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., 2021, Identification of reduced host transcriptomic signatures for tuberculosis disease and digital PCR-based validation and quantification, Frontiers in Immunology, Vol:12, ISSN:1664-3224
Nguyen SH, Cao MD, Coin LJM, 2021, Real-time resolution of short-read assembly graph using ONT long reads, Plos Computational Biology, Vol:17, ISSN:1553-734X
et al., 2020, Comparison of long-read methods for sequencing and assembly of a plant genome, Gigascience, Vol:9, ISSN:2047-217X
et al., 2020, Whole-exome sequencing for the identification of rare variants in primary immunodeficiency genes in children with sepsis - a prospective population-based cohort study., Clinical Infectious Diseases, Vol:71, ISSN:1058-4838, Pages:e614-e623
et al., 2020, Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations, Nature Genetics, Vol:52, ISSN:1061-4036, Pages:1256-+