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Diverse Regulation of YB-1 and YB-3 Abundance in Mammals.
Published in:
Biochemistry (00062979), 2022, v. 87, n. 1, p. S48, doi. 10.1134/S000629792214005X
By:
- Eliseeva, Irina A.;
- Sogorina, Ekaterina M.;
- Smolin, Egor A.;
- Kulakovskiy, Ivan V.;
- Lyabin, Dmitry N.
Publication type:
Article
Human Tissues Exhibit Diverse Composition of Translation Machinery.
Published in:
International Journal of Molecular Sciences, 2023, v. 24, n. 9, p. 8361, doi. 10.3390/ijms24098361
By:
- Anisimova, Aleksandra S.;
- Kolyupanova, Natalia M.;
- Makarova, Nadezhda E.;
- Egorov, Artyom A.;
- Kulakovskiy, Ivan V.;
- Dmitriev, Sergey E.
Publication type:
Article
A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease.
Published in:
BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-07109-5
By:
- 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
Publication type:
Article
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
Published in:
Nucleic Acids Research, 2018, v. 46, n. D1, p. D252, doi. 10.1093/nar/gkx1106
By:
- 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
Publication type:
Article
Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 15, p. 7228, doi. 10.1093/nar/gkw371
By:
- Zolotarev, Nikolay;
- Fedotova, Anna;
- Kyrchanova, Olga;
- Bonchuk, Artem;
- Penin, Aleksey A.;
- Lando, Andrey S.;
- Eliseeva, Irina A.;
- Kulakovskiy, Ivan V.;
- Maksimenko, Oksana;
- Georgiev, Pavel
Publication type:
Article
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 1, p. D116, doi. 10.1093/nar/gkv1249
By:
- 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.
Publication type:
Article
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models.
Published in:
Nucleic Acids Research, 2013, v. 41, p. D195, doi. 10.1093/nar/gks1089
By:
- Kulakovskiy, Ivan V.;
- Medvedeva, Yulia A.;
- Schaefer, Ulf;
- Kasianov, Artem S.;
- Vorontsov, Ilya E.;
- Bajic, Vladimir B.;
- Makeev, Vsevolod J.
Publication type:
Article
Landscape of allele-specific transcription factor binding in the human genome.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23007-0
By:
- 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.
Publication type:
Article
An update to database TraVA: organ-specific cold stress response in Arabidopsis thaliana.
Published in:
BMC Plant Biology, 2019, v. 19, n. 1, p. N.PAG, doi. 10.1186/s12870-019-1636-y
By:
- Klepikova, Anna V.;
- Kulakovskiy, Ivan V.;
- Kasianov, Artem S.;
- Logacheva, Maria D.;
- Penin, Aleksey A.
Publication type:
Article
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus.
Published in:
BMC Evolutionary Biology, 2017, v. 17, p. 5, doi. 10.1186/s12862-017-1103-z
By:
- Moskalev, Alexey A.;
- Kudryavtseva, Anna V.;
- Graphodatsky, Alexander S.;
- Beklemisheva, Violetta R.;
- Serdyukova, Natalya A.;
- Krutovsky, Konstantin V.;
- Sharov, Vadim V.;
- Kulakovskiy, Ivan V.;
- Lando, Andrey S.;
- Kasianov, Artem S.;
- Kuzmin, Dmitry A.;
- Putintseva, Yuliya A.;
- Feranchuk, Sergey I.;
- Shaposhnikov, Mikhail V.;
- Fraifeld, Vadim E.;
- Toren, Dmitri;
- Snezhkina, Anastasia V.;
- Sitnik, Vasily V.
Publication type:
Article
LegNet: a best-in-class deep learning model for short DNA regulatory regions.
Published in:
Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad457
By:
- Penzar, Dmitry;
- Nogina, Daria;
- Noskova, Elizaveta;
- Zinkevich, Arsenii;
- Meshcheryakov, Georgy;
- Lando, Andrey;
- Rafi, Abdul Muntakim;
- Boer, Carl de;
- Kulakovskiy, Ivan V
Publication type:
Article
High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution.
Published in:
Plant Journal, 2017, v. 91, n. 2, p. 278, doi. 10.1111/tpj.13563
By:
- Kasianov, Artem S.;
- Klepikova, Anna V.;
- Kulakovskiy, Ivan V.;
- Gerasimov, Evgeny S.;
- Fedotova, Anna V.;
- Besedina, Elizaveta G.;
- Kondrashov, Alexey S.;
- Logacheva, Maria D.;
- Penin, Aleksey A.
Publication type:
Article
Alternative Forms of Y-Box Binding Protein 1 and <i>YB-1</i> mRNA.
Published in:
PLoS ONE, 2014, v. 9, n. 8, p. 1, doi. 10.1371/journal.pone.0104513
By:
- Lyabin, Dmitry N.;
- Doronin, Alexander N.;
- Eliseeva, Irina A.;
- Guens, Gelena P.;
- Kulakovskiy, Ivan V.;
- Ovchinnikov, Lev P.
Publication type:
Article
Negative selection maintains transcription factor binding motifs in human cancer.
Published in:
BMC Genomics, 2016, v. 17, p. 263, doi. 10.1186/s12864-016-2728-9
By:
- Vorontsov, Ilya E.;
- Khimulya, Grigory;
- Lukianova, Elena N.;
- Nikolaeva, Daria D.;
- Eliseeva, Irina A.;
- Kulakovskiy, Ivan V.;
- Makeev, Vsevolod J.
Publication type:
Article
Analysis of functional importance of binding sites in the Drosophila gap gene network model.
Published in:
BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/1471-2164-16-S13-S7
By:
- Kozlov, Konstantin;
- Gursky, Vitaly V.;
- Kulakovskiy, Ivan V.;
- Dymova, Arina;
- Samsonova, Maria
Publication type:
Article
EpiFactors: a comprehensive database of human epigenetic factors and complexes.
Published in:
Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav067
By:
- Medvedeva, Yulia A.;
- Lennartsson, Andreas;
- Ehsani, Rezvan;
- Kulakovskiy, Ivan V.;
- Vorontsov, Ilya E.;
- Panahandeh, Pouda;
- Khimulya, Grigory;
- Takeya Kasukawa;
- Drabløs, Finn
Publication type:
Article
Brain-related genes are specifically enriched with long phase 1 introns.
Published in:
PLoS ONE, 2020, v. 15, n. 5, p. 1, doi. 10.1371/journal.pone.0233978
By:
- Baulin, Eugene F.;
- Kulakovskiy, Ivan V.;
- Roytberg, Mikhail A.;
- Astakhova, Tatiana V.
Publication type:
Article
VTC4 Polyphosphate Polymerase Knockout Increases Stress Resistance of Saccharomyces cerevisiae Cells.
Published in:
Biology (2079-7737), 2021, v. 10, n. 6, p. 487, doi. 10.3390/biology10060487
By:
- Tomashevsky, Alexander;
- Kulakovskaya, Ekaterina;
- Trilisenko, Ludmila;
- Kulakovskiy, Ivan V.;
- Kulakovskaya, Tatiana;
- Fedorov, Alexey;
- Eldarov, Mikhail
Publication type:
Article
The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region.
Published in:
PLoS ONE, 2017, v. 12, n. 2, p. 1, doi. 10.1371/journal.pone.0172681
By:
- 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.
Publication type:
Article
The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae.
Published in:
Cells (2073-4409), 2019, v. 8, n. 5, p. 461, doi. 10.3390/cells8050461
By:
- Trilisenko, Ludmila;
- Zvonarev, Anton;
- Valiakhmetov, Airat;
- Penin, Alexey A.;
- Eliseeva, Irina A.;
- Ostroumov, Vladimir;
- Kulakovskiy, Ivan V.;
- Kulakovskaya, Tatiana
Publication type:
Article
HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.
Published in:
Nucleic Acids Research, 2024, v. 52, n. D1, p. D154, doi. 10.1093/nar/gkad1077
By:
- 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
Publication type:
Article
Crol contributes to PRE-mediated repression and Polycomb group proteins recruitment in Drosophila.
Published in:
Nucleic Acids Research, 2023, v. 51, n. 12, p. 6087, doi. 10.1093/nar/gkad336
By:
- Erokhin, Maksim;
- Brown, J Lesley;
- Lomaev, Dmitry;
- Vorobyeva, Nadezhda E;
- Zhang, Liangliang;
- Fab, Lika V;
- Mazina, Marina Yu;
- Kulakovskiy, Ivan V;
- Ziganshin, Rustam H;
- Schedl, Paul;
- Georgiev, Pavel;
- Sun, Ming-an;
- Kassis, Judith A;
- Chetverina, Darya
Publication type:
Article
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes.
Published in:
Nucleic Acids Research, 2023, v. 51, n. D1, p. D564, doi. 10.1093/nar/gkac989
By:
- Marakulina, Daria;
- Vorontsov, Ilya E;
- Kulakovskiy, Ivan V;
- Lennartsson, Andreas;
- Drabløs, Finn;
- Medvedeva, Yulia A
Publication type:
Article
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.
Published in:
Nucleic Acids Research, 2022, v. 50, n. W1, p. W51, doi. 10.1093/nar/gkac262
By:
- 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
Publication type:
Article
Ribosomal leaky scanning through a translated uORF requires eIF4G2.
Published in:
Nucleic Acids Research, 2022, v. 50, n. 2, p. 1111, doi. 10.1093/nar/gkab1286
By:
- Smirnova, Victoria V;
- Shestakova, Ekaterina D;
- Nogina, Daria S;
- Mishchenko, Polina A;
- Prikazchikova, Tatiana A;
- Zatsepin, Timofei S;
- Kulakovskiy, Ivan V;
- Shatsky, Ivan N;
- Terenin, Ilya M
Publication type:
Article
standard knockout procedure alters expression of adjacent loci at the translational level.
Published in:
Nucleic Acids Research, 2021, v. 49, n. 19, p. 11134, doi. 10.1093/nar/gkab872
By:
- Egorov, Artyom A;
- Alexandrov, Alexander I;
- Urakov, Valery N;
- Makeeva, Desislava S;
- Edakin, Roman O;
- Kushchenko, Artem S;
- Gladyshev, Vadim N;
- Kulakovskiy, Ivan V;
- Dmitriev, Sergey E
Publication type:
Article
GTRD: an integrated view of transcription regulation.
Published in:
Nucleic Acids Research, 2021, v. 49, n. D1, p. D104, doi. 10.1093/nar/gkaa1057
By:
- Kolmykov, Semyon;
- Yevshin, Ivan;
- Kulyashov, Mikhail;
- Sharipov, Ruslan;
- Kondrakhin, Yury;
- Makeev, Vsevolod J;
- Kulakovskiy, Ivan V;
- Kel, Alexander;
- Kolpakov, Fedor
Publication type:
Article
CpG traffic lights are markers of regulatory regions in human genome.
Published in:
BMC Genomics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12864-018-5387-1
By:
- Lioznova, Anna V.;
- Khamis, Abdullah M.;
- Artemov, Artem V.;
- Besedina, Elizaveta;
- Ramensky, Vasily;
- Bajic, Vladimir B.;
- Kulakovskiy, Ivan V.;
- Medvedeva, Yulia A.
Publication type:
Article
svist4get: a simple visualization tool for genomic tracks from sequencing experiments.
Published in:
BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2706-8
By:
- Egorov, Artyom A.;
- Sakharova, Ekaterina A.;
- Anisimova, Aleksandra S.;
- Dmitriev, Sergey E.;
- Gladyshev, Vadim N.;
- Kulakovskiy, Ivan V.
Publication type:
Article
Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.
Published in:
Human Mutation, 2019, v. 40, n. 9, p. 1280, doi. 10.1002/humu.23797
By:
- Shigaki, Dustin;
- Adato, Orit;
- Adhikari, Aashish N.;
- Dong, Shengcheng;
- Hawkins‐Hooker, Alex;
- Inoue, Fumitaka;
- Juven‐Gershon, Tamar;
- Kenlay, Henry;
- Martin, Beth;
- Patra, Ayoti;
- Penzar, Dmitry D.;
- Schubach, Max;
- Xiong, Chenling;
- Yan, Zhongxia;
- Boyle, Alan P.;
- Kreimer, Anat;
- Kulakovskiy, Ivan V.;
- Reid, John;
- Unger, Ron;
- Yosef, Nir
Publication type:
Article
Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data.
Published in:
BMC Research Notes, 2018, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13104-018-3856-x
By:
- Vorontsov, Ilya E.;
- Fedorova, Alla D.;
- Yevshin, Ivan S.;
- Sharipov, Ruslan N.;
- Kolpakov, Fedor A.;
- Makeev, Vsevolod J.;
- Kulakovskiy, Ivan V.
Publication type:
Article
Y-Box-Binding Proteins Have a Dual Impact on Cellular Translation.
Published in:
International Journal of Molecular Sciences, 2024, v. 25, n. 3, p. 1736, doi. 10.3390/ijms25031736
By:
- Eliseeva, Irina A.;
- Buyan, Andrey I.;
- Smolin, Egor A.;
- Kaliadzenka, Karina S.;
- Popov, Sergey;
- Kulakovskiy, Ivan V.;
- Lyabin, Dmitry N.
Publication type:
Article
rs71327024 Associated with COVID-19 Hospitalization Reduces CXCR6 Promoter Activity in Human CD4 + T Cells via Disruption of c-Myb Binding.
Published in:
International Journal of Molecular Sciences, 2023, v. 24, n. 18, p. 13790, doi. 10.3390/ijms241813790
By:
- Uvarova, Aksinya N.;
- Stasevich, Ekaterina M.;
- Ustiugova, Alina S.;
- Mitkin, Nikita A.;
- Zheremyan, Elina A.;
- Sheetikov, Savely A.;
- Zornikova, Ksenia V.;
- Bogolyubova, Apollinariya V.;
- Rubtsov, Mikhail A.;
- Kulakovskiy, Ivan V.;
- Kuprash, Dmitry V.;
- Korneev, Kirill V.;
- Schwartz, Anton M.
Publication type:
Article
Effects of cytosine methylation on transcription factor binding sites.
Published in:
BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-119
By:
- Medvedeva, Yulia A.;
- Khamis, Abdullah M.;
- Kulakovskiy, Ivan V.;
- Wail Ba-Alawi;
- Bhuyan, Md Shariful I.;
- Kawaji, Hideya;
- Lassmann, Timo;
- Harbers, Matthias;
- Forrest, Alistair R. R.;
- Bajic, Vladimir B.
Publication type:
Article
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data.
Published in:
BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-80
By:
- Levitsky, Victor G.;
- Kulakovskiy, Ivan V.;
- Ershov, Nikita I.;
- Yu Oschepkov, Dmitry;
- Makeev, Vsevolod J.;
- Hodgman, T. C.;
- Merkulova, Tatyana I.
Publication type:
Article
Intergenic, gene terminal, and intragenic CpG islands in the human genome.
Published in:
BMC Genomics, 2010, v. 11, p. 1, doi. 10.1186/1471-2164-11-48
By:
- Medvedeva, Yulia A;
- Fridman, Marina V;
- Oparina, Nina J;
- Malko, Dmitry B;
- Ermakova, Ekaterina O;
- Kulakovskiy, Ivan V;
- Heinzel, Andreas;
- Makeev, Vsevolod J
Publication type:
Article
Motif discovery and motif finding from genome-mapped DNase footprint data.
Published in:
Bioinformatics, 2009, v. 25, n. 18, p. 2318, doi. 10.1093/bioinformatics/btp434
By:
- Kulakovskiy, Ivan V.;
- Favorov, Alexander V.;
- Makeev, Vsevolod J.
Publication type:
Article
Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network.
Published in:
PLoS ONE, 2017, v. 12, n. 9, p. 1, doi. 10.1371/journal.pone.0184657
By:
- Gursky, Vitaly V.;
- Kozlov, Konstantin N.;
- Kulakovskiy, Ivan V.;
- Zubair, Asif;
- Marjoram, Paul;
- Lawrie, David S.;
- Nuzhdin, Sergey V.;
- Samsonova, Maria G.
Publication type:
Article

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