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Algorithms for Molecular Biology : AMB|March 25, 2011
Efficient algorithms for the discovery of gapped factorsAlberto Apostolico, Cinzia Pizzi, Esko UkkonenIEEE/ACM Transactions on Computational Biology and Bioinformatics|November 13, 2010
Finding significant matches of position weight matrices in linear timeCinzia Pizzi, Pasi Rastas, Esko UkkonenBioinformatics (Oxford, England)|September 24, 2009
MOODS: fast search for position weight matrix matches in DNA sequencesJanne Korhonen, Petri Martinmäki, Cinzia Pizzi, et al.Current Opinion in Biotechnology|February 23, 2010
Computational methods for metabolic reconstructionEsa Pitkänen, Juho Rousu, Esko UkkonenNature Protocols|April 5, 2007
Locating potential enhancer elements by comparative genomics using the EEL softwareKimmo Palin, Jussi Taipale, Esko UkkonenJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|August 8, 2013
Fast matching of transcription factor motifs using generalized position weight matrix modelsEmanuele Giaquinta, Szymon Grabowski, Esko UkkonenAlgorithms for Molecular Biology : AMB|April 23, 2016
MissMax: alignment-free sequence comparison with mismatches through filtering and heuristicsCinzia PizziJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|July 30, 2010
The subsequence composition of polypeptidesAlberto Apostolico, Fabio CunialAlgorithms for Molecular Biology : AMB|October 30, 2008
Fast algorithms for computing sequence distances by exhaustive substring compositionAlberto Apostolico, Olgert DenasJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|April 10, 2004
Incremental paradigms of motif discoveryAlberto Apostolico, Laxmi ParidaPageof 6