Pesquisa | BVS Doenças Infecciosas e Parasitárias

1.

The role of insulators and transcription in 3D chromatin organization of flies.

Chathoth, Keerthi T; Mikheeva, Liudmila A; Crevel, Gilles; Wolfe, Jareth C; Hunter, Ioni; Beckett-Doyle, Saskia; Cotterill, Sue; Dai, Hongsheng; Harrison, Andrew; Zabet, Nicolae Radu.

Genome Res ; 32(4): 682-698, 2022 04.

Artigo em Inglês | MEDLINE | ID: mdl-35354608

2.

Identification of mammalian transcription factors that bind to inaccessible chromatin.

Pop, Romana T; Pisante, Alessandra; Nagy, Dorka; Martin, Patrick C N; Mikheeva, Liudmila A; Hayat, Ateequllah; Ficz, Gabriella; Zabet, Nicolae Radu.

Nucleic Acids Res ; 51(16): 8480-8495, 2023 09 08.

Artigo em Inglês | MEDLINE | ID: mdl-37486787

3.

Locus-specific chromatin profiling of evolutionarily young transposable elements.

Taylor, Darren; Lowe, Robert; Philippe, Claude; Cheng, Kevin C L; Grant, Olivia A; Zabet, Nicolae Radu; Cristofari, Gael; Branco, Miguel R.

Nucleic Acids Res ; 50(6): e33, 2022 04 08.

Artigo em Inglês | MEDLINE | ID: mdl-34908129

4.

ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data.

Osuntoki, Itunu G; Harrison, Andrew; Dai, Hongsheng; Bao, Yanchun; Zabet, Nicolae Radu.

Bioinformatics ; 38(14): 3523-3531, 2022 07 11.

Artigo em Inglês | MEDLINE | ID: mdl-35678507

5.

Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome.

Chathoth, Keerthi T; Zabet, Nicolae Radu.

Genome Res ; 29(4): 613-625, 2019 04.

Artigo em Inglês | MEDLINE | ID: mdl-30709849

6.

DNA sequence properties that predict susceptibility to epiallelic switching.

Catoni, Marco; Griffiths, Jayne; Becker, Claude; Zabet, Nicolae Radu; Bayon, Carlos; Dapp, Mélanie; Lieberman-Lazarovich, Michal; Weigel, Detlef; Paszkowski, Jerzy.

EMBO J ; 36(5): 617-628, 2017 03 01.

Artigo em Inglês | MEDLINE | ID: mdl-28069706

7.

DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts.

Catoni, Marco; Tsang, Jonathan Mf; Greco, Alessandro P; Zabet, Nicolae Radu.

Nucleic Acids Res ; 46(19): e114, 2018 11 02.

Artigo em Inglês | MEDLINE | ID: mdl-29986099

8.

Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies.

Zabet, Nicolae Radu; Catoni, Marco; Prischi, Filippo; Paszkowski, Jerzy.

Nucleic Acids Res ; 45(7): 3777-3784, 2017 04 20.

Artigo em Inglês | MEDLINE | ID: mdl-28053115

9.

Estimating binding properties of transcription factors from genome-wide binding profiles.

Zabet, Nicolae Radu; Adryan, Boris.

Nucleic Acids Res ; 43(1): 84-94, 2015 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-25432957

10.

Physical constraints determine the logic of bacterial promoter architectures.

Ezer, Daphne; Zabet, Nicolae Radu; Adryan, Boris.

Nucleic Acids Res ; 42(7): 4196-207, 2014 Apr.

Artigo em Inglês | MEDLINE | ID: mdl-24476912

11.

A comprehensive computational model of facilitated diffusion in prokaryotes.

Zabet, Nicolae Radu; Adryan, Boris.

Bioinformatics ; 28(11): 1517-24, 2012 Jun 01.

Artigo em Inglês | MEDLINE | ID: mdl-22492644

12.

GRiP: a computational tool to simulate transcription factor binding in prokaryotes.

Zabet, Nicolae Radu; Adryan, Boris.

Bioinformatics ; 28(9): 1287-9, 2012 May 01.

Artigo em Inglês | MEDLINE | ID: mdl-22426343

13.

H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function.

Pal, Debosree; Patel, Manthan; Boulet, Fanny; Sundarraj, Jayakumar; Grant, Olivia A; Branco, Miguel R; Basu, Srinjan; Santos, Silvia D M; Zabet, Nicolae Radu; Scaffidi, Paola; Pradeepa, Madapura M.

Nat Struct Mol Biol ; 30(7): 935-947, 2023 07.

Artigo em Inglês | MEDLINE | ID: mdl-37308596

14.

Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array.

Grant, Olivia A; Wang, Yucheng; Kumari, Meena; Zabet, Nicolae Radu; Schalkwyk, Leonard.

Clin Epigenetics ; 14(1): 62, 2022 05 14.

Artigo em Inglês | MEDLINE | ID: mdl-35568878

15.

Combination of BMI1 and MAPK/ERK inhibitors is effective in medulloblastoma.

Badodi, Sara; Pomella, Nicola; Lim, Yau Mun; Brandner, Sebastian; Morrison, Gillian; Pollard, Steven M; Zhang, Xinyu; Zabet, Nicolae Radu; Marino, Silvia.

Neuro Oncol ; 24(8): 1273-1285, 2022 08 01.

Artigo em Inglês | MEDLINE | ID: mdl-35213723

16.

Negative feedback and physical limits of genes.

Zabet, Nicolae Radu.

J Theor Biol ; 284(1): 82-91, 2011 Sep 07.

Artigo em Inglês | MEDLINE | ID: mdl-21723295

17.

Analysis of Plant DNA Methylation Profiles Using R.

Catoni, Marco; Zabet, Nicolae Radu.

Methods Mol Biol ; 2250: 219-238, 2021.

Artigo em Inglês | MEDLINE | ID: mdl-33900608

18.

An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila.

Wolfe, Jareth C; Mikheeva, Liudmila A; Hagras, Hani; Zabet, Nicolae Radu.

Genome Biol ; 22(1): 308, 2021 11 08.

Artigo em Inglês | MEDLINE | ID: mdl-34749786

19.

Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.

Martin, Patrick C N; Zabet, Nicolae Radu.

Comput Struct Biotechnol J ; 18: 3590-3605, 2020.

Artigo em Inglês | MEDLINE | ID: mdl-33304457

20.

Models of transcription factor binding: sensitivity of activation functions to model assumptions.

Chu, Dominique; Zabet, Nicolae Radu; Mitavskiy, Boris.

J Theor Biol ; 257(3): 419-29, 2009 Apr 07.

Artigo em Inglês | MEDLINE | ID: mdl-19121637

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The role of insulators and transcription in 3D chromatin organization of flies.

Identification of mammalian transcription factors that bind to inaccessible chromatin.

Locus-specific chromatin profiling of evolutionarily young transposable elements.

ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data.

Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome.

DNA sequence properties that predict susceptibility to epiallelic switching.

DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts.

Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies.

Estimating binding properties of transcription factors from genome-wide binding profiles.

Physical constraints determine the logic of bacterial promoter architectures.

A comprehensive computational model of facilitated diffusion in prokaryotes.

GRiP: a computational tool to simulate transcription factor binding in prokaryotes.

H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function.

Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array.

Combination of BMI1 and MAPK/ERK inhibitors is effective in medulloblastoma.

Negative feedback and physical limits of genes.

Analysis of Plant DNA Methylation Profiles Using R.

An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila.

Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.

Models of transcription factor binding: sensitivity of activation functions to model assumptions.