Seed-driven Learning of Position Probability Matrices from Large Sequence Sets. - Jarkko Toivonen; Jussi Taipale; Esko Ukkonen (WABI, 2017)

Modeling and learning monomeric and dimeric transcription factor binding motifs. - Jarkko Toivonen (2019)

MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs. - Jarkko Toivonen; Pratyush K. Das; Jussi Taipale; Esko Ukkonen (Bioinform., 2020)