Academia

Below are links to my various published papers and their related github pages.

Many of my papers come from having been a contributor of the COVID-19 Genomics UK Consortium at The University of Liverpool (source).

2025

Comparison of different microbiome analysis pipelines to validate their reproducibility of gastric mucosal microbiome composition

Link: https://journals.asm.org/doi/10.1128/msystems.01358-24

2024

Optimised human stool sample collection for multi-omic microbiota analysis

Link: https://www.nature.com/articles/s41598-024-67499-4

R Code Bookdown: https://m-gemmell.github.io/Gemmell_et_al_2023/01-Intro.html

2023

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

Link: https://www.sciencedirect.com/science/article/pii/S0195670123000671

The Hypolimnas misippus genome supports a common origin of the W chromosome in Lepidoptera

Link: https://www.biorxiv.org/content/10.1101/2023.03.24.533969v2.abstract

The ecology of viruses in urban rodents with a focus on SARS-CoV-2

Link: https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2217940

2021

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

Link: https://www.cell.com/cell/pdf/S0092-8674(20)31537-3.pdf

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

Link: https://www.cell.com/cell-reports/pdf/S2211-1247(21)00663-X.pdf

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

Link: https://www.thelancet.com/journals/lanpub/article/PIIS2468-2667(21)00055-4/fulltext

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Link: https://www.science.org/doi/full/10.1126/science.abl9551

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

Link: https://www.cell.com/iscience/pdf/S2589-0042(21)01322-5.pdf

Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission

Link: https://www.sciencedirect.com/science/article/pii/S1198743X21004353

Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS

Link: https://journals.asm.org/doi/full/10.1128/msphere.00219-21

2020

Oral bacterial diversity is inversely correlated with mucosal inflammation

Link: https://onlinelibrary.wiley.com/doi/full/10.1111/odi.13420

2019

P093 CD4 T-cell transcriptome analysis at baseline predicts clinical remission to anti-TNF agents in ulcerative colitis (UC)

Link: https://academic.oup.com/ecco-jcc/article/13/Supplement_1/S132/5300569?login=false

Draft genome sequences of a Campylobacter curvus and three Campylobacter ureolyticus strains isolated from human colonic mucosal tissue

Link: https://www.microbiotajournal.com/wp-content/uploads/sites/7/2020/01/e148-Draft-genome-sequences-of-a-Campylobacter-curvus-and-three-Campylobacter-ureolyticus-strains-isolated-from-human-colonic-mucosal-tissue-.pdf

2018

Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential

Link: https://www.tandfonline.com/doi/full/10.1038/s41426-018-0118-x

Draft Genome Assembly of the Poultry Red Mite, Dermanyssus gallinae

Link: https://journals.asm.org/doi/full/10.1128/mra.01221-18

Comparative genomics and genome biology of Campylobacter showae

Link: https://www.tandfonline.com/doi/full/10.1080/22221751.2019.1622455

Novel Campylobacter concisus lipooligosaccharide is a determinant of inflammatory potential and virulence

Link: https://www.jlr.org/article/S0022-2275(20)34181-X/fulltext

2016

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies

Link: https://link.springer.com/article/10.1186/s40168-016-0207-9