Kui Hua, Xuegong Zhang, A case study on the detailed reproducibility of a human cell altas project, https://doi.org/10.1007/s40484-018-0164-3, Quantitative Biology Yue Hu, Xuegong Zhang, SCeQTL, an R package for identifying eQTL from single-cell parallel sequencing data, bioRxiv, http://dx.doi.org/10.1101/499863 Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang*, Generation of synthetic electronic medical record text, Proc. IEEE BIBM2018, pp.374-380, 2018 Jiaxing Cui, Hongfei Cui, Mingran Yang, Shiyu Du, Junfeng Li, Yingxue Li, Liyang Liu, Xuegong Zhang, Shao Li, Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade, Protein Cell, https://doi.org/10.1007/s13238-018-0596-6, 2018 Sijie Chen, Zheng Wei, Yang Chen, Kui Hua, Wei Zhang, Changyi Liu, Haoxiang Gao, Hao Sun, Zhenyi Wang, Qijin Yin, Shengquan Chen, Shaoming Song, Chen Feng, Hairong Lu, Rui Jiang, Xiaowo Wang, Jin Gu, Xuegong Zhang, SIP: an interchangeable pipeline for scRNA-seq data processing, doi: https://doi.org/10.1101/456772, https://www.biorxiv.org/content/early/2018/10/30/456772 Wenchang Chen, Xuegong Zhang, scMetric: An R package of metric learning and visualization for single-cell RNA-seq data, doi: https://doi.org/10.1101/456814, https://www.biorxiv.org/content/early/2018/10/30/456814 Huijuan Feng, Tingting Li, Xuegong Zhang, Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data, BMC Genomics, 19(Suppl 6): 564, 2018 S.M. Weyn-Vanhentenryck, H. Feng, D. Ustianenko, R. Duffie, Q. Yan, M. Jacko, J.C. Martinez, M. Goodwin, X. Zhang, U. Hengst, S. Lomvardas, M.S. Swanson, C. Zhang, Precise temporal regulation of alternative splicing during neural development, Nature Communications, 9: 2189, 2018 Aziz Khan, Anthony Mathelier, Xuegong Zhang, Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers, Epigenetics, 2018 Jing-Ren Zhang, Lihong He, Dongyang Luo, Fan Yang, Chris Li, Xuegong Zhang, and Haiteng Deng, Multiple Domains of Bacterial and Human Lon Proteases Define Substrate Selectivity, Emerging Microbes & Infections Aziz Khan & Xuegong Zhang*, Making genome browsers portable and personal, Genome Biology, 19: 93, 2018 Zhun Miao, Ke Deng, Xiaowo Wang, Xuegong Zhang*, DEsingle for detecting three types of differential expression in single-cell RNA-seq data, Bioinformatics, 2018, https://doi.org/10.1093/bioinformatics/bty332 Zhiyi Qin, Peter Stoilov, Xuegong Zhang*, Yi Xing*, SEASTAR: systematic evaluation of alternative transcription start sites in RNA, NAR, 46(8): e45, 2018 Shansong Liu, Kui Hua, Sijie Chen, Xuegong Zhang*, Comprehensive simulation of metagenomics sequencing data with non-uniform sampling distribution, Quantitative Biology, 6(2): 175-185, 2018 Top 2017 Lu Zhang, Shiyong Li, Yoon-La Choi, Jinseon Lee, Zhuolin Gong, Xiaoqiao Liu, Yunfei Pei, Awei Jiang, Mingzhi Ye, Mao Mao, Xuegong Zhang, Jhingook Kim, Ronghua Chen, Systematic identification of cancer-related long noncoding RNAs and aberrant alternative splicing of quintuple-negative lung adenocarcinoma through RNA-Seq, Lung Cancer, 2017 Zhiyi Qin, Xuegong Zhang, The identification of switch like alternative splicing exons among multiple samples with RNA Seq data, PLoS ONE, 12(5): e0178320, 2017 https://doi.org/10.1371/journal.pone.0178320 Syed Shujaat Ali Zaidi, Xuegong Zhang, Computational operon prediction in whole-genomes and metagenomes, Briefings in Functional Genomics, 16(4): 181-193, 2017 Qian Yang, Yue Hu, Jun Li, Xuegong Zhang, ulfasQTL: an ultra-fast method of composite splicing QTL analysis, BMC Genomics, 18(Suppl 1): 963, DOI 10.1186/s12864-016-3258-1, 2017 Xiangyu Li, Weizheng Chen, Yang Chen, Xuegong Zhang, Jun Gu, Michael Q. Zhang, Network embedding-based representation learning for single cell RNA-seq data, Nucleic Acids Research, 49(19): e166, 2017 doi: 10.1093/nar/gkx750 Xuegong Zhang*, Shansong Liu, Hongfei Cui, Ting Chen, Reading the underlying information from massive metagenomic sequencing data, Proceedings of the IEEE, 105(3): 459-473, 2017 doi: 10.1109/JPROC.2016.2604406 Top 2016 Zhun Miao, Xuegong Zhang, Differential expression analyses for single-cell RNA-Seq: old questions on new data, Quantitative Biology, 4(4): 243-260, 2016 张学工*，江瑞，汪小我，古槿，陈挺，从生物大数据到知识大发现，《科学通报》，61(36): 3869-3877, 2016 Binbin Wang, Taoyun Ji, Xueya Zhou, Jing Wang, Xi Wang, Jingmin Wang, Dingliang Zhu, Xuejun Zhang, Pak Chung Sham, Xuegong Zhang, Xu Ma, Yuwu Jiang, CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens, Scientific Reports, 6: 25954, 2016 Hui Chen, Xueya Zhou, Jing Wang, Xi Wang, Liyang Liu, Shinan Wu, Tenyan Li, Si Chen, Jingwen Yang, Pak Chung Sham, Guangming Zhu, Xuegong Zhang, Binbin Wang, Exome sequencing and gene prioritization correct misdiagnosis in a Chinese kindred with familial amyloid polyneuropathy, Scientific Reports, 6: 26362, 2016 Qifeng Xu, Xuegong Zhang*, The influence of the global gene expression shift on downstream analyses, PLoS ONE, 11(4): e0153903, 2016 Jing Li, Jing-Wen Li, Zhixing Feng, Juanjuan Wang, Haoran An, Yanni Liu, Yang Wang, Kailing Wang, Xuegong Zhang, Zhun Miao, Wenbo Liang, Robert Sebra, Guilin Wang, Wen-Ching Wang, Jing-Ren Zhang, Epigenetic switch driven by DNA inversions dictates phase variation in Streptococcus pneumonia, PLoS Pathogens, 12(7): e1005762, 2016 Lu Zhang, Xiaoqiao Liu, Xuegong Zhang*, Ronghua Chen*, Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets, Molecular Genetics and Genomics, 291(3): 1035-1051, (DOI 10.1007/s00438-015-1163-y), 2016 Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michal Wojciech Szczesnik, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, Ali Mortazavi, A survey of best practices for RNA-seq data analysis, Genome Biology, 17:13, 2016 Tatiana C. Mangericao, Zhanhao Peng, Xuegong Zhang*, Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls, BMC Systems Biology, 10(Suppl 1): 5, 2016 Aziz Khan Xuegong Zhang*, dbSUPER: a database of super-enhancers in mouse and human genome, Nucleic Acids Research, 44(D1): D164-D171, Jan 2016 Hongfei Cui, Yingxue Li, Xuegong Zhang*, An overview of major metagenomic studies on human microbiomes in health and disease, Quantitative Biology, DOI 10.1007/s40484-016-0078-x, 4(3): 192-206, 2016 Huijuan Feng, Tingting Li, Xuegong Zhang*, Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-seq data, bioRxiv, doi: http://dx.doi.org/10.1101/061085, June 2016 Top 2015 Huijuan Feng, Xuegong Zhang, Chaolin Zhang, mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data, Nature Communications, 6: 7836, 2015 Junfeng Li, Junyi Zhang, Liyang Liu, Yucai Fan, Lianshuo Li, Yunfeng Yang, Zuhong Lu, Xuegong Zhang, Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu, Scientific Reports, 5: 15488, 2015 Chao Ye, Bo Jiang, Xuegong Zhang*, Jun S. Liu*, dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis, Bioinformatics, 31(11): 1842-1844, 2015 Top 2014 Zhixing Feng, Jing Li, Jing-Ren Zhang*, Xuegong Zhang*, qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data, Nucleic Acids Research, 42(22): 13488-13499, 2014 Leying Guan, Qian Yang, Mengting Gu, Liang Chen, Xuegong Zhang*, Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation, Quantitative Biology, 2(2): 71-79, 2014 Guang-Zhong Wang, Simone Marini, Xinyun Ma, Qiang Yang, Xuegong Zhang*, Yan Zhu*, Improvement of Dscam hemophilic binding affinity throughout Drosophila evolution, BMC Evolutionary Biology, 4: 186, 2014 YingXue Li, XueNing Liu, XiaoWo Wang, XueGong Zhang*, Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae, Science China Life Sciences, 57(1): 52-58, 2014 Xavier Roge, Xuegong Zhang*, RNAseqViewer: visualization tool for RNA-Seq data, Bioinformatics, 30(6): 891-892, 2014 Yong Chen, Yunfeng Ding, Yi Yang, Jinhai Yu, Guiing Liu, Xumin Wang, Shuyan Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo, Yang Wang, Yalan Du, Huina Zhang, Peng Zhang, Huimin Na, Shimeng Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang Wang, Zhonghua Fan, Honglei Liu, Xiaowo Wang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Alexander Steinbuchel, Toyoshi Fujimoto, Simon Cichello, Jun Yu, Pingsheng Liu, Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630, Nucleic Acids Research, 42(2): 1042-1064, 2014 Shufang Zhang, Xueya Zhou, Shengnan Liu, Tingting Bai, Yingai Zhang, Jing Wang, Shunlan Wang, Xuegong Zhang, Binbin, Wang, MYH9-related disease: description of a large Chinese pedigree and a survey of reported mutations, Acta Haematologica, 132: 193-198, 2014 Jing Cheng, Xueya Zhou, Yu Lu, Jing Chen, Bing Han, Yuhua Zhu, Liyang Liu, Kwong-Wai Choy, Dongyi Han, Pak C. Sham, Michael Q. Zhang, Xuegong Zhang, Huijun Yuan, Exom sequencing identifies a novel frameshift mutation of MYO6 as the cause of autosomal dominant nonsyndromic hearing loss in a Chinese Family, Annals of Human Genetics, 78: 410-423, 2014 Yu Lu, Xueya Zhou, Zhanguo Jin, Jing Cheng, Weidong Shen, Fei Ji, Liyang Liu, Xuegong Zhang, Michael Zhang, Ye Cao, Dongyi Han, KwongWai Choy, Huijun Yuan, Resolving the genetic heterogeneity of prelingual hearing loss within one family: performance comparison and application of two targeted next generation sequencing approaches, Journal of Human Genetics, 59: 599-607, 2014 Chao Ye, Xuegong Zhang, A simulation study on gene expression regulation via stochastic model, Proceedings of the 33rd Chinese Control Conference, pp. 6885-6888, July 28-30, 2014, Nanjing, China Qifeng Xu, Xuegong Zhang, Multiclass feature selection algorithms based on R-SVM, IEEE ChinaSIP, 525-529, 2014 RNA序列数据可视化软件[简称: RNASeqViewer] V1.0，中华人民共和国计算机软件著作权登记，第0744989号，2014.6.11
