Publications

1 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
2 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
3 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
4 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)
5 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
6 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
7 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
8 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
9 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
10 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
11 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
12 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
13 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
14 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]
15 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
16 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
17 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
18 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
19 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
20 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.
21 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.
22 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
23 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
24 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.
25 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
26 Liang Niu, Guoliang Li, Shili Lin (2014) Statistical Models for Detecting Differential Chromatin Interactions Mediated by a Protein PLoS One, 9, e97560
27 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
28 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
29 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
30 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
31 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 associationsNature, vol. 504, pp. 306-310, 2013
32 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
33 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
34 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
35 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
36 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
37 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
38 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
39 The ENCODE Project Consortium (including Guoliang Li). 2012 An integrated encyclopedia of DNA elements in the human genome Nature 489(7414): 57-74
40 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
41 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
42 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
43 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
44 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
45 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
46 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
47 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
48 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
49 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
50 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
51 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
52 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
53 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
54 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
55 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
56 Guoliang Li and Tze-Yun Leong Feature Selection for the Prediction of Translation Initiation Sites Genomics, Proteomics Bioinformatics, 2005. 3(2): p. 73-83