Category Archives: Publications

Field-based, real-time metagenomics and phylogenomics for responsive pathogen detection: lessons from nanopore analyses of Acute Oak Decline (AOD) sites in the UK.

Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018


In a globalised world of increasing trade, novel threats to animal and plant health, as well as human diseases, can cross political and geographical borders spontaneously and rapidly. One such example is the rise of Acute Oak Decline (AOD) in the UK, a multifactorial decline syndrome with uncertain aetiology, vectors, and host risk factors first reported in the UK a decade ago. Affected oaks display significant morbidity and mortality, with symptoms including vascular interruption, crown loss and characteristic striking bark lesions breaching cambium and filled with a viscous, aromatic, dark-brown/black exudate, which may sometimes be released under considerable pressure. Although multiple bacterial species have been associated to lesion sites in affected oaks, and a putative insect vector identified, the basic risk factors, transmission, progression and treatment of the syndrome remain unclear.

This dispiriting state of affairs presents an ideal opportunity to exploit recent developments in nanopore sequencing to develop and test field-based methods of real-time phylogenomics and metagenomics to establish baseline data for healthy oaks, and contrast these with affected / dying oaks to shed light on syndrome causes and management. WGS metagenomic sampling was carried out on leaf and bark tissue from 37 affected, asymptomatic, and recovering individuals (nine Quercus species) at three field sites over a year. Extraction and DNA sequencing were performed in the field for a subset of samples with MinION nanopore rapid sequencing kits, and also using MinION and paired-end Illumina sequencing under laboratory conditions. Metagenomic analyses to determine microbial community composition were carried out, and real-time phylogenomic methods were also developed and applied. Early results from these analyses and lessons for future work are presented.

Metagenomic datasets can be rapidly generated in the field with minimal equipment using nanopore sequencing, providing a responsive capability for emerging disease threats and reducing transmission risks associated with transporting quantities of potentially infectious samples from outbreaks of novel diseases. Furthermore, real-time data analysis can provide rapid feedback to field teams, both to inform management decisions and also to allow for adaptive experimental protocols that dynamically target data collection to extract maximum information per unit effort.

Inference and informatics in a ‘sequenced’ world

Short lecture relating my recent work on real-time phylogenomics, implications for bioinformatics research and future directions of genomic/phylogenetic modelling to explicitly account for phylogeny, synteny and identity through coloured graphs.

University of Reading, 2nd August 2017

Slides [SlideShare]: cc-by-nd

Using field-based DNA sequencing to accelerate phylogenomics

Invited seminar at the Department of Zoology, Oxford University, 30th November 2016.

Summary of our field-based real-time phylogenomics (MinION DNA sequencing) experiments this year, and applicability to broad-scale tree-of-life phylogenomics and macroevolutionary biology.

Slides [SlideShare]: cc-by-nd

Single-molecule real-time (SMRT) Nanopore sequencing for Plant Pathology applications

A short presentation to the British Society for Plant Pathology’s ‘Grand Challenges in Plant Pathology’ workshop on the uses of real-time DNA/RNA sequencing technology for plant health applications.

Doctoral Training Centre, University of Oxford, 14th September 2016.

Slides [SlideShare]: cc-by-nc-nd

Application note: ‘Befi-BaTS’ version 0.10.1 – Error rate and statistical power of distance-based measures of phylogeny-trait association.

In prep.


Building on work presented previously (Parker et al., 2008), we study a number of more complex measures of phylogeny-trait association (implemented in the program Befi-BaTS / BaTS v0.10.1) which take into account the branch lengths of a phylogenetic tree in addition to the topographical relationship between taxa. Extensive simulation is performed to measure the Type II error rate (statistical power) of these statistics including those introduced in Parker et al. (2008), as well as the relationship between power and tree shape. The technique is applied to an empirical hepatitis C virus data set presented by Sobesky et al. (2007); their original conclusion that compartmentalization exists between viruses sampled from tumorous and non-tumorous cirrhotic nodules and the plasma is upheld. The association index (AI), migration (PS), phylodynamic diversity (PD) and unique fraction (UF) statistics offer the best combination of Type I error and statistical power to investigate phylogeny-trait association in RNA virus data, while the maximum monophyletic clade size (MC) and nearest taxon (NT) statistics suffer from reduced power in some regions of tree space.

Keywords: BaTS, hepatitis C virus, Markov-chain Monte Carlo, Phylogeny-trait association, Phylogenetic uncertainty, simulation.

Manuscripts in progress (all rights reserved – you may not copy or distribute these files; content and conclusions subject to change; strictly embargoed until publication in a peer-reviewed journal/book):

  • v1: (): .doc
  • v2 (01/01/2014): .docx
  • v3 (16/06/2017): .pdf
  • View this project on GitHub