Students Staff

Academic Staff

Dr Nicolae Radu Zabet

Staff positionLecturer
Emailnzabet@essex.ac.uk
Room3SW.3.16
Biography
  • September 2015 - present, Lecturer, School of Biological Sciences, University of Essex, Colchester UK.
  • June 2014 - September 2015, Research Associate, The Sainsbury Laboratory, University of Cambridge, Cambridge UK.
  • May 2011 - April 2014, MRC Bioinformatics Training Fellow, Department of Genetics, University of Cambridge, Cambridge UK.
  • October 2010 - March 2011, Research Associate, Centre for Molecular Processing, University of Kent, Canterbury UK.

Websitehttps://zabetlab.wordpress.com/
Qualifications
  • PhD degree in Computer Science at School of Computing, University of Kent, UK, 2007-2010. “Towards Modular, Scalable and Optimal Design of Transcriptional Logic Systems”
  • M.Eng. degree in Open Architecture Systems at Department of Automatic Control and Industrial Informatics, Faculty of Automatic Control and Computers, 'Politechnica' University of Bucharest, Romania, 2006-2008.
  • B.Eng. degree in Automatic Control and Industrial Informatics at Department of Automatic Control and Industrial Informatics, Faculty of Automatic Control and Computers, `Politechnica' University of Bucharest, Romania, 2001-2006.
Current research

My research covers two main areas of chromatin and epigenetics:

1. Mechanistic models of how TFs regulate gene expression in 3D. 

Postdoc: Dr Keerthi Chathoth

PhD student: Mr Patrick Martin

2. DNA methylation patterns in plants and mamals. From tools to functional genomics. 

Research interests
  • Mechanistic understanding of gene regulation
  • Diffusion of transcription factors
  • Noise in gene expression
  • DNA methylation
  • Methods and software
Teaching responsibilities

Module supervisor BS231: Computational Data Analysis: R for Life Sciences

Publications

Google Scholar - ORCiD

  • Catoni, M.; Griffiths, J.; Becker, C.; Zabet, N. R.; Bayon, C.; Dapp, M.; Liebermanā€Lazarovich, M.; Weigel, D. & Paszkowski, J., ‘DNA sequence properties that predict susceptibility to epiallelic switching’, The EMBO Journal, doi: 10.15252/embj.201695602.
  • Zabet, N. R.1c ; Catoni, M.; Prischi, F. & Paszkowski, J. (2017), ‘Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies’, Nucleic Acids Research, 45 (7): 3777-3784, doi: 10.1093/nar/gkw1330.
  • Zabet, N. R.1c & Adryan, B (2015), ‘Estimating binding properties of transcription factors from genome-wide binding profiles’, Nucleic Acids Research 43(1): 84-94, doi: 10.1093/nar/gku1269.
  • Schoech, A. P. & Zabet, N. R.c (2014), ‘Facilitated diffusion buffers noise in gene expression’, Phys. Rev. E 90(3): 032701, doi:10.1103/PhysRevE.90.032701.
  • Ezer, D; Zabet, N. R.1c & 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, 10(17): 63-69, doi:0.1016/j.csbj.2014.07.005. (Review Article)
  • Ezer, D; Zabet, N. R.1c & Adryan, B (2014), `Physical constraints determine the logic of bacterial promoter architectures’, Nucleic Acids Research, 42(7): 4196-4207, doi:10.1093/nar/gku078.
  • Zabet, N. R.1c; Foy, R & Adryan, B (2013), `The influence of transcription factor competition on the relationship between occupancy and affinity', PLoS ONE, 8(9): e73714, doi:10.1371/journal.pone.0073714.
  • Zabet, N. R.1c & Adryan, B (2013), `The effects of transcription factor competition on gene regulation’, Frontiers in Genetics 4: 197, doi:10.3389/fgene.2013.00197.
  • Zabet, N. R.1c (2012),`System size reduction in stochastic simulations of the facilitated diffusion mechanism', BMC Systems Biology 6 (1): 121, doi:10.1186/1752-0509-6-121.
  • Zabet, N. R.1c & Adryan, B (2012),`Computational models for large-scale simulations of facilitated diffusion', Molecular Biosystems 8 (11): 2815-2827, doi:10.1039/C2MB25201E. (Review Article)
  • Zabet, N. R.1c & Adryan, B (2012),`A comprehensive computational model of facilitated diffusion in prokaryotes', Bioinformatics 28 (11): 1517-1524, doi:10.1093/bioinformatics/bts178.
  • Zabet, N. R.1c & Adryan, B (2012),`GRiP: a computational tool to simulate transcription factor binding in prokaryotes', Bioinformatics 28 (9): 1287-1289, 2012, doi:10.1093/bioinformatics/bts132.
  • Chu, D. F.; Zabet, N. & von der Haar, T. (2012),`A novel and versatile computational tool to model translation',  Bioinformatics 28(2), 292-293. doi: 10.1093/bioinformatics/btr650.
  • Zabet, N. R.1c (2011), `Negative Feedback and Physical Limits of Genes', Journal of Theoretical Biology 248(1), 82-91. doi: 10.1016/j.jtbi.2011.06.021
  • Chu, D. F.; Zabet, N. R. & Hone, A. N. W. (2011), `Optimal parameter settings for information processing in gene regulatory networks', BioSystems 104(2-3), 99-108. doi: 10.1016/j.biosystems.2011.01.006.
  • Zabet, N. R.1c & Chu, D. F. (2010), `Computational limits to binary genes', Journal of the Royal Society Interface 7(47), 945-954. doi: 10.1098/rsif.2009.0474.
  • Chu, D.; Zabet, N. R. & Mitavskiy, B. (2009), `Models of transcription factor binding: Sensitivity of activation functions to model assumptions', Journal of Theoretical Biology 257(3), 419-429 doi:10.1016/j.jtbi.2008.11.026.

superscript 1 indicates first (co)authorship and c indicates corresponding author.

Conferences/presentations
  • Zabet, N. R.1c; Hone, A. N. W. & Chu, D. F. (2010), `Design principles of transcriptional logic circuits', In Artificial Life XII Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, pp 186-193, 19-23 August, Odense, Denmark, MIT Press, http://mitpress.mit.edu/sites/default/files/titles/alife/0262290758chap39.pdf
  • Zabet, N. R.1c & Chu, D. F. (2010), `Stochasticity and robustness in bi-stable systems', In Bioinformatics and Biomedical Engineering (iCBBE), 2010 4th International Conference on, pp 1-4, June 18-20, Chengdu, China, IEEE Xplore, doi: 10.1109/ICBBE.2010.5518099.

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