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Fedor Kolpakov
Fedor Kolpakov
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Cited by
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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
17981998
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
10482009
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
7272018
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
2902011
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
2512016
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
2152019
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
2112016
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
1962020
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
1462021
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
1411998
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
862000
Gene networks
NA Kolchanov, EA Anan’ko, FA Kolpakov, OA Podkolodnaya, ...
Molecular biology 34, 449-460, 2000
812000
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
652021
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
522019
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
502019
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
481999
BioUML-Framework for visual modeling and simulation of biological systems
FA Kolpakov
Proceedings of the international conference on bioinformatics of genome …, 2002
452002
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
342006
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
321997
Integrated databases and computer systems for studying eukaryotic gene expression.
NA Kolchanov, MP Ponomarenko, AS Frolov, EA Ananko, FA Kolpakov, ...
Bioinformatics (Oxford, England) 15 (7), 669-686, 1999
311999
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