Bobby

Robert Bentham

PhD student, CoMPLEX
Physics Building, Gower Street, UCL
London, WC1E 6BT

robert.bentham.11@ucl.ac.uk

About

In 2011 I joined CoMPLEX (Centre of Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology), entering the MRes/PhD programm. After completing the MRes year in October 2012 I started a PhD on "The bioinformatic analysis of the interface between mitochondrial biogenesis and cell death signalling pathways", supervised by Dr Gyorgy Szabadkai and Dr Kevin Bryson. Before coming to UCL from 2007 to 2011 I studied at Imperial College London, graduating with a MSci in Mathematics.

PhD (2012 - Present)

Bioinformatic analysis of the interface between mitochondrial biogenesis and cell death signalling pathways

Disease states are often associated with radical rearrangements of cellular metabolism. In cancer, this fosters increased proliferation; leading to unique gene expression patterns. Mitochondria are central to many of these pathways. This suggests that the transcriptome underlying mitochondrial biogenesis will follow a distinctive pattern.

My PhD investigates this change in mitochondrial biogenesis by analysing big gene expression data sets (e.g. Cancer Cell Line Encyclopedia), and when necessary creating new bioinformatic tools to elucidate the role of mitochondrial biogenesis.

Publications
Astin, R., Bentham, R., Djafarzadeh, S., Horscroft, J. A., Kuc, R. E., Leung, P. S., ... & Szabadkai, G. (2013). No evidence for a local renin-angiotensin system in liver mitochondria. Scientific reports, 3.
show/hide descriptions

MRes (2011 - 2012)

During the MRes year I had the opportunity to work on a wide variety of topics, here is a summary of my work:

CP1: Evolution of shape in Diatoms.
Supervised by Dr. Karen Page and Dr. Eileen Cox.
I investigated the evolution of shape in centric diatoms by probabilistic means on phylogenetic data using the Bayes Traits software, developed by Mark Pagel, which uses Markov Chain Monte Carlo (MCMC) methods to estimate ancestral characteristics.

CP2: Bioinformatic analysis of the interface between mitochondrial biogenesis and apoptotic cell death signaling pathways in Parkinson's disease.
Supervised by Dr. Gyorgy Szabadkai and Dr. Kevin Bryson.
I investigated microarray data from patients with Parkinson's disease, using gene set enrichment analysis (GSEA) packages from R Bioconductor, I showed that in these patients besides down-regulated mitochondrial pathways, pathways involving DNA damage were also altered.

CP3: Perturbations of networks and the transition to cancer. Supervised by Dr. Simone Severini and Dr. Andrew Teschendorff.
I applied a model of cascade failure in an attempt to explain how a healthy cell develops into a cancerous cell, this was done using large gene expression data sets and the known protein interaction network.

Summer Project: The application of sparse supervised machine learning to predict variables affecting the mitochondrial biogenesis pathway in cancer.
Supervised by Dr. Gyorgy Szabadkai and Dr. Kevin Bryson.
Using the CCLE (Cancer Cell Line Encyclopedia) I attempted to use machine learning methods to predict the activity of mitochondrial biogenesis in different cancer cell lines from gene expression data. Sparse linear models such as the LASSO method as well as SVMs and random forest methods were used.