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 | 1826 | 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 | 1076 | 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 | 865 | 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 | 302 | 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 | 269 | 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 | 254 | 2020 |
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 | 244 | 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 | 242 | 2016 |
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 | 215 | 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 | 145 | 1998 |
Gene networks NA Kolchanov, EA Anan’ko, FA Kolpakov, OA Podkolodnaya, ... Molecular biology 34, 449-460, 2000 | 96 | 2000 |
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 | 91 | 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 | 88 | 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 | 61 | 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 | 58 | 2019 |
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 | 49 | 2024 |
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 |
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 | 43 | 2020 |
BioUML: visual modeling, automated code generation and simulation of biological systems F Kolpakov, M Puzanov, A Koshukov Proceedings of the 5th International Conference on Bioinformatics of Genome …, 2006 | 35 | 2006 |