I am working on various statistical and mathematical problems in genomics. I am particularly interested in building mathematical models to identify genetic variants in high-throughput genomics data - including genotyping microarrays and next generation sequence data - with the ultimate aim of understanding the functional impact and evolutionary history of these variants.
Software can be found on my github page:
ECCB 2012 report
Yhap software for identifying haplogroups from low coverage sequence data: Yhap_0.51
ExomeCNVTest software : ExomeCNVTest_0.51
SOAP-popIndel software for genotyping indels in exome data
cnvHiTSeq - software for detecting and genotyping CNVs in WGS data: cnvHitSeq
cnvPipe - software to enable CNV meta analysis: cnvPipe_v0.82
Software for converting IMPUTE format to format used by MultiPhen software: convertImpute
MultiPhen software: MultiPhen
vntrTest is a program for assessing association of VNTR fragment length genotypes with either continuous or case-control outcomes.
cnvHap is a program for joint copy number genotyping, which uses a haplotype model of copy number variation and integrates data from multiple platforms. It also carries out CN association.
polyHap is a program for phasing polyploids and copy number regions.
See http://dx.doi.org/10.1186/1471-2105-9-513 for more details.
The first version was designed just for phasing polyploid regions (with the restriction that the ploidy is fixed across the entire region of analysis).
We have extended polyHap to remove this restriction, so that it can phase CNV regions (from pre-calculated CNV/SNP genotypes):
AncesHC is a program for determining the haplotype structure of a population sample from genotype data, and then testing for association of these haplotypes with either a binary or continous outcome.
See http://dx.doi.org/10.1093/bioinformatics/btn071 for more details.
metaMapper is a program for flexible, scalable GWAS meta-analysis and visualisation.
Software for simulating sequence level data with inversions. See http://dx.doi.org/10.1093/bioinformatics/btq029 for more details. Developed in conjunction with Clive Hoggart and Paul O'Reilly.
Pseudogene inference from loss of constraint (PSILC)
Software for identifying pseudogenes via loss of evolutionary constraint:
PSILC version 1.21
Supplementary information from paper "Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases"
et al., 2024, Plasma Protein Biomarkers Distinguish Multisystem Inflammatory Syndrome in Children From Other Pediatric Infectious and Inflammatory Diseases., Pediatr Infect Dis J
et al., 2024, Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis., Microbiol Spectr, Vol:12
et al., 2024, Serum Levels of Vitamin C and Thiamin in Children With Suspected Sepsis: A Prospective Observational Cohort Study., Pediatr Crit Care Med, Vol:25, ISSN:1529-7535, Pages:171-176
et al., 2024, PLANNER: a multi-scale deep language model for the origins of replication site prediction., Ieee J Biomed Health Inform, Vol:PP
et al., 2023, Wastewater-based epidemiology of Campylobacter spp.: A systematic review and meta-analysis of influent, effluent, and removal of wastewater treatment plants, Science of the Total Environment, Vol:903, ISSN:0048-9697