张学工 博士
模式识别与生物信息学 教授
清华信息科学与技术国家实验室（筹）
生物信息学部主任
合成与系统生物学研究中心常务副主任
生物信息学教育部重点实验室副主任
北京100084 清华大学自动化系
FIT楼1-107
电话：86-10-62794919，62795578 ext. 888
传真：86-10-62773552
招聘生物信息学或模式识别方向研究生和博士后，
欢迎信息类、数理类、生物类、基础医学类各专业背景同学申请。
最近更新：2021年2月8日
l 机器学习，尤其是小样本学习和发现式学习
l 数基生命系统与智能健康
l 人类细胞与分子画像的信息体系
1994年3月于清华大学获模式识别与智能系统专业工学博士学位
1989年7月于清华大学获工业自动化专业工学学士学位
工作经历
2003 – 今 清华信息科学与技术国家实验室（筹）生物信息学部主任
2010 - 今 清华信息科学与技术国家实验室（筹）合成与系统生物学研究中心常务副主任
2002 – 今 清华大学自动化系 模式识别与生物信息学 教授
2002 – 今 清华大学生物信息学教育部重点实验室 副主任
2007.3 - 4 南加州大学分子与计算生物学系访问学者
2006.2 - 3 哈佛大学公共卫生学院访问科学家
2001 – 2002 哈佛大学公共卫生学院生物统计系高级访问学者
1999 – 2007 清华大学自动化系信息处理研究所 所长
1996 – 2002 清华大学自动化系 模式识别理论及应用 副教授
1994 – 1996 清华大学自动化系 讲师
开设课程
计算分子生物学引论（研究生，2002秋-）
统计学习理论导论（研究生，2000秋，2002秋-）
科学规范与表达（研究生，2005-2007夏，2013春-）
模式识别基础（本科生，1998秋-，国家级精品课）
Machine Learning（研究生， 2018- , 全英文课程）
曾获奖励
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
主要学术论文
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
Jiaqi Guan, Runzhe
Li, Sheng Yu, Xuegong Zhang*, A method for generating synthetic
electronic medical record text, IEEE TCBB, in press
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
Chao
Ye, Bo Jiang, 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 (corresponding author), 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
特邀报告与讲座
1. Xuegong Zhang, Computational prediction of miRNA-regulated pathways in the differentiation of histological grades in breast cancer, ACM-HK Bioinformatics Symposium, March 27, HK, 2010
2. Xuegong Zhang, Estimating variances of pattern classifiers’ performances with given samples, ISciDE (Sino-foreign-interchange Workshop on Intelligence Science and Intelligent Data Engineering), June 3-5, Harbin, 2010
3. Xuegong Zhang, Estimating gene expression values from RNA-seq data, IEEE International Conference on Bioinformatics & Biomedicine (BIBM2010), HK, Dec.18-21, 2010
4. Xuegong Zhang, Estimating gene expression values from RNA-seq data, The 8th ICSA International Conference: Frontiers of Interdisciplinary and Methodological Statistical Research, Guangzhou, Dec.19-22, 2010
5. Xuegong Zhang, Computational prediction of microRNA-regulated pathways in the differentiation of histological grades in breast cancer, Opportunities for Integrative Bionetworks to Enable Dynamic Models of Diseases – Beijing Summit, Beijing, Nov.20, 2009
6. Xuegong Zhang, Putting more biology in learning machines, Planery Keynote Speech at APBC2008,Jan 14-17, 2008, Kyoto
7. Xuegong Zhang, Studying molecular features of breast cancer with learning machines, invited talk at CAS International Symposium on Developmental Systems Biology, May 18-20, 2008, Beijing
8. Xuegong Zhang, Bioinformatics Study of the Molecular Features of Breast Cancer, invited keynote talk at the 5th International Conference on Information Technology and Applications in Biomedicine (ITAB’08), May 30-31, 2008, Shenzhen
9. Xuegong Zhang, Learning Biology with Machines: examples from alternative splicing and DNA methylation, invited talk at 2008 International Bioinformatics Workshop,June 7-9, 2008, Kunming
10. Xuegong Zhang, Understanding lymph node metastasis in breast cancers: a case study of microarray data analysis, invited talk, NSF Sponsored International Conference on Bioinformatics, June 10-14, 2007, Hangzhou
11. Xuegong Zhang, A bioinformatics study on lymph node metastasis of breast cancers, invited talk, International Symposium on Biochip Technology and Molecular Classification of Disease, May 6-8, Shanghai, 2007
12. Xuegong Zhang, Some new challenges for pattern recognition on high-throughput genomics/proteomics data, ICCTA2007, Kolkata, India, Mar 3-7, 2007
13. Xuegong Zhang, Effects of re-mapping the oligo probes onto the updated genome on high-level analyses of microarray data, BNI&IFBT2006, Beijing, Oct. 10, 2006
14. Xuegong Zhang, Machine learning in high-throughput genomics and proteomics, Tutorial at ICONIP2006 (http://iconip2006.cse.cuhk.edu.hk/program/Tutorial-3), Hong Kong, Oct.3, 2006
15. Fang Fang, Xuegong Zhang and Michael Q. Zhang, Computational studies in epigenetics, The First International Conference on Computational Systems Biology, Shanghai, July 20-23, 2006
16. Xuegong Zhang, Building gene networks by fusing literature and microarray data, Transcripteom 2005, Shanghai, Nov.5-9, 2005
17. Xuegong Zhang, Computational Analysis of Haplotype Blocks and Human Recombination Hotspots, Changchun International Bioinformatics Workshop, Changchun, July 5-7, 2005
18. 张学工，再看高通量表达数据的机器学习分析，东方科技论坛：计算生物学最新进展，上海，2005年7月2日
19. Xuegong Zhang, Computation Analysis of Human Recombination Hotspots, 1st International Workshop on Computational and Systems Biology, Beijing, May 23, 2005
20. 张学工, 生物信息学中的若干计算问题，中国计算机学会青年计算机科技论坛，2005年4月22日
21. Xuegong Zhang, Learning Specific Gene Relation Networks from Literatures, 2005 Sina-German Workshop on Networks: from Biology to Theory, Beijing, Apr 4-8, 2005
22. Xuegong Zhang, SVM and Its Application Examples in Computational Biology, CSHL bioinformaics seminar, Feb 9, 2005
23. Xuegong Zhang, Computational Analysis of Haplotype Blocks and Recombination Hotspots, Dr. Jun Liu’s lab seminar at Harvard University, Feb 1, 2005
24. Xuegong Zhang, Significance of Gene Ranking for Classification of Microarray Samples, SRCCS 2004 International Workshop for Statistics, Seoul National University, Korea, June 2004
25. Xuegong Zhang, Considerations on Sample Classification and Gene Selection with Microarray Data using Machine Learning Approaches, Statistical Method in Microarray Analysis Workshop at NUS, Singapore, Jan 2004
26. 张学工，基因表达数据中模式识别问题的一些特点，中国科协中国科学青年科学家论坛第81次论坛“生物信息学中的若干前沿问题的探讨”，2003年11月28-29日
教材、专著与章节
1. 张学工，《模式识别》（第三版），清华大学出版社，2010.8
2. 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
3. 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
4. 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
5. 张学工、刘业新编著, 《X Window /Motif编程速成》，清华大学出版社，1998.3
6. 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