Xuegong Zhang, Ph.D.

Professor of Pattern Recognition and Bioinformatics

Director, Bioinformatics Division, TNLIST (Tsinghua National Laboratory for Information Science &Technology)

Department of Automation, Tsinghua University

FIT 1-107, Tsinghua University, Beijing 100084, China

Phone: 86-10-62794919, 62795578 ext. 888

Fax: 86-10-62773552

Email: zhangxg@tsinghua.edu.cn

Last update：Feb 08, 2021

Research

l Machine Learning, especially small-sample learning and discovery learning

l Digital twin systems of life and Intelligent Health

l The informatics architecture of human cellular and molecular portraitures

Education

March, 1994, Ph.D. of Pattern Recognition and Intelligent Systems, Tsinghua University

July, 1989, BS of Industrial Automation, Tsinghua University

Work Experiences

2003 – present Director, Bioinformatics Division, TNLIST (Tsinghua National Laboratory of Information Science and Technology)

2002 – present Professor of Pattern Recognition and Bioinformatics, Department of Automation, Tsinghua University

2002 – present Deputy Director, MOE Key Laboratory of Bioinformatics

2007. Mar-Apr Visiting Scholar, MCB, USC

2006. Feb-Mar Visiting Scientist, Harvard School of Public Health

2001 – 2002 Visiting Scholar, Harvard School of Public Health

1999 – 2007 Director, Institute of Information Processing, Department of Automation, Tsinghua University

1996 – 2002 Associate Professor of Pattern Recognition, Department of Automation, Tsinghua University

1994 – 1996 Lecturer, Department of Automation, Tsinghua University

Courses Given

Introductory Computational Molecular Biology (graduate)

Introduction to Statistical Learning Theory (graduate)

Scientific Ethics and Exposition (graduate)

Fundamental Pattern Recognition (undergraduate)

Machine Learning (graduate)

Awards

2016年全国优秀科技工作者

2009年国家教学成果二等奖

2008年北京市教学成果一等奖

2006年国家杰出青年基金

2004年教育部新世纪优秀人才支持计划

2002年国家科技进步二等奖

2001年中国海洋石油总公司科技进步一等奖

1995年国家教委科技进步二等奖

Selected Publications

2021

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

2020

Xinmiao Fan, Lu Ping, Hao Sun, Yushan Chen, Pu Wang, Tao Liu, Rui Jiang, Xuegong Zhang*, Xiaowei Chen*, Whole-exom sequencing of discordant monozygotic twin families for identification of candidate genes for Microtia-Atresia, Frontiers in Genetics, 11: 568052, 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

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

Minsheng Hao, Kui Hua, Xuegong Zhang, SOMDE: A scalable method for identifying spatially variable genes with self-organizing map, bioRxiv preprint doi: https://doi.org/10.1101/2020.12.10.419549

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 https://doi.org/10.1007/s13238-018-0596-6

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, https://doi.org/10.1093/bioinformatics/btz262, 2019

Xuegong Zhang, QB: Embracing the future of quantitative understanding and engineering of life, Quantitative Biology, 7(1): 1-2, 2019 https://doi.org/10.1007/s40484-019-0168-7

Aziz Khan & Xuegong Zhang*, Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers, Scientific Reports, 9: 2877, 2019 https://doi.org/10.1038/s41598-019-38979-9

Kui Hua, Xuegong Zhang*, Estimating the total genome length of a metagenomic sample using k-mers, BMC Genomics, 20 (Suppl 2):183 https://doi.org/10.1186/s12864-019-5467-x WOS:000464120900001

Kui Hua, Xuegong Zhang*, A case study on the detailed reproducibility of a human cell altas project, Quantitative Biology, 7(2): 162-169, 2019 https://doi.org/10.1007/s40484-018-0164-3

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 https://doi.org/10.1186/s12864-018-4925-1

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, Xuegong 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 https://doi.org/10.11992/tis.201808019

2018

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

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

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, in press, 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

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

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

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

2015

Aziz Khan & Xuegong Zhang, dbSUPER: a database of super-enhancers in mouse and human genome, Nucleic Acids Research, advanced access Oct.4, 2015

Huijuan Feng, Xuegong Zhang, Chaolin Zhang, mRNA 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

Zhixing Feng, Gang Fang, Jonas Korlach, Tyson Clark, Khai Luong, Xuegong Zhang, Wing Wong, Eric Schadt, Detecting DNA modification from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic, PLoS Computational Biology, 9(3): e1002935, March 2013

Weichen Wang, Zhiyi Qin, Zhixing Feng, Xi Wang, Xuegong Zhang, Identifying differentially spliced genes from two groups of RNA-seq samples, GENE, 518: 164-170, 2013

Ali Nowrouze, Wing T. Cheung, Tingting Li, Xuegong Zhang, Anne Arens, Anna Paruzynski, Simon N. Waddington, Emma Osejindu, Safia Reja, Christof von Kalle, Yoahe Wang, Faisal Al-Allaf, Lisa Gregory, Matthew Themis, Maxine Holder, Niraja Dighe, Alaine Ruthe, Suzanne MK Buckley, Brian Bigger, Eugenio Montini, Adrian J. Thrasher, Robert Andrews, Terry P. Roberts, Robert F. Newbold, Charles Coutelle, Manfred Schmidt, Mike Themis, The fetal mouse is a sensitive genotoxicity model that exposes lentiviral-associated mutagenesis resulting in liver oncogenesis, Molecular Therapy, 21: 324-337, Feb. 2013

2012

Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun, Xuegong Zhang, Comparison of metagenomic samples using sequence signatures, BMC Genomics, 13: 730, 2012

Bai Jiang, Xujun Liang, Yang Chen, Tao Ma, Liyang Liu, Junfeng Li, Rui Jiang, Ting Chen, Xuegong Zhang, Shao Li, Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome, Scientific Reports, 2: 936, 2012

Huijuan Feng, Zhiyi Qin, Xuegong Zhang, Opportunities and methods for studying alternative splicing in cancer with RNA-Seq, Cancer Letters, doi: http://dx.doi.org/10.1016/j.canlet.2012.11.010, 2012

Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun, Xuegong Zhang, Cmoparison of metagenomic samples using sequence signatures, BMC Genomics, 13: 730, 2012

Chao Wu, Jun Zhu, Xuegong Zhang, Inegrating gene expression and protein-protein interaction network to prioritize cancer-associated genes, BMC Bioinformatics, 13: 182, 2012

Tingting Li, Yipeng Du, Likun Wang, Lei Huang, Wenlin Li, Ming Lu, Xuegong Zhang, Wei-Guo Zhu, Characterization and prediction of lysine(k)-acetyl-transferase specific acetylation sites, Molecular & Cellular Proteomics, 11(1): M111.011080, Jan 2012

2011

Xi Wang, Xuegong Zhang, Pinpointing Transcription Factor Binding Sites from ChIP-seq Data with SeqSite, BMC Systems Biology, 5(Suppl 2): S3, 2011

周雪崖，张学工，基于拷贝数变异的遗传关联研究，《科学通报》，56(6): 370-382, 2011

Chao Ye, Linxi Liu, Xi Wang, Xuegong Zhang, Observations on potential novel transcripts from RNA-Seq data, Front. Electr. Electron. Eng. China,6(2): 275-282, 2011

Weichen Wang & Xuegong Zhang, Network-based group variable selection for detecting expression quantitative trait loci (eQTL), BMC Bioinformatics, 12: 269, 2011

N. Kato et al, Meta-analysis of genome-wide association studies identifies five novel variants associated with blood pressure in east Asians, Nature Genetics, 43(6): 531-538, 2011

Chao Ye, Ying Liu, Xuegong Zhang, Observations on shifted cumulative regulation, Genome Biology, 12:404, 2011

Likun Wang, Xiaowo Wang, Xi Wang, Yanchun Liang, Xuegong Zhang, Observations on novel splice junctions from RNA sequencing data, Biochemical and Biophysical Research Communications, 409: 299-303, 2011

Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman, Sequence alignment as hypothesis testing, Journal of Computational Biology, 18(5): 677-691, May 2011

Zhengpeng Wu, Xi Wang, Xuegong Zhang, Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq, Bioinformatics, 27(4): 502-508, 2011

2010

Xi Wang, Zhengpeng Wu, Xuegong Zhang, Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq, Journal of Bioinformatics and Computational Biology, 8(Suppl.1): 177-192, 2010

Ting Zhang, Xuegong Zhang, Zhirong Sun, Identifying changed protein-protein interactions in biological processes by gene coexpression analysis, Chinese Science Bulletin, 55(14): 1396-1402, 2010

王曦、汪小我、王立坤、冯智星、张学工，新一代高通量RNA测序数据的处理与分析，《生物化学与生物物理进展》，37(8): 834-846, 2010

The MAQC Consortium, The MAQC-II project: a comprehensive study of common practices for the development and validation of microarray-based predictive models, Nature Biotechnology, 28(8): 827-841, 2010

Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, 26(1): 136-138, 2010

PEI YunFei, WANG ZhiMin, Fei Fei, SHAO ZhiMing, HUANG Wei, ZHANG XueGong. Bioinformatics study indicates possible microRNA-regulated pathways in the differentiation of breast cancer, Chinese Science Bulletin, 55(10): 927-93, 2010

Tingting Li, Bingbing Wan, Jian Huang, Xuegong Zhang, Comparison of gene expression in hepatocellular carcinoma, liver development and liver regeneration, Mol Genet Genomics, 283: 485-492, 2010

2009

Ying Liu, Bo Jiang, Xuegong Zhang, Gene set analysis identifies master transcription factors in developmental courses, Genomics, 94: 1-10, 2009 (cover story)

Tingting Li, Jian Huang, Ying Jiang, Yan Zeng, Fuchu He, Michael Q. Zhang, Zeguang Han, Xuegong Zhang, Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development, Genomics, 93: 235-242, 2009

Shicai Fan, Xuegong Zhang, CpG island methylation pattern in different human tissues and its correlation with gene expression, BBRC, 383(2009): 421-425

Yunfei Pei, Ting Zhang, Victor Renault, Xuegong Zhang, An overview of hepatocellular carcinoma study by omics-based methods, Acta Biochimica et Biophysica Sinica, 41(1): 1-15, 2009

YunfeiPei, Xi Wang, Xuegong Zhang, Predicting the fate of microRNA target genes based on sequence features, Journal of Theoretical Biology, 261: 17-22, 2009

凡时财，张学工，DNA甲基化的生物信息学研究进展, 《生物化学与生物物理进展》，36(2): 143-150, 2009

Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang, Introduction: the seventh Asia Pacific Bioinformatics Conference (APBC2009), BMC Bioinformatics, 10(Suppl 1): S1, 2009

Li Zhu, Wanwan Tang, Guisen Li, Jicheng Lv, Jiaxiang Ding, Lei Yu, Minghui Zhao, Yanda Li, Xuegong Zhang, Yan Shen, Hong Zhang, Haiyan Wang, Interaction between variants of two glycosyltransferase genes in IgA nephropathy, Kidney International, 76: 190-198, 2009

2008

Bo Jiang, Xuegong Zhang, Tianxi Cai, Estimating the confidence interval for prediction errors of support vector machine classifiers, Journal of Machine Learning Research, 9(March): 521-540, 2008

Xuesong Lu, Xin Lu, Zhigang C. Wang, J. Dirk Iglehart, Xuegong Zhang and Andrea L. Richardson, Predicting features of breast cancer with gene expression patterns, Breast Cancer Research and Treatment, 108(2): 191-201, March 2008 (published online: May, 2007) (4.671)

Tingting Li, Fei Li, Xuegong Zhang, Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach, Proteins: Structure, Function, and Bioinformatics, 70: 404-414, 2008

李婷婷，蒋博，汪小我，张学工，转录因子结合位点的计算分析方法，《生物物理学报》，24(5): 334-346, 2008

Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Xuegong Zhang, Michael Zhang, Multiobjective fuzzy biclustering in microarray data: method and a new performance measure, IEEE Congress on Evolutionary Computation 2008 (CEC2008), pp. 1536-1543, June 1-6, 2008

Shicai Fan, Michael Q. Zhang, Xuegong Zhang, Histone methylation marks play important roles in predicting the methylation status of CpG islands, Biochemical and Biophysical Research Communications,374: 559-564, 2008

Tao Peng, Chenghai Xue, Jianning Bi, Tingting Li, Xiaowo Wang, Xuegong Zhang and Yanda Li, Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse, BMC Genomics, 9: 191, 2008

Xiaowo Wang, Xuegong Zhang, Yanda Li, Complicated evolutionary patterns of microRNAs in Vertebrates, Science in China, 51(6):552-9, 2008

2007

Yonghong Peng, Xuegong Zhang, Guest Editorial: Integrative data mining in systems biology: from text to network mining, Artificial Intelligence in Medicine, 41(2): 83-86, 2007

Tingting Li, Hu Fu, and Xuegong Zhang, Prediction of kinase-specific phosphorylation sites by one-class SVMs, Proceedings of 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM2007), pp. 217-222, 2007

Xi Wang, Sanghamitra Bandyopadhyay, Zhenyu Xuan, Xiaoyue Zhao, Michael Q. Zhang, Xuegong Zhang, Prediction of transcription start site based on feature selection using AMOSA, CSB2007 Conference Proceedings, volume 6, pp.183-193, San Diego, Aug 13-17, 2007

Bo Jiang, Michael Q. Zhang, Xuegong Zhang, OSCAR: one-class SVM for accurate recognition of cis-elements, Bioinformatics, 23(5): 531-537, 2007

Shicai Fan, Fang Fang, Xuegong Zhang, Michael Q. Zhang, Putative zinc finger protein binding sites are enriched in the boundaries of methylation-resistant CpG islands in the human genome, PLoS ONE, 2(11): e1184, 2007

Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li, Identifications of conserved 7-mers in the 3’-UTRs and microRNAs in Drosophila, BMC Bioinformatics, 8:432, 2007

S Li, ZQ Zhang, LJ Wu, XG Zhang, YD Li, YY Wang Understanding ZHENG in Traditional Chinese Medicine in the context of neuro-endocrine-immune network, IEESystems Biology, 1(1): 51-60, 2007

Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang and Michael Q. Zhang, Computing exact P-values for DNA motifs, Bioinformatics, 23(5): 531-537, 2007

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, Pen-Yuan Yang, Hong-Yang Wang, Ze-Guang Han, Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS), BMC Genomics, 8: 207, 2007

Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Neighbor number, valley seeking and clustering, Pattern Recognition Letters, 28: 173-180, 2007

2006

Jun Li, Michael Q. Zhang, Xuegong Zhang, A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data, American Journal of Human Genetics, 79: 628-639, Oct 2006

Shao Li, Ruiqin Wang, Yulong Zhang, Xuegong Zhang, A. Joseph Layon, Yanda Li and Mingzhe Chen, Symptom combinations associated with outcome and therapeutic effects in a cohort of cases with SARS, The American Journal of Chinese Medicine, 34(6): 937-947, 2006

Jin Gu, Tao He, Yunfei Pei, Fei Li, Xiaowo Wang, Jing Zhang, Xuegong Zhang, Yanda Li, Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking seqeuences, Mammalian Genome, 17: 1033-1041, 2006

Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Neighbor number, valley seeking and clustering, Pattern Recognition Letters, 28: 173-180, 2006

Fang Fang, Shicai Fan, Xuegong Zhang and Michael Q. Zhang, Predicting methylation status of CpG islands in the human brain, Bioinformatics, 22(18): 2204-2209, 2006

Xuesong Lu, Xuegong Zhang, The effect of GeneChip gene definitions on the microarray study of cancers, BioEssays, 28(7): 739-746, 2006

Chaolin Zhang, Xuesong Lu, Xuegong Zhang, Significance of gene ranking for classification of microarray samples, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(3): 312-320, 2006

Xuegong Zhang, Xin Lu, Qian Shi, Xiu-qin Xu, Hon-chiu E Leung, Lyndsay N Harris, James D Iglehart, Alexander Miron, Jun S Liu and Wing H Wong, Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data, BMC Bioinformatics, 7:197, 2006 (10Apr2006)

刘沭华，张学工，周群，孙素琴，近红外漫反射光谱法和模式识别技术鉴别中药材产地，《光谱学与光谱分析》，26(4): 629-632, Apr. 2006

许建华，张学工，经典线性算法的非线性核形式，《控制与决策》，vol.21, no.1, pp. 1-12, 2006

Xu Jian-hua, Zhang, Xue-gong, Li Yan-da, Regularized kernel forms of minimum squared error method, Front. Electr. Electron. Eng. China, (2006)1: 1-7

Jianhua XU, Xuegong Zhang, Suqin Sun. Tuning SVM Parameters for Classifying Geographical Origins of Chinese Medical Herbs. International Journal of Wavelet, Multimedia and Information Processing, 2006, 4(3)

2005

Shicai Fan & Xuegong Zhang, Characterizing the microenvironment surrounding phosphorylated protein sites, Genomics, Proteomics & Bioinformatics, 3(4): 213-217, 2005

S. Weng, C. Zhang, Z. Liu, and X. Zhang, Mining the structural knowledge of high-dimensional medical data using Isomap, Medical & Biological Engineering & Computing, 43(3): 410-412, 2005

Jianhua Xu, Xuegong Zhang. A Multiclass Kernel Perceptron Algorithm. In: Proceedings of International Conference on Neural Networks and Brain(Mingsheng Zhao and Zhongzhi Shi, editors). Vol. 2, pp. 717-721, Oct. 13-15, 2005, Beijing, China. New York: IEEE Press

Chenghai Xue, Fei Li, Tao He, Guoping Liu, Yanda Li, Xuegong Zhang, Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine, BMC Bioinformatics, 6: 310, 2005

Xiangqing Sun, Zhongqi Zhang, Yulong Zhang, Xuegong Zhang, Yanda Li, Multi-locus penetrance variance analysis method for association study in complex diseases, Human Heredity, 60(3): 143-149, 2005

Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li, MicroRNA identification based on sequence and structure alignment, Bioinformatics, 21(18): 3610-3614, 2005

Jianning Bi, Huiyu Xia, Fei Li, Xuegong Zhang, Yanda Li, The effect of U1 snRNA binding free energy on the selection of 5' splice sites, Biochemical and Biophysical Research Communications, 333: 64-69, 2005

刘沭华，张学工，周群，孙素琴，模式识别和红外光谱法相结合鉴别中药材产地，《光谱学与光谱分析》，2005，v.25, no.6, 878-881 (Use of FTIR and pattern recognition to detemine geographical origins of Chinese midical herbs, Spectroscopy and Spectral Analysis)

Shuhua Liu, Xuegong Zhang, Suqin Sun, Discrimination and feature selection of geographic origins of traditional Chinese medicine herbs with NIR spectroscopy, Chinese Science Bulletin, 50(2): 179-184, 2005

Keyue Ding, Jing Zhang, Kaixin Zhou, Yan Shen, Xuegong Zhang, htSNPer1.0: software for haplotype block partition and htSNPs selection, BMC Bioinformatics, 6:38, 2005 (1 March 2005)

Keyue Ding, Kaixin Zhou, Jing Zhang, Joanne Knight, Xuegong Zhang, Yan Shen, The effect of haplotype block definations on inference of haplotype block structure and htSNPs selection, Molecular Biology and Evolution, 22(1): 148-159, 2005

2004

Jing Zhang, Fei Li, Jun Li, Michael Q. Zhang, Xuegong Zhang, Evidence and characteristics of putative human alpha recombination hotspots, Human Molecular Genetics, 13(22): 2823-2828, 2004

Xi Ma, Jun Cai, Wei Hu, Yimin Zhang, Yanda Li, Xuegong Zhang, Discovering possible context dependences around SNP Sites in human genes with Bayesian wetwork learning, ICARCV 2004, pp.1315-1319, Dec.2004

Xuesong Lu, Yanda Li, Xuegong Zhang, A simple strategy for detecting outlier samples in microarray data, ICARCV 2004, pp.1331-1335, Dec.2004

孙向青，贾彦彬，张学工，许琪，沈岩，李衍达，多巴胺通路的基因与精神分裂症风险的多位点关联研究，《中国科学》（C辑），34(5): 465-470, 2004

X-Q. Xu, C.K. Leow, X. Lu, X. Zhang, J.S. Liu, W.H. Wong, A. Asperger, S. Deininger, H.E. Leung, Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics, Proteomics, 4: 3235-3245, 2004

Jianhua Xu, Xuegong Zhang, A learning algorithm with Gaussian regularizer for kernel neuron, Advances in Neural Networks – ISNN 2004, part I, pp.252-257, Dalian, Aug., 2004

Jianhua Xu, Xuegong Zhang, Kernels based on weighted Levenshtein distance, IJCNN2004, pp.3015-3018, Budapest, July 2004

许建华，张学工，李衍达，支持向量机的新发展，《控制与决策》，vol.19,no.5, pp.481-484, 2004年5月

李衍达，张学工，李飞，生命信息技术前沿热点—小RNA基因及基因组非编码区的信息挖掘，中国科学院《2004高技术发展报告》，科学出版社，2004年3月 pp. 124-131

Fang Wen, Fei Li, Huiyu Xia, Xin Lu, Xuegong Zhang, Yanda Li, The impact of very short alternative splicing on protein structures and functions in the human genome, Trends in Genetics, vol.20, no.5, May 2004, pp.232-236

Xuesong Lu, Xing Wang, Ying Huang, Wei Hu, Guang R. Gao, Yanda Li, Xuegong Zhang, On some choices in Bayesian network learning for reconstructing regulatory networks,Proceedings of RECOMB04, March 2004, pp. 126-127

Chaolin Zhang, Yanda Li, Xuegong Zhang, gMap: extracting and interactively visualizing nonlinear relationships of genes from expression, Proceedings of RECOMB04,March 2004, pp. 228-229

许建华，张学工，李衍达，最小平方误差算法的正则化核形式，《自动化学报》，vol.30, no.1, Jan. 2004, pp.27-36

Books and Book Chapters

1. Rui Jiang, Xuegong Zhang, Michael Q. Zhang, Basics of Bioinformatics, Tsinghua University Press and Springer, 2014

2. 张学工，《模式识别》（第三版），清华大学出版社，2010.8

3. V. Vapnik著，许建华、张学工译，《统计学习理论》，电子工业出版社，2004.6

4. 边肇祺、张学工等编著，《模式识别》(第二版)，清华大学出版社，2000.1

5. V. Vapnik著，张学工译，《统计学习理论的本质》，清华大学出版社，2000.8

6. 张学工、刘业新编著, 《X Window /Motif编程速成》，清华大学出版社，1998.3

7. Xuegong Zhang and Yanda Li, The application of artificial neural networks in editing noisy seismic data, Chapter 7, in F.Aminzadeh & M. Jamshidi eds., Soft Computing: Fuzzy Logic, Neural Networks, and Distributed Artificial Intelligence, PTR Prentice Hall, NY, 1994