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Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.
Vorontsov IE, Kozin I, Abramov S, Boytsov A, Jolma A, Albu M, Ambrosini G, Faltejskova K, Gralak AJ, Gryzunov N, Inukai S, Kolmykov S, Kravchenko P, Kribelbauer-Swietek JF, Laverty KU, Nozdrin V, Patel ZM, Penzar D, Plescher ML, Pour SE, Razavi R, Yang AWH, Yevshin I, Zinkevich A, Weirauch MT, Bucher P, Deplancke B, Fornes O, Grau J, Grosse I, Kolpakov FA; Codebook/GRECO-BIT Consortium; Makeev VJ, Hughes TR, Kulakovskiy IV. Vorontsov IE, et al. Among authors: yevshin i. bioRxiv [Preprint]. 2024 Nov 13:2024.11.11.619379. doi: 10.1101/2024.11.11.619379. bioRxiv. 2024. PMID: 39605530 Free PMC article. Preprint.
HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.
Vorontsov IE, Eliseeva IA, Zinkevich A, Nikonov M, Abramov S, Boytsov A, Kamenets V, Kasianova A, Kolmykov S, Yevshin IS, Favorov A, Medvedeva YA, Jolma A, Kolpakov F, Makeev VJ, Kulakovskiy IV. Vorontsov IE, et al. Among authors: yevshin is. Nucleic Acids Res. 2024 Jan 5;52(D1):D154-D163. doi: 10.1093/nar/gkad1077. Nucleic Acids Res. 2024. PMID: 37971293 Free PMC article.
BioUML-towards a universal research platform.
Kolpakov F, Akberdin I, Kiselev I, Kolmykov S, Kondrakhin Y, Kulyashov M, Kutumova E, Pintus S, Ryabova A, Sharipov R, Yevshin I, Zhatchenko S, Kel A. Kolpakov F, et al. Among authors: yevshin i. Nucleic Acids Res. 2022 Jul 5;50(W1):W124-W131. doi: 10.1093/nar/gkac286. Nucleic Acids Res. 2022. PMID: 35536253 Free PMC article.
Genome-Wide Atlas of Promoter Expression Reveals Contribution of Transcribed Regulatory Elements to Genetic Control of Disuse-Mediated Atrophy of Skeletal Muscle.
Pintus SS, Akberdin IR, Yevshin I, Makhnovskii P, Tyapkina O, Nigmetzyanov I, Nurullin L, Devyatiyarov R, Shagimardanova E, Popov D, Kolpakov FA, Gusev O, Gazizova GR. Pintus SS, et al. Among authors: yevshin i. Biology (Basel). 2021 Jun 20;10(6):557. doi: 10.3390/biology10060557. Biology (Basel). 2021. PMID: 34203013 Free PMC article.
Landscape of allele-specific transcription factor binding in the human genome.
Abramov S, Boytsov A, Bykova D, Penzar DD, Yevshin I, Kolmykov SK, Fridman MV, Favorov AV, Vorontsov IE, Baulin E, Kolpakov F, Makeev VJ, Kulakovskiy IV. Abramov S, et al. Among authors: yevshin i. Nat Commun. 2021 May 12;12(1):2751. doi: 10.1038/s41467-021-23007-0. Nat Commun. 2021. PMID: 33980847 Free PMC article.
GTRD: an integrated view of transcription regulation.
Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ, Kulakovskiy IV, Kel A, Kolpakov F. Kolmykov S, et al. Among authors: yevshin i. Nucleic Acids Res. 2021 Jan 8;49(D1):D104-D111. doi: 10.1093/nar/gkaa1057. Nucleic Acids Res. 2021. PMID: 33231677 Free PMC article.
24 results