| GTRD: a database on gene transcription regulation—2019 update I Yevshin, R Sharipov, S Kolmykov, Y Kondrakhin, F Kolpakov Nucleic acids research 47 (D1), D100-D105, 2019 | 217 | 2019 |
| GTRD: an integrated view of transcription regulation S Kolmykov, I Yevshin, M Kulyashov, R Sharipov, Y Kondrakhin, ... Nucleic acids research 49 (D1), D104-D111, 2021 | 147 | 2021 |
| Landscape of allele-specific transcription factor binding in the human genome S Abramov, A Boytsov, D Bykova, DD Penzar, I Yevshin, SK Kolmykov, ... Nature communications 12 (1), 2751, 2021 | 68 | 2021 |
| BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data F Kolpakov, I Akberdin, T Kashapov, L Kiselev, S Kolmykov, Y Kondrakhin, ... Nucleic acids research 47 (W1), W225-W233, 2019 | 52 | 2019 |
| The effect of xenobiotics on microRNA expression in the rat liver LF Gulyaeva, MD Chanyshev, SK Kolmykov, DS Ushakov, SS Nechkin Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry 10, 258-263, 2016 | 18 | 2016 |
| BioUML—Towards a universal research platform F Kolpakov, I Akberdin, I Kiselev, S Kolmykov, Y Kondrakhin, M Kulyashov, ... Nucleic Acids Research 50 (W1), W124-W131, 2022 | 12 | 2022 |
| Population size estimation for quality control of ChIP-Seq datasets SK Kolmykov, YV Kondrakhin, IS Yevshin, RN Sharipov, AS Ryabova, ... PloS one 14 (8), e0221760, 2019 | 11 | 2019 |
| Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome M Ponomarenko, M Kleshchev, P Ponomarenko, I Chadaeva, ... BMC genetics 21, 1-17, 2020 | 9 | 2020 |
| ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs A Boytsov, S Abramov, AZ Aiusheeva, AM Kasianova, E Baulin, ... Nucleic Acids Research 50 (W1), W51-W56, 2022 | 7 | 2022 |
| Whole-exome sequencing analysis of human semen quality in Russian multiethnic population S Kolmykov, G Vasiliev, L Osadchuk, M Kleschev, A Osadchuk Frontiers in genetics 12, 662846, 2021 | 7 | 2021 |
| HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors IE Vorontsov, IA Eliseeva, A Zinkevich, M Nikonov, S Abramov, A Boytsov, ... Nucleic Acids Research 52 (D1), D154-D163, 2024 | 6 | 2024 |
| Meta-analysis of ChIP-seq datasets through the rank aggregation approach SK Kolmykov, YV Kondrakhin, RN Sharipov, IS Yevshi, AS Ryabova, ... 2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB), 180-184, 2020 | 2 | 2020 |
| Description, characteristic and algorithm for creation of a dictionary of cell types and tissues in the GTRD database MA Kulyashov, SK Kolmykov, IS Evshin, FA Kolpakov CEUR Workshop Proceedings 2569, 13-18, 2020 | 2 | 2020 |
| Peak caller comparison through quality control of ChIP-Seq datasets RN Sharipov, IS Yevshin, YV Kondrakhin, AS Ryabova, SK Kolmykov, ... Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB …, 2020 | 1 | 2020 |
| New method for estimation of number of transcription factor binding sites using results of processing of ChIP-seq data by different peak callers S Kolmykov, Y Kondrakhin, F Kolpakov Systems Biology and Bioinformatics (SBB-2018), 52-52, 2018 | 1 | 2018 |
| Untranslated Region Sequences and the Efficacy of mRNA Vaccines against Tuberculosis V Reshetnikov, I Terenin, G Shepelkova, V Yeremeev, S Kolmykov, ... International Journal of Molecular Sciences 25 (2), 888, 2024 | | 2024 |
| State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs MA Kulyashov, SK Kolmykov, TM Khlebodarova, IR Akberdin Microorganisms 11 (12), 2987, 2023 | | 2023 |
| Relationship Between Transcription Factor Binding Regions and Open Chromatin Regions in Human Based on GTRD Data SK Kolmykov, YV Kondrakhin, FA Kolpakov Proceedings of 11th Moscow Conference on Computational Molecular Biology …, 2023 | | 2023 |
| Statistical framework for calling allelic imbalance in high-throughput sequencing data A Andrey Buyan, G Meshcheryakov, V Safronov, S Abramov, A Boytsov, ... bioRxiv, 2023.11. 07.565968, 2023 | | 2023 |
| Reconstruction of a genome-scale metabolic model for chicken whole embryo considering transcriptomics data IR Akberdin, MA Kulyashov, SK Kolmykov, SS Pintus, IS Yevshin, ... Bioinformatics of genome regulation and structure/systems biology (BGRS/SB …, 2022 | | 2022 |
