Grants, Software & Publications
Reservoirs of mobile antibiotic resistance genes in the gut microbiome of preterm infants
Institute of Integrative Biology funding scheme; competitively awarded during PostDoc
2 rounds of competitive funding, awarded during PhD
Here are a selection of my most recent projects. Please click on the links to find out more or visit my GitHub page.
appromiately weighted variation graphs for haplotype identification
a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples (a.k.a. Resistome Profiling).
a tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
A pipeline for Detecting Resistome Associated taXa
Co-first author publications are indicated by *. Please visit Google Scholar for the most current list.
When The Levee Breaks: a practical guide to sketching algorithms for processing the flood of genomic data
Genome Biology. 2019
The diversity, evolution and ecology of Salmonella in venomous snakes
PLOS Neglected Tropical Diseases. 2019
A Fast Machine Learning Workflow for Rapid Phenotype Prediction from Whole Shotgun Metagenomes
Streaming histogram sketching for rapid microbiome analytics
Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580
PLoS biology. 2019
Indexed variation graphs for efficient and accurate resistome profiling
Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa
Genome medicine. 2017
Detection of the florfenicol resistance gene floR in Chryseobacterium isolates from rainbow trout. Exception to the general rule?
FEMS microbiology ecology. 2017
Overexpression of antibiotic resistance genes in hospital effluents over time
Journal of Antimicrobial Chemotherapy. 2017
Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment
Water Science and Technology. 2016
Search engine for antimicrobial resistance: a cloud compatible pipeline and web interface for rapidly detecting antimicrobial resistance genes directly from sequence data
PLoS One. 2015
Host subtraction, filtering and assembly validations for novel viral discovery using next generation sequencing data
PLoS One. 2015
Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant
Genome research. 2011