• Haochen Li#, Tianxing Ma#, Zetong Zhao#, Yixin Chen, Xi Xi, Xiaofei Zhao, Xiaoxiang Zhou, Yibo Gao, Lei Wei*, Xuegong Zhang, scTML: a pan-cancerl single-cell landscape of multiple mutation types, Nucleic Acids Research, 2024, in press
• Shihua Dou, Zhuofeng Li, Zhenbin Qiu, Jing Zhang, Yaxi Chen, Shuyuan You, Mengmin Wang, Hongsheng Xie, Xiaoxiang Huang, Yun Yi Li, Jingjing Liu, Yuxin Wen, Jingshan Gong, Fanli Peng, Wenzhao Zhong, Xuegong Zhang, Lin Yang, Improving prediction accuracy of spread through air spaces in clinical-stage T1N0 lung adenocarinoma using computed tomography imaging models, JTCVS Open, 2024, in press
• Wenrui Li, Wei Zhang, Qinghao Zhang, Xuegong Zhang, Xiaowo Wang, Weakly-supervised causal discovery based on fuzzy knowledge and complex data complementarity, IEEE Transactions on Fuzzy Systems, 2024, in press
• Erpai Luo#, Minsheng Hao#, Lei Wei, Xuegong Zhang*, scDiffusion: conditional generation of high-quality single-cell data using diffusion model, Bioinformatics, 40(9), btae518, 2024
• Minsheng Hao, Lei Wei, Fan Yang, Jianhua Yao*, Christina V. Theodoris*, Bo Wang*, Xin Li*, Ge Yang*, Xuegong Zhang*, Current opinions on large cellular models, Quantitative Biology, 12:433-443, 2024
• Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, Jianzhu Ma*, Xuegong Zhang*, Le Song*, Large-scale foundation model on single-cell transcriptomics, Nature Methods, 21: 1481-1491, Aug. 2024
• Rui Jiang, Xiaoxu Yin, Pengshuai Yang, Lingchao Cheng, Juan Hu, Jiao Yang, Ying Wang, Xiaodan Fu, Li Shang, Liling Li, Wei Lin, Huan Zhou, Fufeng Chen, Xuegong Zhang*, Zhongliang Hu*, Hairong Lv*, A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of giomas, Nature Machine Intelligence, https://doi.org/10.1038/s42256-024-00868-w, 2024
• Xinyue Chen, Yin Huang, Liangfeng Huang, Ziliang Huang, Zhao-Zhe Hao, Lahong Xu, Nana Xu, Zhi Li, Yonggao Mou, Mingli Ye, Renke You, Xuegong Zhang, Sheng Liu*, Zhichao Miao*, A brain cell atlas integrating single-cell transcriptomes across human brain regions, Nature Medicine, 2024 https://doi.org/10.1038/s41591-024-03150-z
• Xue Bai, Sijie Chen, Xinxin Chi, Bowen Xie, Xinyi Guo, Han Feng, Peng Wei, Di Zhang, Shan Xie, Tian Xie, Yongzhen Chen, Mengting Gou, Qin Qiao, Xinwei Liu, Wei Jin, Wei Xu, Zixuan Zhao, Qi Xing, Xiaohu Wang, Xuegong Zhang, Chen Dong*, Reciprocal regulation of T follicular helper cells and dendritic cells drives colitis development, Nature Immunology, https://doi.org/10.1038/s41590-024-01882-1
• Haiyang Bian#, Yixin Chen#, Xiaomin Dong#, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei*, Xuegong Zhang*, scMulan: a multitask generative pre-trained language model for single-cell analysis, in J. Ma (Ed.): RECOMB 2024, LNCS 14758, pp. 479-482, 2024
• Minsheng Hao, Erpai Luo, Yixin Chen, Yanhong Wu, Chen Li, Sijie Chen, Haoxiang Gao, Haiyang Bian, Jin Gu, Lei Wei*, Xuegong Zhang*, STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning, Communications Biology, 7:56, 2024
• Tianyu Zhang, Chengbin Hou*, Rui Jiang, Xuegong Zhang, Chenghu Zhou, Ke Tang, Hairong Lv*, Label informed constrastive pretraining for node importance estimation on knowledge graphs, IEEE Transactions on Neural Networks and Machine Learning, in press, 2024
• Tianxing Ma, Zetong Zhao, Haochen Li, Lei Wei, Xuegong Zhang*, NeoHunter: flexible software for systematically detecting neoantigens from sequencing data, Quantitative Biology, http://doi.org/10.1002/qub2.28, 2024
• Yifan Sun, jingyan Shen, Yunfan Jiang, Zhaohuii Huang, Minsheng Hao, Xuegong Zhang*, MMA-RNN: a multi-level multi-task attention-based recurrent neural network for discrimination and localization of atrial fibrillation, Biomedical Signal Processing and Control, 89(2024): 105747, 2024
• Qiuchen Meng, Lei Wei*, Kun Ma, Ming Shi, Xinyi Lin, Joshua W.K. Ho, Yinqing Li*, Xuegong Zhang, scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq, Briefings in Bioinformatics, 25(2): 1-10, 2024
• Gan Liu#*, Qifan Hu#, Shuguang Peng#, Hui Ning#, Jiajia Mai, Xi Chen, Minzhen Tao, Qiang Liu, Huiya Huang, Yun Jiang, Yanhua Ding*, Xuegong Zhang*, Jin Gu*, Zhen Xie*, The spatial and single-cell analysis reveals remodeled immune miscroenvironment induced by synthetic oncolytic adenovirus treatment, Cancer Letters, 581: 216485, 2024
• Jiachen Liu#, Jiaoyan Lv#, Sijie Chen#, Jie Ma#, Jiaying Yao#, Zan Yuan, Chunyuan Yang, Xiao Li, Xuegong Zhang*, Yunping Zhu*, Jianhong Zhang*, Li Wu*, Single-cell profiling highlight pathogenic myeloid features in house dust mite-induced murine model of airway inflammation, Allergy, 2024
• Gan Liu*, Qifan Hu, Shuguang Peng, Hui Ning, Jiajia Mai, Xi Chen, Minzhen Tao, Qiang Liu, Huiya Huang, Yun Jiang, Yanhua Ding*, Xuegong Zhang*, Jin Gu*, Zhen Xie*, The spatial and single-cell analysis reveals remodeled immune microenvironment induced by synthetic oncolytic adenovirus treatment, Cancer Letters, 581: 216485, 2024

• Xuegong Zhang*, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv, Building digital life systems for future biology and medicine, Quantitative Biology 11(3): 207-213, 2023
• Zhan Wang#, Haiyang Bian#, Jiaqi Li, Jin Xu, Haining Fan, Xinze Wu, Yuntai Cao, Bin Guo, Xiaole Xu, Haiju Wang, Liangqiang Zhang, Hu Zhou, Jianfeng Fan, Youyou Ren, Yunping Geng, Xiaobin Feng, Luming Li, Lei Wei, Xuegong Zhang*, Detecting and subtyping of hepatic echinococcosis from plan CT images with deep learning: a retrospective, muticentre study, The Lancet Digit Health, 5(11): e754-e762, 2023
• Jing Gong#, Minsheng Hao#, Xingyi Cheng*, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song*, xTrimoGene: An efficient and scalable representation learner for single-cell RNA-seq data, NeurIPS, 2023
• Yifan Zhou, Yusra B. Medik, Bhakti Patel, Daniel B. Zamler, Sijie Chen, Thomas Chapman, Sarah Schneider, Elizabeth M. Park, Rachel L. Babcock, Taylor T. Chrisikos, Laura M. Kahn, Allison M. Dyevoich, Josue E. Pineda, Matthew C. Wong, Aditya K. Mishra, Samuel H. Cass, Alexandria P. Cogdill, Daniel H. Johnson, Sarah B. Johnson, Khalida Wani, Debora A. Ledesma, Courtney W. Hudgens, Jingjing Wang, Md Abdul Wadud Khan, Christine B. Peterson, Aron Y. Joon, Weiyi Peng, Haiyan S. Li, Reetakshi Arora, Ximing Tang, Maria Gabriela Raso, Xuegong Zhang, Wai Chin Foo, Michael T. Tetzlaff, Gretchen E. Diehl, Karen Clise-Dwyer, Elizabeth M. Whitley, Matthew M. Gubin, James P. Allison, Patrick Hwu, Nadim J. Ajami, Adi Diab, Jennifer A. Wargo, and Stephanie S. Watowich, Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration, Journal of Experimental Medicine, 220(2): e20221333, 2023 https://doi.org/10.1084/jem.20221333
• Jiaqi Li, Zhenbin Qiu, Chao Zhang, Sijie Chen, Mengmin Wang, Qiuchen Meng, Haiming Lu, Lei Wei, Hairong Lv, Wenzhao Zhong*, Xuegong Zhang*, ITHscore: comprehensive quantification of intra-tumor heterogeneity in NSCLC by multi-scale radiomic features, European Radiology, 33:893-903, 2023 https://doi.org/10.1007/s00330-022-09055-0
• Jiaqi Li, Zhuofeng Li, Lei Wei, Xuegong Zhang*, Machine learning in lung cancer radiomics, Machine Intelligence Research, https://doi.org/10.1007/s11633-022-1364-x, 2023

• Xi Xi, Haochen Li, Shengquan Chen, Tingting Lv, Tianxing Ma, Rui Jiang, Ping Zhang, Wing Hung Wong, Xuegong Zhang, Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling, iScience, 25: 104790, 2022
• Weili Fu#*, Sijie Chen#, Runze Yang, Chen Li, Haoxiang Gao, Jian Li, Xuegong Zhang*, Cellular features of localized microenvironments in human meniscal degeneration: a single-cell transcriptomic study, eLife 2022; 11:e79585, https://doi.org/10.7554/eLife.79585
• Tianxing Ma, Haochen Li, Xuegong Zhang*, Discovering single-cell eQTLs from scRNA-seq data only, Gene, 829(2022): 146520, April 2022
• Sijie Chen#, Yanting Luo#, Haoxiang Gao#, Fanhong Li#, Yixin Chen#, Jiaqi Li#, 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*, hECA: The cell-centric assembly of a cell atlas, iScience, 25: 104318, 2022
• Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijiang Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang*, Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding, Nature Machine Intelligence, 4: 116-126, Feb, 2022, https://doi.org/10.1038/s42256-021-00432-w
• Liang Chen#, Kui Hua#, Ningning Zhang, Jingyu Wang, Jian Meng, Zhenliang Hu, Haoxiang Gao, Fanhong Li, Yang Chen, Jie Ren, Liyang Liu, Qiming Zhou, Jin Gu, Jiangping Song*, Xuegong Zhang*, and Shengshou Hu*, Multifaceted spatial and functional zonation of cardiac cells in adult human heart, Circulation, 145: 315-318, 2022 (https://doi.org/10.1161/CIRCULATIONAHA.121.055690)
• Sijie Chen#, Yanting Luo#, Haoxiang Gao#, Fanhong Li#, Jiaqi Li#, Yixin Chen, Renke You, Hairong Lv, Kui Hua, Rui Jiang, Xuegong Zhang*, Toward a unified information framework for cell atlas assembly, National Science Review, 9: nwab179, https://doi.org/10.1093/nsr/nwab179, 27 Sept, 2021

• 张学工，未来智能医健之路——数基生命系统，《中国人工智能学会通讯》，2021年第11卷第1期，pp.34-37，2021
• Minsheng Hao, Kui Hua*, Xuegong Zhang*, SOMDE: a scalable method for identifying spatially variable genes with self-organizing map, Bioinformatics, 37(23): 4392-4398, https://doi.org/10.1093/bioinformatics/btab471, Dec. 2021
• Ziheng Zou#, Kui Hua#*, Xuegong Zhang*, HGC: fast hierarchical clustering for large-scale single-cell data, Bioinformatics, 37(21): 3964-3965, Nov. 2021 https://doi.org/10.1093/bioinformatics/btab420
• Jiaqi Guan*, Runzhe Li, Sheng Yu, Xuegong Zhang, A method for generating synthetic electronic medical record text, IEEE TCBB, 18(1): 173-182, 2021
• Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang*, stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics, Bioinformatics, 37: i299-307, 2021
• Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang*, OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions, Nucleic Acids Research, 49 (Web Server Issue): W483-490, 2021
• Wei Zhang#, Hanwen Xu#, Rong Qiao, Bixi Zhong, Xianglin Zhang, Jin Gu, Xuegong Zhang, Lei Wei*, Xiaowo Wang*, ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data, Briefings in Bioinformatics, bbab362, 2021
• Tao Hu, Shixiong Xu, Lei Wei, Xuegong Zhang, Xiaowo Wang*, CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images, Bioinformatics, 37(2): 285-287, 2021
• Tao Hu#, Lei Wei#, Shuailin Li, Tianrun Cheng, Xuegong Zhang, Xiaowo Wang*, Single-cell transcriptomes reveal characteristics of microRNA in gene expression noise reduction, Genomics, Proteomics & Bioinformatics, 19: 394-407, 2021 https://doi.org/10.1016/j.gpb.2021.05.002
• Congmin Zhu, Junyi Zhang, Xin Wang, Yuqing Yang, Ning Chen, Zuhong Lu, Qinyu Ge, Rui Jiang, Xuegong Zhang, Yunfeng Yang, and Ting Chen*, Responses of cyanobacterial aggregate microbial communities to algal blooms. Water Research. 2021; 196: 117014. https://doi.org/10.1016/j.watres.2021.117014.

• 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

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

• 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

• 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

• 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

• 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

• 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

• Eric E. Schadt, Onureena Banerjee, Gang Fangs, Zhixing Feng, Wing H. Wong, Xuegong Zhang, Andrey Kislyuk, Tyson A. Clark, Khai Luong, Alona Keren-Paz, Andrew Chess, Vipin Kumar, Alice Chen-Plotkin, Neal Sondheimer, Jonas Korlach, Andrew Kasarskis, Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases, Genome Research, 23: 129-141, 2013
• Xuegong Zhang, Fengzhu Sun, Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology), Quantitative Biology, 1(2): 175-181, 2013
• Yan Wang, Yi Zhang, Yan Li, Xueya Zhou, Xiaofeng Wang, Pingjin Gao, Li Jin, Xuegong Zhang, Dingliang Zhu, Common variants in the ATP2B1 gene are associated with hypertension and arterial stiffness in Chinese population, Molecular Biology Reports, 40: 1867-1873, 2013
• Xueya Zhou, Suying Bao, Binbin Wang, Xuegong Zhang, You-Qiang Song, Short read mapping for exome sequencing, Chapter 6 of Noam Shomron (ed.), Deep Sequencing Data Analysis, Methods, in Molecular Biology, vol. 1038, NY: Springer, 2013
• Suying Bao, Xueya Zhou, Liangcai Zhang, Jie Zhou, Kelvin Kai-Wang To, Binbin Wang, Liqiu Wang, Xuegong Zhang, You-Qiang Song, Prioritizing genes responsible for host resistance to influenza using network approaches, BMC Genomics, 14: 816, 2013
• Chao Wu, Jun Zhu, Xuegong Zhang, Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma, BMC Bioinformatics, 14: 365, 2013
• Hongfei Cui, Xuegong Zhang, Alignment-free supervised classification of metagenomes by recursive SVM, BMC Genomics, 14: 641, 2013
• Qiongshi Lu, Siin Ren, Ming Lu, Yong Zhang, Dahai Zhu, Xuegong Zhang, Tingting Li, Computational prediction of associations between long non-coding RNAs and proteins, BMC Genomics, 14: 651, 2013
• 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, 340: 179-191, 2013
• Xinyun Ma, Xuegong Zhang, NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data, BMC Bioinformatics, 14: 220, 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
• Yong Chen, Jingjing Hao, Wei Jiang, Tong He, Xuegong Zhang, Tao Jiang, Rui Jiang, Identifying potential cancer driver genes by genomic data integration, Scientific Reports, 3: 3538, 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
• Hongshan Jiang, Ying Zhao, Wenguang Chen, Weimin Zheng, Xuegong Zhang, Improving cis-regulatory elements modeling by consensus scaffolded mixture models, Science in China - Information Sciences, 56: 012501:1-012501:11, 2013

• 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
• 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

• 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 common variants associated with blood pressure variation 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
• Xuegong Zhang, Bioinformatics study of RNA-seq data, Next Generation Sequencing Asia Congress 2011, Oct.3-4, Singapore

• 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
• Ting Zhang, Xuegong Zhang, Zhirong Sun, Global network analysis of lipid-raft-related proteins reveals their centrality in the network and their roles in multiple biological processes, Journal of Molecular Biology, 402(4): 761-773, 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 MicroArray Quality Control (MAQC)-II 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
• 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
• Xuegong Zhang, Pattern Recognition in Bioinformatics: some examples and challenges, HKUST, March 26, 2010
• 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
• 张学工，对转录调控的一些尝试研究，国家自然科学基金委第51届双清论坛，武汉，11.8-9, 2010
• 张学工，Estimating variances of pattern classifiers’ performances with given samples, 2010年生物信息学学术研讨会，西宁，2010.7.23-25
• Xuegong Zhang, Estimating gene expression values from RNA-seq data, IEEE International Conference on Bioinformatics & Biomedicine (BIBM2010), HK, Dec.18-21, 2010
• 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
• 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
• Ying Liu, Bo Jiang, Xuegong Zhang, Gene set analysis identifies master transcription factors in developmental courses, Genomics, 94: 1-10, 2009
• Shicai Fan, Xuegong Zhang, CpG island methylation pattern in different human tissues and its correlation with gene expression, BBRC, 383(2009): 421-425
• 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 (3.613)
• 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 (1.017)
• 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 （Progress in Biochemistry and Biophysics）
• Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang, The Seventh Asia Pacific Bioinformatics Conference (APBC2009) Introduction, BMC Bioinformatics, 10(Suppl 1): S1, 2009 (3.493)
• Yunfei Pei, Xi Wang, Xuegong Zhang, The microRNAs’ effect on the repression of target genes at mRNA and protein levels, APBC2009, Jan, 2009, Beijing
• Feng Zeng, Xuebing Wu, Xuegong Zhang, Rui Jiang, A functional canonical correlation analysis approach to reverse engineering of in silico gene regulatory networks, APBC2009, Jan, 2009, Beijing
• 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
• 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, Michael Zhang, Xuegong 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 (2.749)
• 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 (4.029)
• Xiaowo Wang, Xuegong Zhang, Yanda Li, Complicated evolutionary patterns of microRNAs in Vertebrates, Science in China, 51(6):552-9, 2008 (0.533)
• 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 (2.682)
• 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 (published online: 6 Aug 2007) (3.354)
• Xuegong Zhang, Putting more biology in learning machines, Planery Keynote Speech at APBC2008, Kyoto, Jan 14-17, 2008
• 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
• 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), Shenzhen, May 30-31, 2008
• Xuegong Zhang, Lea50rning Biology with Machines: examples from alternative splicing and DNA methylation, invited talk at International Bioinformatics Workshop, 2008, Kunming, June 7-9, 2008
• Zhengpeng Wu, Jiangni Ao, Xuegong Zhang, Finding distinct biclusters from background in gene expression matrices, Bioinformation, 2(5): 207-215, 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 (1.634)
• 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 (doi: 10.1093/bioinformatics/btm473) (4.894)
• Bo Jiang, Michael Q. Zhang, Xuegong Zhang, A novel approach for accurate recognition of cis-regulatory elements, Poster at ISBM’07 & ECCB’07, Vienna, Austria, July 21-25, 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 (3.617)
• 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 (4.029)
• Shao Li, Zhongqi Zhang, Lijiang Wu, Xuegong Zhang, Yanda Li & Yongyan Wang, Understanding ZHENG in Traditional Chinese Medicine in the context of neuro-endocrine-immune network, IET. Systems 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 (4.894)
• Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Neighbor number, valley seeking and clustering, Pattern Recognition Letters, 28: 173-180, 2007 (0.952)
• Xuegong Zhang, Understanding lymph node metastasis in breast cancers: a case study of microarray data analysis, NSF Sponsored International Conference on Bioinformatics, June 10-14, 2007, Hangzhou
• 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
• Xuegong Zhang, Some new challenges for pattern recognition on high-throughput genomics/proteomics data, invited talk, ICCTA2007, Kolkata, India, Mar 3-7, 2007
• Jianhua Xu, Xuegong Zhang, Suqin Sun, Tuning SVM parameters for classifying geographical origins of Chinese medical herbs, International Journal of Wavelets, Multiresolution and Information Processing, 4(4): 643-657, 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 (0.710)
• 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(4): 628-639, Oct 2006 (IF 12.629)
• Gu J, He T, Pei Y, Li F, Wang X, Zhang J, Zhang X, Li Y. Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences, Mamm Genome, 17(10):1033-1041, 2006 (2.279)
• 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 (IF 6.019) (4.894)
• Xuesong Lu, Xuegong Zhang, The effect of GeneChip gene definitions on the microarray study of cancers, BioEssays, 28(7): 739-746, 2006 (IF 6.787) (5.965)
• Fang Fang, Xuegong Zhang and Michael Q. Zhang, Computational studies in epigenetics, invited talk at the 1st International Conference on Computational Systems Biology, July 20-23, 2006, Shanghai
• 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) (3.617)
• 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 （SCI影响因子0.666）
• 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
• 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, July-Sept, 2006 (2.283)
• Xuegong Zhang, Effects of re-mapping the oligo probes onto the updated genome on high-level analyses of microarray data, invited talk, BNI&IFBT2006, Beijing, Oct. 10, 2006
• 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
• 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 (IF 1.070)
• 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 (3.617)
• 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 (IF 2.051)
• 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, 25(6): 878-881)（SCI影响因子0.666）
• 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 (IF 5.742) (4.894)
• 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 (IF 2.855)
• Hua Xu, Peifa Jia, Xuegong Zhang, A neural network based method for shape measurement in steel plate forming robot, J. Wang, X. Liao & Z. Yi (eds.): ISNN2005, Lecture Notes in Computer Science, vol 3498, pp.291-296, 2005 （IF 0.513）
• Hua Xu, Peifa Jia, Xuegong Zhang, A novel chamber scheduling method in etching tools using adaptive neural networks, J. Wang, X. Liao & Z. Yi (eds.): ISNN2005, Lecture Notes in Computer Science, vol 3498, pp.908-913, 2005
• 刘沭华，张学工，孙素琴，中药材产地的近红外光谱自动鉴别和特征谱段选择，《科学通报》，50(4): 393-398, 2005 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 （IF 0.722）
• Keyue Ding, Jing Zhang, Kaixin Zhou, Yan Shen, Xuegong Zhang, htSNPer1.0: software for haplotype block partition and htSNPs selection, BMC Bioinformatics, 2005, 6:38 (1 March 2005) doi:10.1186/1471-2105-6-38 (3.617)
• 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 (published online on Sept 15, 2004) （IF 6.726）
• Fang Fang, Xuegong Zhang, Michael Q. Zhang, Predicting methylation of CpG islands in human brain, International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC), 2005
• Xuegong Zhang, Building gene networks by fusing literature and microarray data, Invited talk at Transcriptome2005, Shanghai, Dec. 5-9, 2005 (国际会议特邀报告)
• Xuegong Zhang, Learning specific gene relation networks from literatures, Invited talk at 2005 Sino-Germany Workshop on Networks: from Biology to Theory, Beijing, Apr.4-6, 2005 (国际会议特邀报告)
• Xuegong Zhang, Computational analysis of haplotype blocks and recombination hotspots, Invited talk at 2005 International Bioinformatics Workshop, Changchun, July 5-7, 2005 (国际会议特邀报告)
• 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 (0.533)
• Jing Zhang, Fei Li, Jun Li, Michael Q. Zhang, Xuegong Zhang, Evidence and characteristics of putative human alpha recombination hotspots, Human Molecular Genetics, vol.13, issue 22, pp.2823-2828, 2004 (published online on September 22, 2004) (8.099)
• 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 (5.735)
• 翁时锋，张长水，张学工，非线性降维在高维医学数据处理中的应用，《清华大学学报（自然科学版）》，v 44, n 4, April, 2004, p 485-488
• Jianhua XU, Xuegong ZHANG. A Learning Algorithm with Gaussian Regularizer for Kernel Neuron. Advances in Neural Networks - 2004 International Symposium on Neural Networks (ISNN2004). Lecture Notes in Computer Science –3173: 252-257. Dalian, China, August 19-21, 2004. Springer-Verlag, Berlin Heidelberg, 2004. (SCIE收录)
• 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
• Xuegong Zhang, Significance of Gene Ranking for Classification of Microarray Samples, Invited talk at SRCCS 2004 International Workshop for Statistics, Seoul National University, Korea, June27-29 2004
• 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
• 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
• 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, pp. 232-236, May, 2004 （SCI影响因子12.047）(9.950)
• 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
• 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 (Regularized kernel forms of minimum squared error methods, Acta Automatica Sinica)
• Xuegong Zhang, Significance of Gene Ranking for Classification of Microarray Samples, SRCCS 2004 International Workshop for Statistics: New Issues in Large Dimensional Models, Seoul, Korea, June 27-29, 2009
• Xuegong Zhang, Considerations on Sample Classification and Gene Selection with Microarray Data using Machine Learning Approaches, Invited talk at Statistical Method in Microarray Analysis Workshop at NUS, Singapore, Jan 3-10, 2004
• 李岩，张学工，应用图像处理方法自动检测路口车辆排队长度，《计算机应用与软件》，vol.20, n.12, pp.47-49, 2003
• Jianhua Xu, Xuegong Zhang, Yanda Li, Sparse training procedure for kernel neuron, IEEE Int. Conf. Neural Networks & Signal Processing, Nanjing, China, Dec.14-17, 2003, pp49-53
• Xiaotong Shen, George C. Tseng, Xuegong Zhang, Wing Hung Wong, On psi-learning, Journal of the American Statistical Association, vol.98: number: 463, pp.724-734, Sept. 2003 (2.171)
• 李梢，张学工，季梁，李衍达，复杂性疾病生物信息学研究的策略与方法，《世界华人消化杂志》, v.11, n.10, 1465-1469，Oct. 2003 （World Chinese Journal Digestology）
• O'Hagan RC, Brennan CW, Strahs A, Zhang X, Kannan K, Donovan M, Cauwels C, Sharpless NE, Wong WH, Chin L., Array Comparative Genome Hybridization for Tumor Classification and Gene Discovery in Mouse Models of Malignant Melanoma. Cancer Res. 63(17):5352-5356, Sept.1, 2003 （IF 7.656）
• 许建华，张学工，李衍达，基于核函数的非线性口袋算法，《电子学报》，vo.31, no.4, 612-615, 2003.4 (Nonlinear pocket algorithm with kernels, Acta Electronica Sinica)
• Wenkai Lu, Xuegong Zhang, Yanda Li, Multiple removal based on detection and estimation of localized coherent signal, Geophysics, vol.68, no.2, pp.745-750, Mar. 2003 (IF 1.228)
• 吴翔，谭李，陆文凯，张学工，提高超大规模SVM训练计算速度的研究，《模式识别与人工智能》，vol.16, no.1, 2003, pp.46-49 (Research on increasing the computation speed of huge-scale SVM training, Pattern Recognition and Artificial Intelligence, March 2003)
• 国防专利：张学工，熊高君，陆文凯，许建华，姚凯丰，章珂，“利用地震信号自动确定飞机投弹炸点位置的方法”，申请号01100974.8，申请日：2001年3月20日，授予日期2003年8月29日
• 许建华，张学工，李衍达，经典线性算法核化研究的新进展，第十二届全国神经计算学术大会（特邀论文），pp.117-122，2002
• 许建华，张学工，李衍达，基于最小二乘支持向量机的油气判别技术，《模式识别于人工智能》，v.15, n.4, 507-509, 2002年12月
• 吴君文，张学工，应用小波变换和PCA进行车辆的静态图像检测，《清华大学学报》，v.42, n.11, 2002, pp.1560-1564 (Wu Junwen, Zhang Xuegong, Wavelet transform and PCA to detect cars in static images, J. Tsinghua Uinv. (Sci & Tech))
• 熊高君，张学工，贺振华，吴正伯，三维定位原理与三维反射波长模拟，《矿物岩石》，vol.22, no.3, pp.93-97, 2002
• 阎辉，张学工，马云潜，李衍达，“基于变异函数的径向基核函数参数估计”，《自动化学报》，vol.28, no.3, 2002, pp.450-455
• 许建华，张学工，李衍达，“一种基于核函数的非线性感知器算法”，《计算机学报》，v.25, n.7, 2002, pp.689-695（XU Jian-Hua, ZHANG Xue-Gong, LI Yan-Da, A nonlinear perceptron algorithm based on kernel functions, Chinese J. Computers）
• Kou, Z., Ji, Liang & Zhang, X., Karyotyping of comparative genomic hybridization human metaphases by using support vector machines, Cytometry, v.47, n.1, pp.17-23, 2002 (IF 2.698)
• Kai Yu, Liang Ji, Xuegong Zhang, Kernel nearest-neighbor algorithm, Neural Processing Letters, vol.15, no.2, 2002, pp.147-156 (IF 0.605)
• 阎辉，张学工，李衍达，“基于核函数的最大间隔聚类算法”，《清华大学学报（自然科学版）》，v.42, n.1, 2002, pp.132-134 (YAN Hui, ZHANG Xuegong, LI Yanda, Kernel-based maximal-margin clustering algorithm)
• 许建华，张学工，李衍达，“应用核Fisher判别技术预测油气储集层”，《石油地球物理勘探》，vol.37, n.2, 2002, pp.170-174 (Xu Jianhua et al, “Application of kernel Fisher discriminanting technique to prediction of hydrocarbon reservoir”, Oil Geophysical Prospecting)
• Xuegong Zhang, Wing H. Wong, Recursive sample classification and gene selection based on SVM: method and software description, Technical Report, Department of Biostatistics, Harvard School of Public Health, 2001
• 阎辉，张学工，李衍达，“支持向量机与最小二乘法的关系研究”，《清华大学学报（自然科学版）》，v.41, n.9, 2001, pp.77-80 (YAN Hui, ZHANG Xuegong, LI Yanda, Relation between a support vector machine and the least square method)
• 冯占林，张学工，李衍达，“基于小波变换的地震勘探数据压缩的工程分析”，《清华大学学报（自然科学版）》，v.41, n.4/5, April, 2001, pp.170-173 (FENG Zhanlin, ZHANG Xuegong, LI Yanda, Some practical aspects of seismic data compression based on wavelet transform, Journal of Tsinghua University (Science and Technology))
• 阎辉，张学工，张贤达，“基于小波变换的自适应多井对比技术”，《石油物探》，vol.40, n.1, 2001.3, pp.49-55 (Yan Hui et al, Adaptive multiwell correlation based on wavelet transformation, Geophysical Prospecting for Petroleum)
• 陆文凯，张学工，李衍达，何汉漪，温书亮，刘永江，“时间域零炮检距地震道拟合”，《石油地球物理勘探》，vol.36, n.1, 2001, pp.56-59 (Lu Wenkai et al, Fitting a zero-offset seismic trace in time-frequency domain, Oil Geophysical Prospecting)
• 冯太林，张学工，李衍达，白天成，李云，杨贵祥，陆修莲，“折射波地震记录叠加成像方法研究”，《地球物理学报》，v.44, n.1, 2001, pp.129-134 (Feng Tai-Lin et al, Research on methodology of stack imaging of refractive seismic recording, Chinese Journal of Geophysics) （SCI索引，IDS Number: 415CA）
• Jianhua XU, Xuegong ZHANG, Yanda LI. Kernel Neuron and its Training Algorithm. Proc. of 8th Intl Conf on Neural Information Processing, Vol.2, pp. 861-866, Shanghai, China, Nov., 2001
• Zhenzhen Kou, Jianhua Xu, Xuegong Zhang, Liang Ji，An Improved Support Vector Machine Using Class-Median Vectors. Proc. of 8th Intl Conf on Neural Information Processing, Vol. 2, pp. 883-887, Shanghai, China, Nov., 2001
• Junwen Wu, Xuegong Zhang & Jie Zhou, Vehicle detection in static road images with PCA-and-wavelet-based classifier, Proc. of IEEE ITSC 2001, pp.742-746, Aug. 2001
• Junwen Wu & Xuegong Zhang, A PCA classifier and its application in vehicle detection, Proc. of IJCNN’01, pp. 600-604, July 2001
• Haixin Ke & Xuegong Zhang, Editing support vector machines, Proc. of IJCNN’01, pp.1464-1467, July 2001
• Jianhua Xu, Xuegong Zhang & Yanda Li, Large margin kernel pocket algorithm, Proc. of IJCNN’01, pp.1480-1485, July 2001
• Jianhua Xu, Xuegong Zhang & Yanda Li, Kernel MSE algorithm: a unified framework for KFD, LS-SVM and KRR, Proc. of IJCNN”01, pp.1486-1491, July 2001
• 冯太林，张学工，李衍达，“三分量地震资料野外采集应遵守的重要原则”，《物探与化探》，vol.25, no.1, 2001年2月，pp.70-74 (“The important principles in the acquisition of three-component seismic data”, Geophysical and Geochemical Exploration)
• Kun-Peng Li, Yan-Da Li, Xue-Gong Zhang, “A method to compensate earth filtering based on wavelet packet”, Chinese Journal of Geophysics, vol.43, no.4, 2000, pp.576-583
• Hui Yan, Kun-Peng Li, Xue-Gong Zhang, Yan-Da Li, “The application of wavelet transform in automatic segmentation”, Chinese Journal of Geophysics, vol.43, no.4, 2000, pp.602-608
• Xuegong Zhang & Haixin Ke, “ALL/AML cancer classification by gene expression data using SVM and CSVM approach”, Genome Informatics 2000, Universal Academy Press, (The 11th Workshop on Genome Informatics - GIW2000), Dec. 2000, Tokyo, pp.237-239
• Yan Hui, Zhang Xuegong, Zhang Xianda, “Training support vector machines: an application in welllog data classification”, Proc. of 5th Intl. Conf. On Signal Processing (ICSP2000), vol.3, pp.1427-1431, Aug., 2000
• Yan Hui, Zhang Xuegong, Li Yanda, Shen Liqin, Zhu Weibin, “The signal reconstruction of speech by KPCA”, Proc. of 6th Intl. Conf. On Spoken Language Processing (ICSLP2000), vol.III, pp.91-94, Oct., 2000
• Wenkai Lu, Xuegong Zhang, Yanda Li, Liqin Shen, Weibin Zhu, Joint speech signal enhancement based on spectral subtraction and SVD filter, Proc. of 6th Intl. Conf. On Spoken Language Processing (ICSLP2000), vol.III, pp.656-659, 2000
• 阎辉，张学工，李衍达，“应用SVM方法进行沉积微相识别”，《物探化探计算技术》，vol.22, no.2, May 2000, pp.158-164 (“Support vector machine methods in pattern recognition of sedimentary facies”, Computing Techniques for Geophysical and Geochemical Exploration)
• 阎辉，张学工，李衍达，“应用自组织神经网络进行自动地层划分的设计与实现”，《模式识别与人工智能》，vol.13, no.3, Sept. 2000, pp.309-313(“The application of self-organizing neural network in automatic stratum segmenntation”, Pattern Recognition and Artifical Intelligence)
• 张学工，“关于统计学习理论与支持向量机”，《自动化学报》，vol.26, no.1, 2000.1, 32-42 (Introduction to statistical learning theory and support vector machines”, Acta Automatica Sinaca)
• 张学工，“信息融合技术具有很强的军用背景”，《国际学术动态》，2000年第3期，18-19 (International Academic Developments)
• 马云潜、张学工，“支持向量机函数拟合在分形插值中的应用”，《清华大学学报》, vol.40, no.3, 2000.3, 76-78 (“Application of support vector machines function regression in fractal interpolation”, Jounral of Tsinghua University (Sci & Tech))
• 李鲲鹏，李衍达，张学工， “基于小波包分解的地层吸收补偿”，《地球物理学报》，vol.43, no.4, 2000.7, 542-549 (“A method to compensate earth filtering based on wavelet packet”, Chinese Jounral of Geophysics – Chinese Edition) SCI Web: IDS Number: 340MU, ISSN: 0001-5733
• 阎辉，李鲲鹏，张学工，李衍达，“测井曲线的小波变换特性在自动分层中的应用”，《地球物理学报》，vol.43, no.4, 2000.7, 568-573 (“Wavelet transform properties of well log and their application in automatic segmentation”, Chinese Journal of Geophysics) (SCI索引，IDS Number: 340MU)
• 冯太林 张学工等，“三维三分量地震资料交互处理系统PSD3的研制”，31(The development of 3D3C data processing system PSD3)，中国地球物理学会年刊2000(Annual of the Chinese Geophysical Society 2000)，中国地球物理学会编，中国地质大学出版社，2000.9
• 冯太林 张学工等，“三维转换波地震资料CCP道集快速抽取”，32(The quick CCP gathering of 3D converted wave seismic data), ibid.
• 冯太林 张学工等，“多次覆盖地震记录中的折射波成像”，33(Refracted waves imaging of multi-fold seismic recordings), ibid.
• 阎辉，张学工，李衍达，“一种新的主成分分析方法”， 312 (A new method for analysis of major component), ibid.
• Xuegong Zhang, Using class-center vectors to build support vector machines, Neural Networks for Signal Processing IX - Proceedings of the 1999 IEEE Workshop, IEEE Inc., 3-11, 1999.8 (EI CODEN: 85QHAU)
• Xuegong Zhang, Collaboration of information from different sources for petroleum reservoir prediction, Proc. of the 2nd Int'l Conf. On Information Fusion, Sunnyvale, USA, 1085-1089, 1999.7
• Wenkai Lu, Xuegong Zhang & Yanda Li, Petroleum reservoir framework prediction by information fusion, Proc. of the 2nd Int'l Conf. On Information Fusion, Sunnyvale, USA, 1090-93, 1999.7
• Ke Zhang, Xuegong Zhang & Yanda Li, Improving resolution of seismic sections based on method of information fusion with well-log data, Proc. of the 2nd Int'l Conf. On Information Fusion, Sunnyvale, USA, 1150-1155, 1999.7
• Tailin Feng & Xuegong Zhang, Complex Analysis Theory and Its Application, The 1st Int'l Conf. on Advances in Structural Engineering and Mechanics, Seoul, Korea, 1999.8
• Tailin Feng & Xuegong Zhang, Comparative Study between Multi-wave Seismic Exploration and P-wave’s, The 1st Int'l Conf. on Advances in Structural Engineering and Mechanics, Seoul, Korea, 1999.8
• 章珂、张学工等，“多尺度时变地震信号反褶积”，《信号处理》, vol.14, no.4, 296-303, 1998.12
• 章珂、张学工等，“一种新的地震子波估计方法”，《信号处理》, vol.14, no.3, 226-232, 1998.9
• 张学工、盛硕、李衍达，“几种现代信息处理技术和计算机网络在勘探地球物理中的应用”，《地球物理学报》, vol.40, 增刊, 1997
• Xuegong Zhang et.al., Estimating reservoir’s lithological parameters from seismic data using neural network, SEG 65th Annual Meeting, Houston, USA, 1995.10
• Xuegong Zhang et.al, Early-stage reservoir analysis with SOMA - a neural network approach, SEG 65th Annual Meeting, Houston, USA, 1995.10
• 张学工、刘业新、李衍达, “综合应用智能信息处理技术进行油藏描述的基本思想”，《计算机智能接口与智能应用的新进展》，清华大学出版社，1995.7

• Rui Jiang, Xuegong Zhang, Michael Zhang eds. Basics of Bioinformatics, Tsinghua University Press, Beijing and Springer, Heidelberg, New York, Dordrecht, London, 2013
• 许建华，张学工译，V. Vapnik著，《统计学习理论》，电子工业出版社，2004.6
• 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
• 张学工译，V. Vapnik著，《统计学习理论的本质》，清华大学出版社，2000.8
• 张学工、刘业新编著, 《X Window /Motif编程速成》，清华大学出版社，1998.3
• 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