Charles Breeze, PhD Student
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.
Anna Koeferle, PhD student
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.
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.
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.