Professor of Pattern Recognition and Bioinformatics
Director, Bioinformatics Division, TNLIST (Tsinghua National Laboratory for Information Science &Technology)
Department of Automation, Tsinghua University
FIT 1-107, Tsinghua University,
Beijing 100084, China
Phone: 86-10-62794919, 62795578
ext. 888
Fax: 86-10-62773552
Email: zhangxg@tsinghua.edu.cn
Last update Apr 22, 2025
l Life Foundation Models and Digital Life Systems
l Machine Learning and Bio-Medical Big Data Analyses
l Single-cell Bioinformatics, Human Cell Atlas and Digital Twins
March, 1994, Ph.D. of Pattern Recognition and Intelligent Systems, Tsinghua University
July, 1989, BS of Industrial Automation, Tsinghua University
Work Experiences
2003 C present Director, Bioinformatics Division, TNLIST (Tsinghua National Laboratory of Information Science and Technology)
2002 C present Professor of Pattern Recognition and Bioinformatics, Department of Automation, Tsinghua University
2002 C present Deputy Director, MOE Key Laboratory of Bioinformatics
2007. Mar-Apr Visiting Scholar, MCB, USC
2006. Feb-Mar Visiting Scientist, Harvard School of Public Health
2001 C 2002 Visiting Scholar, Harvard School of Public Health
1999 C 2007 Director, Institute of Information Processing, Department of Automation, Tsinghua University
1996 C 2002 Associate Professor of Pattern Recognition, Department of Automation, Tsinghua University
1994 C 1996 Lecturer, Department of Automation, Tsinghua University
Courses
Given
Introductory Computational Molecular Biology (graduate)
Introduction to Statistical Learning Theory (graduate)
Scientific Ethics and Exposition (graduate)
Fundamental
Pattern Recognition (undergraduate)
Machine Learning (graduate)
Awards
2016 ȫ Ƽ
2009 ҽ ѧ ɹ Ƚ
2008 걱 н ѧ ɹ һ Ƚ
2006 ҽܳ
2004 ˲ ֧ ּƻ
2002 ҿƼ Ƚ
2001 й ʯ ܹ ˾ Ƽ һ Ƚ
1995 ҽ ί Ƽ Ƚ
Selected Publications
2024
Chen Li#, Haoxiang Gao#, Yuli She#, Haiyang Bian, Qing Chen, Kai Liu*, Lei Wei*, Xuegong Zhang*, Benchmarking AI models for in silico gene preturbation of cells, bioRxiv, https://doi.org/10.1101/2024.12.20.629581, 2024
Najeebullah Shah, Qiuchen Meng, Ziheng Zou, Xuegong Zhang*, Bioinformatics Advances, 2024, 00, vbae 109, https://doi.org/10.1093/bioadv/vbae109, 2024
Chuxi Xiao#, Yixin Chen#, Qiuchen Meng, Lei Wei*, Xuegong Zhang, Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data, Briefings in Bioinformatics, 25(2): bbae095, https://doi.org/10.1093/bib/bbae095, 2024
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, https://doi.org/10.1093/nar/gkae898, 2024
Haiyang Bian, Yixin Chen, Erpai Luo, Xinze Wu, Minsheng Hao, Lei Wei, Xuegong Zhang*, General-purpose pre-trained large cellular models for single-cell transcriptomics, National Science Review, 11: nwae340, 2024
Wenbo Guo, Xinqi Li, Dongfang Wang, Nan Yan, Qifan Hu, Fan Yang, Xuegong Zhang, Jin Gu*, scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes, Genome Biology, 25: 297, 2024
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, https://doi.org/10.1016/j.xjon.2024.07.018, 2024
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, 32(12): 7002-7014, 2024
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 gliomas, Nature Machine Intelligence, 6: 876-891, 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
Xuegong Zhang, 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, 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
Haoxiang Gao#, Kui Hua#, Xinze Wu#, Lei Wei, Sijie Chen, Qijin Yin, Rui Jiang, Xuegong Zhang*, Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model, Communications Biology, 7: 977, 2024
Tianyu Zhang, Chengbin Hou*, Rui Jiang, Xuegong Zhang, Chenghu Zhou, Ke Tang, Hairong Lv*, Label informed contrastive 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, Zhaohui 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 microenvironment 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 highlights 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
2023
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, multicentre study, The Lancet Digit Health, 5(11): e754-e762, 2023
Chen Li#, Xiaoyang Chen#, Shengquan Chen, Rui Jiang*, Xuegong Zhang*, simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data, Bioinformatics, 39(8): btad453, 2023
Haochen Li, Tianxing Ma, Minsheng Hao, Wenbo Guo, Jin Gu, Xuegong Zhang*, Lei Wei*, Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics, Briefings in Bioinformatics, 24(6): 1-13, 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, 20: 753-782, 2023 https://doi.org/10.1007/s11633-022-1364-x
Najeebullah Shah, Fanhong Li, Xuegong Zhang*, Hidden knowledge recovery from GAN-generated single-cell RNA-seq data, bioRxiv, 2023 https://doi.org/10.1101/2023.11.27.568840
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
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
Tianxing Ma, Haochen Li, Xuegong Zhang*, Discovering single-cell eQTLs from scRNA-seq data only, Gene, 829(2022): 146520, April 2022
Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang*, DualGCN: a dual graph convolutional network model to predict cancer drug response, BMC Bioinformatics, 23:129, 2023
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 https://doi.org/10.1016/j.isci.2022.104318
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)
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
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
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
2020
Xinmiao Fan, Lu Ping, Hao Sun, Yushan Chen, Pu Wang, Tao Liu, Rui Jiang, Xuegong Zhang*, Xiaowei
Chen*, Whole-exom sequencing of discordant
monozygotic twin families for identification of candidate genes for
Microtia-Atresia, Frontiers in Genetics, 11: 568052, 2020
Yixin Chen, Sijie
Chen, Xuegong Zhang*, Using DenseFly
algorithm for cell searching on massive scRNA-seq
datasets, BMC Genomics, 21 (Suppl 5): 222, 2020
Najeebullah Shah, Jiaqi
Li, Fanhong Li, Wenchang Chen, Haoxiang
Gao, Sijie Chen, Kui Hua, Xuegong Zhang*, An experiment on ab initio
discovery of biological knowledge from scRNA-seq data
using machine learning, Patterns, 1: 100071, 2020
https://doi.org/10.1016/j.patter.2020.100071
Yue Hu, Xi Xi,
Qian Yang, Xuegong Zhang*, SCeQTL:
an R package for indentifying
eQTL from single-cell parallel sequencing data, BMC
Bioinformatics, 21: 184, 2020 https://doi.org/10.1186/s12859-020-3534-6
Wendao Liu, Xuegong Zhang*, Single-cell alternative splicing analysis reveals
dominance of single transcript variant, Genomics, 112: 2418-2425, 2020
Qin Yu, Geng
Chen, Jiaqi Li, Xiaolong
Liu, Xuegong Zhang, Haiming
Lu, Predicting microvascular invasion of hepatocellular carcinoma by texture
analysis of multi-phase MR image, Eulenstein &
Al-Mubaid (eds.) BICOB 2020 (EPiC
Series in Computing, vol.70), pp.238-246, 2020
Minsheng Hao, Kui Hua, Xuegong Zhang,
SOMDE: A scalable method for identifying spatially variable genes with
self-organizing map, bioRxiv preprint doi: https://doi.org/10.1101/2020.12.10.419549
2019
Jiaqi Li, Haiming
Lu, Xiang Fang, Sijie Chen, Xuegong Zhang*, Pixel-level clustering reveals intra-tumor heterogeneity
in non-small cell lung cancer, IEEE BIBM 2019, pp.1536-1939
Jiaxing Cui, Hongfei Cui, Mingran Yang, Shiyu Du, Junfeng Li, Yingxue Li, Liyang Liu, Xuegong Zhang*, Shao Li*, Tongue coating
microbiome as a potential biomarker for gastritis including precancerous
cascade, Protein Cell, 10(7): 496-509, 2019 https://doi.org/10.1007/s13238-018-0596-6
Sijie Chen, Yixin
Chen, Fengzhu Sun, Michael S. Waterman, Xuegong Zhang*, A new statistic for efficient
detection of repetitive sequences, Bioinformatics, 35(22): pp.4596-4606,
https://doi.org/10.1093/bioinformatics/btz262, 2019
Xuegong Zhang, QB: Embracing the future of quantitative understanding and
engineering of life, Quantitative Biology, 7(1): 1-2, 2019
https://doi.org/10.1007/s40484-019-0168-7
Aziz Khan & Xuegong Zhang*, Integrative modeling reveals
key chromatin and sequence signatures predicting super-enhancers, Scientific
Reports, 9: 2877, 2019 https://doi.org/10.1038/s41598-019-38979-9
Kui Hua, Xuegong Zhang*, Estimating the total genome length of a metagenomic sample
using k-mers, BMC Genomics, 20 (Suppl 2):183
https://doi.org/10.1186/s12864-019-5467-x WOS:000464120900001
Kui Hua, Xuegong Zhang*, A case study on the detailed reproducibility of a human
cell altas project, Quantitative Biology, 7(2):
162-169, 2019 https://doi.org/10.1007/s40484-018-0164-3
Huijuan Feng, Tingting
Li, Xuegong Zhang*, Characterization of kinase
gene expression and splicing profile in prostate cancer with RNA-seq data, BMC
Genomics, 19 (Suppl 6): S64, 2019 https://doi.org/10.1186/s12864-018-4925-1
Chao Zhang, Xing Sun, Kang
Dang, Ke Li, Xiao-wei Gao, Zong-qiao Yu, Fei-yue Huang,
Yun-sheng Wu, Zhu Liang, Zai-yi Liu, Xuegong Zhang, Xing-lin
Gao, Shao-hong Huang, Jie
Qin, Wei-neng Feng, Tao Zhou, Yan-bin Zhang, Wei-jun Fang, Ming-fang Zhao, Xue-ning
Yang, Qing Zhou, Yi-long Wu, Wen-zhao Zhong, Toward
an expert level of lung cancer detection and classification using a deep
convolutional neural network, The Oncologist, 24: 1-7, 2019
Խ · ѧ ѧϰ ۣ ϵͳѧ 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
ѧ * С ң ͦ ݵ ֪ʶ ֣ ѧͨ 61(36): 3869-3877, 2016
Yu Xue,
Eric-Wubbo Lameijer, Kai
Ye, Kunlin Zhang, Suhua
Chang, Xiaoyue Wang, Jianmin
Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jingfa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang,
Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu, Precision medicine: what challenges are
we facing? Genomics Proteomics
Bioinformatics, 14: 253-261, 2016
Binbin Wang, Taoyun
Ji, Xueya Zhou, Jing Wang, Xi Wang, Jingmin Wang, Dingliang Zhu, Xuejun Zhang, Pak Chung Sham, Xuegong Zhang, Xu Ma, Yuwu Jiang, CNV analysis in Chinese children of
mental retardation highlights a sex differentiation in parental contribution to
de novo and inherited mutational burdens, Scientific
Reports, 6: 25954, 2016
Hui Chen, Xueya
Zhou, Jing Wang, Xi Wang, Liyang Liu, Shinan Wu, Tenyan Li, Si Chen, Jingwen Yang, Pak Chung Sham, Guangming
Zhu, Xuegong
Zhang, Binbin Wang, Exome sequencing and gene
prioritization correct misdiagnosis in a Chinese kindred
with familial amyloid polyneuropathy, Scientific
Reports, 6: 26362, 2016
Qifeng Xu, Xuegong Zhang*, The influence of the global gene expression shift on
downstream analyses, PLoS
ONE, 11(4): e0153903, 2016
Jing Li, Jing-Wen Li, Zhixing Feng, Juanjuan Wang, Haoran An, Yanni
Liu, Yang Wang, Kailing Wang, Xuegong Zhang, Zhun Miao, Wenbo
Liang, Robert Sebra, Guilin Wang, Wen-Ching Wang,
Jing-Ren Zhang, Epigenetic switch driven by DNA inversions dictates phase
variation in Streptococcus pneumonia, PLoS Pathogens,
12(7): e1005762, 2016
Ana Conesa, Pedro Madrigal,
Sonia Tarazona, David Gomez-Cabrero,
Alejandra Cervera, Andrew McPherson, Michal Wojciech Szczesnik, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, Ali Mortazavi, A survey of best
practices for RNA-seq data analysis, Genome
Biology, 17:13, 2016
Tatiana C. Mangericao,
Zhanhao Peng, Xuegong Zhang,
Computational prediction of CRISPR cassettes in gut metagenome samples from
Chinese type-2 diabetic patients and healthy controls, BMC Systems Biology, 10(Suppl 1): 5, 2016
Aziz Khan & Xuegong Zhang*, dbSUPER:
a database of super-enhancers in mouse and human genome, Nucleic Acids Research, 44(D1): D164-D171, Jan 2016
Hongfei Cui, Yingxue
Li, Xuegong Zhang*, An overview of major
metagenomic studies on human microbiomes in health and disease, Quantitative Biology, DOI
10.1007/s40484-016-0078-x, 4(3): 192-206, 2016
Huijuan Feng, Tingting
Li, Xuegong
Zhang*, Characterization of kinase gene expression and splicing profile in
prostate cancer with RNA-seq data, bioRxiv, doi:
http://dx.doi.org/10.1101/061085, June 2016
2015
Aziz Khan & Xuegong Zhang, dbSUPER:
a database of super-enhancers in mouse and human genome, Nucleic Acids Research, advanced access Oct.4, 2015
Huijuan Feng, Xuegong Zhang, Chaolin Zhang, mRNA for direct
assessment of genome-wide and gene-specific mRNA integrity from large-scale
RNA-sequencing data, Nature
Communications, 6: 7836, 2015
Junfeng Li, Junyi
Zhang, Liyang Liu, Yucai
Fan, Lianshuo Li, Yunfeng
Yang, Zuhong Lu, Xuegong Zhang, Annual periodicity in planktonic bacterial and archaeal
community composition of eutrophic Lake Taihu, Scientific Reports, 5: 15488, 2015
Chao Ye, Bo Jiang, Xuegong Zhang, Jun S. Liu, dslice: an R package for
nonparametric testing of associations with application in QTL and gene set
analysis, Bioinformatics, 31(11): 1842-1844, 2015
2014
Zhixing Feng, Jing Li, Jing-Ren Zhang,
Xuegong Zhang, qDNAmod:
a statistical model-based tool to reveal intercellular heterogeneity of DNA
modification from SMRT sequencing data, Nucleic Acids Research, 42(22):
13488-13499, 2014
Leying Guan, Qian Yang, Mengting Gu, Liang Chen, Xuegong
Zhang, Exon expression QTL (eeQTL) analysis
highlights distant genomic variations associated with splicing regulation, Quantitative
Biology, 2(2): 71-79, 2014
Guang-Zhong Wang, Simone Marini, Xinyun Ma, Qiang Yang, Xuegong Zhang, Yan Zhu*, Improvement of Dscam hemophilic binding affinity throughout Drosophila
evolution, BMC Evolutionary Biology, 4: 186, 2014
YingXue Li, XueNing
Liu, XiaoWo Wang, Xuegong
Zhang, Sequence signatures of genes with accompanying antisense transcripts
in Saccharomyces cerevisiae, Science China Life Sciences, 57(1): 52-58,
2014
Xavier Roge,
Xuegong Zhang, RNAseqViewer:
visualization tool for RNA-Seq data, Bioinformatics, 30(6): 891-892,
2014
Yong Chen, Yunfeng
Ding, Yi Yang, Jinhai Yu, Guiing
Liu, Xumin Wang, Shuyan
Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo,
Yang Wang, Yalan Du, Huina
Zhang, Peng Zhang, Huimin Na, Shimeng
Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang
Wang, Zhonghua Fan, Honglei
Liu, Xiaowo Wang, Xuegong
Zhang, Michael Q. Zhang, Yanda Li, Alexander Steinbuchel, Toyoshi Fujimoto,
Simon Cichello, Jun Yu, Pingsheng
Liu, Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630, Nucleic
Acids Research, 42(2): 1042-1064, 2014
Shufang Zhang, Xueya
Zhou, Shengnan Liu, Tingting
Bai, Yingai Zhang, Jing Wang, Shunlan
Wang, Xuegong Zhang, Binbin, Wang, MYH9‑related disease: description of a large Chinese
pedigree and a survey of reported mutations, Acta Haematologica,
132: 193-198, 2014
Jing Cheng, Xueya
Zhou, Yu Lu, Jing Chen, Bing Han, Yuhua Zhu, Liyang Liu, Kwong‑Wai Choy,
Dongyi Han, Pak C. Sham, Michael Q. Zhang, Xuegong
Zhang, Huijun Yuan, Exom
sequencing identifies a novel frameshift mutation of MYO6 as the cause of
autosomal dominant nonsyndromic hearing loss in a
Chinese Family, Annals of Human Genetics, 78: 410-423, 2014
Yu Lu, Xueya
Zhou, Zhanguo Jin, Jing
Cheng, Weidong Shen, Fei Ji, Liyang
Liu, Xuegong Zhang, Michael Zhang, Ye
Cao, Dongyi Han, KwongWai Choy, Huijun
Yuan, Resolving the genetic heterogeneity of prelingual hearing loss within one
family: performance comparison and application of two targeted next generation
sequencing approaches, Journal of Human Genetics, 59: 599-607, 2014
Chao Ye, Xuegong
Zhang, A simulation study on gene expression regulation via stochastic
model, Proceedings of the 33rd Chinese Control Conference, pp.
6885-6888, July 28-30, 2014, Nanjing, China
Qifeng Xu, Xuegong
Zhang, Multiclass feature selection algorithms based on R-SVM, IEEE ChinaSIP, 525-529, 2014
2013
Zhixing Feng, Gang Fang, Jonas Korlach, Tyson Clark, Khai Luong,
Xuegong Zhang, Wing Wong, Eric Schadt, Detecting DNA modification from SMRT sequencing
data by modeling sequence context dependence of polymerase kinetic, PLoS Computational Biology, 9(3): e1002935,
March 2013
Weichen Wang, Zhiyi
Qin, Zhixing Feng, Xi Wang, Xuegong
Zhang, Identifying differentially spliced genes from two groups of RNA-seq
samples, GENE, 518: 164-170, 2013
Ali Nowrouze,
Wing T. Cheung, Tingting Li, Xuegong
Zhang, Anne Arens, Anna Paruzynski,
Simon N. Waddington, Emma Osejindu, Safia Reja, Christof von Kalle, Yoahe Wang, Faisal Al-Allaf, Lisa Gregory, Matthew Themis, Maxine Holder, Niraja Dighe, Alaine Ruthe,
Suzanne MK Buckley, Brian Bigger, Eugenio Montini,
Adrian J. Thrasher, Robert Andrews, Terry P. Roberts, Robert F. Newbold,
Charles Coutelle, Manfred Schmidt, Mike Themis, The
fetal mouse is a sensitive genotoxicity model that exposes
lentiviral-associated mutagenesis resulting in liver oncogenesis, Molecular
Therapy, 21: 324-337, Feb. 2013
2012
Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun, Xuegong Zhang, Comparison of metagenomic samples using sequence signatures, BMC Genomics, 13: 730, 2012
Bai Jiang, Xujun Liang, Yang Chen, Tao Ma, Liyang Liu, Junfeng Li, Rui Jiang, Ting Chen, Xuegong Zhang, Shao Li, Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome, Scientific Reports, 2: 936, 2012
Huijuan Feng, Zhiyi Qin, Xuegong Zhang, Opportunities and methods for studying alternative splicing in cancer with RNA-Seq, Cancer Letters, doi: http://dx.doi.org/10.1016/j.canlet.2012.11.010, 2012
Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun, Xuegong Zhang, Cmoparison of metagenomic samples using sequence signatures, BMC Genomics, 13: 730, 2012
Chao Wu, Jun Zhu, Xuegong Zhang, Inegrating gene expression and protein-protein interaction network to prioritize cancer-associated genes, BMC Bioinformatics, 13: 182, 2012
Tingting Li, Yipeng Du, Likun Wang, Lei Huang, Wenlin Li, Ming Lu, Xuegong Zhang, Wei-Guo Zhu, Characterization and prediction of lysine(k)-acetyl-transferase specific acetylation sites, Molecular & Cellular Proteomics, 11(1): M111.011080, Jan 2012
2011
Xi Wang, Xuegong Zhang, Pinpointing Transcription Factor Binding Sites from ChIP-seq Data with SeqSite, BMC Systems Biology, 5(Suppl 2): S3, 2011
ѩ ѧ ڿ Ŵ о ѧͨ 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
ء С ҡ ǡ ѧ һ ͨ RNA ݵĴ ﻯѧ չ 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
ʱ ѧ DNA Ϣѧ о չ, ﻯѧ չ 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
ã С ң ѧ ת¼ ӽ λ ļ ѧ 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)
ѧ Ⱥ ٣ ģʽʶ ҩ IJ أ ѧ 26(4): 629-632, Apr. 2006
ѧ 㷨 ķ Ժ ʽ ߡ 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
ѧ Ⱥ ٣ ģʽʶ ͺ ϼ ҩ IJ أ ѧ 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
࣬ ѧ ң ܴ Ͱ ͨ· Ļ 뾫 ֢ յĶ λ о й ѧ C 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 C 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
ѧ ܴ֧ · չ ߡ vol.19,no.5, pp.481-484, 2004 5
ܴ ѧ ɣ Ϣ ǰ ȵ СRNA DZ Ϣ ھ й ѧԺ 2004 չ 桷 ѧ 磬2004 3 pp. 124-131
Fang Wen, Fei Li, Huiyu Xia, Xin Lu, Xuegong Zhang, Yanda Li, The impact of very short alternative splicing on protein structures and functions in the human genome, Trends in Genetics, vol.20, no.5, May 2004, pp.232-236
Xuesong Lu, Xing Wang, Ying Huang, Wei Hu, Guang R. Gao, Yanda Li, Xuegong Zhang, On some choices in Bayesian network learning for reconstructing regulatory networks,Proceedings of RECOMB04, March 2004, pp. 126-127
Chaolin Zhang, Yanda Li, Xuegong Zhang, gMap: extracting and interactively visualizing nonlinear relationships of genes from expression, Proceedings of RECOMB04,March 2004, pp. 228-229
ѧ ܴ Сƽ 㷨 ʽ Զ ѧ vol.30, no.1, Jan. 2004, pp.27-36
Books and Book Chapters
1.
Rui Jiang, Xuegong Zhang, Michael Q. Zhang, Basics of Bioinformatics, Tsinghua
University Press and Springer, 2014
2.
ѧ ģʽʶ 𡷣 棩 廪 ѧ 磬2010.8
3. V. Vapnik ѧ 룬 ͳ ѧϰ ۡ ӹ ҵ 磬2004.6
4. ѧ ȱ ģʽʶ ( ڶ ) 廪 ѧ 磬2000.1
5. V. Vapnik ѧ 룬 ͳ ѧϰ ۵ı ʡ 廪 ѧ 磬2000.8
6. ѧ ҵ ± , X Window /Motif ٳɡ 廪 ѧ 磬1998.3
7. Xuegong Zhang and Yanda Li, The application of artificial neural networks in editing noisy seismic data, Chapter 7, in F.Aminzadeh & M. Jamshidi eds., Soft Computing: Fuzzy Logic, Neural Networks, and Distributed Artificial Intelligence, PTR Prentice Hall, NY, 1994