Dr Radu Zabet

Profile

Radu Zabet did his PhD in Computer Science at University of Kent working on understanding the physical limits of gene regulatory networks. Following the PhD, Radu had a six-month postdoc with Dr Tobias von der Haar at University of Kent, working on translation machinery in yeast. In 2011, he was awarded an MRC Training Fellowship in Bioinformatics and joined Dr Boris Adryan lab at Department of Genetics, University of Cambridge. Here, Radu investigated the role of the diffusion of transcription factors on gene regulation, focusing on the combination of 3D diffusion in the nucleus combined with the 1D random walk on the DNA. During 2014-2015, Radu moved into Dr Jerzy Paszkowski’s lab at The Sainsbury Laboratory, University of Cambridge, where he worked on plant epigenetics (focusing on transgenerational stability of DNA methylation patterns in plant genomes). In September 2015, Radu started his own group at School of Life Sciences at University of Essex. Radu’s lab has relocated to Blizard Institute in July 2020. 

Our lab is interested to understand how different mechanisms contribute to gene regulation and, in particular, we aim to decode the relative role to gene regulation of transcription factors (TFs) and their binding to DNA, 3D genome organisation and epigenetics (DNA methylation and histone modifications). We are highly interdisciplinary and combine computational biology, machine learning, AI, genomics and molecular biology. 

www.zabetlab.wordpress.com

Research

Research Interests:

Radu’s research group combines computational biology and molecular biology to develop new mechanistic models of how gene regulation works and its interplay with 3D gene architecture and epigenetic factors. In particular, his lab focuses on: (i) modelling binding of Transcription Factors (TFs) to DNA using mathematical models and machine learning, (ii) understanding the mechanisms and functional role of 3D chromatin organisation and (iii) investigating the functional role of histone modifications and DNA methylation on gene regulation using statistical models, machine learning and explainable AI. 

Current projects on chromatin and epigenetics in the lab include: 

1. Investigation of the role of architectural proteins and active transcription in 3D genome organisation and the functional role of 3D genome organisation on gene regulation. We are combining conformation capture and molecular biology experiments with existing and new statistical models to disentangle the relationship between 3D genome organisation, binding of architectural proteins, chromatin state (histone modifications) and active transcription. 

2. Understanding the combinations of histone modifications that define enhancer regions and favour the binding of TFs. To achieve that we are using machine learning and explainable artificial intelligence together with histone modification ChIP data and STARR-seq enhancer annotation. 

3. Characterisation of TF binding mechanisms to the DNA in fruit fly and mammalian systems. In particular, we use new statistical models developed in the lab together with genomics and molecular biology techniques to classify TF based on their binding behaviour and extract their binding parameters.

4. Determining the epigenetic signatures of exposure to air pollution. We are using new statistical models together with social data and DNA methylation profiles from Understanding Society to map and further investigate differentially methylated regions of the genome that correlate with exposure to high level of air pollution.

Radu’s lab is a part of QMUL Epigenetics Hub.

Group Members

• Duarte Polvora Brandao
  
  

Publications

Key Publications

Chathoth, K.T., Mikheeva, L.A., Crevel, G., Wolfe, J.C., Hunter, I., Beckett-Doyle, S., Cotterill, S., Dai, H., Harrison, A. and Zabet, N.R.*, (2022) ‘The role of insulators and transcription in 3D chromatin organisation of flies.’ Genome Research, 32: 682-698, doi: 10.1101/gr.275809.121. [3D chromatin organisation, architectural proteins, gene regulation]

Grant, O.A., Wang, Y., Kumari, M., Zabet, N.R.* and Schalkwyk, L.C., (2022) ‘Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array.’ Clinical Epigenetics, 14 (62) doi: 10.1101/2021.09.02.458717. [DNA methylation, sex differences, whole blood]

Wolfe, J. C., Mikheeva, L. A., Hagras, H. Zabet, N.R.*, (2021) ‘An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila.’ Genome Biology, 22: 308, doi: 10.1186/s13059-021-02532-7. [explainable Artificial Intelligence, enhancers, gene regulation]

Chathoth, K.T., and Zabet, N. R.*, (2019). ‘Chromatin architecture reorganisation during neuronal cell differentiation in Drosophila genome.’ Genome Research, 29(4):613-625, doi: 10.1101/gr.246710.118. [3D chromatin organisation, architectural proteins, gene regulation]

Catoni, M., Tsang, J. M. F., Greco, A. P. and Zabet, N. R.*, (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, doi: 10.1093/nar/gky602. [DNA methylation, new method]

*corresponding author

All Publications

Supervision

Olivia Grant (PhD student)
Ines Hofer (PhD student)
Robyn Emerson (PhD student)
Salma Elsahhar (PhD student)
Khizra Maqsood (PhD student)