2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007
Phase separation as a possible mechanism for dosage sensitivity.
Liang Yang#, Jiali Lyu#, Xi Li#, Gaigai Guo# ,Xueya Zhou , Taoyu Chen, Yi Lin, Tingting Li*.
----------Genome Biol. 2024 Jan 15;25(1):17. doi: 10.1186/s13059-023-03128-z
Dissolution of oncofusion transcription factor condensates for cancer therapy.
Yuan Wang#, Chunyu Yu#, Gaofeng Pei#, Wen Jia, Tingting Li*, and Pilong Li*.
----------Nature Chemical Biology, 2023 Oct. doi:10.1038/s41589-023-01376-5.
Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol.
Peiyu Zhu#, Chao Hou#, Manlin Liu, Taoyu Chen,Tingting Li*, Likun Wang*..
----------BMC genomics vol. 24,1 493. 28 Aug. 2023, doi:10.1186/s12864-023-09600-1.
Circadian clocks are modulated by compartmentalized oscillating translation.
Yanrong Zhuang , Zhiyuan Li , Shiyue Xiong , Chujie Sun , Boya Li , Shuangcheng Alivia Wu , Jiali Lyu , Xiang Shi , Liang Yang , Yutong Chen , Zhangbin Bao , Xi Li , Chuhanwen Sun , Yuling Chen , Haiteng Deng , Tingting Li, Qingfeng Wu , Ling Qi , Yue Huang , Xuerui Yang*, Yi Lin*.
----------Cell. 2022 Feb 28. doi: 10.1038/s41392-022-00909-z.
VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis.
Xiaofeng Xu , Ying Li , Taoyu Chen , Chao Hou, Liang Yang , Peiyu Zhu , Yi Zhang , Tingting Li*
----------Brief Bioinform. 2023 Nov 22;25(1):bbad480. doi: 10.1093/bib/bbad480
Sequence variations of phase-separating proteins and resources for studying biomolecular condensates.
Gaigai Guo , Xinxin Wang , Yi Zhang,Tingting Li*.
----------Acta Biochim Biophys Sin (Shanghai). 2023 Jul 18;55(7):1119-1132. doi: 10.3724/abbs.2023131
PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information
Chao Hou#, Xinxin Wang#, Haotai Xie#, Taoyu Chen, Peiyu Zhu, Xiaofeng Xu, Kaiqiang You, Tingting Li*.
----------Nucleic Acids Research, gkac783, 17 September 2022. https://doi.org/10.1093/nar/gkac783
Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.
Chao Hou, Yuxuan Li, Mengyao Wang, Hong Wu, Tingting Li*.
----------BMC Biology 20, 162 (2022). 14 July 2022. doi: 10.1186/s12915-022-01364-6.
Screening membraneless organelle participants with machine-learning models that integrate multimodal features.
Zhaoming Chen#, Chao Hou#, Liang Wang#, Chunyu Yu, Taoyu Chen, Boyan Shen, Yaoyao Hou, Pilong Li*, Tingting Li*.
----------Proc Natl Acad Sci U S A. 2022 Jun 14. doi: 10.1073/pnas.2115369119.
Serum Antigenome Profiling Reveals Diagnostic Models for Rheumatoid Arthritis.
Peng Han, Chao Hou, Xi Zheng, Lulu Cao, Xiaomeng Shi, Xiaohui Zhang, Hua Ye, Hudan Pan, Liang Liu, Tingting Li*, Fanlei Hu* and Zhanguo Li*.
----------Front. Immunol. 20 April 2022. https://doi.org/10.3389/fimmu.2022.884462
A novel strategy for identifying biomarker in serum of patient with COVID-19 using immune complex.
Fugang Duan#, Yifan Wang#, Taoyu Chen#, Zhu Zhu#, Meng Yu, Hui Dai, Shangen Zheng, Yinying Lu*, Tingting Li*, and Xiaoyan Qiu*.
----------Signal Transduct Target Ther. 2022 Feb 28. doi: 10.1038/s41392-022-00909-z.
High-throughput experimental methods for investigating biomolecular condensates.
Taoyu Chen, Qi Lei, Minglei Shi, Tingting Li*.
----------Quantitative Biololgy. 2021, Vol. 9 Issue (3) : 255-266. DOI: 10.15302/J-QB-021-0264.
Distinctive Network Topology of Phase-Separated Proteins in Human Interactome.
Chunyu Yu#, Yunzhi Lang#, Chao Hou, Ence Yang, Xianwen Ren, Tingting Li*.
----------Journal of Molecular Biology. 2021 Oct 6;167292. doi: 10.1016/j.jmb.2021.167292.
Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index.
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*.
----------Genome Biology. 2021 Aug 17;22(1):229. doi: 10.1186/s13059-021-02456-2.
Computational Screening of Biological Phase-separating Proteins.
BoyanShen#, Zhaoming Chen#, Chunyu Yu, Taoyu Chen, Minglei Shi and Tingting Li*.
----------Genomics Proteomics Bioinformatics, 2021 Feb 18;S1672-0229(21)00022-X.
MloDisDB: a manually curated database of the relations between membraneless organelles and diseases.
Chao Hou#, Haotai Xie#, Yang Fu#, Yao Ma# and Tingting Li*.
----------Briefings in Bioinformatics, 2020 Oct 30;bbaa271.
Proteome-scale analysis of phase-separated proteins in immunofluorescence images.
Chunyu Yu, Boyan Shen, Kaiqiang You, Qi Huang, Minglei Shi, Congying Wu, Yang Chen, Chaolin Zhang and Tingting Li*.
----------Briefings in Bioinformatics, 2020 Sep 2;bbaa187.
PhaSepDB: a database of liquid–liquid phase separation related proteins.
Kaiqiang You#, Qi Huang#, Chunyu Yu#, Boyan Shen, Cristoffer Sevilla, Minglei Shi, Henning Hermjakob*, Yang Chen* and Tingting Li*.
----------Nucleic Acids Research, 2020 Jan 8;48(D1):D354-D359.
Phosphoproteomics Enables Molecular Subtyping and Nomination of KinaseCandidates for Individual Patients of Diffuse-Type Gastric Cancer.
Mengsha Tong#, Chunyu Yu#, Jinwen Shi#, Wenwen Huang#, Sai Ge#, Mingwei Liu, Lei Song, Dongdong Zhan, Xia Xia, Wanlin Liu, Jinwen Feng, Wenhao Shi, Jiafu Ji, Jing Gao, Tieliu Shi, Weimin Zhu, Chen Ding, Yi Wang, Fuchu He*, Lin Shen*, Tingting Li*, and Jun Qin*.
----------iScience 2019 Dec 20;22:44-57.
Systematic Characterization and Prediction of Post-Translational Modification Cross-Talk between proteins.
Rongting Huang#, Yuanhua Huang#, YubinGuo#, Shangwei Ji, Ming Lu and Tingting Li*.
----------Bioinformatics 2019 Aug 1;35(15):2626-2633.
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: reanalysis of CPTAC ovarian cancer.
Mengsha Tong#&, Chunyu Yu#, Dongdong Zhan, Ming Zhang, Bei Zhen, Weimin Zhu, Yi Wang, Congying Wu, Fuchu He*, Jun Qin* and Tingting Li*.
----------EBioMedicine 2019 Feb; 40: 305–317.
SIRT5 deacylates metabolism-related proteins and attenuates hepatic steatosis in ob/ob mice.
Yipeng Du*#, Hao Hu#, Saisi Qu#, Jifeng Wang, Chaoju Hua, Jialing Zhang, Peng Wei, Xiaolong He, Junfeng Hao, Pingsheng Liu, Fuquan Yang, Tingting Li*, Taotao Wei*.
---------- EBioMedicine, 2018 Oct;36:347-357. doi: 10.1016/j.ebiom.2018.09.037.
Long non-coding RNA SNHG15 interacts with and stabilizes transcription factor Slug and promotes colon cancer progression.
Hao Jiang, Tingting Li, Yi Qu, Xiang Wang, Bing Li, Jiagui Song, Xiaoran Sun, Yan Tang, Junhu Wan, Yu Yu, Jun Zhan, Hongquan Zhang*.
----------Cancer Letters. 2018 Jul 1;425:78-87. doi: 10.1016/j.canlet.2018.03.038.
Co-occurring protein phosphorylation are functionally associated.
Ying Li#, Xueya Zhou#, Zichao Zhai, Tingting Li*.
----------PLoS Computational Biology. 2017 May 1;13(5):e1005502. doi: 10.1371/journal.pcbi.1005502.
Identifying human SIRT1 substrates by integrating heterogeneous information from various sources.
Zichao Zhai#, Ming Tang#, Yue Yang, Ming Lu, Wei-Guo Zhu*, and Tingting Li*.
----------Scientific Reports. 2017 Jul 4;7(1):4614. doi: 10.1038/s41598-017-04847-7.
Quantitative proteome-based systematic identification of SIRT7 substrates.
Chaohua Zhang#, Zichao Zhai#, Ming Tang, Zhongyi Cheng, Tingting Li*, Wang Haiying*, Wei-Guo Zhu*.
----------Proteomics. 2017 Jul;17(13-14). doi: 10.1002/pmic.201600395.
Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD.
Xiaohua Yu#, Yong Zhang#*, Tingting Li, Zhao Ma, Haixue Jia, Qian Chen, Yixia Zhao, Lili Zhai, Ran Zhong, Changyin Li, Xiaoting Zou, Jiao Meng, Antony K Chen, Pier Lorenzo Puri, Meihong Chen, Dahai Zhu*.
----------Nature Communications. 2017 Jan 16;8:14016. doi: 10.1038/ncomms14016.
Prediction of protein lysine acylation by integrating primary sequence information with multiple functional features.
Yipeng Du#, Zichao Zhai#, Ying Li, Ming Lu, Tanxi Cai, Bo Zhou, Lei Huang, Taotao Wei*, and Tingting Li*.
----------Journal of Proteome Research. 2016 Dec 2;15(12):4234-4244.
Pluripotency-associated miR-290/302 family of microRNAs promote the dismantling of naive pluripotency.
Kai-Li Gu#, Qiang Zhang#, Ying Yan#, Ting-Ting Li#, Fei-Fei Duan, Jing Hao, Xi-Wen Wang, Ming Shi, Da-Ren Wu, Wen-Ting Guo, and Yangming Wang*.
----------Cell Research. 2016 Mar;26(3):350-66. doi: 10.1038/cr.2016.2.
Systematic characterization and prediction of post-translational modification cross-talk.
Yuanhua Huang#, Bosen Xu, Xueya Zhou, Ying Li, Ming Lu, Rui Jiang, Tingting Li*.
----------Molecular&Cellular Proteomics. 2015 Mar;14(3):761-70. doi: 10.1074/mcp.M114.037994.
Epigenetic regulation of autophagy by the methyltransferase EZH2 through an MTOR-dependent pathway.
Fu-Zheng Wei#, Ziyang Cao#, Xi Wang, Hui Wang, Mu-Yan Cai, Tingting Li, Naoko Hattori, Donglai Wang, Yipeng Du, Boyan Song, Lin-Lin Cao, Changchun Shen, Lina Wang, Haiying Wang, Yang Yang, Dan Xie, Fan Wang, Toshikazu Ushijima, Ying Zhao*, and Wei-Guo Zhu*.
----------Autophagy. 2015;11(12):2309-22. doi: 10.1080/15548627.2015.1117734.
Lysine malonylation is elevated in type 2 diabetic mouse models and enriched in metabolic associated proteins.
Yipeng Du#, Tanxi Cai#, Tingting Li, Peng Xue, Bo Zhou, Xiaolong He, Peng Wei, Pingsheng Liu, Fuquan Yang*, Taotao Wei*.
----------Molecular&Cellular Proteomics. 2015 Jan;14(1):227-36. doi: 10.1074/mcp.M114.041947.
Systematic identification of Class I HDAC substrates.
Tingting Li#*, Boyan Song#, Zheng Wu, Ming Lu, Wei-Guo Zhu*.
----------Briefings in Bioinformatics. 2014 Nov;15(6):963-72. doi: 10.1093/bib/bbt060.
Prediction of substrate sites for protein phosphatases 1B, SHP-1, and SHP-2 based on sequence features.
Zheng Wu#, Ming Lu, Tingting Li*.
----------Amino Acids. 2014 Aug;46(8):1919-28. doi: 10.1007/s00726-014-1739-6.
Computational prediction of associations between long non-coding RNAs and proteins.
Qiongshi Lu#, Sijin Ren, Ming Lu, Yong Zhang, Dahai Zhu, Xuegong Zhang, and Tingting Li*.
----------BMC Genomics. 2013 Sep 24;14:651. doi: 10.1186/1471-2164-14-651.
A comprehensive analysis of GATA-1-regulated miRNAs reveals miR-23a to be a positive modulator of erythropoiesis.
Yong Zhu#, Dongsheng Wang#, Fang Wang#, Tingting Li#, Lei Dong, Huiwen Liu, Yanni Ma, Fengbing Jiang, Haixin Yin, Wenting Yan, Min Luo, Zhong Tang, Guoyuan Zhang, Qiang Wang, Junwu Zhang, Jingguo Zhou*, and Jia Yu*.
----------Nucleic Acids Res. 2013 Apr;41(7):4129-43. doi: 10.1093/nar/gkt093.
ASEB: a web server for KAT-specific acetylation site prediction.
Likun Wang#, Yipeng Du, Ming Lu, and Tingting Li*.
----------Nucleic Acids Res. 2012 Jul;40(Web Server issue):W376-9. doi: 10.1093/nar/gks437.
Characterization and prediction of lysine (K)-acetyl-transferase specific acetylation sites.
Tingting Li#, Yipeng Du#, Likun Wang, Lei Huang, Wenlin Li, Ming Lu, Xuegong Zhang, Wei-Guo Zhu*.
----------Molecular&Cellular Proteomics. 2012 Jan;11(1):M111.011080. doi: 10.1074/mcp.M111.011080.
Tingting Li#, Suya Wang, Rimao Wu, Xueya Zhou, Dahai Zhu*, Yong Zhang*.Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing.
----------Genomics. 2012 May;99(5):292-8. doi: 10.1016/j.ygeno.2012.02.003.
MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs.
Chenxing Liu#, Fuquan Zhang, Tingting Li, Ming Lu, Lifang Wang, Weihua Yue, Dai Zhang*.
----------BMC Genomics. 2012 Nov 23;13:661. doi: 10.1186/1471-2164-13-661.
A systematic analysis of the skeletal muscle miRNA transcriptome of chicken varieties with divergent skeletal muscle growth identifies novel miRNAs and differentially expressed miRNAs.
Tingting Li#, Rimao Wu#, Yong Zhang, Dahai Zhu*.
----------BMC Genomics. 2011 Apr 13;12:186. doi: 10.1186/1471-2164-12-186.
hUbiquitome: a database of experimentally verified ubiquitination cascades in humans.
Yipeng Du#, Nanfang Xu#, Ming Lu, Tingting Li*.
----------Database (Oxford). 2011 Nov 30;2011:bar055. doi: 10.1093/database/bar055.
Identifying human kinase-specific protein phosphorylation sites by integrating heterogeneous information from various sources.
Tingting Li*, Pufeng Du, Nanfang Xu.
----------PLoS One. 2010 Nov 15;5(11):e15411. doi: 10.1371/journal.pone.0015411.
Comparison of gene expression in hepatocellular carcinoma, liver development, and liver regeneration.
Tingting Li*, Bingbing Wan, Jian Huang, Xuegong Zhang.
----------Mol Genet Genomics. 2010 May;283(5):485-92. doi: 10.1007/s00438-010-0530-y.
Identification and Characterization of Human snoRNA Core Promoters.
Tingting Li#, Xueya Zhou, Xiaowo Wang, Dahai Zhu*, Yong Zhang*.
----------Genomics. 2010 Jul;96(1):50-6. doi: 10.1016/j.ygeno.2010.03.010.
Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs.
Yong Zhang#, Jun Liu#, Chunshi Jia, Tingting Li, Rimao Wu, Jie Wang, Ying Chen, Xiaoting Zou, Runsheng Chen, Xiujie Wang*, and Dahai Zhu*.
----------BMC Genomics. 2010 Jan 25;11:61. doi: 10.1186/1471-2164-11-61.
Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development.
Tingting Li#, Jian Huang#, Ying Jiang, Yan Zeng, Fuchu He, Michael Zhang, Zeguang Han*, Xuegong Zhang*.
----------Genomics. 2009 Mar;93(3):235-42. doi: 10.1016/j.ygeno.2008.10.006.
Cepred: predicting the co-expression patterns of the human intronic microRNAs with their host genes.
Dong Wang#, Ming Lu, Jing Miao, Tingting Li, Edwin Wang, Qinghua Cui*.
----------PLoS One. 2009;4(2):e4421. doi: 10.1371/journal.pone.0004421.
Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach.
Tingting Li#, Fei Li, Xuegong Zhang*.
----------Proteins. 2008 Feb 1;70(2):404-14.
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.
Tao Peng#, Chenghai Xue, Jianning Bi, Tingting Li, Xiaowo Wang, Xuegong Zhang, Yanda Li*.
----------BMC Genomics. 2008 Apr 26;9:191. doi: 10.1186/1471-2164-9-191.
Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).
Jian Huang#, Pei Hao#, Yun-Li Zhang#, Fu-Xing Deng, Qing Deng, Yi Hong, Xiao-Wo Wang, Yun Wang, Ting-Ting Li, Xue-Gong Zhang, Yi-Xue Li, Peng-Yuan Yang*, Hong-Yang Wang*, and Ze-Guang Han*.
----------BMC Genomics. 2007 Jul 2;8:207.
