Medical Genomics Group Members
Group Leader: Professor Stephan Beck
The laboratory has broad interests in the genomics and epigenomics of phenotypic plasticity in health and disease. In addition to genetic variations, we study epigenetic variations such as DNA methylation, histone modifications and microRNAs and how they modulate genome function. Central to our research is the development of systems approaches for integration of multi-dimensional data and their application to epigenome-wide association studies (EWAS) in cancer and other common diseases to advance translational, regenerative and personalized medicine. The Medical Genomics Group offers state-of-the-art facilities and a stimulating environment for graduate and post-doctoral training.
James Barrett, Research Associate
Further Details: I am interested in the statistical analysis of biomedical data. The integration of multiple genomic datasets, dimensionality reduction techniques, Bayesian methods, and survival analysis (especially competing risks) are of particular interest. I am attempting to derive low dimensional biomarkers from genomic data that are useful for predicting clinical outcomes, making accurate diagnoses, or determining drug response. I am developing new mathematical and statistical tools to do this. I joined the Medical Genomics group at UCL in 2014 and am collaborating with the OncoTrack consortium. I obtained a PhD in Applied Mathematics from King’s College London in 2014 (with Ton Coolen at the Institute for Mathematical and Molecular Biomedicine). I also completed an MSc in Mathematics at King’s College London (in the Disordered Systems Group). My undergraduate degree was in Theoretical Physics at Trinity College Dublin
Charles Breeze, PhD Student
+44 (0)20 7679 0997
Further Details: I studied Biochemistry and Bioinformatics at the University of Navarra, Spain, graduating in 2013. During my studies at university I was awarded two research placements at the University of Oxford, with Prof. Charles Lawrie (Ballabio et al, 2012) and Prof. Alison Banham (LLR studentship). I joined Prof. Stephan Beck’s group with a Marie Curie PhD fellowship to research the epigenetics of complex traits and diseases, as part of the EpiTRAIN Initial Training Network. I am one of the organisers of the Quantitative Genomics 2016 conference.
Pawan Dhami, Research Associate
+44 (0)20 7679 0997
Further Details: After completing my post graduation studies in India in the field of Human Genetics, I moved to the UK to pursue a career in research. Subsequently, I completed my PhD in 2006 under the supervision of Dr. Dave Vetrie based at the Sanger Institute, Cambridge. My PhD thesis involved elucidation of DNA-protein interactions using ChIP-chip to study the transcriptional regulation of SCL gene during haematopoietic development. I also used ChIP-chip assay to build maps of DNA-protein interactions at a genome-wide scale in the human and mouse genomes to identify and elucidate various classes of cis-regulatory functional elements, e.g. promoters, enhancers, insulators etc. and link these functional elements to biological processes. In May 2008, I joined Prof. Stephan Beck's lab to understand how DNA methylation plays a role in vertebrate development.
Andrew Feber, Research Associate
+44 (0)20 7679 0963
Further Details: I completed my BSc (Hons) degree at the University of Newcastle Upon Tyne. In 2001 I joined the Institute of Cancer Research, where under the supervision of Prof. Colin Cooper I carried out my PhD, investigating the genomic alterations associated with the development and progression of urological cancers. In September 2005 I joined the laboratory of Dr. Tony Godfrey at Mount Sinai Medical School, New York, to start my postdoctoral training. During my time in New York I worked on the integration of high resolution genomic copy number, gene expression and miRNA expression data to define molecular signatures associated with esophageal cancer patient survival and to identify novel therapeutic targets. In March 2008, I returned to the UK to join the laboratory of Prof. Stephan Beck, at the UCL Cancer Institute, London, to investigate the role of methylation in the development and progression of cancer.
Anna Koeferle, PhD student
+44 (0)20 7679 0963
Further Details: I completed an undergraduate degree in Biochemistry at the University of Oxford in 2012. My dissertation project, which I undertook in Prof. Peter Cook’s lab at the Sir William Dunn School of Pathology, focused on a model in which transcription occurs in ‘specialized transcription factories’. I attempted to test this model through targeted manipulation of a well-characterised gene loop using a zinc-finger nuclease. In September 2013, I joined Prof. Stephan Beck’s lab in order to commence my PhD, for which I receive funding from CR-UK. I have a general interest in how epigenetic changes contribute to tumorigenesis and plan to use a TALE/CRISPR-based system for targeted epigenetic reprogramming of cancer cells.
Miljana Tanic, Research Associate
+44 (0)20 7679 6004
Further Details: I graduated in 2008 at the University of Belgrade in Molecular Biology and Physiology. The following year I earned an MSc, and in 2012 a PhD from the Faculty of Medicine at the Universidad Autonoma de Madrid. I carried out my PhD under the supervision of Prof. Javier Benitez at the Spanish National Cancer Research Centre (CNIO), where I was studying the role of miRNAs in hereditary breast cancer. As a part of my PhD training I did a secondment in the group of Jose Silva at Columbia University, developing a new method for high-throughput miRNA screening. In 2012 I returned to my home country, to work in the Institute for Oncology and Radiology of Serbia (IORS), where I studied molecular mechanisms of resistance to preoperative radiotherapy in locally advanced breast cancer. In 2015, I joined Prof. Stephan Beck’s group, at the UCL Cancer Institute, to develop new methods for targeted bisulfite sequencing of circulating tumour DNA and to study the evolution of the epigenetic landscape during colorectal cancer progression and therapy resistance.
Emanuele Libertini, Research Associate
+44 (0)20 7679 0999
Further Details: Graduating from the University of London with a PhD in Bioinformatics in 2010, I have two undergraduate degrees: a BSc in Biology (York) and a BA in Creative Writing (Brunel). My PhD was focused on building a gene network using multiple types of data, modelling stress-induced hormone-driven responses in Arabidopsis. In 2010-11, as a UCL teaching fellow, I taught a Biology course in Astana, including lectures, tutorials and practicals (laboratory and computer-based). As a post-doc, my work at Institut Pasteur Paris has brought me in close collaboration with the bacterial-human cell interaction group led by Pascale Cossart. Based at the Epigenomics and Transcriptomics unit (PF2) led by Jean-Yves Coppé, I have been working as key developer of workflows for the analysis of sequencing data, focussing on DNA methylation, protein occupacy and transcription. The EpiLis project (led by Helene Bierne) has been my main focus: working with mammalian cells, developing an insight onto chromatin remodellers and DNA methylation within bacterial infection-induced epigenetic pathways. I joined Stephan Beck's group in January 2014 to contribute to the next generation sequencing analysis and work as resident computational biologist.
Chris Pipinikas, Research Associate
Sabrina Stewart, PhD student
+44 (0)20 7679 0999
Christina Thirlwell, Cancer Research UK Clinician Scientist and Senior Lecturer in Medical Oncology
+44 (0)20 7679 0997
Further Details: I graduated in Medicine at UCL in 1997 having undertaken an integrated BSc in Immunology in 1994. I went on to train in Medical Oncology and undertook my PhD with Prof. Ian Tomlinson at the Cancer Research UK London Research Institute in colorectal cancer genetics. I completed my clinical training in Medical Oncology whilst furthering my research interests in cancer epigenetics between 2008 and 2010 as post-doc in Stephan Becks lab at the UCL Cancer Institute. In 2010 I started my first Clinician Scientist post and currently work as a Consultant in Medical Oncology at the Royal Free Hospital specialising in Neuroenodocrine Tumours – where we are a European Centre of Excellence. I also treat Hepatobiliiary cancer. I now have a post-doc Chris Pipinikas and PhD student Anna Karpathakis working with me in the lab where we are performing large-scale integrated genomic analysis of Neuroendocrine tumours. Our ultimate aim is to further our understanding of the biology of these tumours whilst identifying and validating novel biomarkers.