MicroRNA identification based on sequence and structure alignment. - Xiaowo Wang; Jing Zhang 010; Fei Li; Jin Gu; Tao He; Xuegong Zhang; Yanda Li (Bioinform., 2005)

Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. - Xiaowo Wang; Jin Gu; Michael Q. Zhang; Yanda Li (Bioinform., 2008)

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. - Likun Wang 003; Zhixing Feng; Xi Wang 002; Xiaowo Wang; Xuegong Zhang (Bioinform., 2010)

OP-Synthetic: identification of optimal genetic manipulations for the overproduction of native and non-native metabolites. - Honglei Liu; Yanda Li; Xiaowo Wang (Quant. Biol., 2014)

MICC: an R package for identifying chromatin interactions from ChIA-PET data. - Chao He; Michael Q. Zhang; Xiaowo Wang (Bioinform., 2015)

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. - Honglei Liu; Zheng Wei; Antonia Dominguez; Yanda Li; Xiaowo Wang; Lei S. Qi (Bioinform., 2015)

Advances in computational ChIA-PET data analysis. - Chao He; Guipeng Li; Mohamed Nadhir Djekidel; Yang Chen; Xiaowo Wang; Michael Q. Zhang (Quant. Biol., 2016)

A quantitative understanding of microRNA-mediated competing endogenous RNA regulation. - Ye Yuan; Xinying Ren; Zhen Xie; Xiaowo Wang (Quant. Biol., 2016)

Regulation by competing: A hidden layer of gene regulatory networks. - Xiaowo Wang (CASE, 2017)

DEsingle for detecting three types of differential expression in single-cell RNA-seq data. - Zhun Miao; Ke Deng; Xiaowo Wang; Xuegong Zhang (Bioinform., 2018)

esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis. - Zheng Wei; Wei Zhang 241; Huan Fang 003; Yanda Li; Xiaowo Wang (Bioinform., 2018)

Regulation by competition: a hidden layer of gene regulatory network. - Lei Wei; Ye Yuan; Tao Hu; Shuailin Li; Tianrun Cheng; Jinzhi Lei; Zhen Xie; Michael Q. Zhang; Xiaowo Wang (Quant. Biol., 2019)

DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads. - Jiaqi Li; Lei Wei; Xianglin Zhang; Wei Zhang 241; Haochen Wang; Bixi Zhong; Zhen Xie; Hairong Lv; Xiaowo Wang (Briefings Bioinform., 2021)

CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images. - Tao Hu; Shixiong Xu; Lei Wei; Xuegong Zhang; Xiaowo Wang (Bioinform., 2021)

Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction. - Tao Hu; Lei Wei; Shuailin Li; Tianrun Cheng; Xuegong Zhang; Xiaowo Wang (Genom. Proteom. Bioinform., 2021)

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. - Shengquan Chen; Qiao Liu 008; Xuejian Cui; Zhan-Ying Feng; Chunquan Li; Xiaowo Wang; Xuegong Zhang; Yong Wang; Rui Jiang 001 (Nucleic Acids Res., 2021)

cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data. - Wei Zhang 241; Lei Wei; Jiaqi Huang; Bixi Zhong; Jiaqi Li; Hanwen Xu; Shuying He; Yu Liu; Juhong Liu; Hairong Lv; Xiaowo Wang (Bioinform., 2021)

Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA. - Xianglin Zhang; Xiaodong Jia; Bixi Zhong; Lei Wei; Jiaqi Li; Wei Zhang 241; Huan Fang 003; Yanda Li; Yinying Lu; Xiaowo Wang (Briefings Bioinform., 2022)

ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data. - Wei Zhang 241; Hanwen Xu; Rong Qiao; Bixi Zhong; Xianglin Zhang; Jin Gu; Xuegong Zhang; Lei Wei; Xiaowo Wang (Briefings Bioinform., 2022)

MeConcord: a new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites. - Xianglin Zhang; Xiaowo Wang (Bioinform., 2022)

DeSP: a systematic DNA storage error simulation pipeline. - Lekang Yuan; Zhen Xie; Ye Wang; Xiaowo Wang (BMC Bioinform., 2022)

Correction to: DeSP: a systematic DNA storage error simulation pipeline. - Lekang Yuan; Zhen Xie; Ye Wang; Xiaowo Wang (BMC Bioinform., 2022)

Building digital life systems for future biology and medicine. - Xuegong Zhang; Lei Wei; Rui Jiang 001; Xiaowo Wang; Jin Gu; Zhen Xie; Hairong Lv (Quant. Biol., 2023)

Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models. - Ziting Zhang; Wenxu Wu; Lei Wei; Xiaowo Wang (RECOMB, 2024)

Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network. - Xiaocheng Zeng; Zheng Wei; Qixiu Du; Jiaqi Li; Zhen Xie; Xiaowo Wang (Bioinform., 2024)

Weakly Supervised Causal Discovery Based on Fuzzy Knowledge and Complex Data Complementarity. - Wenrui Li; Wei Zhang 241; Qinghao Zhang; Xuegong Zhang; Xiaowo Wang (IEEE Trans. Fuzzy Syst., 2024)

Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity. - Xianglin Zhang; Wei Zhang 241; Jinyi Zhang; Xiuhong Lyu; Haoran Pan; Tianwei Jia; Ting Wang; Xiaowo Wang; Haiyang Guo (Briefings Bioinform., 2025)

Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data. - Wei Zhang 241; Xianglin Zhang; Qiao Liu 008; Lei Wei; Xu Qiao; Rui Gao 006; Zhiping Liu; Xiaowo Wang (Genom. Proteom. Bioinform., 2025)

Non-Contact Dexterous Micromanipulation With Multiple Optoelectronic Robots. - Yongyi Jia; Shu Miao; Ao Wang; Caiding Ni; Lin Feng 002; Xiaowo Wang; Xiang Li 009 (IEEE Robotics Autom. Lett., 2025)