MaskerAid : a performance enhancement to RepeatMasker. - Joseph A. Bedell; Ian Korf; Warren Gish (Bioinform., 2000)

MPBLAST : improved BLAST performance with multiplexed queries. - Ian Korf; Warren Gish (Bioinform., 2000)

Integrating genomic homology into gene structure prediction. - Ian Korf; Paul Flicek; Daniel Duan; Michael R. Brent (ISMB (Supplement of Bioinformatics), 2001)

BLAST - an essential guide to the basic local alignment search tool. - Ian Korf; Mark Yandell; Joseph A. Bedell (O'Reilly, 2003)

Serial BLAST searching. - Ian Korf (Bioinform., 2003)

Gene finding in novel genomes. - Ian Korf (BMC Bioinform., 2004)

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. - Genis Parra; Keith Bradnam; Ian Korf (Bioinform., 2007)

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. - Danielle G. Lemay; William F. Martin; Angie S. Hinrichs; Monique Rijnkels; J. Bruce German; Ian Korf; Katherine S. Pollard (BMC Bioinform., 2012)

StochHMM: a flexible hidden Markov model tool and C++ library. - Paul C. Lott; Ian Korf (Bioinform., 2014)

SAMSA: a comprehensive metatranscriptome analysis pipeline. - Samuel T. Westreich; Ian Korf; David A. Mills; Danielle G. Lemay (BMC Bioinform., 2016)

SAMSA2: a standalone metatranscriptome analysis pipeline. - Samuel T. Westreich; Michelle L. Treiber; David A. Mills; Ian Korf; Danielle G. Lemay (BMC Bioinform., 2018)

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. - Michelle L. Treiber; Diana H. Taft; Ian Korf; David A. Mills; Danielle G. Lemay (BMC Bioinform., 2020)