CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. - Fedor A. Kolpakov; Vladimir Poroikov; Ruslan N. Sharipov; Yury V. Kondrakhin; Alexey V. Zakharov; Alexey Lagunin; Luciano Milanesi; Alexander E. Kel (Nucleic Acids Res., 2007)

Identification of Differentially Expressed Genes by Meta-Analysis of Microarray Data on Breast Cancer. - Yury V. Kondrakhin; Ruslan N. Sharipov; Alexander E. Kel; Fedor A. Kolpakov (Silico Biol., 2008)

Model composition through model reduction: a combined model of CD95 and NF-κ. - Elena Kutumova; Andrei Yu. Zinovyev; Ruslan N. Sharipov; Fedor A. Kolpakov (BMC Syst. Biol., 2013)

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)

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)

Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features. - Oxana A. Volkova; Yury V. Kondrakhin; Timur A. Kashapov; Ruslan N. Sharipov (J. Bioinform. Comput. Biol., 2018)

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)

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)

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)