Learning Advanced TFBS Models from Chip-Seq Data - diChIPMunk: Effective Construction of Dinucleotide Positional Weight Matrices. - Ivan V. Kulakovskiy; Victor G. Levitsky; Dmitry G. Oschepkov; Ilya E. Vorontsov; Vsevolod J. Makeev (BIOINFORMATICS, 2013)

Jaccard index based similarity measure to compare transcription factor binding site models. - Ilya E. Vorontsov; Ivan V. Kulakovskiy; Vsevolod J. Makeev (Algorithms Mol. Biol., 2013)

From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites. - Ivan V. Kulakovskiy; Victor G. Levitsky; Dmitry Yu. Oshchepkov; Leonid Bryzgalov; Ilya E. Vorontsov; Vsevolod J. Makeev (J. Bioinform. Comput. Biol., 2013)

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. - Ivan V. Kulakovskiy; Yulia A. Medvedeva; Ulf Schaefer; Artem S. Kasianov; Ilya E. Vorontsov; Vladimir B. Bajic; Vsevolod J. Makeev (Nucleic Acids Res., 2013)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation. - Ilya E. Vorontsov; Ivan V. Kulakovskiy; Grigory Khimulya; Daria D. Nikolaeva; Vsevolod J. Makeev (BIOINFORMATICS, 2015)

EpiFactors: a comprehensive database of human epigenetic factors and complexes. - Yulia A. Medvedeva; Andreas Lennartsson; Rezvan Ehsani; Ivan V. Kulakovskiy; Ilya E. Vorontsov; Pouda Panahandeh; Grigory Khimulya; Takeya Kasukawa; Finn Drabløs (Database J. Biol. Databases Curation, 2015)

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. - Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Anastasiia V. Soboleva; Artem S. Kasianov; Haitham Ashoor; Wail Ba-alawi; Vladimir B. Bajic; Yulia A. Medvedeva; Fedor A. Kolpakov; Vsevolod J. Makeev (Nucleic Acids Res., 2016)

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. - Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Ruslan N. Sharipov; Alla D. Fedorova; Eugene I. Rumynskiy; Yulia A. Medvedeva; Arturo Magana-Mora; Vladimir B. Bajic; Dmitri A. Papatsenko; Fedor A. Kolpakov; Vsevolod J. Makeev (Nucleic Acids Res., 2018)

ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs. - Alexandr Boytsov; Sergey Abramov; Ariuna Z. Aiusheeva; Alexandra M. Kasianova; Eugene Baulin; Ivan A. Kuznetsov; Yurii S. Aulchenko; Semyon Kolmykov; Ivan S. Yevshin; Fedor A. Kolpakov; Ilya E. Vorontsov; Vsevolod J. Makeev; et al. (Nucleic Acids Res., 2022)

EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes. - Daria Marakulina; Ilya E. Vorontsov; Ivan V. Kulakovskiy; Andreas Lennartsson; Finn Drabløs; Yulia A. Medvedeva (Nucleic Acids Res., 2023)