Michelle Kendall

The University of Warwick · Department of Statistics

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detec...

Vignette for the R package treescape treescape on CRAN: https://cran.r-project.org/web/packages/treescape/index.html treescape web app: http://shiny.imperial-stats-experimental.co.uk/users/mlkendal/treescape/ treescape development on GitHub: https://github.com/thibautjombart/treescape

Key predistribution schemes for resource-constrained networks are methods for allocating symmetric keys to devices in such a way as to provide an efficient trade-off between key storage, connectivity and resilience. While there have been many suggested constructions for key predistribution schemes, a general understanding of the design principles o...

We present a formalisation of a category of schemes that we refer to as broadcast-enhanced key predistribution schemes (BEKPSs). These schemes are suitable for networks with access to a trusted base station and an authenticated broadcast channel. We demonstrate that the access to these extra resources allows for the creation of BEKPSs with advantag...

Motivation: The ability to distinguish imported cases from locally acquired cases has important consequences for the selection of public health control strategies. Genomic data can be useful for this, for example using a phylogeographic analysis in which genomic data from multiple locations is compared to determine likely migration events between...

Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack...

Quarantining close contacts of individuals infected with SARS-CoV-2 for 10 to 14 days is a key strategy in reducing transmission. However, quarantine requirements are often unpopular, with low adherence, especially when a large fraction of the population has been vaccinated. Daily contact testing (DCT), in which contacts are required to isolate onl...

SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how best to navigate through the ongoing epidemic, with computational models being used to predict the spread of infection and assess the impact of public health measures. Here, we present OpenABM...

The COVID-19 pandemic has seen digital contact tracing emerge around the world to help prevent spread of the disease. A mobile phone app records proximity events between app users, and when a user tests positive for COVID-19, their recent contacts can be notified instantly. Theoretical evidence has supported this new public health intervention1–6,...

Digital contact tracing is a public health intervention. It should be integrated with local health policy, provide rapid and accurate notifications to exposed individuals, and encourage high app uptake and adherence to quarantine. Real-time monitoring and evaluation of effectiveness of app-based contact tracing is key for improvement and public tru...

Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not directly informative about transmission events betwee...

Background In May 2020, the UK National Health Service (NHS) Test and Trace programme was launched in England in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included version 1 of the NHS contact tracing app. The aim of the study was to make a preliminary assessment of the epidemiological impact of...

SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how best to navigate through the ongoing epidemic, with models being used to predict the spread of infection and assess the impact of public health measures. Here, we present OpenABM-Covid19: an a...

The timing of SARS-CoV-2 transmission is a critical factor to understand the epidemic trajectory and the impact of isolation, contact tracing and other non- pharmaceutical interventions on the spread of COVID-19 epidemics. We examined the distribution of transmission events with respect to exposure and onset of symptoms. We show that for symptomati...

In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Lo...

Instantaneous contact tracing New analyses indicate that severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) is more infectious and less virulent than the earlier SARS-CoV-1, which emerged in China in 2002. Unfortunately, the current virus has greater epidemic potential because it is difficult to trace mild or presymptomatic infections. As...

Mobile phone apps implementing algorithmic contact tracing can speed up the process of tracing newly diagnosed individuals, spreading information instantaneously back through a past contact network to inform them that they are at risk of being infected, and thus allow them to take appropriate social distancing and testing measures. The aim of non-p...

Background : Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods : We simulate...

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated...

Reconstructing who infected whom is a central challenge in analysing epidemiological data. Recently, advances in sequencing technology have led to increasing interest in Bayesian approaches to inferring who infected whom using genetic data from pathogens. The logic behind such approaches is that isolates that are nearly genetically identical are mo...

Trees that illustrate patterns of ancestry and evolution are a central tool in many areas of biology. Comparing evolutionary trees to each other has widespread applications in comparing the evolutionary stories told by different sources of data, assessing the quality of inference methods, and highlighting areas where patterns of ancestry are uncert...

Background Multidrug-resistant tuberculosis poses a major threat to the success of tuberculosis control programs worldwide. Understanding how drug-resistant tuberculosis evolves can inform the development of new therapeutic and preventive strategies. Methods Here, we use novel genome-wide analysis techniques to identify polymorphisms that are asso...

Hotspots of correlation between homoplastic sites. White and yellow indicate significant positive correlation (p<0.05) while red indicates significant negative correlation (p<0.05). (EPS)

Genome wide analysis with correction for population structure by principle components and Bonferroni correction for rifampicin, isoniazid, pyrazinamide and ethambutol drug resistance polymorphisms in M. tuberculosis. (EPS)

Homoplastic polymorphisms detected by phyC. (DOCX)

The cophenetic correlation coefficient of whole genome sequence, MIRU, MIRU and spoligotype combined (MIRU Spol) and spoligotype dendrograms. (EPS)

Genome wide analysis with correction for population structure by principle components and Bonferroni correction for streptomycin, kanamycin, capreomycin and ciprofloxacin drug resistance polymorphisms in M. tuberculosis. (EPS)

The most homoplastic polymorphisms. (DOCX)

The most topologically influential polymorphisms. (DOCX)

Accession numbers for genomes sequenced. (DOCX)

To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the “Phylogenetics and Networks for Generalised HIV Epidemics in Africa” consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai...

To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the 'Phylogenetics and Networks for Generalised HIV Epidemics in Africa' consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai...

The increasing availability of large genomic datasets as well as the advent of Bayesian phylogenetics facilitate the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect me...

BACKGROUND: Multidrug-resistant tuberculosis poses a major threat to the success of tuberculosis control programs worldwide. Understanding how drug-resistant tuberculosis evolves can inform the development of new therapeutic and preventive strategies. METHODS: Here, we use novel genome-wide analysis techniques to identify polymorphisms that are ass...

R package for calculating and viewing topological properties of phylogenetic trees.

Viral phylogenetic methods contribute to understanding how HIV spreads in populations, and thereby help guide the design of prevention interventions. So far, most analyses have been applied to well-sampled concentrated HIV-1 epidemics in wealthy countries. To direct the use of phylogenetic tools to where the impact of HIV-1 is greatest, the Phyloge...

Evolutionary relationships are described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. Obtaining credible trees that capture the relationships present in complex data is one of the fundamental challenges in evolution today. We present a way to map tree...

R package for statistical exploration of landscapes of phylogenetic trees

Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources (e.g. several genes from the same organisms) and different inference methods. We propose a new metric for robus...

A commonly used metric for comparing the resilience of key predistribution schemes is fail s , which measures the proportion of network connections which are 'broken' by an adversary which has compromised s nodes. In 'Random key predistribution schemes for sensor networks', Chan, Perrig and Song present a formula for measuring the resilience in a c...

Providing security for a wireless sensor network composed of small sensor nodes with limited battery power and memory can be a non-trivial task. A variety of key predistribution schemes have been proposed which allocate symmetric keys to the sensor nodes before deployment. In this paper we examine the role of expander graphs in key predistribution...