DAGchainer: a tool for mining segmental genome duplications and synteny. - Brian J. Haas; Arthur L. Delcher; Jennifer R. Wortman; Steven Salzberg (Bioinform., 2004)

UCHIME improves sensitivity and speed of chimera detection. - Robert C. Edgar; Brian J. Haas; José Carlos Clemente; Christopher Quince; Rob Knight 001 (Bioinform., 2011)

Trinity RNA-Seq assembler performance optimization. - Robert Henschel; Matthias Lieber; Le-Shin Wu; Phillip M. Nista; Brian J. Haas; Richard D. LeDuc (XSEDE, 2012)

Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily. - Jonathan M. Goldberg; Allison D. Griggs; Janet L. Smith; Brian J. Haas; Jennifer R. Wortman; Qiandong Zeng (Bioinform., 2013)

A universal genomic coordinate translator for comparative genomics. - Neda Zamani; Görel Sundström; Jennifer R. S. Meadows; Marc P. Höppner; Jacques Dainat; Henrik Lantz; Brian J. Haas; Manfred G. Grabherr (BMC Bioinform., 2014)