ResearchGate

Publons

Publications
1 Zhixian Zhu, Qiangwei Zhou, Yuanhui Sun, Fuming Lai, Zhenji Wang, Zhigang Hao, Guoliang Li MethMarkerDB: a comprehensive cancer DNA methylation biomarker database Nucleic Acids Research, 2023, DOI: https://doi.org/10.1093/nar/gkad923
2 Shitong Lin, Yuanhui Sun, Canhui Cao, Zhixian Zhu, Yashi Xu, Binghan Liu, Bai Hu, Ting Peng, Wenhua Zhi, Miaochun Xu, Wencheng Ding, Fang Ren, Ding Ma, Guoliang Li, Peng Wu Single-nucleus RNA sequencing reveals heterogenous microenvironments and specific drug response between cervical squamous cell carcinoma and adenocarcinoma eBioMedicine, 2023, DOI: https://doi.org/10.1016/j.ebiom.2023.104846
3 Zhixian Zhu, Qiangwei Zhou, Pengpeng Guan, Yuanhui Sun, Guoliang Li Novel DNA methylation biomarkers in enhancer regions with chromatin interactions for diagnosis of non-small-cell lung cancer MedComm - Oncology, 2023, DOI: https://doi.org/10.1002/mog2.51
4 Ying Zhang, Guoting Chen, Li Deng, Baibai Gao, Jing Yang, Cheng Ding, Qing Zhang, Weizhi Ouyang, Minrong Guo, Wenxia Wang, Beibei Liu, Qinghua Zhang, Wing-Kin Sung, Jiapei Yan, Guoliang Li, Xingwang Li Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice Nucleic Acids Research, 2023, DOI: https://doi.org/10.1093/nar/gkad658
5 Li Deng, Qiangwei Zhou, Jie Zhou, Qing Zhang, Zhibo Jia, Guangfeng Zhu, Sheng Cheng, Lulu Cheng, Caijun Yin, Chao Yang, Jinxiong Shen, Junwei Nie, Jian-Kang Zhu, Guoliang Li & Lun Zhao 3D organization of regulatory elements for transcriptional regulation in Arabidopsis Genome Biology, 2023, DOI: https://doi.org/10.1186/s13059-023-03018-4
6 Wei Zhang, Huanhuan Wang, Yuning Ma, Baibai Gao, Pengpeng Guan, Xingyu Huang, Weizhi Ouyang, Minrong Guo, Guoting Chen, Guoliang Li, Xingwang Li Domains Rearranged Methylase 2 maintains DNA methylation at large DNA hypomethylated shores and long-range chromatin interactions in rice Plant Biotechnology Journal, 2023, DOI: https://doi.org/10.1111/pbi.14134
7 Xi Zeng, Yuyouye Wang, Binghan Liu, Xinjie Rao, Canhui Cao, Fang Peng, Wenhua Zhi, Ping Wu, Ting Peng, Ye Wei, Tian Chu, Miaochun Xu, Yashi Xu, Wencheng Ding, Guoliang Li, Shitong Lin, Peng Wu Multi-omics data reveals novel impacts of human papillomavirus integration on the epigenomic and transcriptomic signatures of cervical tumorigenesis Journal of Medical Virology, 2023, DOI: https://doi.org/10.1002/jmv.28789
8 Zhigang Hao, Wolfgang Mayer, Jingbo Xia, Guoliang Li, Li Qin, Zaiwen Feng Ontology alignment with semantic and structural embeddings Journal of Web Semantics, 2023, DOI: https://doi.org/10.1016/j.websem.2023.100798
9 Zhenji Wang, Minghao Liu, Fuming Lai, Qiangqiang Fu, Liang Xie, Yaping Fang, Qiangwei Zhou and Guoliang Li AraENCODE: A comprehensive epigenomic database of Arabidopsis thaliana Molecular Plant, 2023, DOI:https://doi.org/10.1016/j.molp.2023.06.005
10 LiPing Yang, GuoLiang Li, Li Qin & FuChuan Ni Research on Experimental Teaching Reform of Computer Principles Course Based on Logisim Simulation Software Computer Science and Education, 2023, DOI: https://doi.org/10.1007/978-981-99-2449-3_13
11 Weizhi Ouyang, Xiwen Zhang, Minrong Guo, Jing Wang, Xiaoting Wang, Runxin Gao, Meng Ma, Xu Xiang, Shiping Luan, Feng Xing, Zhilin Cao, Jiapei Yan, Guoliang Li, and Xingwang Li Haplotype mapping of H3K27me3-associated chromatin interactions defines topological regulation of gene silencing in rice Cell Reports, 2023, DOI: https://doi.org/10.1016/j.celrep.2023.112350
12 Yan Zhang, Jingwen Zhang, Wei Zhang, Mohan Wang, Shuangqi Wang, Yao Xu, Lun Zhao, Xingwang Li, Guoliang Li Mapping Multiple Factors-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes Genomics, Proteomics & Bioinformatics, 2023, DOI: https://doi.org/10.1016/j.gpb.2023.01.004
13 Yigeng Shang, Zhigang Hao, Chao Yao, Guoliang Li Improving Graph Neural Network Models in Link Prediction Task via A Policy-Based Training Method Applied Sciences, 2022, DOI: https://doi.org/10.3390/app13010297
14 Qiangwei Zhou, Sheng Cheng, Shanshan Zheng, Zhenji Wang, Pengpeng Guan, Zhixian Zhu, Xingyu Huang, Cong Zhou, Guoliang Li ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms Nucleic Acids Research, 2022, DOI: https://doi.org/10.1093/nar/gkac893
15 Da Lin, Weize Xu, Ping Hong, Chengchao Wu, Zhihui Zhang, Siheng Zhang, Lingyu Xing, Bing Yang, Wei Zhou, Qin Xiao, Jinyue Wang, Cong Wang, Yu He, Xi Chen, Xiaojian Cao, Jiangwei Man, Aikebaier Reheman, Xiaofeng Wu, Xingjie Hao, Zhe Hu, Chunli Chen, Zimeng Cao, Rong Yin, Zhen F. Fu, Rong Zhou, Zhaowei Teng, Guoliang Li & Gang Cao Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation Nature Communications, 2022, DOI: https://doi.org/10.1038/s41467-022-33558-5
16 Lun Zhao, Qiangwei Zhou, Li He, Li Deng, Rosa Lozano-Duran, Guoliang Li & Jian-Kang Zhu DNA methylation underpins the epigenomic landscape regulating genome transcription in Arabidopsis Genome Biology, 2022, DOI: https://doi.org/10.1186/s13059-022-02768-x
17 Simon Zhongyuan Tian, Guoliang Li, Duo Ning, Kai Jing, Yewen Xu, Yang Yang, Melissa J Fullwood, Pengfei Yin, Guangyu Huang, Dariusz Plewczynski, Jixian Zhai, Ziwei Dai, Wei Chen, Meizhen Zheng MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification Briefings in Bioinformatics, 2022, DOI: https://doi.org/10.1093/bib/bbac380
18 Zhenfei Sun, Yunlong Wang, Zhaojian Song, Hui Zhang, Yuanda Wang, Kunpeng Liu, Min Ma, Pan Wang, Yaping Fang, Detian Cai, Guoliang Li, Yuda Fang DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication Journal of Advanced Research, 2022, DOI: https://doi.org/10.1016/j.jare.2022.07.007
19 Muhammad Muzammal Adeel, Khaista Rehman, Yan Zhang, Yibeltal Arega, Guoliang Li Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data Genes, 2022, DOI: https://doi.org/10.3390/genes13071170
20 Na Yao, Fuchuan Ni, Minghao Wu, Haiyan Wang, Guoliang Li, Wing-Kin Sung Deep Learning-Based Segmentation of Peach Diseases Using Convolutional Neural Network Frontiers in Plant Science, 2022, DOI: https://doi.org/10.3389/fpls.2022.876357
21 Yifan Meng, Shitong Lin, Yi Zhou, Xiao Yi, Ping Wu, Qing Zhang, Weigang Ge, Canhui Cao, Peipei Gao, Wenhua Zhi, Ting Peng, Juncheng Wei, Wencheng Ding, Ding Ma, Guoliang Li, Qin Yang, Tiannan Guo, Xi Zeng, Peng Wu RAB2A promotes cervical cancer progression as revealed by comprehensive analysis of HPV integration and proteome in longitudinal cervical samples Clinical and Translational Medicine, 2022, DOI: https://doi.org/10.1002/ctm2.767
22 Qin Xiao, Xingyu Huang, Yan Zhang, Wei Xu, Yongqing Yang, Qing Zhang, Zhe Hu, Feng Xing, Qianwen Sun, Guoliang Li & Xingwang Li The landscape of promoter-centred RNA–DNA interactions in rice Nature Plants, 2022, DOI: https://doi.org/10.1038/s41477-021-01089-4
23 Li Deng, Baibai Gao, Lun Zhao, Ying Zhang, Qing Zhang, Minrong Guo, Yongqing Yang, Shuangqi Wang, Liang Xie, Hao Lou, Meng Ma, Wei Zhang, Zhilin Cao, Qinghua Zhang, C. Robertson McClung, Guoliang Li & Xingwang Li Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice Genome Biology, 2022, DOI: https://doi.org/10.1186/s13059-021-02594-7
24 Weizhi Ouyang, Shiping Luan, Xu Xiang, Minrong Guo, Yan Zhang ,Guoliang Li, Xingwang Li Profiling Plant Histone Modification at Single‐cell Resolution Using snCUT&Tag Plant Biotechnology Journal, 2021, DOI: https://doi.org/10.1111/pbi.13768
25 Weize Xu, Quan Zhong, Da Lin, Ya Zuo, Jinxia Dai, Guoliang Li & Gang Cao CoolBox: a flexible toolkit for visual analysis of genomics data BMC Bioinformatics, 2021, DOI: https://doi.org/10.1186/s12859-021-04408-w
26 Zhipeng Tai, Pengpeng Guan, Ting Zhang, Wenye Liu, LingyaLi, You Wua, Guoliang Li, Jing-Xia Liu Effects of parental environmental copper stress on offspring development: DNA methylation modification and responses of differentially methylated region-related genes in transcriptional expression Journal of Hazardous Materials, 2021, DOI: https://doi.org/10.1016/j.jhazmat.2021.127600
27 Qiangwei Zhou, Pengpeng Guan, Zhixian Zhu, Sheng Cheng, Cong Zhou, Huanhuan Wang, Qian Xu, Wing-kin Sung, Guoliang Li ASMdb: A comprehensive database for allele-specific DNA methylation in diverse organisms Nucleic Acids Research, 2021, DOI: https://doi.org/10.1093/nar/gkab937
28 Liang Xie, Minghao Liu, Lun Zhao, Kai Cao, Peng Wang, Wenhao Xu, Wing-Kin Sung, Xingwang Li, Guoliang Li RiceENCODE: A comprehensive epigenomic database as a rice Encyclopedia of DNA Elements Molecular Plant, 2021, DOI: https://doi.org/10.1016/j.molp.2021.08.018
29 Muhammad Muzammal Adeel, Hao Jiang, Yibeltal Arega, Kai Cao, Da Lin, Canhui Cao, Gang Cao, Peng Wu,* and Guoliang Li,* Structural Variations of the 3D Genome Architecture in Cervical Cancer Development Frontiers in Cell and Developmental Biology, 2021, DOI: https://doi.org/10.3389/fcell.2021.706375
30 Ke Xiao,† Dan Xiong,† Gong Chen, Jinsong Yu, Yue Li, Kening Chen, Lu Zhang, Yangyang Xu, Qian Xu, Xi Huang, Anran Gao, Kai Cao, Keji Yan, Jinxia Dai, Xueying Hu, Yijun Ruan, Zhenfang Fu*, Guoliang Li,* Gang Cao* RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription Science Advances, 2021, DOI: https://doi.org/10.1126/sciadv.abf8962
31 Zhengfeng Zhang, Yao Xu, Fei Yang, Benze Xiao, Guoliang Li RiceLncPedia: a comprehensive database of rice long non‐coding RNAs Plant Biotechnology Journal, 2021, DOI: https://doi.org/10.1111/pbi.13639
32 Yunlong Wang, Yaqi Liu, Qian Xu, Yao Xu, Kai Cao, Nan Deng, Ruimin Wang, Xueying Zhang, Ruiqin Zheng, Guoliang Li, Yaping Fang TAD boundary and strength prediction by integrating sequence and epigenetic profile information Briefings in Bioinformatics, 2021, DOI: https://doi.org/10.1093/bib/bbab139
33 Na Yao, Fuchuan Ni, Ziyan Wang, Jun Luo, Wing-Kin Sung, Chaoxi Luo & Guoliang Li L2MXception: an improved Xception network for classification of peach diseases Plant Methods, 2021, DOI: https://doi.org/10.1186/s13007-021-00736-3
34 Weizhi Ouyang, Xiwen Zhang, Yong Peng, Qing Zhang, Zhilin Cao,, Guoliang Li, and Xingwang Li* Rapid and Low-Input Profiling of Histone Marks in Plants Using Nucleus CUT&Tag Frontiers in Plant Science, 2021, DOI: https://doi.org/10.3389/fpls.2021.634679
35 Liuling Pei, Guoliang Li, Keith Lindsey, Xianlong Zhang, Maojun Wang Plant 3D genomics: the exploration and application of chromatin organization New Phytologist, 2021, DOI: https://doi.org/10.1111/nph.17262
36 Ting Pan, Qi Qin, Chubing Nong, Shan Gao, Lili Wang, Bingcheng Cai, Ming Zhang, Chong Wu, Hanchen Chen, Tong Li, Dan Xiong, Guoliang Li, Shui Wang and Shunping Yan A novel WEE1 pathway for replication stress responses Nature Plants, 2021, DOI: https://doi.org/10.1038/s41477-021-00855-8
37 Xi Zeng, Linghao Zhao, Chenhang Shen, Yi Zhou, Guoliang Li, Wing-Kin Sung HIVID2: an accurate tool to detect virus integrations in the host genome Bioinformatics, 2021, DOI: https://doi.org/10.1093/bioinformatics/btab031
38 Ramesh Rajaby, Yi Zhou, Yifan Meng, Xi Zeng, Guoliang Li, Peng Wu, Wing-Kin Sung SurVirus: a repeat-aware virus integration caller Nucleic Acids Research, 2021, DOI: https://doi.org/10.1093/nar/gkaa1237
39 Yibeltal Arega, Hao Jiang, Shuangqi Wang, Jingwen Zhang, Xiaohui Niu and Guoliang Li ChIAMM: A Mixture Model for Statistical Analysis of Long-Range Chromatin Interactions From ChIA-PET Experiments Frontiers in Genetics, 2020, DOI: https://doi.org/10.3389/fgene.2020.616160
40 Zhihui Zhang, Chengchao Wu, Khaista Rahman, Weize Xu, Guoliang Li, Da Lin, Gang Cao Robust capturing chromosome conformation using the DLO Hi-C 2.0 method Journal of Genetics and Genomics, 2020, DOI: https://doi.org/10.1016/j.jgg.2020.11.003
41 Qing Zhang, Pengpeng Guan, Lun Zhao, Meng Ma, Liang Xie, Yue Li, Ruiqin Zheng, Weizhi Ouyang, Shunyao Wang, Hongmeijuan Li, Ying Zhang, Yong Peng, Zhilin Cao, Wei Zhang, Qin Xiao, Yuanling Xiao, Tingdong Fu, Guoliang Li, Xingwang Li, Jinxiong Shen, Qing Zhang, Pengpeng Guan, Lun Zhao, Meng Ma, Liang Xie, Yue Li, Ruiqin Zheng, Weizhi Ouyang, Shunyao Wang, Hongmeijuan Li, Ying Zhang, Yong Peng, Zhilin Cao, Wei Zhang, Qin Xiao, Yuanling Xiao, Tingdong Fu, Guoliang Li, Xingwang Li, Jinxiong Shen Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus Molecular Plant, 2020, DOI:https://doi.org/10.1016/j.molp.2020.12.020
42 Weizhi Ouyang, Qin Xiao, Guoliang Li,* and Xingwang Li Technologies for Capturing 3D Genome Architecture in Plants Trends in Plant Science, 2020, DOI: 10.1016/j.tplants.2020.10.007
43 Weizhi Ouyang, Dan Xiong, Guoliang Li,* and Xingwang Li* Unraveling the 3D Genome Architecture in Plants: Present and Future Molecular Plant, 2020, DOI: https://doi.org/10.1016/j.molp.2020.10.002
44 Qiangwei Zhou, Ze Wang, Jing Li, Wing-Kin Sung & Guoliang Li MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification BMC Bioinformatics, 2020, DOI: https://doi.org/10.1186/s12859-020-03798-7
45 Canhui Cao, Qian Xu, Shitong Lin, Wenhua Zhi, Cordelle Lazare, Yifan Meng, Ping Wu, Peipei Gao, Kezhen Li, Juncheng Wei, Peng Wu, Guoliang Li Mapping long-range contacts between risk loci and target genes in human diseases with Capture Hi-C Clinical and Translational Medicine, 2020, DOI: https://doi.org/10.1002/ctm2.183
46 Yonghao Sun, Liang Dong, Ying Zhang, Da Lin, Weize Xu, Changxiong Ke, Linqian Han, Lulu Deng, Guoliang Li, David Jackson, Xingwang Li & Fang Yang 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize. Genome Biology, 2020, DOI: 10.1186/s13059-020-02063-7
47 Ouyang Weizhi, Cao Zhilin, Xiong Dan Li Guoliang, Li Xingwang Decoding plant genome: from epigenome to 3D organization. Journal of Genetics and Genomics, 2020, DOI: 10.1016/j.jgg.2020.06.007
48 Ting Zhang, PengPeng Guan, WenYe Liu, Guang Zhao, YaPing Fang, Hui Fu, Jian-Fang Gui, GuoLiang Li, Jing-Xia Liu Copper stress induces zebrafish central neural system myelin defects via WNT/NOTCH-hoxb5b signaling and pou3f1/fam168a/fam168b DNA methylation. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2020, DOI: 10.1016/j.bbagrm.2020.194612
49 Canhui Cao, Ping Hong, Xingyu Huang, Da Lin, Gang Cao, Liming Wang, Bei Feng,Ping Wu, Hui Shen, Qian Xu, Ci Ren, Yifan Meng, Wenhua Zhi, Ruidi Yu, JunchengWei, Wencheng Ding, Xun Tian, Qinghua Zhang, Wei Li, Qinglei Gao, Gang Chen,Kezhen Li, Wing-Kin Sung, Zheng Hu, Hui Wang, Guoliang Li, Peng Wu HPV-CCDC106 integration alters local chromosome architecture and hijacks anenhancer by 3D genome structure remodeling in cervical cancer. Journal of Genetics and Genomics, 2020, DOI: 10.1016/j.jgg.2020.05.006
50 Zhengfeng Zhang, Yao Xu, Fei Yang, Benze Xiao, Guoliang Li RiceLncPedia: a comprehensive database of rice long non-coding RNAs bioRxiv, 2020, DOI: 10.1101/2020.05.22.110569
51 Na Yao, Fuchuan Ni, Ziyan Wang, Jun Luo, Wing-Kin Sung, Chaoxi Luo, Guoliang Li L2MXception: An Improved Xception Network for Classification of Peach diseases. DOI: 10.21203/rs.3.rs-31469/v1
52 Yan Zhang, Guoliang Li Advances in technologies for 3D genomics research. Science China Life Sciences, 2020, DOI: 10.1007/s11427-019-1704-2
53 Da LIN , SiHeng ZHANG , ZhiHui ZHANG , WeiZe XU , Ping HONG , GuoLiang LI *, Gang CAO * The “toolbox” for chromatin conformation capture. Scientia Sinica Vitae, 2020, DOI: 10.1360/SSV-2019-0224
54 Lun Zhao, Liang Xie, Qing Zhang, Weizhi Ouyang, Li Deng, Pengpeng Guan, Meng Ma, Yue Li, Ying Zhang, Qin Xiao, Jingwen Zhang, Hongmeijuan Li, Shunyao Wang, Jiangwei Man, Zhilin Cao, Qinghua Zhang, Qifa Zhang, Guoliang Li & Xingwang Li Integrative analysis of reference epigenomes in 20 rice varieties. Nature Communications, 2020, DOI: 10.1038/s41467-020-16457-5
55 Ping Hong, Hao Jiang, Weize Xu, Da Lin, Qian Xu, Gang Cao, Guoliang Li The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis. Genes, 2020, DOI: 10.3390/genes11030289
56 Yoshiki Higashijima, Yusuke Matsui, Teppei Shimamura, Ryo Nakaki, Nao Nagai, Shuichi Tsutsumi, Yohei Abe, Verena M Link, Mizuko Osaka, Masayuki Yoshida, Ryo Watanabe, Toshihiro Tanaka, Akashi Taguchi, Mai Miura, Xiaoan Ruan, Guoliang Li, Tsuyoshi Inoue, Masaomi Nangaku, Hiroshi Kimura, Tetsushi Furukawa, Hiroyuki Aburatani, Youichiro Wada, Yijun Ruan, Christopher K Glass, Yasuharu Kanki Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells. The EMBO Journal, 2020, DOI: 10.15252/embj.2019103949.
57 Lun Zhao#, Shuangqi Wang#, Zhilin Cao#, Weizhi Ouyang, Qing Zhang, Liang Xie, Ruiqin Zheng, Minrong Guo, Meng Ma, Zhe Hu, Wing-Kin Sung, Qifa Zhang, Guoliang Li*, Xingwang Li* Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation. Nature Communications, DOI: 10.1038/s41467-019-11535-9, (2019)
58 Guoliang Li*, Tongkai Sun, Huidan Chang, Liuyang Cai, Ping Hong, Qiangwei Zhou Chromatin interaction analysis with updated ChIA-PET Tool (V3). Genes, 2019, 10, 554, https://doi.org/10.3390/genes10070554. bioRxiv 627257, doi: https://doi.org/10.1101/627257 (2019)
59 Hui Zhang, Ruiqin Zheng, Yunlong Wang, Yu Zhang, Ping Hong, Yaping Fang, Guoliang Li*, Yuda Fang* The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation. Nucleic Acids Research, DOI: 10.1093/nar/gkz511 (2019)
60 Yong Peng#, Dan Xiong#, Lun Zhao, Weizhi Ouyang, Shuangqi Wang, Jun Sun, Qing Zhang, Pengpeng Guan, Liang Xie, Wenqiang Li, Guoliang Li*, Jianbing Yan*, Xingwang Li* Chromatin Interaction Maps Reveal Genetic Regulation for Quantitative Traits in Maize. Nature Communications, DOI: 10.1038/s41467-019-10602-5, (2019)
61 Yuriy L. Orlov, Alex V. Kochetov, Guoliang Li and Nikolay A. Kolchanov Genomics research at Bioinformatics of Genome Regulation and Structure\ Systems Biology (BGRS\SB) conferences in Novosibirsk. BMC Genomics 2019 20(Suppl 3):322, https://doi.org/10.1186/s12864-019-5707-0 (2019)
62 Ruimin Wang, Yunlong Wang, Xueying Zhang, Yaliang Zhang, Xiaoyong Du, Yaping Fang*, Guoliang Li* Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data. BMC Genomics, 2019, 20 (Suppl 3):296, DOI: 10.1186/s12864-019-5535-2
63 张競文#，续倩#，李国亮* 癌症发生发展中的表观遗传学研究 《遗传》，2019, 41 (7): 567-581. doi: 10.16288/j.yczz.19-077
64 Qiangwei Zhou, Jing-Quan Lim, Wing-Kin Sung, Guoliang Li An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping. BMC Bioinformatics 2019, 20:47. https://doi.org/10.1186/s12859-018-2593-4
65 Jian Jun Jin, Wei Lv, Pan Xia, Zai Yan Xu, An Dai Zheng, Xiao Jing Wang, Shan Shan Wang, Rui Zeng, Hong Mei Luo, Guo Liang Li, Bo Zuo Long noncoding RNA SYISL regulates myogenesis by interacting with polycomb repressive complex 2 Proceedings of the National Academy of Sciences Oct 2018, 201801471; DOI: 10.1073/pnas.1801471115
66 林达#，洪萍#，李国亮*，曹罡* DLO Hi-C染色体构象捕获技术 南京农业大学学报，2018, 41(4):577-579
67 Q. H. Xu, P. Guan, T. Zhang, C. Lu, Guoliang Li, and J. X. Liu Silver nanoparticles impair zebrafish skeletal and cardiac myofibrillogenesis and sarcomere formation Aquat Toxicol, vol. 200, pp. 102-113, Apr 30 2018
68 Da Lin#, Ping Hong#, Liang Li, Siheng Zhang, Weize Xu, Muhammad Jamal, Keji Yan, Yingying Lei, Yijun Ruan, Zhenfang Fu, Guoliang Li* & Gang Cao* Digestion-Ligation-Only Hi-C, a Simple, Cost-effective, and Highly Efficient Method for Chromosome Conformation Capture Nature Genetics, volume 50, pages 754–763, doi:10.1038/s41588-018-0111-2 (2018)
69 Hai-Feng Liu*#, Cheng Luo#, Wu Song#, Hai-Tao Shen#, Guoliang Li, Zhi-Gang He, Wen-Gang Chen, Yan-Yan Cao, Fang Huang, Shou-Wu Tang, Ping Hong, En-Feng Zhao, Jian-Bo Zhu, Da-Jun He, Shao-Ming Wang, Guang-Ying Huo, Hailiang Liu* Flavonoid Biosynthesis Controls Fiber Color in Naturally Colored Cotton PeerJ, 6:e4537 https://doi.org/10.7717/peerj.4537, 2018
70 Bo Zhang, Men-Yun Chen, Yu-Jun Shen, Xian-Bo Zhuo, Ping Gao, Fu-Sheng Zhou, Bo Liang, Jun Zu, Qin Zhang, Sufyan Suleman, Yi-Hui Xu, Min-Gui Xu, Jin-Kai Xu, Chen- Cheng Liu, Nikolaos Giannareas, Ji-Han Xia, Yuan Zhao, Zhong-Lian Huang, Zhen Yang, Huaidong Cheng, Na Li, Yan-Yan Hong, Wei Li, Min-Jun Zhang, Ke-Da Yu, Guoliang Li, Meng-Hong Sun, Zhen-Dong Chen, Gong-Hong Wei, and Zhi-Ming Shao A large-scale, exome-wide association study of Han Chinese women identifies three novel loci predisposing to breast cancer Cancer Research, 2018 Mar 23. pii: canres.1721.2017. doi: 10.1158/0008-5472.CAN-17-1721
71 Maojun Wang, Pengcheng Wang, Min Lin, Zhengxiu Ye, Guoliang Li, Lili Tu, Chao Shen,Jianying Li, Qingyong Yang and Xianlong Zhang Evolutionary dynamics of 3D genome architecture following polyploidization in cotton Nature Plants, vol. 4, pp. 90-97, Feb 2018
72 Sizun Jiang, Hufeng Zhou, Jun Liang, Catherine Gerdt, Chong Wang, Liangru Ke, Yohei Narita, Yijie Ma, Tyler Colson, Benjamin Gewurz, Guoliang Li, Elliott Kieff*, Bo Zhao* The Epstein-Barr Virus Regulome in Lymphoblastoid Cells Cell Host and Microbe, 22, 561–573, 2017
73 Yiwen Guo, Jingnan Wang, Mingfei Zhu, Rui Zeng, Zaiyan Xu, Guoliang Li, and Bo Zuo Identification of MyoD-Responsive Transcripts Reveals a Novel Long Non-coding RNA (lncRNA-AK143003) that Negatively Regulates Myoblast Differentiation Scientific Reports 7 (1) :2828, 2017
74 Xingwang Li, Oscar Junhong Luo, Ping Wang, Meizhen Zheng, Danjuan Wang, Emaly Piecuch, Jacqueline Jufen Zhu, Simon Zhongyuan Tian, Zhonghui Tang, Guoliang Li, Yijun Ruan Long-read ChIA-PET for base-pair resolution mapping of haplotype-specific chromatin interactions Nature Protocol, 2017 May;12(5):899-915. PubMed PMID: 28358394
75 Liuyang Cai, Huidan Chang, Yaping Fang, Guoliang Li* A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions Scientific Reports 6, (2016), doi:10.1038/srep36572
76 方亚平，彭城，阮一骏，李国亮* 染色质的高级结构（二）：三维基因组学与精准医学 表观遗传与精准医学，书号：978-7-313-18411-5，上海交通大学出版社，2018，227-268
77 Yaping Fang,Yunlong Wang, Qin Zhu,JiaWang, Guoliang Li (2016). In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences (accepted). Scientific reports 6: 2016 Sep 01 pg 32476
78 Shaoli Zhou, Xiaoyu Liu, Chao Zhou, Qiangwei Zhou, Yu zhao, Guoliang Li, Dao-Xiu Zhou (2016). Cooperation between the H3K27me3 chromatin marker and non-CG methylation in epigenetic regulation (accepted). Plant Physiology [2016, 172(2):1131-1141]
79 Wei Zong, Ning Tang, Jun Yang, Lei Peng, Siqi Ma, Yan Xu, Guoliang Li, Lizhong Xiong (2016). Feedback regulation of ABA signaling and biosynthesis by OsbZIP23 that targets diverse drought resistance related genes in rice. Plant Physiology, 171(4):2810-25, 2016, doi: 10.1104/pp.16.00469
80 Chao Wang, Haixiang Yu, Li Luo, Liujian Duan, Liuyang Cai, Xinxing He, Jiangqi Wen, Kirankumar S Mysore, Guoliang Li, Aifang Xiao, Deqiang Duanmu, Yangrong Cao, Zonglie Hong, Zhongming Zhang (2016). NODULES WITH ACTIVATED DEFENSE 1 is required for maintenance of rhizobial endosymbiosis in Medicago truncatula. New Phytologist, 2016, DOI: 10.1111/nph.14017
81 Feng Tan, Chao Zhou, Qiangwei Zhou, Shaoli Zhou, Wenjing Yang, Yu Zhao, Guoliang Li, Dao-Xiu Zhou (2016) The ortholog of DDM1 is mainly required for CHG and CG methylation of heterochromatin and is involved in DRM2-mediated CHH methylation that targets mostly genic regions of the rice genome (accepted). Plant Physiology, 2016
82 朱菊芬, 李国亮, 阮一骏 (2016) 三维基因组学及其精准医学意义 科学发展报告，2016
83 Tang, Z., O. J. Luo, X. Li, M. Zheng, J. J. Zhu, P. Szalaj, P. Trzaskoma, A. Magalska, J. Wlodarczyk, B. Ruszczycki, P. Michalski, E. Piecuch, P. Wang, D. Wang, S. Z. Tian, M. Penrad-Mobayed, L. M. Sachs, X. Ruan, C. L. Wei, E. T. Liu, G. M. Wilczynski, D. Plewczynski, Guoliang Li and Y. Ruan (2015). CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell 163(7): 1611-1627
84 GKuznetsova, T., S. Y. Wang, N. A. Rao, A. Mandoli, J. H. Martens, N. Rother, A. Aartse, L. Groh, E. M. Janssen-Megens, Guoliang Li, Y. Ruan, C. Logie and H. G. Stunnenberg (2015). Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization. Genome Biology 16(1): 264.
85 Yuan, D., Z. Tang, M. Wang, W. Gao, L. Tu, X. Jin, L. Chen, Y. He, L. Zhang, L. Zhu, Y. Li, Q. Liang, Z. Lin, X. Yang, N. Liu, S. Jin, Y. Lei, Y. Ding, Guoliang Li, X. Ruan, Y. Ruan and X. Zhang (2015). The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. Scientific Reports 5: 17662.
86 Fei Yao, ..., Guoliang Li, ..., Axel M. Hillmer Genome structure variation analysis identified recurrent fusion genes in gastric cancer with CLDN18-ARHGAP26 mediating loss of epithelial integrity Cell Reports, 12(2):272–285, 2015
87 Guoliang Li, Liuyang Cai, Huidan Chang, Ping Hong, Qiangwei Zhou, Ekaterina V Kukakova, Nikolay A Kolchanov and Yijun Ruan. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application BMC Genomics，2014, S12, S11
88 彭城#，李国亮#，张红雨，阮一骏 染色质三维结构重建及其生物学意义 《中国科学：生命科学》，794-802.
89 Maejima, T., Inoue, T., Kanki, Y., Kohro, T., Guoliang Li, Ohta, Y., Kimura, H., Kobayashi, M., Taguchi, A., Tsutsumi, S., et al. Direct Evidence for Pitavastatin Induced Chromatin Structure Change in the KLF4 Gene in Endothelial Cells PLoS ONE, 9, e96005
90 Liang Niu, Guoliang Li, Shili Lin (2014) Statistical Models for Detecting Differential Chromatin Interactions Mediated by a Protein PLoS One, 9, e97560
91 李国亮，阮一骏，谷瑞升，杜生明 起航三维基因组学研究 2014, 59, 1165-1172
92 T. Inoue, T. Kohro, T. Tanaka, Y. Kanki, Guoliang Li, H. M. Poh, I. Mimura, M. Kobayashi, A. Taguchi, T. Maejima, J. I. Suehiro, A. Sugiyama, K. Kaneki, H. Aruga, S. Dong, J. F. Stevens, S. Yamamoto, S. Tsutsumi, T. Fujita, X. Ruan, H. Aburatani, M. Nangaku, Y. Ruan, T. Kodama, and Y. Wada Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements Genome Biology, vol. 15, p. R63, Apr 10 2014
93 Dijun Chen, Liang-Yu Fu, Zhao Zhang, Guoliang Li, Hang Zhang, Li Jiang, Andrew P. Harrison, Hugh P. Shanahan, Christian Klukas, Hong-Yu Zhang, Yijun Ruan, Ling-ling Chen and Ming Chen Dissecting the chromatin interactome of microRNA genes Nucleic Acids Research, 42, pp. 3028-3043, 2014
94 Kyong-Rim Kieffer Kwon, Zhonghui Tang, Ewy Mathe, Jason Qian, Myong-Hee Sung, Guoliang Li, Wolfgang Resch, Songjoon Baek, Nathanael Pruett, Lars Grontvend, Laura Vian, Steevenson Nelson, Hossein Zare, Ofir Hakim, Deepak Reyon, Arito Yamane, Hirotaka Nakahashi, Alexander L. Kovalchuk, Jizhong Zou, J. Keith Joung, Vittorio Sartorelli, Chia-Lin Wei, Xiaoan Ruan, Gordon L. Hager, Yijun Ruan, Rafael Casellas Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation Cell, 155, 1507-1520, 2013
95 Yubo Zhang, Chee-Hong Wong, Ramon Y. Birnbaum, Guoliang Li, Rebecca Favaro, Chew Yee Ngan, Joanne Lim, Eunice Tai, Huay Mei Poh, Eleanor Wong, Fabianus Hendriyan Mulawadi, Ken Sung, Silvia Nicolis, Nadav Ahituv, Yijun Ruan and Chia-Lin Wei Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations Nature, vol. 504, pp. 306-310, 2013
96 T. R. Mercer, S. L. Edwards, M. B. Clark, S. J. Neph, H. Wang, A. B. Stergachis, S. John, R. Sandstrom, Guoliang Li, K. S. Sandhu, Y. Ruan, L. K. Nielsen, J. S. Mattick, and J. A. Stamatoyannopoulos DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements Nature Genetics, vol. 45, pp. 852-859, 2013
97 Zhizhuo Zhang, Guoliang Li, Kim-Chuan Toh and Wing-Kin Sung 3D Chromosome Modeling with Semi-definite Programming and Hi-C Data Journal of Computational Biology, 20, 831-846, 2013
98 Arkasubhra Ghosh, Gaye Saginc, Shi Chi Leow, Eun Myong Shin, Marc Wong, Ting Dong Yan, Zhizhuo Zhang, Guoliang Li, Wing-Kin Sung, Jianbiao Zhou, Wee Joo Chng, Shang Li, Edison Liu, Vinay Tergaonkar Telomerase directly regulates NFκB dependent transcription Nature Cell Biology, 14(12) (Dec 2012): 1270-1281
99 Argyris Papantonis, Takahide Kohro, Sabyasachi Baboo, Joshua D Larkin, Binwei Deng, Shuichi Tsutsumi, Stephen Taylor, Mika Kobayashi, Guoliang Li, Huay Mei Poh, Xiaoan Ruan, Hiroyuki Aburatani, Yijun Ruan, Tatsuhiko Kodama, Youichiro Wada, Peter Richard Cook TNFa signals through specialized factories where responsive coding and miRNA genes are transcribed EMBO Journal, 31, 23 (Nov 28 2012), 4404-4414
100 Kuljeet S. Sandhu, Guoliang Li, Huay Mei Poh, Yu Ling Kelly Quek, Yee Yen Sia, Su Qin Peh, Fabianus H Mulawadi, Jingyao Zhang, Joanne Lim, Mile Sikic, Francesca Menghi, Anbupalam Thalamuthu, Wing Kin Sung, Xiaoan Ruan, Melissa J Fullwood, Edison Liu, Peter Csermely, Yijun Ruan Large scale functional organization of long-range chromatin interaction networks Cell Reports, 2, 5 (Nov 29 2012), 1207-1219
101 Jingyao Zhang, Huay Mei Poh, Su Qin Peh, Yee Yen Sia, Guoliang Li, Fabianus Hendriyan Mulawadi, Yufen Goh, Melissa J. Fullwood, Wing-Kin Sung, Xiaoan Ruan, Yijun Ruan ChIA-PET Analysis of Transcriptional Chromatin Interactions Methods (2012), 58, 3 (Nov 2012), 289-299
102 Fei Yao, Pramila N. Ariyaratne, Axel M. Hillmer, Wah Heng Lee, Guoliang Li, Audrey S. M. Teo, Xing Yi Woo, Zhenshui Zhang, Jieqi P. Chen, Wan Ting Poh, Kelson F. B. Zawack, Chee Seng Chan, See Ting Leong, Say Chuan Neo, Poh Sum D. Choi, Song Gao, Niranjan Nagarajan, Hervé Thoreau, Atif Shahab, Xiaoan Ruan, Valère Cacheux-Rataboul, Chia-Lin Wei, Guillaume Bourque, Wing-Kin Sung, Edison T. Liu, Yijun Ruan Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons PLOS ONE 7 (9), e46152
103 The ENCODE Project Consortium (including Guoliang Li). 2012 An integrated encyclopedia of DNA elements in the human genome Nature 489(7414): 57-74
104 Jing-Quan Lim, Chandana Tennakoon, Guoliang Li, Eleanor Wong, Yijun Ruan, Chia-Lin Wei and Wing-Kin Sung BatMeth: Improved Mapper for Bisulfite Sequencing Reads on DNA Methylation Genome Biology, 13:R82 (3 October 2012), 2012
105 Guoliang Li*, Xiaoan Ruan*, Raymond K. Auerbach*, Kuljeet Singh Sandhu*, Meizhen Zheng, Ping Wang, Huay Mei Poh, Yufen Goh, Joanne Lim, Jingyao Zhang, Hui Shan Sim, Su Qin Peh, Fabianus Hendriyan Mulawadi, Chin Thing Ong, Yuriy L. Orlov, Shuzhen Hong, Zhizhuo Zhang, Steve Landt, Debasish Raha, Ghia Euskirchen, Chia-Lin Wei, Weihong Ge, Huaien Wang, Carrie Davis, Katherine I. Fisher-Aylor, Ali Mortazavi, Mark Gerstein, Thomas Gingeras, Barbara Wold, Yi Sun, Melissa J. Fullwood, Edwin Cheung, Edison Liu, Wing-Kin Sung, Michael Snyder, and Yijun Ruan Extensive Promoter-centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation Cell, 148, 84-98
106 Melissa J. Fullwood, Joanne Lee, Lifang Lin, Guoliang Li, Mikael Huss, Patrick Ng, Wing-Kin Sung, Shirish Shenolikar Next-Generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations PLoS ONE, 6, e26054, 2011
107 Say Li Kong*, Guoliang Li*, Siang Lin Loh, Wing-Kin Sung, Edison T. Liu Cellular reprogramming by the conjoint action of ERα, FOXA1 and GATA3 for ligand inducible growth Molecular Systems Biology 2011, 7:526
108 Lusy Handoko*, Han Xu*, Guoliang Li*, Chew Yee Ngan, Elaine Chew, Marie Schnapp, Charlie Wah Heng Lee, Chaopeng Ye, Joanne Lim Hui Ping, Fabianus Mulawadi, Eleanor Wong, Jianpeng Sheng, Yubo Zhang, Thompson Poh, Chee Seng Chan, Galih Kunarso, Atif Shahab, Guillaume Bourque, Valere Cacheux-Ratabou, Wing-Kin Sung, Yijun Ruan, Chia-Lin Wei CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells Nature Genetics 43, 630-638
109 Kuljeet Singh Sandhu, Guoliang Li, Wing-Kin Sung, Yijun Ruan Chromatin Interaction Networks and Higher Order Architectures of Eukaryotic Genomes Journal of Cellular Biochemistry 2011, 112(9):2218-2221
110 Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Guoliang Li, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes Genome Research 21:665-675
111 Li Yuqing, Li Yi, Wedren S, Guoliang Li, Charn TH, Vasant DK, Bonnard C, Czene K, Humphreys K, Darabi H, Einarsdttir K et al Genetic variation of ESR1 and its co-activator PPARGC1B is synergistic in augmenting the risk of estrogen receptor positive breast cancer Breast Cancer Research 2011, 13(1):R10
112 Joseph R, Orlov YL, Huss M, Sun W, Kong SL, Ukil L, Pan YF, Guoliang Li, Lim M, Thomsen JS et al Integrative model of genomic factors for determining binding site selection by estrogen receptor a Molecular Systems Biology 2010, 6:456
113 Guoliang Li*, M.J. Fullwood*, H. Xu*, F.H. Mulawadi, S. Velkov, V. Vega, P.N. Ariyaratne, Y.B. Mohamed, H.-S. Ooi, C. Tennakoon, C.-L. Wei, Y. Ruan, W.-K. Sung ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing Genome Biology 11 (2) (2010) R22, DOI: 10.1186/gb-2010-1111-1182-r1122
114 Louise Laurent, Eleanor Wong, Guoliang Li, T. Huynh, A. Tsirigos, C.T. Ong, H.M. Low, W.-K. Sung, I. Rigoutsos, J. Loring, C.-L. Wei Dynamic changes in the human methylome during differentiation Genome Research 20 (3) (2010) 320-331
115 Guoliang Li, Jian Ma, Louxin Zhang Greedy Selection of Species for Ancestral State Reconstruction on Phylogenies: Elimination Is Better than Insertion PLoS ONE 5 (2) (2010) e8985. doi:8910.1371/journal.pone.0008985
116 Zhang, Louxin, Jian Shen, Jialiang Yang, Guoliang Li Analyzing the Fitch Method for Reconstructing Ancestral States on Ultrametric Phylogenetic Trees Bulletin of Mathematical Biology (2010), 72, 1760-1782, DOI: 10.1007/s11538-11010-19505-11538
117 Guoliang Li, Steel Mike, Louxin Zhang More Taxa Are Not Necessarily Better For the Reconstruction of Ancestral Character States Systematic Biology 57 (4) (2008) 647-653
118 AH. Morris, J. Orme,Jr., JD Truwit, J. Steingrub, C. Grissom, KH Lee, Guoliang Li, BT Thompson, R. Brower, M. Tidswell, G. Bernard, D. Sorenson, K. Sward, H. Zheng, D. Schoenfeld, H. Warner A replicable method for blood glucose control in critically ill patients Critical Care Medicine. 36(6):1787-1795, June 2008
119 Guoliang Li, Tze-Yun Leong, and Louxin Zhang Translation Initiation Sites Prediction with Mixture Gaussian Models in Human cDNA Sequences IEEE Transactions on Knowledge and Data Engineering, 2005. 17(8): p. 1152-1160
120 Guoliang Li and Tze-Yun Leong Feature Selection for the Prediction of Translation Initiation Sites Genomics, Proteomics Bioinformatics, 2005. 3(2): p. 73-83