HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
Kulakovskiy, Ivan V, Vorontsov, Ilya E, Yevshin, Ivan S, Sharipov, Ruslan N, Fedorova, Alla D, Rumynskiy, Eugene I, Medvedeva, Yulia A, Magana-Mora, Arturo, Bajic, Vladimir B, Papatsenko, Dmitry A, Kolpakov, Fedor A, Makeev, Vsevolod J
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
Kulakovskiy, Ivan V, Vorontsov, Ilya E, Yevshin, Ivan S, Soboleva, Anastasiia V, Kasianov, Artem S, Ashoor, Haitham, Ba-Alawi, Wail, Bajic, Vladimir B, Medvedeva, Yulia A, Kolpakov, Fedor A, Makeev, Vsevolod J
Published in Nucleic acids research (04.01.2016)
Published in Nucleic acids research (04.01.2016)
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Journal Article
Landscape of allele-specific transcription factor binding in the human genome
Abramov, Sergey, Boytsov, Alexandr, Bykova, Daria, Penzar, Dmitry D., Yevshin, Ivan, Kolmykov, Semyon K., Fridman, Marina V., Favorov, Alexander V., Vorontsov, Ilya E., Baulin, Eugene, Kolpakov, Fedor, Makeev, Vsevolod J., Kulakovskiy, Ivan V.
Published in Nature communications (12.05.2021)
Published in Nature communications (12.05.2021)
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Journal Article
EpiFactors: a comprehensive database of human epigenetic factors and complexes
Medvedeva, Yulia A, Lennartsson, Andreas, Ehsani, Rezvan, Kulakovskiy, Ivan V, Vorontsov, Ilya E, Panahandeh, Pouda, Khimulya, Grigory, Kasukawa, Takeya, Drabløs, Finn
Published in Database : the journal of biological databases and curation (2015)
Published in Database : the journal of biological databases and curation (2015)
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ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
Boytsov, Alexandr, Abramov, Sergey, Aiusheeva, Ariuna Z, Kasianova, Alexandra M, Baulin, Eugene, Kuznetsov, Ivan A, Aulchenko, Yurii S, Kolmykov, Semyon, Yevshin, Ivan, Kolpakov, Fedor, Vorontsov, Ilya E, Makeev, Vsevolod J, Kulakovskiy, Ivan V
Published in Nucleic acids research (05.07.2022)
Published in Nucleic acids research (05.07.2022)
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A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease
Sethi, Siddharth, Vorontsov, Ilya E, Kulakovskiy, Ivan V, Greenaway, Simon, Williams, John, Makeev, Vsevolod J, Brown, Steve D M, Simon, Michelle M, Mallon, Ann-Marie
Published in BMC genomics (02.11.2020)
Published in BMC genomics (02.11.2020)
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Enhanced C/EBP binding to G·T mismatches facilitates fixation of CpG mutations in cancer and adult stem cells
Ershova, Anna S., Eliseeva, Irina A., Nikonov, Oleg S., Fedorova, Alla D., Vorontsov, Ilya E., Papatsenko, Dmitry, Kulakovskiy, Ivan V.
Published in Cell reports (Cambridge) (13.07.2021)
Published in Cell reports (Cambridge) (13.07.2021)
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Multiple single nucleotide polymorphisms in the first intron of the IL2RA gene affect transcription factor binding and enhancer activity
Schwartz, Anton M., Demin, Denis E., Vorontsov, Ilya E., Kasyanov, Artem S., Putlyaeva, Lidia V., Tatosyan, Karina A., Kulakovskiy, Ivan V., Kuprash, Dmitry V.
Published in Gene (20.02.2017)
Published in Gene (20.02.2017)
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HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
Kulakovskiy, Ivan V., Medvedeva, Yulia A., Schaefer, Ulf, Kasianov, Artem S., Vorontsov, Ilya E., Bajic, Vladimir B., Makeev, Vsevolod J.
Published in Nucleic acids research (01.01.2013)
Published in Nucleic acids research (01.01.2013)
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Journal Article
The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region
Afanasyeva, Marina A, Putlyaeva, Lidia V, Demin, Denis E, Kulakovskiy, Ivan V, Vorontsov, Ilya E, Fridman, Marina V, Makeev, Vsevolod J, Kuprash, Dmitry V, Schwartz, Anton M
Published in PloS one (24.02.2017)
Published in PloS one (24.02.2017)
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What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants
Penzar, Dmitry D., Zinkevich, Arsenii O., Vorontsov, Ilya E., Sitnik, Vasily V., Favorov, Alexander V., Makeev, Vsevolod J., Kulakovskiy, Ivan V.
Published in Frontiers in genetics (31.10.2019)
Published in Frontiers in genetics (31.10.2019)
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Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data
Vorontsov, Ilya E, Fedorova, Alla D, Yevshin, Ivan S, Sharipov, Ruslan N, Kolpakov, Fedor A, Makeev, Vsevolod J, Kulakovskiy, Ivan V
Published in BMC research notes (23.10.2018)
Published in BMC research notes (23.10.2018)
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HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors
Vorontsov, Ilya E, Eliseeva, Irina A, Zinkevich, Arsenii, Nikonov, Mikhail, Abramov, Sergey, Boytsov, Alexandr, Kamenets, Vasily, Kasianova, Alexandra, Kolmykov, Semyon, Yevshin, Ivan S, Favorov, Alexander, Medvedeva, Yulia A, Jolma, Arttu, Kolpakov, Fedor, Makeev, Vsevolod J, Kulakovskiy, Ivan V
Published in Nucleic acids research (05.01.2024)
Published in Nucleic acids research (05.01.2024)
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Journal Article
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes
Marakulina, Daria, Vorontsov, Ilya E, Kulakovskiy, Ivan V, Lennartsson, Andreas, Drabløs, Finn, Medvedeva, Yulia A
Published in Nucleic acids research (06.01.2023)
Published in Nucleic acids research (06.01.2023)
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Journal Article
Enhanced C/EBP binding to G·T mismatches facilitates fixation of CpG mutations in cancer and adult stem cells
Ershova, Anna S., Eliseeva, Irina A., Nikonov, Oleg S., Fedorova, Alla D., Vorontsov, Ilya E., Papatsenko, Dmitry, Kulakovskiy, Ivan V.
Published in Cell reports (Cambridge) (08.06.2021)
Published in Cell reports (Cambridge) (08.06.2021)
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Journal Article
Assessing Ribosome Distribution Along Transcripts with Polarity Scores and Regression Slope Estimates
Vorontsov, Ilya E, Egorov, Artyom A, Anisimova, Aleksandra S, Eliseeva, Irina A, Makeev, Vsevolod J, Gladyshev, Vadim N, Dmitriev, Sergey E, Kulakovskiy, Ivan V
Published in Methods in molecular biology (Clifton, N.J.) (2021)
Published in Methods in molecular biology (Clifton, N.J.) (2021)
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Journal Article
Jaccard index based similarity measure to compare transcription factor binding site models
Vorontsov, Ilya E, Kulakovskiy, Ivan V, Makeev, Vsevolod J
Published in Algorithms for molecular biology (30.09.2013)
Published in Algorithms for molecular biology (30.09.2013)
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Journal Article
Early B-cell factor 1 (EBF1) is critical for transcriptional control of SLAMF1 gene in human B cells
Schwartz, Anton M., Putlyaeva, Lidia V., Covich, Milica, Klepikova, Anna V., Akulich, Kseniya A., Vorontsov, Ilya E., Korneev, Kirill V., Dmitriev, Sergey E., Polanovsky, Oleg L., Sidorenko, Svetlana P., Kulakovskiy, Ivan V., Kuprash, Dmitry V.
Published in Biochimica et biophysica acta (01.10.2016)
Published in Biochimica et biophysica acta (01.10.2016)
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