It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. - Juan Xie; Anjun Ma; Anne Fennell; Qin Ma 003; Jing Zhao (Briefings Bioinform., 2019)

MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome. - Anjun Ma; Minxuan Sun; Adam McDermaid; Bingqiang Liu; Qin Ma 003 (Bioinform., 2019)

Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique. - Xiaoying Wang; Bin Yu 007; Anjun Ma; Cheng Chen; Bingqiang Liu; Qin Ma 003 (Bioinform., 2019)

Clustering and classification methods for single-cell RNA-sequencing data. - Ren Qi; Anjun Ma; Qin Ma 003; Quan Zou 001 (Briefings Bioinform., 2020)

QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. - Juan Xie; Anjun Ma; Yu Zhang; Bingqiang Liu; Sha Cao; Cankun Wang; Jennifer Xu; Chi Zhang 021; Qin Ma 003 (Bioinform., 2020)

SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting. - Bin Yu 007; Wenying Qiu; Cheng Chen; Anjun Ma; Jing Jiang; Hongyan Zhou; Qin Ma 003 (Bioinform., 2020)

IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq. - Anjun Ma; Cankun Wang; Yuzhou Chang; Faith H. Brennan; Adam McDermaid; Bingqiang Liu; Chi Zhang 021; Phillip G. Popovich; Qin Ma 003 (Nucleic Acids Res., 2020)

Network analyses in microbiome based on high-throughput multi-omics data. - Zhaoqian Liu; Anjun Ma; Ewy A. Mathé; Marlena Merling; Qin Ma 003; Bingqiang Liu (Briefings Bioinform., 2021)

Prediction of protein-protein interactions based on elastic net and deep forest. - Bin Yu 007; Cheng Chen; Xiaolin Wang; Zhaomin Yu; Anjun Ma; Bingqiang Liu (Expert Syst. Appl., 2021)

Machine learning development environment for single-cell sequencing data analyses. - Lei Jiang; Yuexu Jiang; Cankun Wang; Clement Essien; Juexin Wang; Anjun Ma; Qin Ma 003; Dong Xu 002 (BIBM, 2022)

Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data. - Shuangquan Zhang; Anjun Ma; Jing Zhao; Dong Xu 002; Qin Ma 003; Yan Wang 028 (Briefings Bioinform., 2022)

MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data. - Shuangquan Zhang; Lili Yang 004; Xiaotian Wu; Nan Sheng; Yuan Fu; Anjun Ma; Yan Wang 028 (Bioinform., 2022)

scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data. - Haocheng Gu; Hao Cheng; Anjun Ma; Yang Li 089; Juexin Wang; Dong Xu 002; Qin Ma 003 (Bioinform., 2022)

Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data. - Zhaoqian Liu; Qi Wang; Anjun Ma; Shaohong Feng; Dongjun Chung; Jing Zhao; Qin Ma 003; Bingqiang Liu (Comput. Biol. Medicine, 2023)

Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data. - Yang Li 089; Anjun Ma; Yizhong Wang; Qi Guo; Cankun Wang; Hongjun Fu; Bingqiang Liu; Qin Ma 003 (Briefings Bioinform., 2024)

A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data. - Yang Li 089; Yizhong Wang; Cankun Wang; Anjun Ma; Qin Ma 003; Bingqiang Liu (Patterns, 2024)