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Research

Publications: Dr Nicolae Radu Zabet

Badodi S, Pomella N, Lim YM, Brandner S, Morrison G, Pollard SM, Zhang X, Zabet NR et al. ( 2022 ) . Combination of BMI1 and MAPK/ERK inhibitors is effective in medulloblastoma . Neuro-Oncology vol. 24 , ( 8 ) 1273 - 1285 .
Osuntoki IG, Harrison AP, Dai H, Bao Y, Zabet NR ( 2022 ) . ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data . Bioinformatics
Grant OA, Yucheng W, Meena K, Zabet NR, Schalkwyk L ( 2022 ) . Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array . Clinical Epigenetics vol. 14 , Article 62 ,
Taylor D, Lowe R, Philippe C, Cheng KCL, Grant OA, Zabet NR, Cristofari G, Branco MR ( 2022 ) . Locus-specific chromatin profiling of evolutionarily young transposable elements . Nucleic Acids Research vol. 50 , ( 6 )
Chathoth KT, Mikheeva LA, Crevel G, Wolfe JC, Hunter I, Beckett-Doyle S, Cotterill S, Dai H et al. ( 2022 ) . The role of insulators and transcription in 3D chromatin organization of flies . Genome Research vol. 32 , 682 - 682 .
Wolfe JC, Mikheeva LA, Hagras H, Zabet NR ( 2021 ) . An Explainable Artificial Intelligence Approach for Decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila . Genome Biology vol. 22 , Article 308 ,
Catoni M, Zabet NR ( 2021 ) . Analysis of Plant DNA Methylation Profiles Using R . Methods in Molecular Biology , vol. 2250 ,
Martin P, Zabet NR ( 2020 ) . Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework . Computational and Structural Biotechnology Journal vol. 18 , 3590 - 3605 .
Fiorilli V, Catoni M, Lanfranco L, Zabet NR ( 2020 ) . Editorial: Interactions of Plants With Bacteria and Fungi: Molecular and Epigenetic Plasticity of the Host . Frontiers in Plant Science vol. 11 ,
Chathoth KT, Zabet NR ( 2019 ) . Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome . Genome Research vol. 29 , ( 4 ) 613 - 625 .
Catoni M, Tsang JMF, Greco AP, 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 vol. 46 , ( 19 )
Bottani S, Zabet NR, Wendel JF, Veitia RA ( 2018 ) . Gene Expression Dominance in Allopolyploids: Hypotheses and Models . Trends in Plant Science vol. 23 , ( 5 ) 393 - 402 .
Sanchez DH, Gaubert H, Drost HG, Zabet NR, Paszkowski J ( 2017 ) . High-frequency recombination between members of an LTR retrotransposon family during transposition bursts . Nature Communications vol. 8 , ( 1 )
Catoni M, Griffiths J, Becker C, Zabet NR, Bayon C, Dapp M, Lieberman-Lazarovich M, Weigel D et al. ( 2017 ) . DNA sequence properties that predict susceptibility to epiallelic switching . EMBO Journal vol. 36 , ( 5 ) 617 - 628 .
Zabet NR, Catoni M, Prischi F, Paszkowski J ( 2017 ) . Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies . Nucleic Acids Research vol. 45 , ( 7 ) 3777 - 3784 .
Zabet NR, Adryan B ( 2015 ) . Estimating binding properties of transcription factors from genome-wide binding profiles . Nucleic Acids Research vol. 43 , ( 1 ) 84 - 94 .
Schoech AP, Zabet NR ( 2014 ) . Facilitated diffusion buffers noise in gene expression . Physical Review E - Statistical, Nonlinear, and Soft Matter Physics vol. 90 , ( 3 )
Ezer D, Zabet NR, Adryan B ( 2014 ) . Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression . Computational and Structural Biotechnology Journal vol. 10 , ( 17 ) 63 - 69 .
Ezer D, Zabet NR, Adryan B ( 2014 ) . Physical constraints determine the logic of bacterial promoter architectures . Nucleic Acids Research vol. 42 , ( 7 ) 4196 - 4207 .
Zabet NR, Adryan B ( 2013 ) . The effects of transcription factor competition on gene regulation . Frontiers in Genetics vol. 4 , ( OCT )
Zabet NR, Foy R, Adryan B ( 2013 ) . The Influence of Transcription Factor Competition on the Relationship between Occupancy and Affinity . PLoS ONE vol. 8 , ( 9 )
Zabet NR, Adryan B ( 2012 ) . Computational models for large-scale simulations of facilitated diffusion . Molecular BioSystems vol. 8 , ( 11 ) 2815 - 2827 .
Zabet NR ( 2012 ) . System size reduction in stochastic simulations of the facilitated diffusion mechanism . BMC Systems Biology vol. 6 ,
Zabet NR, Adryan B ( 2012 ) . A comprehensive computational model of facilitated diffusion in prokaryotes . Bioinformatics vol. 28 , ( 11 ) 1517 - 1524 .
Zabet NR, Adryan B ( 2012 ) . GRIP: A computational tool to simulate transcription factor binding in prokaryotes . Bioinformatics vol. 28 , ( 9 ) 1287 - 1289 .
Zabet NR, Adryan B ( 2012 ) . A comprehensive computational model to simulate transcription factor binding in prokaryotes . Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) . vol. 7223 LNCS , 35 - 37 .
Chu D, Zabet N, von der Haar T ( 2012 ) . A novel and versatile computational tool to model translation . Bioinformatics vol. 28 , ( 2 ) 292 - 293 .
Zabet NR ( 2011 ) . Negative feedback and physical limits of genes . Journal of Theoretical Biology vol. 284 , ( 1 ) 82 - 91 .
Chu DF, Zabet NR, Hone ANW ( 2011 ) . Optimal parameter settings for information processing in gene regulatory networks . BioSystems vol. 104 , ( 2-3 ) 99 - 108 .
Zabet NR, Hone ANW, Chu DF ( 2010 ) . Design principles of transcriptional logic circuits . Artificial Life XII: Proceedings of the 12th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2010 . 186 - 193 .
Zabet NR, Chu DF ( 2010 ) . Stochasticity and robustness in bi-stable systems . 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010 .
Zabet NR, Chu DF ( 2010 ) . Computational limits to binary genes . Journal of the Royal Society Interface vol. 7 , ( 47 ) 945 - 954 .
Chu D, Zabet NR, Mitavskiy B ( 2009 ) . Models of transcription factor binding: Sensitivity of activation functions to model assumptions . Journal of Theoretical Biology vol. 257 , ( 3 ) 419 - 429 .