- University of HullPhD Bioinformatics, 2010 - 2015
- University of YorkBioinformatician, 2015 - present
Genome Biology | Full text | Dragging scientific publishing into the 21s...
Scientific publishers must shake off three centuries of publishing on paper and embrace 21st century technology to make scientific communica
BMC Bioinformatics | Full text | CLAST: CUDA implemented large-scale ali...
Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searchin
BMC Bioinformatics | Full text | ANGSD: Analysis of Next Generation Sequ...
High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are nee
BMC Bioinformatics | Full text | CAR: contig assembly of prokaryotic dra...
Next generation sequencing technology has allowed efficient production of draft genomes for many organisms of interest. However, most draft
HTSeq—a Python framework to work with high-throughput sequencing data
Abstract Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. Howeve
BMC Evolutionary Biology | Abstract | Divergent evolutionary rates in ve...
The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles du
The Ensembl REST API: Ensembl Data for Any Language
Abstract Motivation: We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server e
ballaxy: web services for structural bioinformatics
Abstract Motivation: Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinfo
poRe: an R package for the visualization and analysis of nanopore sequen...
Abstract Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by t
Insights into structural variations and genome rearrangements in prokary...
Abstract Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversion
BigDataScript: a scripting language for data pipelines
Abstract Motivation: The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large
Monte Carlo algorithms for Brownian phylogenetic models
Abstract Motivation: Brownian models have been introduced in phylogenetics for describing variation in substitution rates through time, with