个人简历:  

1989年         获清华大学自动化系学士学位

1994年         获清华大学模式识别与智能系统专业博士学位

2001--2002年    哈佛大学公共卫生学院高级访问学者

                 现为清华大学自动化系教授、生命学院和医学院兼职教授

主要科研领域及方向:         

代表论文:     

2021

张学工、汪小我编著，《模式识别》(第4版)，清华大学出版社，2021.9

Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang*, A method for generating synthetic electronic medical record text, IEEE TCBB, 18(1):173-182, 2021

Minsheng Hao, Kui Hua*, Xuegong Zhang*, SOMDE: a scalable method for identifying spatially variable genes with self-organizing map, Bioinformatics, 2021

Sijie Chen, Yanting Luo, Haoxiang Gao, Fanhong Li, Jiaqi Li, Yixin Chen, Renke You, Minsheng Hao, Haiyang Bian, Xi Xi, Wenrui Li, Weiyu Li, Mingli Ye, Qiuchen Meng, Ziheng Zou, Chen Li, Haochen Li, Yangyuan Zhang, Yanfei Cui, Lei Wei, Fufeng Chen, Xiaowo Wang, Hairong Lv, Kui Hua, Rui Jiang, Xuegong Zhang*, A human ensemble cell atlas (hECA) enables in data cell sorting, bioRxiv 2021.07.21.453289;

Sijie Chen, (陈斯杰), Yanting Luo, (罗燕婷), Haoxiang Gao, (高浩翔), Fanhong Li, (李范红), Jiaqi Li, (李嘉骐), Yixin Chen, (陈奕鑫), Renke You, (尤仁科), Hairong Lv, (闾海荣), Kui Hua, (花奎), Rui Jiang, (江瑞), Xuegong Zhang, (张学工), Toward a unified information framework for cell atlas assembly, National Science Review, 2021;, nwab179

2020

Yue Hu, Xi Xi, Qian Yang, Xuegong Zhang*, SCeQTL: an R package for indentifying eQTL from single-cell parallel sequencing data, BMC Bioinformatics, 21: 184, 2020 https://doi.org/10.1186/s12859-020-3534-6

Wendao Liu, Xuegong Zhang*, Single-cell alternative splicing analysis reveals dominance of single transcript variant, Genomics, 112: 2418-2425, 2020

Qin Yu, Geng Chen, Jiaqi Li, Xiaolong Liu, Xuegong Zhang, Haiming Lu, Predicting microvascular invasion of hepatocellular carcinoma by texture analysis of multi-phase MR image, Eulenstein & Al-Mubaid (eds.) BICOB 2020 (EPiC Series in Computing, vol.70), pp.238-246, 2020

Yixin Chen, Sijie Chen, Xuegong Zhang*, Using DenseFly algorithm for cell searching on massive scRNA-seq datasets, BMC Genomics, 21 (Suppl 5): 222, 2020

Najeebullah Shah, Jiaqi Li, Fanhong Li, Wenchang Chen, Haoxiang Gao, Sijie Chen, Kui Hua, Xuegong Zhang*, An experiment on ab initio discovery of biological knowledge from scRNA-seq data using machine learning, Patterns, 1: 100071, 2020 https://doi.org/10.1016/j.patter.2020.100071

2019

Jiaqi Li, Haiming Lu, Xiang Fang, Sijie Chen, Xuegong Zhang*, Pixel-level clustering reveals intra-tumor heterogeneity in non-small cell lung cancer, IEEE BIBM 2019, pp.1536-1939

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, 10(7): 496-509, 2019

Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S. Waterman, Xuegong Zhang*, A new statistic for efficient detection of repetitive sequences, Bioinformatics, 35(22): pp.4596-4606, 2019

Xuegong Zhang, QB: Embracing the future of quantitative understanding and engineering of life, Quantitative Biology, 7(1): 1-2, 2019

Aziz Khan & Xuegong Zhang, Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers, Scientific Reports, 9: 2877, 2019

Kui Hua, Xuegong Zhang, Estimating the total genome length of a metagenomic sample using k-mers, BMC Genomics, 20 (Suppl 2):183, 2019

Kui Hua, Xuegong Zhang, A case study on the detailed reproducibility of a human cell altas project, Quantitative Biology, 7(2): 162-169, 2019

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): S64, 2019

Chao Zhang, Xing Sun, Kang Dang, Ke Li, Xiao-wei Gao, Zong-qiao Yu, Fei-yue Huang, Yun-sheng Wu, Zhu Liang, Zai-yi Liu, Xue-gong Zhang, Xing-lin Gao, Shao-hong Huang, Jie Qin, Wei-neng Feng, Tao Zhou, Yan-bin Zhang, Wei-jun Fang, Ming-fang Zhao, Xue-ning Yang, Qing Zhou, Yi-long Wu, Wen-zhao Zhong, Toward an expert level of lung cancer detection and classification using a deep convolutional neural network, The Oncologist, 24: 1-7, 2019

胡越，罗东阳，花奎，路海明，张学工，关于深度学习的综述与讨论，《智能系统学报》， 14(1): 1-18, 2019

2018

Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang*, Generation of synthetic electronic medical record text, Proc. IEEE BIBM2018, pp.374-380, 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, in press

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, 34(18): 3223-3224, 2018

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

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, 109: 21-27, 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

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 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

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

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

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, Jun Yu, Precision medicine: what challenges are we facing? Genomics Proteomics Bioinformatics, 14: 253-261, 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, 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, 4(3): 192-206, 2016

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

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

2013及以前见 http://bioinfo.au.tsinghua.edu.cn/member/xuegonglab/Publications.html

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