发表论文

  • Qixiu Du#, Haochen Wang#, Benben Jiang, Xiaowo Wang*，Advancing genetic engineering with active learning: theory, implementations and potential opportunities， Brief Bioinform. 2025;26(4):bbaf286. doi: 10.1093/bib/bbaf286
  • Jiaqi Li, Pencheng Zhang, Xi Xi, Xiaowo Wang*，esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysis. Bioinformatics. 2025;41(6):btaf315. doi: 10.1093/bioinformatics/btaf315
  • Wang H#, Xiang Y#, Liu Z, Yin W, Li B, Qian L, Wang X*, Lou C*.，De novo design of insulated cis-regulatory elements based on deep learning-predicted fitness landscape. Nucleic Acids Res. 2025;53(12):gkaf611. doi: 10.1093/nar/gkaf611.
  • Zhang X, Zhang W, Zhang J, Lyu X, Pan H, Jia T, Wang T, Xiaowo Wang*, Guo H*. Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity. Brief Bioinform. 2025;26(3):bbaf252. doi: 10.1093/bib/bbaf252
  • Pengcheng Zhang#, Qixiu Du#, Ye Wang#, Lei Wei, Xiaowo Wang*，Systematic representation and optimization enable the inverse design of cross-species regulatory sequences in bacteria, Nature Communications. 2025;16(1):1763. doi: 10.1038/s41467-025-57031-1
  • Jiaqi Li#, Pengcheng Zhang#, Xi Xi, Liyang Liu, Lei Wei, Xiaowo Wang*，Modeling and designing enhancers by introducing and harnessing transcription factor binding units，Nature Communications. 2025;16(1):1469. doi: 10.1038/s41467-025-56749-2
  • Xi Xi, Jiaqi Li, Jinmeng Jia, Qiuchen Meng, Chen Li, Xiaowo Wang, Lei Wei, Xuegong Zhang*， A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions，Nature Communications. 2025;16(1):1284. doi: 10.1038/s41467-025-56475-9.
  • Qianming Yan#, Yingying Zhang, Lei Wei, Xuehui Liu*, Xiaowo Wang*, Assessment of anemia recovery using peripheral blood smears by deep semi-supervised learning, Ann Hematol. 2025, doi: 10.1007/s00277-025-06254-9
  • Wei Zhang, Xianglin Zhang, Qian Liu, Lei Wei, Xu Qiao, Rui Gao, Zhiping Liu*, Xiaowo Wang*，Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data, Genomics Proteomics Bioinformatics. 2025. doi: 10.1093/gpbjnl/qzaf009
  • Fei Guo, Renchu Guan, Yaohang Li, Qi Liu, Xiaowo Wang, Can Yang, Jianxin Wang*，Foundation models in bioinformatics. Natl Sci Rev. 2025 Jan 25;12(4):nwaf028. doi: 10.1093/nsr/nwaf028
  • hang D, Li W, Sui X, Yu N, Wang S, Liu Z, Wang X, Yuan Z, Gao R, Zhang W.，Space: reconciling multiple spatial domain identification algorithms via consensus clustering. Bioinform Adv. 2025;5(1):vbaf084. doi: 10.1093/bioadv/vbaf084
  • Haoxiao Cai, Xiaowo Wang*, Lei Wei*, Efficient computation by molecular competition networks, PHYSICAL REVIEW RESEARCH 6, 033208, 2024, DOI: 10.1103/PhysRevResearch.6.033208
  • 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, DOI: 10.1109/TFUZZ.2024.3471187
  • Pengcheng Zhang#, Lei Wei#, Jiaqi Li, Xiaowo Wang*, Artificial intelligence-guided strategies for next-generation biological sequence design, National Science Review, 2024;11(11):nwae343. doi: 10.1093/nsr/nwae343.
  • Xiaocheng Zeng#, Zheng Wei#, Qixiu Du, Jiaqi Li, Zhen Xie, Xiaowo Wang*, Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network，Bioinformatics . 2024，40(Suppl 1):i381-i389. doi: 10.1093/bioinformatics/btae262.
  • Qixiu Du#, May Nee Poon#, Xiaocheng Zeng, Pengcheng Zhang, Zheng Wei,Haochen Wang, Ye Wang, Lei Wei, Xiaowo Wang*. Synthetic promoter design in Escherichia coli based on multinomial diffusion model，iScience . 2024，27(11):111207. doi: 10.1016/j.isci.2024.111207.
  • Haochen Wang#, Qixiu Du#, Ye Wang, Hanwen Xu, Zheng Wei, Xiaowo Wang*, GPro: generative AI-empowered toolkit for promoter design, Bioinformatics, 2024, 40(3):btae123. doi: 10.1093/bioinformatics/btae123.
  • Jieling He, Wenxu Wu, Xiaowo Wang*， Synth Syst Biotechnol. DIProT: A deep learning based interactive toolkit for efficient and effective Protein design, 2024, 9(2):217-222. doi: 10.1016/j.synbio.2024.01.011.
  • Pengcheng Zhang#, Haochen Wang#, Hanwen Xu#, Lei Wei, Liyang Liu, Zhirui Hu, Xiaowo Wang*. Deep flanking sequence engineering for efficient promoter design using DeepSEED. Nature Communications (2023) 14(1):6309
  • Zheng Wei, Kui Hua, Lei Wei, Shining Ma, Rui Jiang, Xuegong Zhang, Yanda Li, Wing H. Wong*, Xiaowo Wang*. NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks. Proceedings of the National Academy of Sciences 120, no. 15, 2023: e2216698120.
  • 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 2023, 11(3):207-213
  • Xian-En Zhang*, Chenli Liu*, Junbiao Dai*, Yingjin Yuan*, Caixia Gao*, Yan Feng*, Bian Wu*, Ping Wei*, Chun You*, Xiaowo Wang*, Tong Si*, Enabling technology and core theory of synthetic biology, Sci China Life Sci . 2023 Aug;66(8):1742-1785.
  • 张学工,王颖,汪小我,江瑞,古槿, 数基生命系统——用控制和系统的观点对生命的数字化建模, 厦门大学学报(自然科学版),2022,61(06),906-907
  • Xianglin Zhang, Xiaowo Wang*, MeConcord: a new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites, Bioinformatics, 2022; 38(Suppl 1):i307-i315.
  • Xianglin Zhang#, Xiaodong Jia#, Bixi Zhong, Lei Wei, Jiaqi Li, Wei Zhang, Huan Fang, Yanda Li, Yinying Lu*, Xiaowo Wang*, Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA, Briefings In Bioinformatics, 2022， 23(4):bbac278.
  • Xiaofei Zhang, Tingting Cong, Lei Wei, Bixi Zhong, Xiaowo Wang, Jin Sun, Shuxia Wang, Meng Michelle Xu, Ping Zhu, Hong Jiang, Jianwei Wang*, YTHDF3 modulates hematopoietic stem cells by recognizing RNA m6A modification on Ccnd1，Haematologica, 2022, 107(10):2381-2394.
  • Lekang Yuan, Zhen Xie, Ye Wang*, Xiaowo Wang*, DeSP: a systematic DNA storage error simulation pipeline, BMC Bioinformatics, 2022; 23(1):185.
  • 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, 2022; 25(5):104318.
  • Lei Wei#*, Shuailin Li#, Xiaowo Wang*，In silico and in vitro protocols for quantifying gene expression noise modulated by microRNAs, STAR Protoc. 2022; 3(1):101205
  • 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, 2022, 23(1):bbab362. doi: 10.1093/bib/bbab362
  • Yanhong Wu, Qifan Hu, Shicheng Wang, Changyi Liu, Yiran Shan, Wenbo Guo, Rui Jiang, Xiaowo Wang, Jin Gu*，Highly Regional Genes: graph-based gene selection for single-cell RNA-seq data，J Genet Genomics . 2022 Feb 8;S1673-8527(22)00033-9
  • Xiaofei Zhang, Tingting Cong, Lei Wei, Bixi Zhong, Xiaowo Wang, Jin Sun, Shuxia Wang, Meng Michelle Xu, Ping Zhu, Hong Jiang, Jianwei Wang*，YTHDF3 modulates hematopoietic stem cells by recognizing RNA m6A modification on Ccnd1，Haematologica . 2022. doi: 10.3324/haematol.2021.279739
  • Lei Wei#, Shuailin Li#, Pengcheng Zhang, Tao Hu, Michael Q Zhang, Zhen Xie, Xiaowo Wang*, Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits, Cell Reports, 2021, 36(8):109573. doi: 10.1016/j.celrep.2021.109573.
  • 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, 2021, 19(3):394-407.
  • 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 Res. 2021; 49(W1):W483-W490
  • Jiaqi Li#, Lei Wei#,*, Xianglin Zhang, Wei Zhang, Haochen Wang, Bixi Zhong, Zhen Xie, Hairong Lv, Xiaowo Wang*，DISMIR: deep learning-based non-invasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads, Briefings In Bioinformatics, 2021, 22(6):bbab250
  • Wei Zhang, Lei Wei*, Jiaqi Huang, Bixi Zhong, Jiaqi Li, Hanwen Xu, Shuying He, Yu Liu, Juhong Liu, Hairong Lv, Xiaowo Wang*, cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data, Bioinformatics, 2021, 37(22):4251–4252. doi: 10.1093/bioinformatics/btab413
  • 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, 2021; 49(W1):W483-W490
  • Xianglin Zhang#, Xuehui Liu#, Zhenhai Du#, Lei Wei, Huan Fang, Qiongye Dong, Jing Niu, Yanda Li, Juntao Gao, Michael Q. Zhang, Wei Xie*, Xiaowo Wang*, The loss of heterochromatin associates with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence, Genome Research, 2021, 31: 1121-1135
  • 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, 2021, 37(2): 285-287
  • Honglei Liu*, Xiaowo Wang, CRISPR-ERA: A Webserver for Guide RNA Design of Gene Editing and Regulation, Methods Mol Biol. 2021;2189:65-69.
  • Jiaqi Liu#, Hengqiang Zhao#, Yukuan Huang#, Shouping Xu#, Yan Zhou, Wei Zhang, Jiaqi Li, Yue Ming, Xinyu Wang, Sen Zhao, Kai Li, Xiying Dong, Yunlong Ma, Tianyi Qian, Xinyi Chen, Zeyu Xing, Yan Zhang, Hongyan Chen, Zhihua Liu, Da Pang, Meng Zhou, Zhihong Wu, Xiaowo Wang, Xiang Wang, Nan Wu*, Jianzhong Su*， Genome-wide cell-free DNA methylation analyses improve accuracy of non-invasive diagnostic imaging for early-stage breast cancer, Molecular Cancer, 2021, 20(1):36
  • 颜钱明，张鹏程，乔榕，古槿，汪小我*．基于细胞—计算机交互的细胞控制方法．自动化学报. 2021, 47(3): 489-500
  • 王也，王昊晨，晏明皓，胡冠华，汪小我*，生物分子序列的人工智能设计，合成生物学，2021,2(01).
  • Ye Wang#, Haochen Wang#, Lei Wei, Shuailin Li, Liyang Liu, Xiaowo Wang*, Synthetic Promoter Design in Escherichia Coli Based on a Deep Generative Network, Nucleic Acids Research. 2020, 48(12):6403-6412
    • NAR Breakthrough Artical & Cover Story of the issue 48(12) https://academic.oup.com/nar/issue/48/12
  • He H, Xu P, Zhang X, Liao M, Dong Q, Cong T, Tang B, Yang X, Ye M, Chang Y, Liu W, Wang XW, Ju Z, Wang J., Aging-induced IL27Ra signaling impairs hematopoietic stem cells. Blood. 2020, 136(2):183-198
  • Zhao Z, Dong QY, Liu XH, Wei L, Liu LY, Li YD, Wang XW*, Dynamic transcriptome profiling in DNA damage-induced cellular senescence and transient cell-cycle arrest. Genomics. 2020, 112(2):1309-1317
  • 方欢，钟碧溪，魏磊，张祥林，张威，汪小我*，血浆游离DNA全基因组甲基化测序的实用稳定性评估，生物工程学报，2019, 35(12):2284-2294
  • Xiong G#, Liu C#, Yang G#, Feng M, Xu J, Zhao F, You L, Zhou L, Zheng L, Hu Y, Wang XW*, Zhang T*, Zhao Y*., Long noncoding RNA GSTM3TV2 upregulates LAT2 and OLR1 by competitively sponging let-7 to promote gemcitabine resistance in pancreatic cancer. J Hematol Oncol. 2019;12(1):97
  • Liu XH#, Wei L#, Dong QY, Liu LY, Zhang MQ, Xie Z, Wang XW*, A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass. Aging. 2019 ;11(12):4011-4031
  • Lei Wei# , Ye Yuan#, Tao Hu, Shuailin Li, Tianrun Cheng, Jinzhi Lei, Zhen Xie, Michael Q. Zhang, Xiaowo Wang*, Regulation by competition: a hidden layer of gene regulatory network, Quantitative Biology, 2019; 7(2): 110–121
  • 张祥林, 方欢, 汪小我*, 三维基因组数据分析方法进展，《生物化学与生物物理进展》 2018, 45(11): 1093-1105
  • 胡冠华，王也，魏磊，汪小我*, 通过合成基因线路实现细胞分类，《生命科学》 2018, 30(8): 799-809
  • Dong Q, Wei L, Zhang MQ*, Wang XW*, Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence, Aging. 2018, 10(6):1489-1505.
  • Miao Z, Deng K, Wang X, Zhang X*, DEsingle for detecting three types of differential expression in single-cell RNA-seq data, Bioinformatics, 2018, 34(18):3223-3224
  • Yaru Liang#, Chang Liu#, Maoyang Lu, Qiongye Dong, Zimu Wang, Zhuoran Wang,Wenxiang Xiong, Nannan Zhang, Jiawei Zhou, Qingfei Liu, Xiaowo Wang*, Zhao Wang*,Calorie restriction is the most reasonable anti-ageing intervention: a meta-analysis of survival curves,Scientific Reports, 2018, 8:5779, DOI:10.1038/s41598-018-24146-z
  • Wei Z#, Zhang W#, Fang H, Li Y, Wang X* esATAC: An Easy-to-use Systematic pipeline for ATAC-seq data analysis. Bioinformatics. 2018, 34(15):2664-2665
  • Li Y, Zheng H, Wang Q, Zhou C, Wei L, Liu X, Zhang W, Zhang Y, Du Z, Wang X, Xie W*.Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys. Genome Biol. 2018 Feb 8;19(1):18
  • Du Z, Zheng H, Huang B, Ma R, Wu J, Zhang X, He J, Xiang Y, Wang Q, Li Y, Ma J, Zhang X, Zhang K, Wang Y, Zhang MQ, Gao J, Dixon JR, Wang X, Zeng J, Xie W*. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature. 2017;547(7662):232-235.
  • Dong Q#, Han H#, Liu X#, Wei L, Zhang W, Zhao Z, Zhang MQ, Wang X*, HCSGD: An integrated database of human cellular senescence genes., J Genet Genomics. 2017;44(5):227-234
  • Honglei Liu, Xiaowo Wang*, Lei S. Qi*, Using CRISPR-ERA Webserver for sgRNA Design, Bio-protocals, 2017,DOI:10.21769/BioProtoc.2522
  • 魏磊, 袁野, 汪小我*, 合成基因线路规模化设计面临的挑战. 生物工程学报. 2017;33(3):372-385.
  • Chao He, Guipeng Li, Diekidel M. Nadhir, Yang Chen*, Xiaowo Wang*, Michael Q. Zhang*, Advances in computational ChIA-PET data analysis, Quantitative Biology, 2016, 4(3): 217-225
  • 张学工*, 江瑞, 汪小我, 古槿, 陈挺，从生物大数据到知识大发现: 十年进展与未来展望，科学通报，2016, 61(36), 3869-3877
  • Ye Yuan, Xinying Ren, Zhen Xie, Xiaowo Wang*, A quantitative understanding of microRNA mediated competing endogenous RNA regulation，Quantitative Biology, 2016, 4(1):47-57
  • Chao He, Michael Q. Zhang*, Xiaowo Wang*, MICC: an R package for identifying chromatin interactions from ChIA-PET data, Bioinformatics, 2015, 31(23):3832-4
  • Honglei Liu, Zheng Wei, Antonia Dominguez, Yanda Li, Xiaowo Wang*, Lei S. Qi*, CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation, Bioinformatics, 2015, 31(22):3676-8
  • 梁亚茹#, 刘畅#, 王卓然, 董琼叶, 汪小我*, 王钊*. 抗衰老药物对线虫生存曲线影响的荟萃分析. 中国科学 生命科学, 2015, 45(5): 479-487
  • Ye Yuan, Bing Liu, Peng Xie, Michael Q. Zhang, Yanda Li, Zhen Xie*, Xiaowo Wang*, Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit, Proc Natl Acad Sci U S A, 2015, 112(10):3158-63
  • Honglei Liu, Yanda Li, Xiaowo Wang*, OP-Synthetic: identification of optimal genetic manipulations for the overproduction of native and non-native metabolites, Quantitative Biology 2014, 2(3): 100?109
  • Chao He, Xiaowo Wang*, Michael Q. Zhang*, Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alphaassociated long-range interactions, Nucleic Acid Research, 2014, 42(11):6935-44
  • Peng Xie, Yu Liu, Yan-da Li, Michael Zhang* and Xiaowo Wang*, MIROR: a method for cell-type specific microRNA occupancy rate prediction, Mol. BioSyst. 2014, 10 (6), 1377 - 1384
  • YingXue Li, XueNing Liu, Xiaowo Wang, XueGong Zhang, Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae, Science China Life Sciences, 2014 Jan;57(1):52-58
  • 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, PengZhang, 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, 2014, 42(2):1052-64
  • Matthew H Larson, Luke A Gilbert, Xiaowo Wang, Wendell A Lim, Jonathan S Weissman & Lei S Qi, CRISPR interference (CRISPRi) for sequence-specific control of gene expression, Nature Protocols, 2013; 8, 2180?2196
  • Ruijuan Li, Weilong Guo, Jin Gu, Michael Q. Zhang, Xiaowo Wang*, Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation, Genomics, 2012 ;100(5):297-302
  • Ozlem Aksoy, Agustin Chicas, Tianying Zeng, Zhen Zhao, Mila McCurach, Xiaowo Wang, Scott Lowe, The atypical E2F family member E2F7 couples the p53 and Rb pathways during cellular senescence, Genes Dev.2012; 26(14):1546-57
  • Agustin Chicas#, Avnish Kapoor#, Xiaowo Wang#, Ozlem Aksoy, Adam G. Evertts, Michael Q. Zhang, Benjamin A. Garcia, Emily Bernstein*, Scott Lowe*, H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence, Proc Natl Acad Sci U S A. 2012 ;109(23):8971-6 (#equally contributed)
  • Ratnakumar K, Duarte LF, Leroy G, Hasson D, Smeets D, Vardabasso C, Bonisch C, Zeng T, Xiang B, Zhang DY, Li H, Wang X, Hake SB, Schermelleh L, Garcia BA, Bernstein E., ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression, Genes Dev. 2012 Mar 1;26(5):433-8.
  • Miao He, Yu Liu, Xiaowo Wang, Michael Q. Zhang, Gregory Hannon, Z. Josh Huang, Cell-type based analysis of microRNA profiles in the mouse brain, Neuron, 2012, 73(1):35-48
  • Chien Y, Scuoppo C, Wang X, Fang X, Balgley B, Bolden JE, Premsrirut P, Luo W, Chicas A, Lee CS, Kogan SC, Lowe SW, Control of the senescence-associated secretory phenotype by NF-κB promotes senescence and enhances chemosensitivity, Genes Dev.;25(20):2125-36, 2011
  • Wang LY, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics. 2011 Dec 1;6(12):1505-12.
  • Likun Wang, Xiaowo Wang, Xi Wang, Xuegong Zhang, Yanchun Liang, Observations on novel splice junctions from RNA sequencing data, Biochemical and Biophysical Research Communications, 409(2):299-303, 2011
  • 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
  • Agustin Chicas, Xiaowo Wang, Chaolin Zhang, Mila McCurrach, Zhen Zhao, Ozlem Mert, Ross A. Dickins, Masashi Narita, Michael Zhang and Scott W. Lowe, Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence, Cancer Cell, 17(4): 376-387, 2010 Comments on Cancer Cell
  • Tingting Li, Xueya Zhou, Xiaowo Wang, Dahai Zhu, Yong Zhang, Identification and characterization of human snoRNA core promoters, Genomics, 96(1):50-6, 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
  • Xiaowo Wang, Zhenyu Xuan, Xiaoyue Zhao, Yanda Li, Michael Q. Zhang, High-resolution human core-promoter prediction with CoreBoost_HM, Genome Research, 19(2):266-75, 2009
  • Xiaowo Wang , Jin Gu, Michael Q. Zhang and Yanda Li., Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species, Bioinformatics, 15;24(2):165-71,2008
  • 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, 26;9:191, 2008
  • Xiaowo Wang , Xuegong Zhang, Yanda Li, Complicated evolutionary patterns of miRNAs in vertebrates, Sci China Ser C-Life Sci, 51(6):552-9 2008
  • 汪小我,张学工,李衍达,脊椎动物中微小RNA进化模式研究, 中国科学C辑：生命科学,2008, 38(4):348-355
  • Jian Huang, Pei Hao, Yun-Li Zhang, Fu-Xing Deng, Qing Deng, Yi Hong, Xiaowo Wang, Yun Wang, Ting-Ting Li, Xue-Gong Zhang, Yi-Xue Li, Peng-Yuan Yang, Hong-Yang Wang and Ze-Guang Han. Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS), BMC Genomics, 8:207,2007
  • Jin Gu, Tao He, Yunfei Pei, Fei Li, Xiaowo Wang, Jing Zhang, Xuegong Zhang and Yanda Li, Primary Transcripts and Expressions of Mammal Intergenic MicroRNAs Detected by Mapping ESTs to Their Flanking Sequences. Mamm Genome, 17(10):1033-1041, 2007
  • Xiaowo Wang, Jing Zhang, Fei Li , Jin Gu , Tao He , Xuegong Zhang and Yanda Li, MicroRNA identification based on sequence and structure alignment. Bioinformatics, 21 (18): 3610-4, 2005

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