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

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

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

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

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

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

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

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

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

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

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