POBO, transcription factor binding site verification with bootstrapping. - Matti Kankainen; Liisa Holm (Nucleic Acids Res., 2004)

POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets. - Matti Kankainen; Liisa Holm (Nucleic Acids Res., 2005)

POXO: a web-enabled tool series to discover transcription factor binding sites. - Matti Kankainen; Petri Pehkonen; Päivi Rosenström; Petri Törönen; Garry Wong; Liisa Holm (Nucleic Acids Res., 2006)

MATLIGN: a motif clustering, comparison and matching tool. - Matti Kankainen; Ari Löytynoja (BMC Bioinform., 2007)

LOCP - locating pilus operons in Gram-positive bacteria. - Ilya Plyusnin; Liisa Holm; Matti Kankainen (Bioinform., 2009)

MPEA - metabolite pathway enrichment analysis. - Matti Kankainen; Peddinti V. Gopalacharyulu; Liisa Holm; Matej Oresic (Bioinform., 2011)

BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. - Matti Kankainen; Teija Ojala; Liisa Holm (BMC Bioinform., 2012)