DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses. - Jinyu Yang; Xin Chen; Adam McDermaid; Qin Ma 003 (Bioinform., 2017)

An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data. - Bingqiang Liu; Jinyu Yang; Yang Li 089; Adam McDermaid; Qin Ma 003 (Briefings Bioinform., 2018)

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes. - Sheng-Yong Niu; Jinyu Yang; Adam McDermaid; Jing Zhao; Yu Kang 004; Qin Ma 003 (Briefings Bioinform., 2018)

Interpretation of differential gene expression results of RNA-seq data: review and integration. - Adam McDermaid; Brandon Monier; Jing Zhao; Bingqiang Liu; Qin Ma 003 (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)

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis. - Brandon Monier; Adam McDermaid; Cankun Wang; Jing Zhao; Allison J. Miller; Anne Fennell; Qin Ma 003 (PLoS Comput. Biol., 2019)

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)