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Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells.
Published in:
BMC Biology, 2020, v. 18, n. 1, p. 1, doi. 10.1186/s12915-020-0752-3
By:
- Dunican, Donnchadh S.;
- Mjoseng, Heidi K.;
- Duthie, Leanne;
- Flyamer, Ilya M.;
- Bickmore, Wendy A.;
- Meehan, Richard R.
Publication type:
Article
Nuclear organisation and replication timing are coupled through RIF1–PP1 interaction.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22899-2
By:
- Gnan, Stefano;
- Flyamer, Ilya M.;
- Klein, Kyle N.;
- Castelli, Eleonora;
- Rapp, Alexander;
- Maiser, Andreas;
- Chen, Naiming;
- Weber, Patrick;
- Enervald, Elin;
- Cardoso, M. Cristina;
- Bickmore, Wendy A.;
- Gilbert, David M.;
- Buonomo, Sara C. B.
Publication type:
Article
Bioframe: operations on genomic intervals in Pandas dataframes.
Published in:
Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae088
By:
- Abdennur, Nezar;
- Fudenberg, Geoffrey;
- Flyamer, Ilya M;
- Galitsyna, Aleksandra A;
- Goloborodko, Anton;
- Imakaev, Maxim;
- Venev, Sergey
Publication type:
Article
Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-09185-y
By:
- Ulianov, Sergey V.;
- Doronin, Semen A.;
- Khrameeva, Ekaterina E.;
- Kos, Pavel I.;
- Luzhin, Artem V.;
- Starikov, Sergei S.;
- Galitsyna, Aleksandra A.;
- Nenasheva, Valentina V.;
- Ilyin, Artem A.;
- Flyamer, Ilya M.;
- Mikhaleva, Elena A.;
- Logacheva, Mariya D.;
- Gelfand, Mikhail S.;
- Chertovich, Alexander V.;
- Gavrilov, Alexey A.;
- Razin, Sergey V.;
- Shevelyov, Yuri Y.
Publication type:
Article
A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.
Published in:
EMBO Journal, 2017, v. 36, n. 24, p. 3600, doi. 10.15252/embj.201798083
By:
- Gassler, Johanna;
- Brandão, Hugo B;
- Imakaev, Maxim;
- Flyamer, Ilya M;
- Ladstätter, Sabrina;
- Bickmore, Wendy A;
- Peters, Jan‐Michael;
- Mirny, Leonid A;
- Tachibana, Kikuë
Publication type:
Article
Evolution of the Genome 3D Organization: Comparison of Fused and Segregated Globin Gene Clusters.
Published in:
Molecular Biology & Evolution, 2017, v. 34, n. 6, p. 1492, doi. 10.1093/molbev/msx100
By:
- Kovina, Anastasia P.;
- Petrova, Natalia V.;
- Gushchanskaya, Ekaterina S.;
- Dolgushin, Konstantin V.;
- Gerasimov, Evgeny S.;
- Galitsyna, Aleksandra A.;
- Penin, Alexey A.;
- Flyamer, Ilya M.;
- Ioudinkova, Elena S.;
- Gavrilov, Alexey A.;
- Vassetzky, Yegor S.;
- Ulianov, Sergey V.;
- Iarovaia, Olga V.;
- Razin, Sergey V.
Publication type:
Article
Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure.
Published in:
Epigenetics & Chromatin, 2017, v. 10, p. 1, doi. 10.1186/s13072-017-0142-4
By:
- Ulianov, Sergey V.;
- Galitsyna, Aleksandra A.;
- Flyamer, Ilya M.;
- Golov, Arkadiy K.;
- Khrameeva, Ekaterina E.;
- Imakaev, Maxim V.;
- Abdennur, Nezar A.;
- Gelfand, Mikhail S.;
- Gavrilov, Alexey A.;
- Razin, Sergey V.
Publication type:
Article
Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity.
Published in:
PLoS Genetics, 2024, v. 20, n. 5, p. 1, doi. 10.1371/journal.pgen.1011277
By:
- Gómez Acuña, Luciana I.;
- Flyamer, Ilya;
- Boyle, Shelagh;
- Friman, Elias T.;
- Bickmore, Wendy A.
Publication type:
Article
Quantitative differences in TAD border strength underly the TAD hierarchy in Drosophila chromosomes.
Published in:
Journal of Cellular Biochemistry, 2019, v. 120, n. 3, p. 4494, doi. 10.1002/jcb.27737
By:
- Luzhin, Artem V.;
- Flyamer, Ilya M.;
- Khrameeva, Ekaterina E.;
- Ulianov, Sergey V.;
- Razin, Sergey V.;
- Gavrilov, Alexey A.
Publication type:
Article
Low Level of Expression of C-Terminally Truncated Human FUS Causes Extensive Changes in the Spinal Cord Transcriptome of Asymptomatic Transgenic Mice.
Published in:
Neurochemical Research, 2020, v. 45, n. 5, p. 1168, doi. 10.1007/s11064-020-02999-z
By:
- Lysikova, Ekaterina A.;
- Funikov, Sergei;
- Rezvykh, Alexander P.;
- Chaprov, Kirill D.;
- Kukharsky, Michail S.;
- Ustyugov, Aleksey;
- Deykin, Alexey V.;
- Flyamer, Ilya M.;
- Boyle, Shelagh;
- Bachurin, Sergey O.;
- Ninkina, Natalia;
- Buchman, Vladimir L.
Publication type:
Article
Cooltools: Enabling high-resolution Hi-C analysis in Python.
Published in:
PLoS Computational Biology, 2024, v. 20, n. 5, p. 1, doi. 10.1371/journal.pcbi.1012067
By:
- Abdennur, Nezar;
- Abraham, Sameer;
- Fudenberg, Geoffrey;
- Flyamer, Ilya M.;
- Galitsyna, Aleksandra A.;
- Goloborodko, Anton;
- Imakaev, Maxim;
- Oksuz, Betul A.;
- Venev, Sergey V.;
- Xiao, Yao
Publication type:
Article
Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters.
Published in:
Cells (2073-4409), 2023, v. 12, n. 15, p. 2001, doi. 10.3390/cells12152001
By:
- Stefanova, Maria E.;
- Ing-Simmons, Elizabeth;
- Stefanov, Stefan;
- Flyamer, Ilya;
- Dorado Garcia, Heathcliff;
- Schöpflin, Robert;
- Henssen, Anton G.;
- Vaquerizas, Juan M.;
- Mundlos, Stefan
Publication type:
Article
Pairtools: From sequencing data to chromosome contacts.
Published in:
PLoS Computational Biology, 2024, v. 20, n. 5, p. 1, doi. 10.1371/journal.pcbi.1012164
By:
- Abdennur, Nezar;
- Fudenberg, Geoffrey;
- Flyamer, Ilya M.;
- Galitsyna, Aleksandra A.;
- Goloborodko, Anton;
- Imakaev, Maxim;
- Venev, Sergey V.
Publication type:
Article
Trisomies Reorganize Human 3D Genome.
Published in:
International Journal of Molecular Sciences, 2023, v. 24, n. 22, p. 16044, doi. 10.3390/ijms242216044
By:
- Zhegalova, Irina V.;
- Vasiluev, Petr A.;
- Flyamer, Ilya M.;
- Shtompel, Anastasia S.;
- Glazyrina, Eugene;
- Shilova, Nadezda;
- Minzhenkova, Marina;
- Markova, Zhanna;
- Petrova, Natalia V.;
- Dashinimaev, Erdem B.;
- Razin, Sergey V.;
- Ulianov, Sergey V.
Publication type:
Article
Coolpup.py: versatile pile-up analysis of Hi-C data.
Published in:
Bioinformatics, 2020, v. 36, n. 10, p. 2980, doi. 10.1093/bioinformatics/btaa073
By:
- Flyamer, Ilya M;
- Illingworth, Robert S;
- Bickmore, Wendy A
Publication type:
Article
Order and stochasticity in the folding of individual Drosophila genomes.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-020-20292-z
By:
- Ulianov, Sergey V.;
- Zakharova, Vlada V.;
- Galitsyna, Aleksandra A.;
- Kos, Pavel I.;
- Polovnikov, Kirill E.;
- Flyamer, Ilya M.;
- Mikhaleva, Elena A.;
- Khrameeva, Ekaterina E.;
- Germini, Diego;
- Logacheva, Mariya D.;
- Gavrilov, Alexey A.;
- Gorsky, Alexander S.;
- Nechaev, Sergey K.;
- Gelfand, Mikhail S.;
- Vassetzky, Yegor S.;
- Chertovich, Alexander V.;
- Shevelyov, Yuri Y.;
- Razin, Sergey V.
Publication type:
Article

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