Kabita Shakya

“Content Evaluation and tool development for knowledge management system: Colon Cancer”

My project aims to develop a set of tools for biomedical research on colon cancer, and to address the fundamental question of model suitability for human colon cancer. Firstly, I addressed the issue of dataset assembly and database curation by data mining and knowledge discovery. Here, I focused on annotation and augmentation of  the StatEpigen biomedical resource (http://statepigen.sci-sym.dcu.ie/), which included manual curation of data as well as automation of possible data curation work. This work incorporated correlating genetic and epigenetic interactions, along with different stages of pathology development. Statepigen is a highly specific database of colon cancer epigenetic statistics. The second focus of my MSc thesis is to determine if cancer has acted as a selective pressure in the evolutionary history of mammals, and if that pressure has been different between human and mouse (since mouse is used as a model organism for many human cancers).  We wished to determine whether, in the 200 million years of independent evolution, if there has been differential rates of functional shift in orthologous proteins in human and mouse and we explored what impact this might have for modeling human cancer. Both aspects of this work have been published – see our publications page. I am now completing my MSc research thesis.

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We are always looking for collaborators and new people to come and work with us. Please get in contact if you are interested in what we do: m.oconnell@leeds.ac.uk