PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments. - Tuomo Hartonen; Biswajyoti Sahu; Kashyap Dave; Teemu Kivioja; Jussi Taipale (Bioinform., 2016)

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

Fast motif matching revisited: high-order PWMs, SNPs and indels. - Janne H. Korhonen; Kimmo Palin; Jussi Taipale; Esko Ukkonen (Bioinform., 2017)

The interaction landscape between transcription factors and the nucleosome. - Fangjie Zhu; Lucas Farnung; Eevi Kaasinen; Biswajyoti Sahu; Yimeng Yin; Bei Wei; Svetlana O. Dodonova; Kazuhiro R. Nitta; Ekaterina Morgunova; Minna Taipale; Patrick Cramer; Jussi Taipale (Nat., 2018)

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