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 鈥淧olitehnica鈥� 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鈥檚 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 糖心Vlog. 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
糖心Vlog
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Lecturer, School of Biological Sciences, 糖心Vlog (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
Zast膮pi艂o, 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 (35)
Vinel, C., Boot, J., Jin, W., Pomella, N., Hadaway, A., Mein, C., Zabet, NR. and Marino, S., (2025). Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets. BMC Biology. 23 (1), 26-
Millner, TO., Panday, P., Xiao, Y., Nicholson, J., Boot, JR., Arpe, Z., Stevens, PA., Rahman, NN., Zhang, X., Mein, C., Kitchen, N., McEvoy, AW., McKintosh, E., McKenna, GS., Paraskevopoulos, D., Zabet, NR., Lewis, R., Badodi, S. and Marino, S., (2025). Disruption of DNA methylation underpins the neuroinflammation induced by targeted CNS radiotherapy. Brain, awaf163-
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., 脫lafsson, 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-
Chera, A., Stancu-Cretu, M., Zabet, NR. and Bucur, O., (2024). Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology. Epigenetics & Chromatin. 17 (1), 39-
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). . Clinical Epigenetics. 14 (1), 62-
Osuntoki, IG., Harrison, A., Dai, H., Bao, Y. and Zabet, NR., (2022). . Bioinformatics. 38 (14), btac387-btac387
Wolfe, JC., Mikheeva, LA., Hagras, H. and Zabet, NR., (2021). . 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). . Computational and Structural Biotechnology Journal. 18, 3590-3605
Chathoth, KT. and Zabet, NR., (2019). . Genome Research. 29 (4), 613-625
Bottani, S., Zabet, NR., Wendel, JF. and Veitia, RA., (2018). . Trends in Plant Science. 23 (5), 393-402
Catoni, M., Tsang, JMF., Greco, AP. and Zabet, NR., (2018). . Nucleic Acids Research. 46 (19), e114-
Zabet, NR., Catoni, M., Prischi, F. and Paszkowski, J., (2017). . Nucleic Acids Research. 45 (7), gkw1330-gkw1330
Catoni, M., Griffiths, J., Becker, C., Zabet, NR., Bayon, C., Dapp, M., Lieberman鈥怢azarovich, M., Weigel, D. and Paszkowski, J., (2017). . The EMBO Journal. 36 (5), 617-628
Sanchez, D., Gaubert, H., Drost, HG., Zabet, NR. and Paszkowski, J., (2017). . Nature Communications. 8 (1), 1283-
Zabet, NR. and Adryan, B., (2015). . Nucleic Acids Research. 43 (1), 84-94
Ezer, D., Zabet, NR. and Adryan, B., (2014). . Computational and Structural Biotechnology Journal. 10 (17), 63-69
Ezer, D., Zabet, NR. and Adryan, B., (2014). . Nucleic Acids Research. 42 (7), 4196-4207
Schoech, AP. and Zabet, NR., (2014). . Physical Review E. 90 (3), 032701-
Zabet, NR., Foy, R. and Adryan, B., (2013). . PLoS ONE. 8 (9), e73714-e73714
Zabet, NR. and Adryan, B., (2013). . Frontiers in Genetics. 4 (OCT), 197-
Zabet, NR. and Adryan, B., (2012). . Bioinformatics. 28 (9), 1287-1289
Zabet, NR. and Adryan, B., (2012). . Bioinformatics. 28 (11), 1517-1524
Zabet, NR. and Adryan, B., (2012). . Molecular BioSystems. 8 (11), 2815-2815
Zabet, NR., (2012). . BMC Systems Biology. 6 (1), 121-121
Chu, D., Zabet, NR. and von der Haar, T., (2012). . Bioinformatics. 28 (2), 292-293
Chu, DF., Zabet, NR. and Hone, ANW., (2011). . Biosystems. 104 (2-3), 99-108
Zabet, NR., (2011). . Journal of Theoretical Biology. 284 (1), 82-91
Zabet, NR. and Chu, DF., (2010). . Journal of The Royal Society Interface. 7 (47), 945-954
Chu, D., Zabet, NR. and Mitavskiy, B., (2009). . 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).
Zabet, NR. and Chu, DF., (2010).
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
