2020
1. Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang*, A method for generating synthetic electronic medical record text, IEEE TCBB, in press
2. Yue Hu, Xi Xi, Qian Yang, Xuegong Zhang*, SCeQTL: an R package for indentifying eQTL from single-cell parallel sequencing data, BMC Bioinformatics, in press
3. Wendao Liu, Xuegong Zhang*, Single-cell alternative splicing analysis reveals dominance of single transcript variant, Genomics, 112: 2418-2425, 2020
4. 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
5. Yixin Chen, Sijie Chen, Xuegong Zhang*, Using DenseFly algorithm for cell searching on massive scRNA-seq datasets, BMC Genomics, in press
2019
6. 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
7. 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
8. Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S. Waterman, Xuegong Zhang*, A new statistic for efficient detection of repetitive sequences, Bioinformatics, 35(22): pp.4596-4606, 2019
9. Xuegong Zhang, QB: Embracing the future of quantitative understanding and engineering of life, Quantitative Biology, 7(1): 1-2, 2019
10. Aziz Khan & Xuegong Zhang, Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers, Scientific Reports, 9: 2877, 2019
11. Kui Hua, Xuegong Zhang, Estimating the total genome length of a metagenomic sample using k-mers, BMC Genomics, 20 (Suppl 2):183, 2019
12. Kui Hua, Xuegong Zhang, A case study on the detailed reproducibility of a human cell altas project, Quantitative Biology, 7(2): 162-169, 2019
13. 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
14. 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
15. 胡越，羅東陽，花奎，路海明，張學工，關於深度學習的綜述與討論，《智能系統學報》， 14(1): 1-18, 2019
2018
16. Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang*, Generation of synthetic electronic medical record text, Proc. IEEE BIBM2018, pp.374-380, 2018
17. 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
18. Aziz Khan, Anthony Mathelier, Xuegong Zhang, Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers, Epigenetics, 2018
19. Jing-Ren Zhang, Lihong He, Dongyang Luo, Fan Yang, Chris Li, Xuegong Zhang, and Haiteng Deng, Multiple Domains of Bacterial and Human Lon Proteases Define Substrate Selectivity, Emerging Microbes & Infections, in press
20. Aziz Khan & Xuegong Zhang*, Making genome browsers portable and personal, Genome Biology, 19: 93, 2018
21. Zhun Miao, Ke Deng, Xiaowo Wang, Xuegong Zhang*, DEsingle for detecting three types of differential expression in single-cell RNA-seq data, Bioinformatics, 34(18): 3223-3224, 2018
22. Zhiyi Qin, Peter Stoilov, Xuegong Zhang*, Yi Xing*, SEASTAR: systematic evaluation of alternative transcription start sites in RNA, NAR, 46(8): e45, 2018
23. 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
24. Lu Zhang, Shiyong Li, Yoon-La Choi, Jinseon Lee, Zhuolin Gong, Xiaoqiao Liu, Yunfei Pei, Awei Jiang, Mingzhi Ye, Mao Mao, Xuegong Zhang, Jhingook Kim, Ronghua Chen, Systematic identification of cancer-related long noncoding RNAs and aberrant alternative splicing of quintuple-negative lung adenocarcinoma through RNA-Seq, Lung Cancer, 109: 21-27, 2017
25. 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
26. Syed Shujaat Ali Zaidi, Xuegong Zhang, Computational operon prediction in whole-genomes and metagenomes, Briefings in Functional Genomics, 16(4): 181-193, 2017
27. Qian Yang, Yue Hu, Jun Li, Xuegong Zhang*, ulfasQTL: an ultra-fast method of composite splicing QTL analysis, BMC Genomics, 18(Suppl 1): 963 2017
28. 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
29. Xuegong Zhang*, Shansong Liu, Hongfei Cui, Ting Chen, Reading the underlying information from massive metagenomic sequencing data, Proceedings of the IEEE, 105(3): 459-473, 2017
2016
30. Zhun Miao, Xuegong Zhang*, Differential expression analyses for single-cell RNA-Seq: old questions on new data, Quantitative Biology, 4(4): 243-260, 2016
31. 張學工*，江瑞，汪小我，古槿，陳挺，從生物大數據到知識大發現，《科學通報》，61(36): 3869-3877, 2016
32. 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
33. 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
34. 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
35. Qifeng Xu, Xuegong Zhang*, The influence of the global gene expression shift on downstream analyses, PLoS ONE, 11(4): e0153903, 2016
36. 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
37. Lu Zhang, Xiaoqiao Liu, Xuegong Zhang*, Ronghua Chen*, Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets, Molecular Genetics and Genomics, 291(3): 1035-1051, 2016
38. 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
39. 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
40. Aziz Khan & Xuegong Zhang*, dbSUPER: a database of super-enhancers in mouse and human genome, Nucleic Acids Research, 44(D1): D164-D171, Jan 2016
41. Hongfei Cui, Yingxue Li, Xuegong Zhang*, An overview of major metagenomic studies on human microbiomes in health and disease, Quantitative Biology, 4(3): 192-206, 2016
2015
42. 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
43. 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
44. 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
45. 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
46. 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
47. 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
48. 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
49. Xavier Roge, Xuegong Zhang*, RNAseqViewer: visualization tool for RNA-Seq data, Bioinformatics, 30(6): 891-892, 2014
50. 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
51. 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
52. 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
53. 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
54. 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
55. Qifeng Xu, Xuegong Zhang, Multiclass feature selection algorithms based on R-SVM, IEEE ChinaSIP, 525-529, 2014
2013
56. 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
57. 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
58. 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
59. 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
60. 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
61. 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
62. Hongfei Cui, Xuegong Zhang*, Alignment-free supervised classification of metagenomes by recursive SVM, BMC Genomics, 14: 641, 2013
63. 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
64. Huijuan Feng, Zhiyi Qin, Xuegong Zhang*, Opportunities and methods for studying alternative splicing in cancer with RNA-Seq, Cancer Letters, 340: 179-191, 2013
65. 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
66. 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
67. 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
68. 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
69. 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
70. 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
2012
71. Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun, Xuegong Zhang*, Comparison of metagenomic samples using sequence signatures, BMC Genomics, 13: 730, 2012
72. 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
73. Chao Wu, Jun Zhu, Xuegong Zhang, Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes, BMC Bioinformatics, 13: 182, 2012
74. 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
75. Xi Wang, Xuegong Zhang*, Pinpointing Transcription Factor Binding Sites from ChIP-seq Data with SeqSite, BMC Systems Biology, 5(Suppl 2): S3, 2011
76. 周雪崖，張學工，基如果你於拷貝數變異的遺傳關聯研究，《科學通報》，56(6): 370-382, 2011
77. 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
78. Weichen Wang & Xuegong Zhang, Network-based group variable selection for detecting expression quantitative trait loci (eQTL), BMC Bioinformatics, 12: 269, 2011
79. 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
80. Chao Ye, Ying Liu, Xuegong Zhang*, Observations on shifted cumulative regulation, Genome Biology, 12:404, 2011
81. 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
82. Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman, Sequence alignment as hypothesis testing, Journal of Computational Biology, 18(5): 677-691, May 2011
83. 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
84. 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
85. 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
86. 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
87. 王曦、汪小我、王立坤、馮智星、張學工，新一代高通量七天之后〒RNA測序數據的處理與分析，《生物化學與生物物理進展》，37(8): 834-846, 2010
88. 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
89. 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
90. 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
91. 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
