Imperial College London


Faculty of MedicineDepartment of Infectious Disease

Honorary Senior Lecturer



+44 (0)20 7594 1930l.coin




172Medical SchoolSt Mary's Campus





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:

More information:

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

Toy example for 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 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 for more details.


metaMapper is a program for flexible, scalable GWAS meta-analysis and visualisation.


Software for simulating sequence level data with inversions. See 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 data
Supplementary information from paper "Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases"



Yeoh S, Estrada-Rivadeneyra D, Jackson H, et al., 2024, Plasma Protein Biomarkers Distinguish Multisystem Inflammatory Syndrome in Children From Other Pediatric Infectious and Inflammatory Diseases., Pediatr Infect Dis J

Harris PNA, Bauer MJ, Lüftinger L, et al., 2024, Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis., Microbiol Spectr, Vol:12

McWhinney B, Ungerer J, LeMarsey R, 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

Wang C, He Z, Jia R, et al., 2024, PLANNER: a multi-scale deep language model for the origins of replication site prediction., Ieee J Biomed Health Inform, Vol:PP

Zhang S, Shi J, Li X, 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

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