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Cell-type specialization is encoded by specific chromatin topologies.
Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, Musella F, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Welch L, Castelo-Branco G, Pombo A. Winick-Ng W, et al. Among authors: kukalev a. Nature. 2021 Nov;599(7886):684-691. doi: 10.1038/s41586-021-04081-2. Epub 2021 Nov 17. Nature. 2021. PMID: 34789882 Free PMC article.
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
Fiorillo L, Musella F, Conte M, Kempfer R, Chiariello AM, Bianco S, Kukalev A, Irastorza-Azcarate I, Esposito A, Abraham A, Prisco A, Pombo A, Nicodemi M. Fiorillo L, et al. Among authors: kukalev a. Nat Methods. 2021 May;18(5):482-490. doi: 10.1038/s41592-021-01135-1. Epub 2021 May 7. Nat Methods. 2021. PMID: 33963348 Free PMC article.
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC; FANTOM consortium; Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH. Grapotte M, et al. Nat Commun. 2021 Jun 2;12(1):3297. doi: 10.1038/s41467-021-23143-7. Nat Commun. 2021. PMID: 34078885 Free PMC article.
SRRM2 splicing factor modulates cell fate in early development.
Carvalho S, Zea-Redondo L, Tang TCC, Stachel-Braum P, Miller D, Caldas P, Kukalev A, Diecke S, Grosswendt S, Grosso AR, Pombo A. Carvalho S, et al. Among authors: kukalev a. Biol Open. 2024 Apr 15;13(4):bio060415. doi: 10.1242/bio.060415. Epub 2024 Apr 24. Biol Open. 2024. PMID: 38656788 Free PMC article.
28 results