PhD student profiles


Liberty Foreman
Joined the Wellcome Trust 4-year Interdisciplinary PhD Programme in Autumn 2011 funded by Birkbeck

Project title
Investigating the use of single element ATR-FTIR spectroscopy as a clinical diagnostic tool

Principle investigator: Professor Peter Rich, ISMB, UCL
Co-investigators: Prof. Laurence Lovat (UCLH) and Prof. Tom Fearn (Dep. of Statistics), UCL

I graduated in Molecular Genetics from the University of Sussex in 2011 where I undertook a bioinformatics project as my final year project. During this time I developed a real passion for computational analysis, where I found that combining lab based and computational research is extremely powerful. I applied for the ISMB rotational PhD programme as it gave me the opportunity to explore this combination of computation and lab based science in different areas of life science.
Rotation projects

Rotation 1: September 2011 – January 2012
Preliminary Characterization of ORF145: An Acidianus Two-tailed Virus (ATV) protein.
Principal investigator: Prof. Finn Werner

This project involved optimisation of the expression and purification protocol for the hyperthermophile crenarcheon viral protein (ORF145). This lead to the preliminary characterization of its structure and function giving insight into how the virus affects transcription using NMR.

Rotation 2: January 2012 – April 2012
Optimizing Molecular Modeling techniques to aid characterization of GPCR P2Y11. 
Principal investigator : Prof. Peter Coveney. Co-investigator: Dr. Andrea Townsend-Nicholson

P2Y11 is a GPCR involved in the slow relaxation of the stomach. By blocking this receptor, it is though possible to prevent the stomach from expanding, opening it up as a drug target for a new weight loss method. However, crystalising GPCRs is notoriously difficult. Therefore to gain a structure computational homology modeling was used, followed by coarse-grained molecular dynamics of single helix dimerization to further characterize this potential drug target.

Rotation 3: April 2012 - present
IR spectroscopy as a clinical diagnostic method of pre-cancerous Barratt’s esophagus.
Principal investigator: Prof. Peter Rich. Co-investigators: Prof. Laurence Lovat (UCLH) and Prof. Tom Fearn (Dep. of Statistics)

Barrett’s oesophagus (BE) is the recognized pre-cursory lesion to oesophageal adenocarcinoma and occurs in patients with chronic gastroesophageal reflux disorder (GERD). The prognosis for esophageal adenocarcinoma (EAC) is poor with a 5 year survival rate, therefore it is extremely important to detect the progression of the disease early.

PhD Project

In this highly interdisciplinary PhD project I am exploring the potential of single element Attenuated Total Reflectance - Fourier Transform Infrared (ATR-FTIR) spectroscopy as a relatively simple means to provide a clinically feasible method for rapid, point-of-care screening of dysplastic BE biopsies before histological analysis. This method could aid clinicians’ decision making, leading to reduced histological sampling, which would ultimately lower the cost of BE surveillance and enable immediate treatment for those identified with dysplastic BE.

To guide detection of signatures of specific diseased cell types, we have used information from FTIR microspectroscopic images of specific cell types. This allowed the single element ATR-FTIR spectra to firstly be sorted into different cell type groups using k-means clustering. Partial least squares (PLS) regression and logistic regression were then used to produce an automated, statistically robust BE screening tool that classifies, using additional misclassification costs, biopsy spectra into either a SQ/NDBE, HGD/EAC or inconclusive class.




Institute of Structural and Molecular Biology, University of London
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