Computational Omics Lab

Publications


Xihao Hu#, Jian Zhang#, Jin Wang, Jingxin Fu, Taiwen Li, Xiaoqi Zheng, Binbin Wang, Shengqing Gu, Peng Jiang, Jingyu Fan, Xiaomin Ying, Jing Zhang, Michael C. Carroll, Kai W. Wucherpfennig, Nir Hacohen, Fan Zhang, Peng Zhang, Jun S. Liu*, Bo Li*, Xiaole Shirley Liu*. Landscape of B cell immunity and related immune evasion in human cancers. Nat Genet. 2019 Mar;51(3):560-567

 

Bao-Feng Jin, Fan Yang, Xiao-Min Ying, Lin Gong, Shuo-Feng Hu, Qing Zhao, Yi-Da Liao, Ke-Zhong Chen, Teng Li, Yan-Hong Tai, Yuan Cao, Xiao Li, Yan Huang, Xiao-Yan Zhan, Xuan-He Qin, Jin Wu, Shuai Chen, Sai-Sai Guo, Yu-Cheng Zhang, Jing Chen, Dan-Hua Shen, Kun-Kun Sun, Lu Chen, Wei-Hua Li, Ai-Ling Li, Na Wang, Qing Xia, Jun Wang, Tao Zhou. Signaling protein signature predicts clinical outcome of non-small-cell lung cancer. BMC cancer, 2018, 18(1):259

 

Feng Changjiang#, Wu Jiaqi#, Yang Fan, Qiu M, Hu Shuofeng, Guo S, Wu J, Ying Xiaomin, Wang Jun. Expression of Bcl-2 is a favorable prognostic biomarker in lung squamous cell carcinoma. Oncology letters. 2018 May;15(5):6925-6930

 

Xiaofang Xing, Jianping Guo, Xianzi Wen, Guangyu Ding, Bo Li, Bin Dong, Qin Feng, Shen Li, Jian Zhang, Xiaojing Cheng, Ting Guo, Hong Du, Ying Hu, Xiaohong Wang, Lin Li, Qingda Li, Meng Xie, Liting Li, Xiangyu Gao, Fei Shan, Ziyu Li, Xiaomin Ying, Tao Zhou, Jiping Wang, and Jiafu Ji. Analysis of PD1, PDL1, PDL2 expression and T cells infiltration in 1014 gastric cancer patients. Oncoimmunology. 2017 Dec 21;7(3):e1356144

 

Yanyan Gao, Xinzheng Wang, Zhihong Sang, Zongcheng Li, Feng Liu, Jie Mao, Dan Yan, Yongqiang Zhao, Hongli Wang, Ping Li, Xiaomin Ying, Xuemin Zhang, Kun He, and Hongxia Wang. Quantitative proteomics by SWATH-MS reveals sophisticated metabolic reprogramming in hepatocellular carcinoma tissues. Sci Rep. 2017 Apr 5;7:45913

 

Jiaqi Wu#, Shuofeng Hu#, Yaowen Chen, Zongcheng Li, Jian Zhang, Hanyu Yuan, Qiang Shi, Ningsheng Shao, and Xiaomin Ying. BCIP: a gene-centered platform for identifying potential regulatory genes in breast cancer. Sci Rep. 2017 Mar 22;7:45235

 

Yaowen Chen, Zongcheng Li, Shuofeng Hu, Jian Zhang, Jiaqi Wu, Ningsheng Shao, Xiaochen Bo, Ming Ni*, and Xiaomin Ying*. Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola. Microbiome. 2017 Feb 1;5(1):15

 

Baocheng Hu, Xiang Wang, Shuofeng Hu, Xiaomin Ying, Ping Wang, Xiangming Zhang, Jian Wang, Hongyan Wang and Ya Wang. miR-21-mediated Radioresistance Occurs via Promoting Repair of DNA Double Strand Breaks. J Biol Chem. 2017 Feb 24;292(8):3531-3540

 

Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jingfa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, and Jun Yu. Precision Medicine: What Challenges Are We Facing? Genomics Proteomics Bioinformatics. 2016 Oct;14(5):253-261

 

Wu Ren, Jian Zhang, Wei Li, Zongcheng Li, Shuofeng Hu, Jian Suo*, and Xiaomin Ying*. A Tumor-Specific Prognostic Long Non-Coding RNA Signature in Gastric Cancer. Med Sci Monit. 2016 Oct 11;22:3647-3657

 

Teng Li, Liang Chen, Juanxian Cheng, Jiang Dai, Yijiao Huang, Jian Zhang, Zhaoshan Liu, Ang Li, Na Li, Hongxia Wang, Xiaomin Ying, Kun He, Ming Yu, Tao Zhou, Xue-Min Zhang, and Qing Xia. SUMOylated NKAP is essential for chromosome alignment by anchoring CENP-E to kinetochores. Nat Commun. 2016 Oct 3;7:12969

 

Zongcheng Li, Yaowen Chen, Shuofeng Hu, Jian Zhang, Jiaqi Wu, Wu Ren, Ningsheng Shao, and Xiaomin Ying. Integrative analysis of protein-coding and non-coding RNAs identifies clinically relevant subtypes of clear cell renal cell carcinoma. Oncotarget. 2016 Dec 13;7(50):82671-82685

 

Hao W, Zhang X, Xiu B, Yang X, Hu S, Liu Z, Duan C, Jin S, Ying X, Zhao Y, Han X, Hao X, Fan Y, Johnson H, Meng D, Persson JL, Zhang H, Feng X, Huang Y. Vitronectin: a promising breast cancer serum biomarker for early diagnosis of breast cancer in patients. Tumour Biol. 2016 Jul;37(7):8909-16

 

Jian Wang, Zongcheng Li#, Bailong Liu, Guangnan Chen, Ningsheng Shao, Xiaomin Ying*, Ya Wang. Systematic studyofcis-antisensemiRNAs in animal species reveals miR-3661 to target PPP2CA in human cells. RNA, 2016 Jan;22(1):87-95 (# Co-first author, *Co-corresponding author)

 

Weike Shen, Yuan Cao, Lei Cha, Xufei Zhang, Xiaomin Ying, Wei Zhang, Kun Ge, Wuju Li and Li Zhong. Predicting linear B-cell epitopes using amino acid anchoring pair composition. BioData Min. 2015 Apr 29;8:14

 

Baocheng Hu, Xiaomin Ying#, Jian Wang, Jittima Piriyapongsa, I. King Jordan, Jipo Sheng, Fang Yu, Po Zhao, Yazhuo Li, Hongyan Wang, Wooi Loon Ng, Shuofeng Hu, Xiang Wang, Chenguang Wang, Xiaofei Zheng, Wuju Li, Walter J. Curran, and Ya Wang. Identification of a Tumor Suppressive Human Specific MicroRNA within the FHIT Tumor Suppressor Gene. Cancer Research, 2014, 74(8):2283-94 (# Co-first author)

 

Wuju Li, Xiaomin Ying, Qixuan Lu, Linxi Chen. Predicting sRNAs and their targets in bacteria. Genomics Proteomics Bioinformatics, 2012, 10(5): 276–284

 

Xiaomin Ying, Yuan Cao, Jiayao Wu, Qian Liu, Lei Cha, Wuju Li. sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization. PLoS One. 2011; 6(7): e22705 (Web server: http://ccb.bmi.ac.cn/starpicker)

 

Yu Liu, Chunhua Mu, Xiaomin Ying, Wuju Li, Na Wu, Jie Dong, Yaping Gao, Ningsheng Shao, Ming Fan, Guang Yang. RNAIII activates map expression by forming an RNA-RNA complex in Staphylococcus aureus. FEBS Lett. 2011, 585(6): 899-905

 

Yuan Cao, Jiayao Wu, Qian Liu, Yalin Zhao, Xiaomin Ying, Lei Cha, Ligui Wang, Wuju Li. sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments. RNA, 2010, 16(11):2051-7 (Database: http://ccb.bmi.ac.cn/srnatarbase)

 

Xiaomin Ying, You Jung Kim, Yiqing Mao, Ming Liu, Yanyan Hou, Hua Li, Xiaolei Wang, Yalin Zhao, Dongsheng Zhao, Jignesh M. Patel, Wuju Li. BatchGenAna: a batch platform for large-scale genomic analysis of mammalian small RNAs. Bioinformation, 2009, 3(8): 346-349

 

Yuan Cao, Na Wang, Xiaomin Ying, Ailing Li, Hengsha wang, Xuemin Zhang, Wuju Li. BioSunMS: a plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry. BMC Medical Informatics and Decision Making, 2009, 9(1):13

 

Yuan Cao, Yalin Zhao, Lei Cha, Xiaomin Ying, Ligui Wang, Ningsheng Shao, Wuju Li. sRNATarget: a web server for prediction of bacterial sRNA targets. Bioinformation, 2009, 3(8): 364-366 (Web server: http://ccb.bmi.ac.cn/srnatarget)

 

Yalin Zhao, Hua Li, Yanyan Hou, Lei Cha, Yuan Cao, Ligui Wang, Xiaomin Ying*, Wuju Li. Construction of two mathematical models for prediction of bacterial sRNA targets. Biochemical and Biophysical Research Communications, 2008, 372:346-350 (Web server: http://ccb.bmi.ac.cn/srnatarget)

 

Bingli Wu, Lei Cha, Zepeng Du, Xiaomin Ying, Hua Li, Xiaofei Zheng, Enmin Li, Wuju Li. Construction of mathematical model for high-level expression of foreign genes in pPIC9 vector and its verification. Biochemical and Biophysical Research Communications, 2007, 354:498-504

 

Xiaomin Ying, Hong Luo, Jingchu Luo and Wuju Li. RDfolder: a web server for prediction of RNA secondary structure. Nucleic Acids Research, 2004, vol.32: W150-W153 (Web server: http://ccb.bmi.ac.cn/RDfolder/)