Genomic features in the breakpoint regions between syntenic blocks. - Phil Trinh; Aoife McLysaght; David Sankoff (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Porter: a new, accurate server for protein secondary structure prediction. - Gianluca Pollastri; Aoife McLysaght (Bioinform., 2005)

Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes. - Yoichiro Nakatani; Aoife McLysaght (Bioinform., 2017)