Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data. - Shuhua Fu; Aaron M. Tarone; Sing-Hoi Sze (ICCABS, 2014)

Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in melilotus. - Shuhua Fu; Peter L. Chang; Maren L. Friesen; Natasha L. Teakle; Aaron M. Tarone; Sing-Hoi Sze (ICCABS, 2017)

IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing. - Shuhua Fu; Yingke Ma; Hui Yao; Zhichao Xu 003; Shilin Chen; Jingyuan Song; Kin Fai Au (Bioinform., 2018)