang, Minghong Li, Sichen Zhang, Xiaotong Zhang*, Yang Chen*. Computational methods for identifying enhancer-promoter interactions. Quantitative Biology, 2023,11(2): 122–142. PDF
- Haiyan Gong#, Fuqiang Ma, Xiaotong Zhang, Yi Yang,Minghong Li, Zhengyuan Chen, Sichen Zhang*, Yang Chen*. A 3D Chromosome Structure Reconstruction method with High Resolution Hi-C Data using Nonlinear Dimensionality Reduction and Divide-and-conquer strategy. IEEE Transactions on NanoBioscience, 18 May 2023. PDF
2022
- Haiyan Gong, Yi Yang, Xiaotong Zhang*, Minghong Li, Sichen Zhang, Yang Chen*. CASPIAN: A Method to Identify Chromatin Topological Associated Domains based on Spatial Density Cluster. Computational and Structural Biotechnology Journal,2022,20:4816-4824. PDF
- Ruiting Wang#, Fengling Chen#, Qian Chen#, Xin Wan#, Minglei Shi, Antony K. Chen, Zhao Ma, Guohong Li, Min Wang, Yachen Ying, Qinyao Liu, Hu Li, Xu Zhang, Jinbiao Ma, Jiayun Zhong, Meihong Chen, Michael Q. Zhang*, Yong Zhang*, Yang Chen*, Dahai Zhu*. MyoD is a 3D genome structure organizer for muscle cell identity. Nature Communications,2022,13:205. PDF
- Wenlong Shen#, Yan Zhang#, Minglei Shi#, Bingyu Ye, Man Yin, Ping Li, Shu Shi, Yifei Jin, Zhang Zhang, Michael Q. Zhang, Yang Chen*, Zhihu Zhao*. Profiling and characterization of constitutive chromatin enriched RNAs. iScience,2022,105349. PDF
- Liang Chen#, Kui Hua#, Ningning Zhang, Jingyu Wang, Jian Meng, Zhenliang Hu, Haoxiang Gao, Fanhong Li, Yang Chen, Jie Ren, Liyang Liu, Qiming Zhou, Jin Gu, Jiangping Song*, Xuegong Zhang*, Shengshou Hu*. Multifaceted Spatial and Functional Zonation of Cardiac Cells in Adult Human Heart. Circulation,2022,145:315–318. PDF
- Tiantian Guo, Yang Chen, Minglei Shi, Xiangyu Li*, Michael Q Zhang*. Integration of single cell data by disentangled representation learning. Nucleic Acids Research,2022,50(2):e8. PDF
- Zhenyi Wang, Yanjie Zhong, Zhaofeng Ye, Lang Zeng, Yang Chen, Minglei Shi, Zhiyuan Yuan, Qiming Zhou, Minping Qian*, Michael Q Zhang*. MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data with transition pathway and critical point detection. Nucleic Acids Research,2022,50(1):46-56. PDF
- Yawei Song, Zhengyu Liang, Jie Zhang, Gongcheng Hu, Juehan Wang, Yaoyi Li, Rong Guo, Xiaotao Dong, Isaac A Babarinde, Wangfang Ping, Ying-Liang Sheng, Huanhuan Li, Zhaoming Chen, Minghui Gao, Yang Chen, Ge Shan, Michael Q Zhang, Andrew P Hutchins, Xiang-Dong Fu*, Hongjie Yao*. CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming. 2022, Cell Reports,39, 110626. PDF
2021
- Zhiyuan Yuan#, Qiming Zhou#, Lesi Cai#, Lin Pan, Weiliang Sun, Shiwei Qumu , Si Yu, Jiaxin Feng, Hansen Zhao, Yongchang Zheng, Minglei Shi, Shao Li, Yang Chen*, Xinrong Zhang*, Michael Q. Zhang*.SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment. Nature Methods,2021,18(10):1223-1232. PDF
- Xuezhu Wang#, Yucheng Dong#, Yongchang Zheng, Yang Chen*. Multi-omics Metabolic and Epigenetics Regulatory Network in Cancer: A Systems Biology Perspective. Journal of Genetics and Genomics,2021,48(7):520-530. PDF
- Minglei Shi#*, Kaiqiang You#, Taoyu Chen, Chao Hou, Zhengyu Liang, Mingwei Liu, Jifeng Wang, Taotao Wei, Jun Qin, Yang Chen*, Michael Q Zhang*, Tingting Li*. Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index. Genome Biology,2021,22:229. PDF
- Shuai Jiang, Hao Li, Hao Hong, Guifang Du, Xin Huang, Yu Sun, Junting Wang, Huan Tao, Kang Xu, Cheng Li, Yang Chen*, Hebing Chen*, Xiaochen Bo*. Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains. Briefings in Bioinformatics,2021,22(3):bbaa210. PDF
- Lu Yang#, Fengling Chen#, Haichuan Zhu#, Yang Chen, Bingjie Dong, Minglei Shi, Weitao Wang, Qian Jiang, Leping Zhang, Xiaojun Huang*, Michael Q Zhang*, Hong Wu*. 3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia. Nature Communications,2021,12(1):3708. PDF
- Feng Wang, Yanan Zhen, Chaozeng Si, Cheng Wang, Lin Pan, Yang Chen, Xiaopeng Liu, Jie Kong, Qiangqiang Nie, Mingsheng Sun, Yongxin Han, Zhidong Ye, Peng Liu*, Jianyan Wen*. WNT5B promotes vascular smooth muscle cell dedifferentiation via mitochondrial dynamics regulation in chronic thromboembolic pulmonary hypertension. Journal of Cellular Physiology,2021. PDF
- Chunyu Yu, Boyan Shen, Kaiqiang You, Qi Huang, Minglei Shi, Congying Wu, Yang Chen, Chaolin Zhang, Tingting Li*. Proteome-scale analysis of phase-separated proteins in immunofluorescence images. Briefings in Bioinformatics,2021,22(3):bbaa187. PDF
2020
- Kaiqiang You#, Qi Huang#, Chunyu Yu#, Boyan Shen, Cristoffer Sevilla, MingleiShi, HenningHermjakob*, Yang Chen*, Tingting Li*. PhaSepDB: a database of liquid–liquid phase separation related proteins. Nucleic Acids Research,2020,48(D1):D354-D359. PDF
- Si Yu, Guanqun Wang, Yue Shi, Haifeng Xu, Yongchang Zheng*, Yang Chen*. MCMs in Cancer: Prognostic Potential and Mechanisms. Analytical Cellular Pathology,2020,2020:3750294. PDF
- Qian Xiong#, Sai Huang#, Yong-Hui Li, Na Lv, Chao Lv, Yi Ding, Wen-Wen Liu, Li-Li Wang, Yang Chen, Liang Sun, Yi Zhao, Sheng-You Liao, Michael Q Zhang, Bao-Li Zhu*, Li Yu*. Single‑cell RNA sequencing of t (8;21) acute myeloid leukemia for risk prediction. Oncology Reports,2020,43(4):1278-1288. PDF
- Lin Fu#, Zhiheng Cheng, Fen Dong, Liang Quan, Longzhen Cui, Yan Liu, Tiansheng Zeng, Wenhui Huang, Jinghong Chen, Ying Pang, Xu Ye, Guangsheng Wu, Tingting Qian*, Yang Chen*, Chaozeng Si*. Enhanced expression of FCER1G predicts positive prognosis in multiple myeloma. Journal of Cancer,2020,11(5):1182-1194. PDF
2019
- Yongchang Zheng#, Yue Shi#, Si Yu#, Yuanyuan Han, Kai Kang, Haifeng Xu, Huajian Gu, Xinting Sang, Yang Chen*, Jingyu Wang*. GTSE1, CDC20, PCNA, and MCM6 Synergistically Affect Regulations in Cell Cycle and Indicate Poor Prognosis in Liver Cancer. Analytical Cellular Pathology,2019,2019:1038069. PDF
- Zhaojun An#, Peng Liu#*, Jiashun Zheng, Chaozeng Si, Tianda Li, Yang Chen, Tianhua Ma, Michael Q Zhang, Qi Zhou, Sheng Ding*. Sox2 and Klf4 as the Functional Core in Pluripotency Induction without Exogenous Oct4. Cell Reports,2019,29(7):1986-2000,e8. PDF
- Rui Xiao#*, Jia-Yu Chen#, Zhengyu Liang#, Daji Luo, Geng Chen, Zhi John Lu, Yang Chen, Bing Zhou, Hairi Li, Xian Du, Yang Yang, Mingkui San, Xintao Wei, Wen Liu, Eric Lécuyer, Brenton R Graveley, Gene W Yeo, Christopher B Burge, Michael Q Zhang, Yu Zhou, Xiang-Dong Fu*. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Cell,2019,178(1):107-121,e18. PDF
- Jianbin Zhang#, Qiangqiang Nie#, Chaozeng Si, Cheng Wang, Yang Chen, Weiliang Sun, Lin Pan, Jing Guo, Jie Kong, Yiyao Cui, Feng Wang, Xueqiang Fan, Zhidong Ye, Jianyan Wen*, Peng Liu*. Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome. Frontiers in Physiology,2019,10:278. PDF
- Zhiheng Cheng, Yifeng Dai, Yifan Pang, Yang Jiao, Hongmian Zhao, Zhihui Zhang, Tong Qin, Ning Hu, Yijie Zhang, Xiaoyan Ke, Yang Chen, Depei Wu*, Jinlong Shi*, Lin Fu*. Enhanced expressions of FHL2 and iASPP predict poor prognosis in acute myeloid leukemia. Cancer Gene Therapy,2019,26(1):17-25. PDF
- Si Liu#, Chaozeng Si#, Yang Yu, Guiping Zhao, Lei Chen, Yu Zhao, Zheng Zhang, Hengcun Li, Yang Chen, Li Min, Shutian Zhang, Shengtao Zhu*. Multi-omics Analysis of Gut Microbiota and Metabolites in Rats With Irritable Bowel Syndrome. Front. Cell. Infect. Microbiol,2019,9:178. PDF
2018
- Fengling Chen#, Guipeng Li#, Michael Q Zhang, Yang Chen*.HiCDB :a sensitive and robust method for detecting contact domain boundaries. Nucleic Acids Research,2018,46:11239-11250. PDF
- Mohamed Nadhir Djekidel#, Yang Chen*, Michael Q. Zhang*. FIND : difFerential chromatin INteractions Detection using a spatial Poisson process. Genome Research,2018,28:1-11. PDF
- Yanjian Li#, Yi He#, Zhengyu Liang, Yang Wang, Fengling Chen, Mohamed Nadhir Djekidel, Guipeng Li, Xu Zhang, Shuqin Xiang, Zejun Wang, Juntao Gao, Michael Q. Zhang*, Yang Chen*. Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation. Cell Death & Disease,2018,9(2):200. PDF
- Mingyao Meng#, Lin Li#, Ruhong Li, Wenju Wang, Yang Chen, Yanhua Xie, Rui Han, Kai Zhu, Wenwen Huang, Lili Yang, Shuo Li, Jianlin Shi, Weiwei Tan, Hui Gao, Yiyi Zhao, Li Yang, Jing Tan*, Zongliu Hou*. A dynamic transcriptomic atlas of cytokine-induced killer cells. Journal of Biological Chemistry,2018,293(51):19600-19612. PDF
- Jing Li, Younghee Lee, Yanjian Li, Yu Jiang, Huiping Lu, Wenjuan Zang, Xiaohong Zhao, Liguo Liu, Yang Chen, Haidong Tan, Zhiying Yang, Michael Q Zhang, Tak W Mak, Ling Ni, Chen Dong*. Co-inhibitory Molecule B7 Superfamily Member 1 Expressed by Tumor-Infiltrating Myeloid Cells Induces Dysfunction of Anti-tumor CD8 + T Cells. Immunity,2018,8(4):773-786,e5. PDF
- Hansen Zhao, Qiming Zhou, Mengchan Xia, Jiaxin Feng, Yang Chen*, Sichun Zhang, Xinrong Zhang*. Characterize Collective Lysosome Heterogeneous Dynamics in Live Cell with a Space- and Time-Resolved Method. Analytical Chemistry,2018,90(15):9138-9147. PDF
2017
- Zhengyu Liang, Guipeng Li, Zejun Wang, Mohamed Nadhir Djekidel, Yanjian Li, Minping Qian, Michael Q. Zhang* and Yang Chen*. BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions. Nature Communications,2017,8:1622. PDF
- Guipeng Li, Yang Chen, Michael P Snyder*, Michael Q Zhang*. ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis. Nucleic Acids Research,2017,45(1):e4. PDF
- Yuanyuan Han, Xiaomei Sun, Dexuan Kuang, Pinfen Tong, Caixia Lu, Wenguang Wang, Na Li, Yang Chen, Xiaoping Wang, Jiejie Dai*, Huatang Zhang*. Characterization of tree shrew (Tupaia belangeri) interleukin-6 and its expression pattern in response to exogenous challenge. International Journal of Molecular Medicine,2017,40(6):1679-1690. PDF
- Xiangyu Li, Weizheng Chen, Yang Chen, Xuegong Zhang, Jin Gu*, Michael Q Zhang*. Network embedding-based representation learning for single cell RNA-seq data. Nucleic Acids Research,2017,45(19):e166. PDF
- Yonghui Li#, Qiaoyang Ning#, Jinlong Shi#, Yang Chen#, Mengmeng Jiang, Li Gao, Wenrong Huang, Yu Jing, Sai Huang, Anqi Liu, Zhirui Hu, Daihong Liu, Lili Wang, Clara Nervi, Yun Dai, Michael Q Zhang, Li Yu*. A novel epigenetic AML1‐ETO/THAP10/miR‐383 mini‐circuitry contributes to t(8;21) leukaemogenesis. EMBO Molecular Medicine,2017,9(7):933-949. PDF
2016
- Chao He#, Guipeng Li#, Diekidel M. Nadhir, Yang Chen*, Xiaowo Wang*, Michael Q. Zhang*. Advances in computational ChIA-PET data analysis. Quantitative Biology,2016,4(3):217-225. PDF
- Jingyu Wang, Fengling Chen, Longwei Liu, Chunxiao Qi, Bingjie Wang, Xiaojun Yan, Chenyu Huang, Wei Hou, Michael Q. Zhang, Yang Chen*, Yanan Du*. Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation. Biomaterials,2016,91:11-22. PDF
Before2016
- Meini Wu, Haixuan Wang, Jiandong Shi, Jing Sun, Zhiqing Duan, Yanhan Li, Jianfang Li, Ningzhu Hu, Yiju Wei, Yang Chen*, Yunzhang Hu*. Gene expression profiles identify both MyD88-independent and MyD88-dependent pathways involved in the maturation of dendritic cells mediated by heparan sulfate a novel adjuvant. Human Vaccines & Immunotherapeutics,2014,10(12):3711-3721. PDF
- Yonghong Feng#, Anca Dorhoi#, Hans-Joachim Mollenkopf, Hongyun Yin, Zhengwei Dong, Ling Mao, Jun Zhou, Aixiao Bi, Stephan Weber, Jeroen Maertzdorf, Gang Chen, Yang Chen, Stefan H. E. Kaufmann*. Platelets direct monocyte differentiation into epithelioid-like multinucleated giant foam cells with suppressive capacity upon mycobacterial stimulation. The Journal of Infectious Diseases,2014,210(11):1700-1710. PDF
- MiaoMiao Sheng#, Ying Zhong#, Yang Chen, JianChao Du, XiangWu Ju, Chen Zhao, GuiGen Zhang, LiFang Zhang, KangTai Liu, Ning Yang, Peng Xie, DangSheng Li, Michael Q Zhang*, ChengYu Jiang*. Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro. Science China Life Sciences,2014,57(10):959-972. PDF
- Jin Gu#*, Yang Chen#, Huiya Huang, Lingyun Yin, Zhen Xie, Michael Q Zhang*. Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Molecular BioSystems,2014,10(12):3249-3254. PDF
- Mohamed Nadhir Djekidel, Zhengyu Liang, Qi Wang, Zhirui Hu, Guipeng Li, Yang Chen*, Michael Q. Zhang*. 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. Genome Biology,2015,16:288. PDF
- Yan Ma#, Chen Zhang#, Xiao-Bo Gao, Hai-Yan Luo, Yang Chen, Hui-hua Li*, Xu Ma*, Cai-Ling Lu*. Folic acid protects against arsenic-mediated embryo toxicity by up-regulating the expression of Dvr1. Scientific Reports,2015,5(1):1-14. PDF
- Teng-Fei Chao, Hui-Hua Xiong, Wei Liu, Yang Chen, Jia-Xuan Zhang*. MiR-21 mediates the radiation resistance of glioblastoma cells by regulating PDCD4 and hMSH2. J Huazhong Univ Sci Technolog Med Sci,2013,33(4):525-529. PDF
- Bai Jiang#, Xujun Liang#, Yang Chen#, Tao Ma, Liyang Liu, Junfeng Li, Rui Jiang, Ting Chen, Xuegong Zhang*, Shao Li*. Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Scientific Reports,2012,2:936. PDF
- Yang Chen#, Jin Gu#, Dan Li, Shao Li*. Time-course network analysis reveals TNF-α can promote G1S transition of cell cycle in vascular endothelial cells. Bioinformatics,2012,28(1):1-4. PDF
- Jin Gu, Yang Chen, Shao Li*, Yanda Li*. Identification of responsive gene modules by network-based gene clustering and extending application to inflammation and angiogenesis. BMC Systems Biology,2010,4:47. PDF
- Jianyan Wen#, Qing Xia#, Cheng Wang, Wei Liu, Yang Chen, Jing Gao, Yanhua Gong, Bin Yin, Yuannan Ke, Boqin Qiang, Jiangang Yuan*, Xiaozhong Peng*. Dok-5 is involved in cardiomyocyte differentiation through PKB/ FOXO3a pathway. Journal of Molecular and Cellular Cardiology,2009,47(6):761-769. PDF
- Pufeng Du#, Yang Chen#, Yanda Li*. Computational evidence of A-to-I RNA editing in nucleus transcriptome of Arabidopsis thaliana. Frontiers of Electrical and Electronic Engineering in China,2009,4(4):349-361.
- Jin Gu, Shao Li, Yang Chen, Yanda Li. Integrative Computational Identifications of the Signaling Pathway Network Related to TNF-alpha Stimulus in Vascular Endothelial Cells. 2009 International Joint Conference on Bioinformatics,Systems Biology and Intelligent Computing,2009,422-427. PDF
- Yu Zhang, Tengfei Chao, Ran Li, Wei Liu, Yang Chen, Xingqi Yan, Yanhua Gong, Bin Yin, Wei Liu, Boqing Qiang, Jizhong Zhao, Jiangang Yuan*, Xiaozhong Peng*. MicroRNA-128 inhibits glioma cells proliferation by targeting transcription factor E2F3a. Journal of Molecular Medicine,2009,87(1):43-51. PDF
- Yang Chen, Wei Liu, Tengfei Chao, Yu Zhang, Xingqi Yan, Yanhua Gong, Boqin Qiang, Jiangang Yuan, Maosheng Sun*, Xiaozhong Peng*. MicroRNA-21 down-regulates the expression of tumor suppressor PDCD4 in human glioblastoma cell T98G. Cancer Letters,2008,272(2):197-205. PDF
- 陈阳, 李健峰, 姬秋彦, 闫玲梅, 龙海亭, 徐维明*.幽门螺杆菌oipA基因的克隆及其生物信息学分析. 世界华人消化杂志, 2005,13(7):867-870. PDF
- 陈阳, 徐维明*. 蛋白质组学技术在幽门螺杆菌研究中的应用. 世界华人消化杂志,2005,13(2):243-245. PDF