Publications

Research and peer reviewing in computational biology, evolutionary genomics, and phylogenetics.

Peer reviewing

85recorded peer reviews

17journals

2009–2026recorded activity

Most frequently reviewed for: Bioinformatics (35), Systematic Biology (11), Molecular Biology and Evolution (7).

Reviewing by journal

Journal reviews recorded on ORCID

Journal	Reviews
Bioinformatics	35
Systematic Biology	11
Molecular Biology and Evolution	7
Infection, Genetics and Evolution	6
FEMS Microbes	4
Microbiome	4
PLOS One	3
BMC Bioinformatics	2
IEEE/ACM Transactions on Computational Biology and Bioinformatics	2
Infection	2
Molecular Phylogenetics and Evolution	2
Bioinformatics Advances	1
Ecology and Evolution	1
Journal of Molecular Evolution	1
Microbial Genomics	1
Proceedings of the National Academy of Sciences	1
Scientific Reports	1

Other peer reviewing: Wellcome Trust (1).

Public reviewing records on ORCID · Refreshed 8 September 2026. Counts reflect recorded review activities, which may include multiple rounds for a manuscript; they may not cover all reviewing undertaken.

85 works from my ORCID record · Refreshed 8 September 2026.

Includes articles, preprints, and other research outputs recorded on ORCID.

2026

1. Whole genome comparative analysis shows limited Escherichia coli co-occurrence within co-habiting humans and dogs

   BMC Genomics · Journal article

   DOI: 10.1186/s12864-026-13236-2

2. Structural and evolutionary insights into the isoprene monooxygenases

   FEMS Microbiology Ecology · Journal article

   DOI: 10.1093/femsec/fiag004

2025

1. Staphylococcus haemolyticus Population Genomics Provides Insights into Pathogenicity and Commensalism

   Preprint

   DOI: 10.1101/2025.11.08.687178

2. A multi-isolate genomic approach identifies diverse Escherichia coli contamination and antimicrobial resistance carriage on retail foods

   Microbial genomics · Journal article

   DOI: 10.1099/mgen.0.001549

3. Temporal dynamics of SARS-CoV-2 shedding in feces and saliva: a longitudinal study in Norfolk, United Kingdom during the 2021–2022 COVID-19 waves

   Microbiology Spectrum · Journal article

   DOI: 10.1128/spectrum.03195-24

4. Population structure and gene flux of Listeria monocytogenes ST121 reveal prophages as a candidate driver of adaptation and persistence in food production environments

   Microbial Genomics · Journal article

   DOI: 10.1099/mgen.0.001397

2024

1. Capturing clinically relevant Campylobacter attributes through direct whole genome sequencing of stool

   Microbial genomics · Journal article

   DOI: 10.1099/mgen.0.001284

2. Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine

   Pathogens · Journal article

   DOI: 10.3390/pathogens13060521

3. Scalable neighbour search and alignment with uvaia

   PeerJ · Journal article

   DOI: 10.7717/peerj.16890

2023

1. The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis.

   PLoS ONE · Journal article

   DOI: 10.1371/journal.pone.0284187

2. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.

   Journal of Hospital Infection · Journal article

   DOI: 10.1016/j.jhin.2023.02.010

3. The impact of SARS-CoV-2 infection in children with rheumatic/autoinflammatory diseases on immunosuppressive treatment: a single centre experience

   Clinical and Experimental Rheumatology · Journal article

   DOI: 10.1038/s41586-021-03470-x

4. Scalable neighbour search and alignment with uvaia

   Other

   DOI: 10.1101/2023.01.31.526458

5. SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis

   South African Medical Journal · Journal article

   DOI: 10.7196/samj.2023.v113i3.16762

6. Repurposing an integrated national influenza platform for genomic surveillance of SARS-CoV-2 in Ghana: a molecular epidemiological analysis

   The Lancet Global Health · Journal article

   DOI: 10.1016/s2214-109x(23)00189-4

2022

1. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

   Scientific Reports · Journal article

   DOI: 10.1038/s41598-022-15661-1

2. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway (vol 7, pg 1161, 2022)

   Nature Microbiology · Journal article

   DOI: 10.1038/s41564-022-01241-6

3. Recurrent SARS-CoV-2 mutations in immunodeficient patients

   Virus Evolution · Journal article

   DOI: 10.1093/ve/veac050

4. Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021

   Epidemiology and Infection · Journal article

   DOI: 10.1017/s0950268822001285

5. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

   Scientific Reports · Journal article

   DOI: 10.1038/s41598-022-14016-0

6. Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.

   Virus Evolution · Journal article

   DOI: 10.1093/ve/veac023

7. Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

   Nature Communications · Journal article

   DOI: 10.1038/s41467-022-28371-z

8. Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

   Nature Communications · Journal article

   DOI: 10.1038/s41467-021-27942-w

9. The new normal? Dynamics and scale of the SARS-CoV-2 variant Omicron epidemic in England

   MedRxiv · Journal article

   DOI: 10.1101/2022.03.29.22273042

10. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

    Science · Journal article

    DOI: 10.1126/science.abq5358

11. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

    Other

    DOI: 10.1101/2022.04.17.22273906

12. Tatajuba: exploring the distribution of homopolymer tracts

    NAR Genomics and Bioinformatics · Journal article

    DOI: 10.1093/nargab/lqac003

13. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

    BMC Infectious Diseases · Journal article

    DOI: 10.1186/s12879-022-07628-4

14. Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

    Microbial Genomics · Journal article

    DOI: 10.1099/mgen.0.000838

15. Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages

    Genome Biology and Evolution · Journal article

    DOI: 10.1093/gbe/evac119

16. Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England

    Nature Communications · Journal article

    DOI: 10.1038/s41467-022-32096-4

17. Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing

    Scientific Data · Journal article

    DOI: 10.1038/s41597-022-01463-7

2021

1. Genomic reconstruction of the SARS-CoV-2 epidemic in England

   Nature · Journal article

   DOI: 10.1038/s41586-021-04069-y

2. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

   iScience · Journal article

   DOI: 10.1016/j.isci.2021.103353

3. SARS- CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021

   Microbial genomics · Journal article

   DOI: 10.1099/mgen.0.000693

4. Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study.

   The Lancet Infectious Diseases · Journal article

   DOI: 10.1016/s1473-3099(21)00475-8

5. Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

   Cell · Journal article

   DOI: 10.1016/j.cell.2021.08.014

6. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

   Cell Reports · Journal article

   DOI: 10.1016/j.celrep.2021.109292

7. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

   Nature · Journal article

   DOI: 10.1038/s41586-021-03412-7

8. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

   The Lancet Public Health · Journal article

   DOI: 10.1016/s2468-2667(21)00055-4

9. SARS-CoV-2 evolution during treatment of chronic infection

   Nature · Journal article

   DOI: 10.1038/s41586-021-03291-y

10. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

    Cell · Journal article

    DOI: 10.1016/j.cell.2021.01.037

11. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

    Cell · Journal article

    DOI: 10.1016/j.cell.2020.11.020

12. Large-scale sequencing of sars-cov-2 genomes from one region allows detailed epidemiology and enables local outbreak management

    Microbial genomics · Journal article

    DOI: 10.1099/mgen.0.000589

13. Tatajuba ― Exploring the distribution of homopolymer tracts

    Other

    DOI: 10.1101/2021.06.02.446710

14. Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern

    The Lancet Microbe · Journal article

    DOI: 10.1016/s2666-5247(21)00061-6

15. SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021

    MedRxiv · Journal article

    DOI: 10.1101/2021.06.04.21258352

16. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

    Other

    DOI: 10.1101/2021.12.17.21267925

17. Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

    MedRxiv · Journal article

    DOI: 10.1101/2021.08.10.21261847

18. Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts (Animals, Fungi and Their Microbial Relatives) and All Other Lineages

    BioRxiv · Journal article

    DOI: 10.1101/2021.02.26.433005

19. Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread

    MedRxiv · Journal article

    DOI: 10.1101/2021.01.04.20232520

20. Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data

    The Lancet Global Health · Journal article

    DOI: 10.1016/s2214-109x(21)00434-4

21. Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs

    Npj Biofilms and Microbiomes · Journal article

    DOI: 10.1038/s41522-020-00178-0

22. CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes

    Genome Medicine · Journal article

    DOI: 10.1186/s13073-021-00839-5

23. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

    Science · Journal article

    DOI: 10.1126/science.abj4336

2020

1. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

   Eurosurveillance · Journal article

   DOI: 10.2807/1560-7917.es.2020.25.32.2001410

2. Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing

   NAR Genomics and Bioinformatics · Journal article

   DOI: 10.1093/nargab/lqz016

3. Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management

   Other

   DOI: 10.1101/2020.09.28.20201475

4. Experimental evolution selects clinically relevant antibiotic resistance in biofilms but with collateral tradeoffs

   Access Microbiology · Journal article

   DOI: 10.1099/acmi.mim2019.po0001

5. CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes

   Other

   DOI: 10.1101/2020.06.24.162156

6. An integrated national scale SARS-CoV-2 genomic surveillance network

   The Lancet Microbe · Journal article

   DOI: 10.1016/s2666-5247(20)30054-9

2019

1. Antibiotics select for novel pathways of resistance in biofilms

   BioRxiv · Preprint

   DOI: 10.1101/605212

2. Taxonomic resolution of the ribosomal RNA operon in bacteria: Implications for its use with long read sequencing

   Other

   DOI: 10.1101/626093

3. Nanoneedle-Mediated Stimulation of Cell Mechanotransduction Machinery

   ACS Nano · Journal article

   DOI: 10.1021/acsnano.8b06998

2017

1. Species Tree Estimation from Genome-Wide Data with guenomu

   Methods in Molecular Biology · Journal article

   DOI: 10.1007/978-1-4939-6622-6_18

2016

1. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

   Systematic Biology · Journal article

   DOI: 10.1093/sysbio/syu082

2. SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

   Systematic Biology · Journal article

   DOI: 10.1093/sysbio/syv082

3. Infinitely long branches and an informal test of common ancestry

   Biology Direct · Journal article

   DOI: 10.1186/s13062-016-0120-y

2015

1. Species Tree Estimation from Genome-wide Data with Guenomu

   BioRxiv · Journal article

   DOI: 10.1101/023861

2. SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

   BioRxiv · Journal article

   DOI: 10.1101/021709

3. Infinitely Long Branches and an Informal Test of Common Ancestry

   Other

   DOI: 10.1101/023903

2014

1. Unsorted Homology within Locus and Species Trees

   Systematic Biology · Journal article

   DOI: 10.1093/sysbio/syu050

2. Testing for Universal Common Ancestry

   Systematic Biology · Journal article

   DOI: 10.1093/sysbio/syu041

2013

1. Codon pairs of the HIV-1 vif gene correlate with CD4+T cell count

   BMC Infectious Diseases · Journal article

   DOI: 10.1186/1471-2334-13-173

2012

1. Proving universal common ancestry with similar sequences.

   Trends in Evolutionary Biology · Journal article

   DOI: 10.4081/eb.2012.e5

2010

1. Evolutionary Process of Deep-Sea Bathymodiolus Mussels

   PLoS ONE · Journal article

   DOI: 10.1371/journal.pone.0010363

2. Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites

   BMC Evolutionary Biology · Journal article

   DOI: 10.1186/1471-2148-10-52

3. Distribution of distances between topologies and its effect on detection of phylogenetic recombination

   Annals of the Institute of Statistical Mathematics · Journal article

   DOI: 10.1007/s10463-009-0259-8

2008

1. Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees

   PLoS ONE · Journal article

   DOI: 10.1371/journal.pone.0002651

2. Evolutionary Dynamics of HIV-1 BF and CB Recombinants and Its Parental Counterparts in South America

   Retrovirology: Research and Treatment · Journal article

   DOI: 10.4137/rrt.s1045

2007

1. A likelihood-based index of protein-protein binding affinities with application to influenza HA escape from antibodies

   Molecular Biology and Evolution (MBE) · Journal article

   DOI: 10.1093/molbev/msm079

2006

1. Evolutionary relationships of deep-sea mussels inferred by mitochondrial DNA sequences

   Marine Biology · Journal article

   DOI: 10.1007/s00227-006-0268-6

2005

1. Phylogeography of loaches of the Genus lefua (Balitoridae, Cypriniformes) inferred from mitochondrial DNA sequences

   Zoological Science · Journal article

   DOI: 10.2108/zsj.22.157

2001

1. Phylogenetic Likelihood

   eLS · Journal article

   DOI: 10.1002/9780470015902.a0005141

2. Estimation of Species Trees

   eLS · Journal article

   DOI: 10.1002/9780470015902.a0025781