A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays. - Huanying Ge; Chao Cheng; Lei M. Li (BMC Bioinform., 2008)

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. - Huanying Ge; Kejun Liu; Todd Juan; Fang Fang; Matthew Newman; Wolfgang Hoeck (Bioinform., 2011)

OSA: a fast and accurate alignment tool for RNA-Seq. - Jun Hu; Huanying Ge; Matthew Newman; Kejun Liu (Bioinform., 2012)

RNA-Seq Analysis Pipeline Based on Oshell Environment. - Jing Li; Jun Hu; Matthew Newman; Kejun Liu; Huanying Ge (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)