Identification and Analysis of Genes and Pseudogenes within Duplicated Regions in the Human and Mouse Genomes. - Mikita Suyama; Eoghan D. Harrington; Peer Bork; David Torrents (PLoS Comput. Biol., 2006)

Sircah: a tool for the detection and visualization of alternative transcripts. - Eoghan D. Harrington; Peer Bork (Bioinform., 2008)

SmashCommunity: a metagenomic annotation and analysis tool. - Manimozhiyan Arumugam; Eoghan D. Harrington; Konrad U. Foerstner; Jeroen Raes; Peer Bork (Bioinform., 2010)

SmashCell: a software framework for the analysis of single-cell amplified genome sequences. - Eoghan D. Harrington; Manimozhiyan Arumugam; Jeroen Raes; Peer Bork; David A. Relman (Bioinform., 2010)