GTRD: an integrated view of transcription regulation
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Published in Nucleic acids research (08.01.2021)
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HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
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Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index
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Published in BMC bioinformatics (13.07.2024)
Published in BMC bioinformatics (13.07.2024)
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HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors
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Published in Nucleic acids research (05.01.2024)
Published in Nucleic acids research (05.01.2024)
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Exploring massive, genome scale datasets with the GenometriCorr package
Favorov, Alexander, Mularoni, Loris, Cope, Leslie M, Medvedeva, Yulia, Mironov, Andrey A, Makeev, Vsevolod J, Wheelan, Sarah J
Published in PLoS computational biology (01.05.2012)
Published in PLoS computational biology (01.05.2012)
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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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De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)
Logacheva, Maria D, Kasianov, Artem S, Vinogradov, Dmitriy V, Samigullin, Tagir H, Gelfand, Mikhail S, Makeev, Vsevolod J, Penin, Aleksey A
Published in BMC genomics (13.01.2011)
Published in BMC genomics (13.01.2011)
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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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Correction: Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index
Guguchkin, Egor, Kasianov, Artem, Belenikin, Maksim, Zobkova, Gaukhar, Kosova, Ekaterina, Makeev, Vsevolod, Karpulevich, Evgeny
Published in BMC bioinformatics (19.08.2024)
Published in BMC bioinformatics (19.08.2024)
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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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Zebrafish pigment cells develop directly from persistent highly multipotent progenitors
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Published in Nature communications (06.03.2023)
Published in Nature communications (06.03.2023)
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Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study
Ambrosini, Giovanna, Vorontsov, Ilya, Penzar, Dmitry, Groux, Romain, Fornes, Oriol, Nikolaeva, Daria D, Ballester, Benoit, Grau, Jan, Grosse, Ivo, Makeev, Vsevolod, Kulakovskiy, Ivan, Bucher, Philipp
Published in Genome Biology (11.05.2020)
Published in Genome Biology (11.05.2020)
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Annotation of nuclear lncRNAs based on chromatin interactions
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Published in PloS one (06.05.2024)
Published in PloS one (06.05.2024)
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Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis
Orekhov, Alexander N, Oishi, Yumiko, Nikiforov, Nikita G, Zhelankin, Andrey V, Dubrovsky, Larisa, Sobenin, Igor A, Kel, Alexander, Stelmashenko, Daria, Makeev, Vsevolod J, Foxx, Kathy, Jin, Xueting, Kruth, Howard S, Bukrinsky, Michael
Published in Current pharmaceutical design (01.01.2018)
Published in Current pharmaceutical design (01.01.2018)
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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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Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response-What is First?
Orekhov, Alexander N, Sukhorukov, Vasily N, Nikiforov, Nikita G, Kubekina, Marina V, Sobenin, Igor A, Foxx, Kathy K, Pintus, Sergey, Stegmaier, Philip, Stelmashenko, Daria, Kel, Alexander, Poznyak, Anastasia V, Wu, Wei-Kai, Kasianov, Artem S, Makeev, Vsevolod Y, Manabe, Ichiro, Oishi, Yumiko
Published in International journal of molecular sciences (14.04.2020)
Published in International journal of molecular sciences (14.04.2020)
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Assessing computational tools for the discovery of transcription factor binding sites
Eskin, Eleazar, Ye, Chun, Mironov, Andrei A, Fu, Yutao, Favorov, Alexander V, Pavesi, Giulio, Li, Nan, Pesole, Graziano, Vandenbogaert, Mathias, Noble, William Stafford, Weng, Zhiping, Régnier, Mireille, Sinha, Saurabh, Makeev, Vsevolod J, Kent, W James, De Moor, Bart, Simonis, Nicolas, Zhu, Zhou, Thijs, Gert, Bailey, Timothy L, Frith, Martin C, Workman, Christopher, Church, George M, Tompa, Martin, van Helden, Jacques
Published in Nature biotechnology (01.01.2005)
Published in Nature biotechnology (01.01.2005)
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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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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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