| Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL T Heinemeyer, E Wingender, I Reuter, H Hermjakob, AE Kel, OV Kel, ... Nucleic acids research 26 (1), 362-367, 1998 | 1805 | 1998 |
| The systems biology graphical notation NL Novère, M Hucka, H Mi, S Moodie, F Schreiber, A Sorokin, E Demir, ... Nature biotechnology 27 (8), 735-741, 2009 | 1049 | 2009 |
| HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis IV Kulakovskiy, IE Vorontsov, IS Yevshin, RN Sharipov, AD Fedorova, ... Nucleic acids research 46 (D1), D252-D259, 2018 | 736 | 2018 |
| Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language D Waltemath, R Adams, FT Bergmann, M Hucka, F Kolpakov, AK Miller, ... BMC systems biology 5, 1-10, 2011 | 291 | 2011 |
| HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models IV Kulakovskiy, IE Vorontsov, IS Yevshin, AV Soboleva, AS Kasianov, ... Nucleic acids research 44 (D1), D116-D125, 2016 | 253 | 2016 |
| 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: a database of transcription factor binding sites identified by ChIP-seq experiments I Yevshin, R Sharipov, T Valeev, A Kel, F Kolpakov Nucleic acids research, gkw951, 2016 | 212 | 2016 |
| SBML Level 3: an extensible format for the exchange and reuse of biological models SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ... Molecular systems biology 16 (8), e9110, 2020 | 203 | 2020 |
| 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 |
| GeneNet: a gene network database and its automated visualization. FA Kolpakov, EA Ananko, GB Kolesov, NA Kolchanov Bioinformatics (Oxford, England) 14 (6), 529-537, 1998 | 141 | 1998 |
| Transcription regulatory regions database (TRRD): its status in 2000 NA Kolchanov, OA Podkolodnaya, EA Ananko, EV Ignatieva, ... Nucleic Acids Research 28 (1), 298-301, 2000 | 87 | 2000 |
| Gene networks NA Kolchanov, EA Anan’ko, FA Kolpakov, OA Podkolodnaya, ... Molecular biology 34, 449-460, 2000 | 82 | 2000 |
| 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 |
| Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer A Kel, U Boyarskikh, P Stegmaier, LS Leskov, AV Sokolov, I Yevshin, ... BMC bioinformatics 20, 1-20, 2019 | 53 | 2019 |
| 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 |
| Transcription regulatory regions database (TRRD): its status in 1999 NA Kolchanov, EA Ananko, OA Podkolodnaya, EV Ignatieva, ... Nucleic acids research 27 (1), 303-306, 1999 | 48 | 1999 |
| BioUML-Framework for visual modeling and simulation of biological systems FA Kolpakov Proceedings of the international conference on bioinformatics of genome …, 2002 | 45 | 2002 |
| BioUML: visual modeling, automated code generation and simulation of biological systems F Kolpakov, M Puzanov, A Koshukov Proceedings of The Fifth International Conference on Bioinformatics of …, 2006 | 34 | 2006 |
| TRRD: database on transcription regulatory regions of eukaryotic genes AE Kel', NA Kolchanov, OV Kel', AG Romashchenko, EA Anan'Ko, ... Molecular Biology 31 (4), 521-530, 1997 | 32 | 1997 |
| Regulation of proteins in human skeletal muscle: the role of transcription PA Makhnovskii, VG Zgoda, RO Bokov, EI Shagimardanova, ... Scientific Reports 10 (1), 3514, 2020 | 31 | 2020 |
