Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. - Brian D. Ondov; Anjana Varadarajan; Karla D. Passalacqua; Nicholas H. Bergman (Bioinform., 2008)

Assessment of Gene Annotation Accuracy by Inferring Transcripts from RNA-Seq. - Jeffrey Martin; Wenhan Zhu; Nicholas H. Bergman; Mark Borodovsky (BIBM, 2009)

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System. - Brian D. Ondov; Charles Cochran; Mark Landers; Gavin D. Meredith; Miroslav Dudas; Nicholas H. Bergman (Bioinform., 2010)

Bacillus anthracis genome organization in light of whole transcriptome sequencing. - Jeffrey Martin; Wenhan Zhu; Karla D. Passalacqua; Nicholas H. Bergman; Mark Borodovsky (BMC Bioinform., 2010)

Interactive metagenomic visualization in a Web browser. - Brian D. Ondov; Nicholas H. Bergman; Adam M. Phillippy (BMC Bioinform., 2011)