DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy. - Brian D. Halligan; Victor Ruotti; Simon N. Twigger; Andrew S. Greene (Nucleic Acids Res., 2005)

Visualizing Quantitative Proteomics Datasets using Treemaps. - Brian D. Halligan; Shama P. Mirza; Molly C. Pellitteri-Hahn; Michael Olivier; Andrew S. Greene (IV, 2007)

Improved rat genome gene prediction by integration of ESTs with RNA-Seq information. - Liping Li; Enguo Chen; Chun Yang; Jun Zhu; Pushkala Jayaraman; Jeff de Pons; Catherine C. Kaczorowski; Howard J. Jacob; Andrew S. Greene; Matthew R. Hodges; Allen W. Cowley Jr.; Mingyu Liang; et al. (Bioinform., 2015)