Ivan V. Kulakovskiy

17 papers Journal 15Unranked 2
YearRankTypeTitle / Venue / Authors
2023 J jnl
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes.
Nucleic Acids Res.
Daria Marakulina, Ilya E. Vorontsov, Ivan V. Kulakovskiy, Andreas Lennartsson, Finn Drabløs, Yulia A. Medvedeva
2023 J jnl
LegNet: a best-in-class deep learning model for short DNA regulatory regions.
Bioinform.
Dmitry Penzar, Daria Nogina, Elizaveta Noskova, Arsenii Zinkevich, Georgy Meshcheryakov, Andrey Lando, Abdul Muntakim Rafi, Carl G. de Boer, Ivan V. Kulakovskiy
2022 J jnl
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.
Nucleic Acids Res.
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
2021 J jnl
GTRD: an integrated view of transcription regulation.
Nucleic Acids Res.
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
2019 J jnl
svist4get: a simple visualization tool for genomic tracks from sequencing experiments.
BMC Bioinform.
Artyom A. Egorov, Ekaterina A. Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev, Ivan V. Kulakovskiy
2018 J jnl
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
Nucleic Acids Res.
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
2016 J jnl
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.
Nucleic Acids Res.
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
2015 J jnl
EpiFactors: a comprehensive database of human epigenetic factors and complexes.
Database J. Biol. Databases Curation
Yulia A. Medvedeva, Andreas Lennartsson, Rezvan Ehsani, Ivan V. Kulakovskiy, Ilya E. Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, Finn Drabløs
2015 — conf
PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation.
BIOINFORMATICS
Ilya E. Vorontsov, Ivan V. Kulakovskiy, Grigory Khimulya, Daria D. Nikolaeva, Vsevolod J. Makeev
2013 J jnl
From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites.
J. Bioinform. Comput. Biol.
Ivan V. Kulakovskiy, Victor G. Levitsky, Dmitry Yu. Oshchepkov, Leonid Bryzgalov, Ilya E. Vorontsov, Vsevolod J. Makeev
2013 J jnl
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models.
Nucleic Acids Res.
Ivan V. Kulakovskiy, Yulia A. Medvedeva, Ulf Schaefer, Artem S. Kasianov, Ilya E. Vorontsov, Vladimir B. Bajic, Vsevolod J. Makeev
2013 J jnl
Jaccard index based similarity measure to compare transcription factor binding site models.
Algorithms Mol. Biol.
Ilya E. Vorontsov, Ivan V. Kulakovskiy, Vsevolod J. Makeev
2013 — conf
Learning Advanced TFBS Models from Chip-Seq Data - diChIPMunk: Effective Construction of Dinucleotide Positional Weight Matrices.
BIOINFORMATICS
Ivan V. Kulakovskiy, Victor G. Levitsky, Dmitry G. Oschepkov, Ilya E. Vorontsov, Vsevolod J. Makeev
2011 J jnl
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites.
Bioinform.
Ivan V. Kulakovskiy, A. A. Belostotsky, Artem S. Kasianov, Natalia G. Esipova, Yulia A. Medvedeva, I. A. Eliseeva, Vsevolod J. Makeev
2010 J jnl
Deep and wide digging for binding motifs in ChIP-Seq data.
Bioinform.
Ivan V. Kulakovskiy, Valentina Boeva, Alexander V. Favorov, Vsevolod J. Makeev
2010 J jnl
Empirical Potentials for ion Binding in proteins.
J. Bioinform. Comput. Biol.
Sergei Rahmanov, Ivan V. Kulakovskiy, Leonid Uroshlev, Vsevolod J. Makeev
2009 J jnl
Motif discovery and motif finding from genome-mapped DNase footprint data.
Bioinform.
Ivan V. Kulakovskiy, Alexander V. Favorov, Vsevolod J. Makeev