Fedor A. Kolpakov

Publication Activity (10 Years)

Years Active: 1996-2022
Publications (10 Years): 9

Top Topics

Colorectal Cancer

Systems Biology

Top Venues

Nucleic Acids Res.

BMC Syst. Biol.

Publications

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) (2022)
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) (2022)
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) (2021)
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. (4) (2019)
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) (2019)
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) (2019)
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) (2018)
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) (2017)
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) (2016)
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 (2013)
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 (2011)
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) (2008)
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) (2007)
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) (2000)
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) (2000)
Fedor A. Kolpakov, Elena A. Ananko
Interactive data input into the GeneNet database. Bioinform. 15 (7) (1999)
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) (1999)
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) (1999)
Fedor A. Kolpakov, Elena A. Ananko, G. B. Kolesov, Nikolay A. Kolchanov
GeneNet: a gene network database and its automated visualization. Bioinform. 14 (6) (1998)
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)
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) (1998)
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)