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Zheng Wei, Kui Hua, Lei Wei, Shining Ma, Rui Jiang, Xuegong Zhang, Yanda Li, Wing H. Wong*, and 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.
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.
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
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)
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
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