Publications: Dr Nicolae Radu Zabet

Chera A, Stancu-Cretu M, Zabet NR, Bucur O ( 2024 ) . Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology . Epigenetics & Chromatin vol. 17 , ( 1 )

Klemm C, Ólafsson G, Wood HR, Mellor C, Zabet NR, Thorpe PH ( 2024 ) . Proteome-wide forced interactions reveal a functional map of cell-cycle phospho-regulation in S. cerevisiae . Nucleus vol. 15 , ( 1 )

Maqsood K, Hagras H, Zabet NR ( 2024 ) . A Type-2 Fuzzy Logic-Based Explainable Artificial Intelligence for the Prediction of Enhancers . Conference: 2024 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE) vol. 00 , 1 - 8 .

Maqsood K, Hagras H, Zabet NR ( 2024 ) . An overview of artificial intelligence in the field of genomics . Discover Artificial Intelligence vol. 4 , ( 1 )

Pop RT, Pisante A, Nagy D, Martin PCN, Mikheeva LA, Hayat A, Ficz G, Zabet NR ( 2023 ) . Identification of mammalian transcription factors that bind to inaccessible chromatin . Nucleic Acids Res vol. 51 , ( 16 ) 8480 - 8495 .

Pal D, Patel M, Boulet F, Sundarraj J, Grant OA, Branco MR, Basu S, Santos SDM et al. ( 2023 ) . H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function . Nature Structural & Molecular Biology vol. 30 , ( 7 ) 935 - 947 .

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

Badodi S, Pomella N, Zhang X, Zabet NR, Basson MA, Marino S ( 2022 ) . MEDB-23. Targeting epigenetic dysregulation in medulloblastoma with poor prognosis . Neuro-Oncology vol. 24 , ( Supplement_1 ) i109 - i110 .

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 ,

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 .

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 .

Badodi S, Pomella N, Zhang X, Zabet NR, Basson MA, Marino S ( 2022 ) . TARGETING EPIGENETIC DYSREGULATION IN MEDULLOBLASTOMA WITH POOR PROGNOSIS . NEURO-ONCOLOGY . vol. 24 , 109 - 109 .

Taylor D, Lowe R, Philippe C, Cheng KCL, Grant OA, Zabet NR, Cristofari G, Branco MR ( 2021 ) . Locus-specific chromatin profiling of evolutionarily young transposable elements . Nucleic Acids Research vol. 50 , ( 6 ) e33 - e33 .

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 . Plant Transposable Elements , vol. 2250 , Springer Nature

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 H-G, 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 . The 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 ( 2014 ) . 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 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, 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 ( 2013 ) . The effects of transcription factor competition on gene regulation . Frontiers in Genetics vol. 4 ,

Zabet NR ( 2012 ) . System size reduction in stochastic simulations of the facilitated diffusion mechanism . BMC Systems Biology vol. 6 , ( 1 )

Zabet NR, Adryan B ( 2012 ) . Computational models for large-scale simulations of facilitated diffusion . Molecular Omics vol. 8 , ( 11 ) 2815 - 2827 .

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 . vol. 7223 , 35 - 37 .

Chu D, Zabet N, von der Haar T ( 2011 ) . 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 . Conference: 2010 4th International Conference on Bioinformatics and Biomedical Engineering1 - 4 .

Zabet NR, Chu DF ( 2009 ) . Computational limits to binary genes . Journal of The Royal Society Interface vol. 7 , ( 47 ) 945 - 954 .

Chu D, Zabet NR, Mitavskiy B ( 2008 ) . Models of transcription factor binding: Sensitivity of activation functions to model assumptions . Journal of Theoretical Biology vol. 257 , ( 3 ) 419 - 429 .