Summary
The development of complex organisms critically depends upon regulation of gene activity across dozens, hundreds or millions of cells in time and space. This regulation ensures the fidelity of development of complex structures and the overall function of the organism. Its disruption therefore often leads to disease.
We study gene regulation at the genomewide level using computational genomics and epigenomics. Our major research interests focus on:
- Structure and function of gene promoters
- Function and genomic distribution of gene regulatory elements
- Function of transcription factors
- Regulation of the production of transcription factors i.e. transcriptional regulatory networks (TRNs)
- Association of different modes of regulation with epigenetic marks and their inheritance
Our recent work centres on the functional classification of core promoters, the development of methods to correctly assign regulatory elements to the genes they regulate, and the role of the epigenome in guiding development.
Publications
Journals
Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, et al., 2024, JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles., Nucleic Acids Res, Vol:52, Pages:D174-D182
Nikumbh S, Lenhard B, 2023, Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation., Plos Comput Biol, Vol:19
Al-Jibury E, King JWD, Guo Y, et al., 2023, A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks, Nature Communications, Vol:14, ISSN:2041-1723
McAllan L, Baranasic D, Villicaña S, et al., 2023, Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes, Nature Communications, Vol:14, ISSN:2041-1723, Pages:1-20
Paterson HAB, Yu S, Artigas N, et al., 2022, Liver RBFOX2 regulates cholesterol homeostasis via Scarb1 alternative splicing in mice, Nature Metabolism, Vol:4, ISSN:2522-5812, Pages:1812-1829