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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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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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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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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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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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
Subkhankulova, Tatiana, Camargo Sosa, Karen, Uroshlev, Leonid A., Nikaido, Masataka, Shriever, Noah, Kasianov, Artem S., Yang, Xueyan, Rodrigues, Frederico S. L. M., Carney, Thomas J., Bavister, Gemma, Schwetlick, Hartmut, Dawes, Jonathan H. P., Rocco, Andrea, Makeev, Vsevolod J., Kelsh, Robert N.
Published in Nature communications (06.03.2023)
Published in Nature communications (06.03.2023)
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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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Annotation of nuclear lncRNAs based on chromatin interactions
Agrawal, Saumya, Buyan, Andrey, Severin, Jessica, Koido, Masaru, Alam, Tanvir, Abugessaisa, Imad, Chang, Howard Y, Dostie, Josée, Itoh, Masayoshi, Kere, Juha, Kondo, Naoto, Li, Yunjing, Makeev, Vsevolod J, Mendez, Mickaël, Okazaki, Yasushi, Ramilowski, Jordan A, Sigorskikh, Andrey I, Strug, Lisa J, Yagi, Ken, Yasuzawa, Kayoko, Yip, Chi Wai, Hon, Chung Chau, Hoffman, Michael M, Terao, Chikashi, Kulakovskiy, Ivan V, Kasukawa, Takeya, Shin, Jay W, Carninci, Piero, de Hoon, Michiel J L
Published in PloS one (06.05.2024)
Published in PloS one (06.05.2024)
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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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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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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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Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal
Papatsenko, Dmitri, Darr, Henia, Kulakovskiy, Ivan V., Waghray, Avinash, Makeev, Vsevolod J., MacArthur, Ben D., Lemischka, Ihor R.
Published in Stem cell reports (11.08.2015)
Published in Stem cell reports (11.08.2015)
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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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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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Use of Primary Macrophages for Searching Novel Immunocorrectors
Nikiforov, Nikita G, Elizova, Natalia V, Bukrinsky, Michael, Dubrovsky, Larisa, Makeev, Vsevolod J, Wakabayashi, Yoshiyuki, Liu, Poching, Foxx, Kathy K, Kruth, Howard S, Jin, Xueting, Zakiev, Emile R, Orekhov, Alexander N
Published in Current pharmaceutical design (01.01.2017)
Published in Current pharmaceutical design (01.01.2017)
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Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance
Odintsova, Tatyana I, Slezina, Marina P, Istomina, Ekaterina A, Korostyleva, Tatyana V, Kasianov, Artem S, Kovtun, Alexey S, Makeev, Vsevolod J, Shcherbakova, Larisa A, Kudryavtsev, Alexander M
Published in PeerJ (San Francisco, CA) (08.01.2019)
Published in PeerJ (San Francisco, CA) (08.01.2019)
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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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