Assessment of translational importance of mammalian mRNA sequence features based on Ribo-Seq and mRNA-Seq data. - Oxana A. Volkova; Yury V. Kondrakhin; Ivan S. Yevshin; Tagir F. Valeev; Ruslan N. Sharipov (J. Bioinform. Comput. Biol., 2016)

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)

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. - Ivan S. Yevshin; Ruslan N. Sharipov; Tagir F. Valeev; Alexander E. Kel; Fedor A. Kolpakov (Nucleic Acids Res., 2017)

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)

Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. - Alexander E. Kel; Ulyana Boyarskikh; Philip Stegmaier; Leonid S. Leskov; Andrey V. Sokolov; Ivan S. Yevshin; Nikita Mandrik; Daria Stelmashenko; Jeannette Koschmann; Olga V. Kel-Margoulis; Mathias Krull; Anna Martínez-Cardús; et al. (BMC Bioinform., 2019)

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. - Fedor A. Kolpakov; Ilya R. Akberdin; Timur A. Kashapov; llya Kiselev; Semyon Kolmykov; Yury V. Kondrakhin; Elena Kutumova; Nikita Mandrik; Sergey S. Pintus; Anna Ryabova; Ruslan N. Sharipov; Ivan S. Yevshin; et al. (Nucleic Acids Res., 2019)

GTRD: a database on gene transcription regulation - 2019 update. - Ivan S. Yevshin; Ruslan N. Sharipov; Semyon Kolmykov; Yury V. Kondrakhin; Fedor A. Kolpakov (Nucleic Acids Res., 2019)

GTRD: an integrated view of transcription regulation. - Semyon Kolmykov; Ivan S. Yevshin; Mikhail Kulyashov; Ruslan N. Sharipov; Yury V. Kondrakhin; Vsevolod J. Makeev; Ivan V. Kulakovskiy; Alexander E. Kel; Fedor A. Kolpakov (Nucleic Acids Res., 2021)

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)

BioUML - towards a universal research platform. - Fedor A. Kolpakov; Ilya R. Akberdin; Ilya Kiselev; Semyon Kolmykov; Yury V. Kondrakhin; Mikhail Kulyashov; Elena Kutumova; Sergey S. Pintus; Anna Ryabova; Ruslan N. Sharipov; Ivan S. Yevshin; Sergey Zhatchenko; et al. (Nucleic Acids Res., 2022)

Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome. - Valentina A. Grushina; Ivan S. Yevshin; Oleg A. Gusev; Fedor A. Kolpakov; Olga I. Stanishevskaya; Elena S. Fedorova; Natalia A. Zinovieva; Sergey S. Pintus (J. Bioinform. Comput. Biol., 2025)