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ORCIDFedor A. Kolpakov
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2020 – today
- 2022
[j20]Alexandr Boytsov
, Sergey Abramov, Ariuna Z. Aiusheeva, Alexandra M. Kasianova, Eugene Baulin, Ivan A. Kuznetsov, Yurii S. Aulchenko, Semyon Kolmykov, Ivan S. Yevshin, Fedor A. Kolpakov, Ilya E. Vorontsov, Vsevolod J. Makeev, Ivan V. Kulakovskiy:
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs. Nucleic Acids Res. 50(W1): 51-56 (2022)- [j19]Fedor A. Kolpakov, Ilya R. Akberdin, Ilya Kiselev, Semyon Kolmykov, Yury V. Kondrakhin, Mikhail Kulyashov, Elena Kutumova, Sergey Pintus, Anna Ryabova, Ruslan N. Sharipov, Ivan S. Yevshin, Sergey Zhatchenko, Alexander E. Kel:
BioUML - towards a universal research platform. Nucleic Acids Res. 50(W1): 124-131 (2022) - 2021
- [j18]Semyon Kolmykov, Ivan S. Yevshin, Mikhail Kulyashov, Ruslan N. Sharipov, Yury V. Kondrakhin, Vsevolod J. Makeev, Ivan V. Kulakovskiy, Alexander E. Kel, Fedor A. Kolpakov:
GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 49(Database-Issue): D104-D111 (2021)
2010 – 2019
- 2019
- [j17]Alexander E. Kel, Ulyana Boyarskikh, Philip Stegmaier, Leonid S. Leskov, Andrey V. Sokolov, Ivan S. Yevshin, Nikita Mandrik, Daria Stelmashenko, Jeannette Koschmann, Olga V. Kel-Margoulis, Mathias Krull, Anna Martínez-Cardús, Sebastian Moran, Manel Esteller, Fedor A. Kolpakov, Maxim Filipenko, Edgar Wingender:
Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. BMC Bioinform. 20-S(4): 119:1-119:20 (2019) - [j16]Ivan S. Yevshin, Ruslan N. Sharipov, Semyon Kolmykov, Yury V. Kondrakhin, Fedor A. Kolpakov:
GTRD: a database on gene transcription regulation - 2019 update. Nucleic Acids Res. 47(Database-Issue): D100-D105 (2019) - [j15]Fedor A. Kolpakov, Ilya R. Akberdin, Timur A. Kashapov, llya Kiselev, Semyon Kolmykov, Yury V. Kondrakhin, Elena Kutumova, Nikita Mandrik, Sergey S. Pintus, Anna Ryabova, Ruslan N. Sharipov, Ivan S. Yevshin, Alexander E. Kel:
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. Nucleic Acids Res. 47(Webserver-Issue): W225-W133 (2019) - 2018
- [j14]Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Ruslan N. Sharipov, Alla D. Fedorova, Eugene I. Rumynskiy, Yulia A. Medvedeva, Arturo Magana-Mora, Vladimir B. Bajic, Dmitri A. Papatsenko, Fedor A. Kolpakov, Vsevolod J. Makeev:
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res. 46(Database-Issue): D252-D259 (2018) - 2017
- [j13]Ivan S. Yevshin, Ruslan N. Sharipov, Tagir F. Valeev, Alexander E. Kel, Fedor A. Kolpakov:
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. Nucleic Acids Res. 45(Database-Issue): D61-D67 (2017) - 2016
- [j12]Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Anastasiia V. Soboleva, Artem S. Kasianov, Haitham Ashoor, Wail Ba-alawi, Vladimir B. Bajic, Yulia A. Medvedeva, Fedor A. Kolpakov, Vsevolod J. Makeev:
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res. 44(Database-Issue): 116-125 (2016) - 2013
- [j11]Elena Kutumova, Andrei Yu. Zinovyev, Ruslan N. Sharipov, Fedor A. Kolpakov:
Model composition through model reduction: a combined model of CD95 and NF-κ. BMC Syst. Biol. 7: 13 (2013) - 2011
- [j10]Dagmar Waltemath, Richard R. Adams, Frank T. Bergmann, Michael Hucka, Fedor A. Kolpakov, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Sven Sahle, Jacky L. Snoep, Nicolas Le Novère:
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Syst. Biol. 5: 198 (2011)
2000 – 2009
- 2008
- [j9]Yury V. Kondrakhin, Ruslan N. Sharipov, Alexander E. Kel, Fedor A. Kolpakov:
Identification of Differentially Expressed Genes by Meta-Analysis of Microarray Data on Breast Cancer. Silico Biol. 8(5-6): 383-411 (2008) - 2007
- [j8]Fedor A. Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury V. Kondrakhin, Alexey V. Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel:
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. Nucleic Acids Res. 35(Database-Issue): 550-556 (2007) - 2000
- [j7]Nikolay A. Kolchanov, Olga A. Podkolodnaya, Elena A. Ananko, Elena V. Ignatieva, Irina L. Stepanenko, Olga V. Kel-Margoulis, Alexander E. Kel, Tatyana I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, Fedor A. Kolpakov, Nikolay L. Podkolodny, Andrey N. Naumochkin, I. M. Korostishevskaya, Aida G. Romashchenko, G. Christian Overton:
Transcription Regulatory Regions Database (TRRD): its status in 2000. Nucleic Acids Res. 28(1): 298-301 (2000) - [j6]Fedor A. Kolpakov, N. L. Podkolodnyi, Sergey V. Lavryushev, Dmitry A. Grigorovich, Mikhail P. Ponomarenko, Nikolay A. Kolchanov:
Methods for integration of heterogeneous information resources in molecular biology in the digital library GeneExpress. Program. Comput. Softw. 26(3): 170-176 (2000)
1990 – 1999
- 1999
- [j5]Nikolay A. Kolchanov, Mikhail P. Ponomarenko, Anatoly S. Frolov, Elena A. Ananko, Fedor A. Kolpakov, Elena V. Ignatieva, Olga A. Podkolodnaya, T. N. Goryachkovskaya, Irina L. Stepanenko, Tatyana I. Merkulova, V. V. Babenko, Y. V. Ponomarenko, Alexey V. Kochetov, Nikolay L. Podkolodny, Denis G. Vorobiev, Sergey V. Lavryushev, Dmitry A. Grigorovich, Yury V. Kondrakhin, Luciano Milanesi, Edgar Wingender, Victor V. Solovyev, G. Christian Overton:
Integrated databases and computer systems for studying eukaryotic gene expression. Bioinform. 15(7): 669-686 (1999) - [j4]Fedor A. Kolpakov, Elena A. Ananko:
Interactive data input into the GeneNet database. Bioinform. 15(7): 713-714 (1999) - [j3]Nikolay A. Kolchanov, Elena A. Ananko, Olga A. Podkolodnaya, Elena V. Ignatieva, Irina L. Stepanenko, Olga V. Kel-Margoulis, Alexander E. Kel, Tatyana I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, Fedor A. Kolpakov, Nikolay L. Podkolodny, Andrey N. Naumochkin, Aida G. Romashchenko:
Transcription Regulatory Regions Database (TRRD): its status in 1999. Nucleic Acids Res. 27(1): 303-306 (1999) - 1998
- [j2]Fedor A. Kolpakov, Elena A. Ananko, G. B. Kolesov, Nikolay A. Kolchanov:
GeneNet: a gene network database and its automated visualization. Bioinform. 14(6): 529-537 (1998) - [j1]T. Heinemeyer, Edgar Wingender, Ingmar Reuter, Henning Hermjakob, Alexander E. Kel, Olga V. Kel-Margoulis, Elena V. Ignatieva, Elena A. Ananko, Olga A. Podkolodnaya, Fedor A. Kolpakov, Nikolay L. Podkolodny, Nikolay A. Kolchanov:
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res. 26(1): 362-367 (1998) - [c2]Nikolay A. Kolchanov, Mikhail P. Ponomarenko, Alexander E. Kel, Yury V. Kondrakhin, Anatoly S. Frolov, Fedor A. Kolpakov, T. N. Goryachkovskaya, O. V. Kel, Elena A. Ananko, Elena V. Ignatieva, Olga A. Podkolodnaya, Vladimir N. Babenko, Irina L. Stepanenko, Aida G. Romashchenko, Tatyana I. Merkulova, Denis G. Vorobiev, Sergey V. Lavryushev, Y. V. Ponomarenko, Alexey V. Kochetov, G. B. Kolesov, Victor V. Solovyev, Luciano Milanesi, Nikolay L. Podkolodny, Edgar Wingender, T. Heinemeyer:
GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome. ISMB 1998: 95-104 - 1996
- [c1]Yury V. Kondrakhin, Fedor A. Kolpakov, Alexander E. Kel, Nikolay A. Kolchanov, Luciano Milanesi:
Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes. German Conference on Bioinformatics 1996: 247-250
Coauthor Index
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