Dr Nicolae Zabet
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Email
nzabet@essex.ac.uk -
Location
3SW.3.16, Colchester Campus
Profile
Biography
I am a computer scientist by training (BSc and MSc in Control Systems Engineering at University “Politehnica” of Bucharest and PhD in Computer Science, University of Kent). During my PhD (2007-2010), I become interested in applying computer sciences and theoretical physics methods to genomics focusing on understanding the physical limits of gene regulatory networks. Following the PhD, I did a six-month postdoc with Dr Tobias von der Haar at University of Kent, working on translation machinery in yeast. In 2011, I was awarded an MRC Training Fellowship in Bioinformatics and joined Dr Boris Adryan lab at Department of Genetics, University of Cambridge. Here, I investigated the role of the diffusion of transcription factors on gene regulation, focusing on facilitated diffusion (the combination of 3D diffusion of transcription factors in the cytoplasm/nucleus combined with the 1D random walk on the DNA). During 2014-2015, I moved to Dr Jerzy Paszkowski’s lab at The Sainsbury Laboratory, University of Cambridge, where I worked on plant epigenetics (focusing on transgenerational stability of DNA methylation patterns in plant genomes). Since September 2015, I have started my own group at School of Biological Sciences at University of Essex. My lab combines computational biology and wet lab to understand the role of chromatin three-dimensional organisation on gene regulation in Drosophila melanogaster.
Qualifications
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PhD in Computer Science University of Kent, (2011)
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M.Eng. degree in Open Architecture Systems Polytechnic University of Bucharest, (2008)
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B.Eng. degree in Automatic Control and Industrial Informatics Polytechnic University of Bucharest, (2006)
Appointments
University of Essex
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Lecturer, School of Biological Sciences, University of Essex (16/9/2015 - present)
Other academic
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Research Associate, The Sainsbury Laboratory, University of Cambridge (1/6/2014 - 15/9/2015)
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MRC Bioinformatics Training Fellow, Department of Genetics, University of Cambridge (1/5/2011 - 30/4/2014)
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Research Associate, Centre for Molecular Processing, University of Kent (1/10/2010 - 31/3/2011)
Research and professional activities
Research interests
Mechanistic understanding of gene regulation
Diffusion of transcription factors
Noise in gene expression
Current research
DNA methylation patterns in plants and mamals. From tools to functional genomics.
Teaching and supervision
Previous supervision
Degree subject: Biological Sciences
Degree type: Doctor of Philosophy
Awarded date: 13/5/2024
Degree subject: Biological Sciences
Degree type: Doctor of Philosophy
Awarded date: 7/3/2023
Degree subject: Statistics
Degree type: Doctor of Philosophy
Awarded date: 23/6/2022
Degree subject: Biological Sciences
Degree type: Doctor of Philosophy
Awarded date: 11/4/2022
Degree subject: Biological Sciences
Degree type: Master of Science (by Dissertation)
Awarded date: 31/1/2022
Degree subject: Biological Sciences
Degree type: Master of Science (by Dissertation)
Awarded date: 10/12/2021
Degree subject: Biological Sciences
Degree type: Doctor of Philosophy
Awarded date: 16/6/2020
Degree subject: Biological Sciences
Degree type: Master of Science (by Dissertation)
Awarded date: 8/6/2020
Publications
Publications (7)
Grant, OA., Kumari, M., Schalkwyk, L. and Zabet, NR., (2024). Systematic investigation of interindividual variation of DNA methylation in human whole blood
Vinel, C., Boot, J., Jin, W., Pomella, N., Mein, C., Zabet, NR. and Marino, S., (2024). Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets
Emmerson, RA., Bechtold, U., Zabet, NR. and Lawson, T., (2024). DNA methylation contributes to plant acclimation to naturally fluctuating light
Zastąpiło, J., Emmerson, R., Mikheeva, LA., Catoni, M., Bechtold, U. and Zabet, NR., (2024). Gene body methylation buffers noise in gene expression in plants
Pop, RT., Pisante, A., Nagy, D., Martin, PCN., Mikheeva, LA., Hayat, A., Ficz, G. and Zabet, NR., (2023). Identification of mammalian transcription factors that bind to inaccessible chromatin
Pal, D., Patel, M., Boulet, F., Sundarraj, J., Grant, OA., Branco, MR., Basu, S., Santos, S., Zabet, NR., Scaffidi, P. and Pradeepa, MM., (2022). H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function
Taylor, D., Lowe, R., Philippe, C., Cheng, KCL., Grant, OA., Zabet, NR., Cristofari, G. and Branco, MR., (2021). Locus-specific chromatin profiling of evolutionarily young transposable elements
Journal articles (32)
Maqsood, K., Hagras, H. and Zabet, NR., (2024). An overview of artificial intelligence in the field of genomics. Discover Artificial Intelligence. 4 (1)
Klemm, C., Ólafsson, G., Wood, HR., Mellor, C., Zabet, NR. and Thorpe, PH., (2024). Proteome-wide forced interactions reveal a functional map of cell-cycle phospho-regulation in S. cerevisiae. Nucleus. 15 (1), 2420129-
Pal, D., Patel, M., Boulet, F., Sundarraj, J., Grant, OA., Branco, MR., Basu, S., Santos, SDM., Zabet, NR., Scaffidi, P. and Pradeepa, MM., (2023). H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function. Nature Structural & Molecular Biology. 30 (7), 935-947
Pop, RT., Pisante, A., Nagy, D., Martin, PCN., Mikheeva, LA., Hayat, A., Ficz, G. and Zabet, NR., (2023). Identification of mammalian transcription factors that bind to inaccessible chromatin. Nucleic Acids Research. 51 (16), 8480-8495
Taylor, D., Lowe, R., Philippe, C., Cheng, KCL., Grant, OA., Zabet, NR., Cristofari, G. and Branco, MR., (2022). Locus-specific chromatin profiling of evolutionarily young transposable elements. Nucleic Acids Research. 50 (6), e33-e33
Badodi, S., Pomella, N., Lim, YM., Brandner, S., Morrison, G., Pollard, SM., Zhang, X., Zabet, NR. and Marino, S., (2022). Combination of BMI1 and MAPK/ERK inhibitors is effective in medulloblastoma. Neuro-Oncology. 24 (8), 1273-1285
Grant, OA., Wang, Y., Kumari, M., Zabet, NR. and Schalkwyk, L., (2022). Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array.. Clinical Epigenetics. 14 (1), 62-
Osuntoki, IG., Harrison, A., Dai, H., Bao, Y. and Zabet, NR., (2022). ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data.. Bioinformatics. 38 (14), btac387-btac387
Wolfe, JC., Mikheeva, LA., Hagras, H. and Zabet, NR., (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-
Fiorilli, V., Catoni, M., Lanfranco, L. and Zabet, NR., (2020). Editorial: Interactions of Plants With Bacteria and Fungi: Molecular and Epigenetic Plasticity of the Host. Frontiers in Plant Science. 11, 274-
Martin, PCN. and Zabet, NR., (2020). Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. Computational and Structural Biotechnology Journal. 18, 3590-3605
Chathoth, KT. and Zabet, NR., (2019). Chromatin architecture reorganisation during neuronal cell differentiation in Drosophila genome. Genome Research. 29 (4), 613-625
Bottani, S., Zabet, NR., Wendel, JF. and Veitia, RA., (2018). Gene expression dominance in allopolyploids: hypotheses and models.. Trends in Plant Science. 23 (5), 393-402
Catoni, M., Tsang, JMF., 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-
Zabet, NR., Catoni, M., Prischi, F. and Paszkowski, J., (2017). Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. Nucleic Acids Research. 45 (7), gkw1330-gkw1330
Catoni, M., Griffiths, J., Becker, C., Zabet, NR., Bayon, C., Dapp, M., Lieberman‐Lazarovich, M., Weigel, D. and Paszkowski, J., (2017).
Sanchez, D., Gaubert, H., Drost, HG., Zabet, NR. and Paszkowski, J., (2017). High-frequency recombination between members of an LTR retrotransposon family during transposition bursts. Nature Communications. 8 (1), 1283-
Zabet, NR. and Adryan, B., (2015). Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Research. 43 (1), 84-94
Ezer, D., Zabet, NR. and 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
Ezer, D., Zabet, NR. and Adryan, B., (2014). Physical constraints determine the logic of bacterial promoter architectures. Nucleic Acids Research. 42 (7), 4196-4207
Schoech, AP. and Zabet, NR., (2014). Facilitated diffusion buffers noise in gene expression. Physical Review E. 90 (3), 032701-
Zabet, NR., Foy, R. and Adryan, B., (2013). The Influence of Transcription Factor Competition on the Relationship between Occupancy and Affinity. PLoS ONE. 8 (9), e73714-e73714
Zabet, NR. and Adryan, B., (2013). The effects of transcription factor competition on gene regulation. Frontiers in Genetics. 4 (OCT), 197-
Zabet, NR. and Adryan, B., (2012). GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Bioinformatics. 28 (9), 1287-1289
Zabet, NR. and Adryan, B., (2012). A comprehensive computational model of facilitated diffusion in prokaryotes. Bioinformatics. 28 (11), 1517-1524
Zabet, NR. and Adryan, B., (2012). Computational models for large-scale simulations of facilitated diffusion. Molecular BioSystems. 8 (11), 2815-2815
Zabet, NR., (2012). System size reduction in stochastic simulations of the facilitated diffusion mechanism. BMC Systems Biology. 6 (1), 121-121
Chu, D., Zabet, NR. and von der Haar, T., (2012). A novel and versatile computational tool to model translation. Bioinformatics. 28 (2), 292-293
Chu, DF., Zabet, NR. and Hone, ANW., (2011). Optimal parameter settings for information processing in gene regulatory networks. Biosystems. 104 (2-3), 99-108
Zabet, NR., (2011). Negative feedback and physical limits of genes. Journal of Theoretical Biology. 284 (1), 82-91
Zabet, NR. and Chu, DF., (2010). Computational limits to binary genes. Journal of The Royal Society Interface. 7 (47), 945-954
Chu, D., Zabet, NR. and Mitavskiy, B., (2009). Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology. 257 (3), 419-429
Book chapters (1)
Catoni, M. and Zabet, NR., (2021). Analysis of Plant DNA Methylation Profiles Using R. In: Methods in Molecular Biology. Springer US. 219- 238. 9781071611333
Conferences (4)
Maqsood, K., Hagras, H. and Zabet, NR., (2024). A Type-2 Fuzzy Logic-Based Explainable Artificial Intelligence for the Prediction of Enhancers
Zabet, NR. and Adryan, B., (2012). A Comprehensive Computational Model to Simulate Transcription Factor Binding in Prokaryotes
Zabet, NR., Hone, ANW. and Chu, DF., (2010). Design principles of transcriptional logic circuits
Zabet, NR. and Chu, DF., (2010). Stochasticity and Robustness in Bi-Stable Systems
Reports and Papers (3)
Chathoth, KT., Mikheeva, LA., Crevel, G., Wolfe, JC., Hunter, I., Beckett-Doyle, S., Cotterill, S., Dai, H., Harrison, A. and Zabet, NR., (2021). The role of insulators and transcription in 3D chromatin organisation of flies
Grant, OA., Wang, Y., Kumari, M., Zabet, NR. and Schalkwyk, L., (2021). Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array
Osuntoki, IG., Harrison, A., Dai, H., Bao, Y. and Zabet, NR., (2021). ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data
Grants and funding
2016
Investigating the effects of chromatin architecture on gene regulation
Wellcome Trust
