iMotifs: an integrated sequence motif visualization and analysis environment. - Matias Piipari; Thomas A. Down; Harpreet Kaur Saini; Anton J. Enright; Tim J. P. Hubbard (Bioinform., 2010)

Metamotifs - a generative model for building families of nucleotide position weight matrices. - Matias Piipari; Thomas A. Down; Tim J. P. Hubbard (BMC Bioinform., 2010)

Dalliance: interactive genome viewing on the web. - Thomas A. Down; Matias Piipari; Tim J. P. Hubbard (Bioinform., 2011)