I am a Research Associate in the EPSRC Centre for Mathematics of Precision Healthcare, working with Dr. Caroline Colijn. My work concerns the mathematical modelling and statistical simulation of disease spread from person to person. Specifically, I am looking at ways to integrate genomic and epidemiological data to infer transmission patterns in tuberculosis outbreaks.
In a disease outbreak, it is of extreme importance for public health authorities to know when and where the outbreak originated from, identify sources of transmission, active transmission clusters, possible missing cases and establish transmission links between cases. Traditional epidemiological approaches to investigating an outbreak have limitations because data is hard to collect and often inaccurate; and whereas molecular typing approaches help identify transmission clusters by comparing specific loci in the TB genome, the process is both time-consuming and costly. As whole-genome-sequencing becomes more cheaper than before, there has been enormous interests in using the genomic information of the pathogens to help infer transmission links between patients. My work focuses on developing quantitative approaches to transmission inference combining pathogen sequence and patients data, drawing on ideas from statistical inference and simulation.
I received my PhD in scientific computing in 2016, from the Centre for Scientific Computing at the University of Warwick, under the supervision of Prof. Mark Rodger (who sadly passed away in 2017). I worked on the development, implementation and application of efficient Monte Carlo conformational sampling methods to lattice protein aggregation models that embodies secondary structures of the proteins in question. Prior to my PhD, I obtained a MSc degree in financial mathematics and computation at the University of Leicester.
et al., 2018, Estimating Transmission from Genetic and Epidemiological Data: A Metric to Compare Transmission Trees, Statistical Science, Vol:33, ISSN:0883-4237, Pages:70-85
Xu Y, Rodger PM, 2017, MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation, Journal of Computational Physics, Vol:333, ISSN:0021-9991, Pages:128-141
Xu Y, Rodger PM, 2015, Improved Estimation of Density of States for Monte Carlo Sampling via MBAR, Journal of Chemical Theory and Computation, Vol:11, ISSN:1549-9618, Pages:4565-4572