Our lab works on fundamental and translational aspects of gene regulation in cell differentiation and cancer using approaches of biophysics, bioinformatics and next generation sequencing (see publications). We also maintain the NucPosDB database and few other community resources.
Our research is centred around nucleosomes. We are investigating how nucleosomes interact with transcription factors and other chromatin players to fine tune gene regulation in cell differentiation and cancer transitions, and how this fundamental information can be translated to the clinic to aid patient diagnostics, stratification and monitoring for personalised medicine. We collaborate with the NHS and other stakeholders to develop a new generation of liquid biopsies based on the nucleosomics analysis of cell-free DNA (cfDNA). Our another long-term theme of work is the interplay of transcription factors with nucleosomes and other chromatin players to direct gene regulation. CTCF is one of our favourite transcription factors, but we also have a few other fovourites 🙂
This web site contains resources relevant to gene regulation, including nucleosome positioning (NucPosDB is a centralised database of experimental nucleosome maps in vivo, cell-free DNA (cfDNA), algorithms to predict nucleosome positioning and computational tools to analyse nucleosome positioning experiments) and protein-DNA binding (e.g. the section TF binding contains information about databases of transcription factors weight matrices, experimental binding datasets and computational tools). A frequently updated section is devoted to upcoming conferences and schools relevant to quantitative gene regulation. Recently we started maintaining the real-time calendar of online events such as webinars. In addition, we maintain a list of undergraduate research opportunities , postdoctoral and PhD fellowships, as well as travel grants. Finally, the Open Science sections contain information about the present and future of science online including the Academic Mastodon/Twitter and the Fragile Nucleosome online discussion community.