A maximum common substructure-based algorithm for searching and predicting drug-like compounds. - Yiqun Cao; Tao Jiang 001; Thomas Girke (ISMB, 2008)

ChemmineR: a compound mining framework for R. - Yiqun Cao; Anna Charisi; Li-Chang Cheng; Tao Jiang 001; Thomas Girke (Bioinform., 2008)

Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing. - Yiqun Cao; Tao Jiang 001; Thomas Girke (Bioinform., 2010)

Single feature polymorphism detection using recombinant inbred line microarray expression data. - Xinping Cui; Na You; Thomas Girke; Richard Michelmore; Allen Van Deynze (Bioinform., 2010)

Predicting conserved protein motifs with Sub-HMMs. - Kevin Horan; Christian R. Shelton; Thomas Girke (BMC Bioinform., 2010)

SEED: efficient clustering of next-generation sequences. - Ergude Bao; Tao Jiang 001; Isgouhi Kaloshian; Thomas Girke (Bioinform., 2011)

ChemMine tools: an online service for analyzing and clustering small molecules. - Tyler W. H. Backman; Yiqun Cao; Thomas Girke (Nucleic Acids Res., 2011)

BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences. - Ergude Bao; Tao Jiang 001; Thomas Girke (Bioinform., 2013)

fmcsR: mismatch tolerant maximum common substructure searching in R. - Yan Wang; Tyler W. H. Backman; Kevin Horan; Thomas Girke (Bioinform., 2013)

Differential gene expression analysis using coexpression and RNA-Seq data. - Ei-Wen Yang; Thomas Girke; Tao Jiang 001 (Bioinform., 2013)

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references. - Ergude Bao; Tao Jiang 001; Thomas Girke (Bioinform., 2014)

systemPipeR: NGS workflow and report generation environment. - Tyler W. H. Backman; Thomas Girke (BMC Bioinform., 2016)

bioassayR: Cross-Target Analysis of Small Molecule Bioactivity. - Tyler W. H. Backman; Thomas Girke (J. Chem. Inf. Model., 2016)