Genomics at the University of Essex

The function of many genes is still unknown and their regulation and interactions even less. Epigenetic 'marks' on chromosomes clearly have a role in recording developmental choices and environmental influences. Powerful new techniques make this is an exciting time for studying epigenetic mechanisms and what they tell us about gene functions. I am working on methods and software for analysing DNA methylation, and epigenomic studies including whole epigenome studies of Alzheimer disease and schizophrenia.

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I am an evolutionary biologist fascinated by the causes that underlie the origins and diversity of the Animal Kingdom, especially the evolution of animal genomes and their body plans, as well as their systematics. My research spans molecular phylogenetics and evolutionary genomics, merging zoology (especially "invertebrates"), genetics and genomics, evodevo, metagenomics and bioinformatics.

Some of the groups I have worked on are the Metazoa (all the multicellular animals), the Opisthokonta (the eukaryote super-group including animals, fungi and choanoflagellates among others), the bilaterian super-clade Lophotrochozoa, the Platyhelminthes (free-living flatworms, but also parasitic ones), the Acoelomorpha, Xenoturbella, Chaetognatha, Gastrotricha and molluscs among many others.

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I am interested in addressing fundamental questions in chromatin biology and gene regulation by employing cutting edge molecular biology, and together with high throughput approaches in cancer and stem cells. My long-term goal is to unravel the mechanism in distal regulation of gene expression and how mutations at regulatory elements lead to specific disease, with the focus on enhancers and lncRNAs.

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Radu is interested in understanding gene regulation mechanistically. In particular, he focuses on two aspects: binding of TFs to the DNA and DNA methylation. Transcription factors (TFs) are proteins that bind to specific positions on the DNA and control gene activity (the rate at which genes are expressed). Radu's work focuses on modelling the diffusion of TFs in the cell and extracting the rules that define where TFs bind to the genome and which genes they regulate. He also developed a new software tool that is able to perform computer simulations of the diffusion of TFs in the cell (GRiP) and also tools to predict computationally how binding profiles of TFs look like (ChIPseqProfile). In addition to TFs binding to the genome, Radu also developed an interest in understanding DNA methylation and, in particular, he focuses on developing a new method to detect differential methylation from whole genome bisulfite sequencing data. This method is available in the form of an R/Bioconductor package called DMRcaller, which is fast and works both for plants and mammalian systems.

Biophysicist by initial education, Vladimir Teif has been working on DNA-protein-drug binding since 1998. A decade later he become interested in nucleosome positioning and chromatin organization, and currently enjoys integrative bioinformatics analysis of next generation sequencing datasets and modeling epigenetic regulation in chromatin, broadly defined. Apart from computational/systems biology, Vladimir Teif is also interested in conceptually new ways of doing science in the Internet era, which he calls 'Science 3.0'.

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Evolution is driven by changes in the genome, not only in their gene products but in their regulatory interactions. My research interest is in evolutionary genomics with a strong focus on gene regulatory mechanisms. My current projects focus on microRNA function and evolution. You can find more about me in my personal site. If you have an interest in history of science you may want to visit my blog.

High throughput omic technologies are generating big data useful to address a number of biological and clinical questions. Recent advances in DNA synthesis methods provide unprecedented opportunities to integrate omic information into synthetic systems to test hypotheses in vivo.

I am working on computational methods to design and analyse genomic information, aiming at understanding its role in fundamental biological processes and diseases. To do this, I developed different approaches, ranging from evolutionary optimization to statistical modelling and network theory.

I obtained a Ph.D. in computer science from the University of Catania in Italy. Successively, I was a postdoctoral fellow at Johns Hopkins University, working on the synthetic yeast project (Sc2.0), and later at the University of Oxford, focusing on cancer genetics. Currently, I am Lecturer at the School of Computer Science and Electronic Engineering.

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Meena is a leading expert in biomarkers and genetics, and has worked to apply insights from these areas to better understand ageing, cardiovascular disease, and health inequalities using the Whitehall II cohort study of British civil servants and the English Longitudinal Study of Ageing. She remains an Honorary Professor at UCL. She continues to lead research on the social-biological interface and genetic epidemiology as an investigator for Understanding Society.

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I explore how the genome, especially in terms of gene expression, is regulated by its dynamic packaging into chromatin and how this allows stem and progenitor cells, e.g., intestinal stem cells, to respond and to adapt to the environment.

An important level of gene regulation occurs at the packaging of genes into the chromatin superstructure. The first building block of chromatin is the nucleosome, composed of histone proteins around which DNA winds. How gene and genome regulation happens dynamically through chromatin remodeling is of fundamental importance, but still requires much illumination. I have a long standing interest in the biochemistry of nucleosome remodelling factors and their role in maintaining specific chromatin states.

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My research and interests are in the field of cell and molecular biology and proteomics with special emphasize on cancer. We use quantitative mass spectrometry, molecular genetics, and computational approaches and statistics to study how aberrant protein expression, protein interactions and phosphorylation affect the tumour phenotype. The long term aim is to contribute to the development of novel diagnostics and therapies for cancer.

--My publications

Nicola is a demographer and statistician interested in the genetics of human reproduction. His work includes genome-wide association studies on fertility traits and gene-environment interactions in social sciences. He is a Reader at the Institute for Social and Economic Research a co-Director of the ESRC Research Centre on Micro-Social Change (MiSoC). 

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I am a structural and evolutionary geneticist interested in the relationship between the structure of the nucleus, and the function of a cell. I develop software tools for high-throughput morphological analysis of microscopy data. I am especially interested in nuclear shape and chromatin organisation in asymmetric cells such as sperm. Recently I have been studying the evolutionary differences in sperm development between strains of mice, the effects of gene knockouts on sperm functionality, and the differences between highly fertile and sub-fertile semen samples.