HOCOMOCO: a comprehensive collection of human transcription factor binding sites models von Kulakovskiy, Ivan V., Medvedeva, Yulia A., Schaefer, Ulf, Kasianov, Artem S., Vorontsov, Ilya E., Bajic, Vladimir B., Makeev, Vsevolod J.

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GTRD: an integrated view of transcription regulation von Kolmykov, Semyon, Yevshin, Ivan, Kulyashov, Mikhail, Sharipov, Ruslan, Kondrakhin, Yury, Makeev, Vsevolod J, Kulakovskiy, Ivan V, Kel, Alexander, Kolpakov, Fedor

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HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis von 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

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HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models von 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

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HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors von 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

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Landscape of allele-specific transcription factor binding in the human genome von 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.

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Exploring massive, genome scale datasets with the GenometriCorr package von Favorov, Alexander, Mularoni, Loris, Cope, Leslie M, Medvedeva, Yulia, Mironov, Andrey A, Makeev, Vsevolod J, Wheelan, Sarah J

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De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum) von Logacheva, Maria D, Kasianov, Artem S, Vinogradov, Dmitriy V, Samigullin, Tagir H, Gelfand, Mikhail S, Makeev, Vsevolod J, Penin, Aleksey A

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Zebrafish pigment cells develop directly from persistent highly multipotent progenitors von 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.

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ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs von 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

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A new cancer/testis long noncoding RNA, the OTP-AS1 RNA von Karnaukhova, Iuliia K., Polev, Dmitrii E., Krukovskaya, Larisa L., Makashov, Andrei A., Masharsky, Alexey E., Nazarenko, Olga V., Poverennaya, Irina V., Makeev, Vsevolod J., Akulova, Ekaterina B., Kozlov, Andrei P.

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Assessing computational tools for the discovery of transcription factor binding sites von 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

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A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease von 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

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Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal von Papatsenko, Dmitri, Darr, Henia, Kulakovskiy, Ivan V., Waghray, Avinash, Makeev, Vsevolod J., MacArthur, Ben D., Lemischka, Ihor R.

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Positional weight matrices have sufficient prediction power for analysis of noncoding variants [version 1; peer review: 2 approved with reservations] von Boytsov, Alexandr, Abramov, Sergey, Makeev, Vsevolod J, Kulakovskiy, Ivan V

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The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region von 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

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Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance von 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

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What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants von Penzar, Dmitry D., Zinkevich, Arsenii O., Vorontsov, Ilya E., Sitnik, Vasily V., Favorov, Alexander V., Makeev, Vsevolod J., Kulakovskiy, Ivan V.

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Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data von Vorontsov, Ilya E, Fedorova, Alla D, Yevshin, Ivan S, Sharipov, Ruslan N, Kolpakov, Fedor A, Makeev, Vsevolod J, Kulakovskiy, Ivan V

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HOCOMOCO: a comprehensive collection of human transcription factor binding sites models von Kulakovskiy, Ivan V, Medvedeva, Yulia A, Schaefer, Ulf, Kasianov, Artem S, Vorontsov, Ilya E, Bajic, Vladimir B, Makeev, Vsevolod J

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