Browse by Person

Osuntoki, Itunu G and Harrison, Andrew and Dai, Hongsheng and Bao, Yanchun and Zabet, Nicolae Radu (2022) ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data. Bioinformatics, 38 (14). btac387-btac387. DOI https://doi.org/10.1093/bioinformatics/btac387

Grant, Olivia A and Wang, Yucheng and Kumari, Meena and Zabet, Nicolae Radu and Schalkwyk, Leonard (2022) Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array. Clinical Epigenetics, 14 (1). 62-. DOI https://doi.org/10.1186/s13148-022-01279-7

Wolfe, Jareth C and Mikheeva, Liudmila A and Hagras, Hani and Zabet, Nicolae Radu (2021) An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila. Genome Biology, 22 (1). 308-. DOI https://doi.org/10.1186/s13059-021-02532-7

Martin, Patrick CN and Zabet, Nicolae Radu (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. Computational and Structural Biotechnology Journal, 18. pp. 3590-3605. DOI https://doi.org/10.1016/j.csbj.2020.11.006

Chathoth, Keerthi T and Zabet, Nicolae Radu (2019) Chromatin architecture reorganisation during neuronal cell differentiation in Drosophila genome. Genome Research, 29 (4). pp. 613-625. DOI https://doi.org/10.1101/gr.246710.118

Catoni, M and Tsang, JMF and Greco, AP and Zabet, NR (2018) DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Research, 46 (19). e114-. DOI https://doi.org/10.1093/nar/gky602

Bottani, S and Zabet, NR and Wendel, JF and Veitia, RA (2018) Gene expression dominance in allopolyploids: hypotheses and models. Trends in Plant Science, 23 (5). pp. 393-402. DOI https://doi.org/10.1016/j.tplants.2018.01.002

Sanchez, D and Gaubert, H and Drost, HG and Zabet, NR and Paszkowski, J (2017) High-frequency recombination between members of an LTR retrotransposon family during transposition bursts. Nature Communications, 8 (1). 1283-. DOI https://doi.org/10.1038/s41467-017-01374-x

Zabet, Nicolae Radu and Catoni, Marco and Prischi, Filippo and Paszkowski, Jerzy (2017) Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. Nucleic Acids Research, 45 (7). gkw1330-gkw1330. DOI https://doi.org/10.1093/nar/gkw1330

Catoni, Marco and Griffiths, Jayne and Becker, Claude and Zabet, Nicolae Radu and Bayon, Carlos and Dapp, Mélanie and Lieberman‐Lazarovich, Michal and Weigel, Detlef and Paszkowski, Jerzy (2017) <scp>DNA</scp> sequence properties that predict susceptibility to epiallelic switching. The EMBO Journal, 36 (5). pp. 617-628. DOI https://doi.org/10.15252/embj.201695602

Zabet, Nicolae Radu and Adryan, Boris (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Research, 43 (1). pp. 84-94. DOI https://doi.org/10.1093/nar/gku1269

Schoech, Armin P and Zabet, Nicolae Radu (2014) Facilitated diffusion buffers noise in gene expression. Physical Review E, 90 (3). 032701-. DOI https://doi.org/10.1103/physreve.90.032701

Ezer, Daphne and Zabet, Nicolae Radu and Adryan, Boris (2014) Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression. Computational and Structural Biotechnology Journal, 10 (17). pp. 63-69. DOI https://doi.org/10.1016/j.csbj.2014.07.005

Ezer, Daphne and Zabet, Nicolae Radu and Adryan, Boris (2014) Physical constraints determine the logic of bacterial promoter architectures. Nucleic Acids Research, 42 (7). pp. 4196-4207. DOI https://doi.org/10.1093/nar/gku078

Zabet, Nicolae Radu and Adryan, Boris (2013) The effects of transcription factor competition on gene regulation. Frontiers in Genetics, 4 (OCT). 197-. DOI https://doi.org/10.3389/fgene.2013.00197

Zabet, Nicolae Radu and Foy, Robert and Adryan, Boris (2013) The Influence of Transcription Factor Competition on the Relationship between Occupancy and Affinity. PLoS ONE, 8 (9). e73714-e73714. DOI https://doi.org/10.1371/journal.pone.0073714

Zabet, Nicolae Radu and Adryan, Boris (2012) A comprehensive computational model of facilitated diffusion in prokaryotes. Bioinformatics, 28 (11). pp. 1517-1524. DOI https://doi.org/10.1093/bioinformatics/bts178

Zabet, Nicolae Radu and Adryan, Boris (2012) GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Bioinformatics, 28 (9). pp. 1287-1289. DOI https://doi.org/10.1093/bioinformatics/bts132

Chu, D and Zabet, NR and von der Haar, T (2012) A novel and versatile computational tool to model translation. Bioinformatics, 28 (2). pp. 292-293. DOI https://doi.org/10.1093/bioinformatics/btr650

Zabet, Nicolae Radu and Adryan, Boris (2012) Computational models for large-scale simulations of facilitated diffusion. Molecular BioSystems, 8 (11). p. 2815. DOI https://doi.org/10.1039/c2mb25201e

Zabet, Nicolae Radu (2012) System size reduction in stochastic simulations of the facilitated diffusion mechanism. BMC Systems Biology, 6 (1). p. 121. DOI https://doi.org/10.1186/1752-0509-6-121

Zabet, Nicolae Radu (2011) Negative feedback and physical limits of genes. Journal of Theoretical Biology, 284 (1). pp. 82-91. DOI https://doi.org/10.1016/j.jtbi.2011.06.021

Chu, Dominique F and Zabet, Nicolae Radu and Hone, Andrew NW (2011) Optimal parameter settings for information processing in gene regulatory networks. Biosystems, 104 (2-3). pp. 99-108. DOI https://doi.org/10.1016/j.biosystems.2011.01.006

Zabet, NR and Hone, ANW and Chu, DF (2010) Design principles of transcriptional logic circuits. In: UNSPECIFIED, ? - ?.

Zabet, Nicolae Radu and Chu, Dominique F (2010) Computational limits to binary genes. Journal of The Royal Society Interface, 7 (47). pp. 945-954. DOI https://doi.org/10.1098/rsif.2009.0474

Zabet, Nicolae Radu and Chu, Dominique F (2010) Stochasticity and Robustness in Bi-Stable Systems. In: 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE), 2010-06-18 - 2010-06-20.

Chu, Dominique and Zabet, Nicolae Radu and Mitavskiy, Boris (2009) Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology, 257 (3). pp. 419-429. DOI https://doi.org/10.1016/j.jtbi.2008.11.026