Publications
This page lists my research publications, organised by employment. Expect some overlap in years for publications arising from transitions between positions.
Sims Group (2020–present)
Fibroblast specialisation across microanatomy in a single-cell atlas of healthy human Achilles tendon 2025
Learning and teaching biological data science in the Bioconductor community. 2025
Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis. 2024
Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. 2022
Sansom Group (2017–2020)
The transcriptional repressor AEBP2 is indispensable for the epigenetic control of mimetic thymic epithelial cell differentiation and central self-tolerance induction 2025
IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies 2021
The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages. 2019
Ratcliffe Group (2016–2017)
This publication arose from a collaboration started during a short-term research position in the group of Prof. David Mole and Prof. Sir Peter Ratcliffe at the University of Oxford.
Wilkins Group (2015–2016)
These publications arose from my first postdoctoral research position in the group of Prof. Martin Wilkins at Imperial College London.
Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia. 2019
De Novo Truncating Mutations in WASF1 Cause Intellectual Disability with Seizures. 2018
Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes. 2018
Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data. 2018
Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease. 2017
Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration. 2017
Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension. 2017
PhD Research (2011–2015)
These publications arose from my doctoral research and collaborations, jointly supervised by Prof. David MacHugh and Prof. Stephen Gordon, at University College Dublin.
RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course. 2021
The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis. 2019
Experimental infection of cattle with Mycobacterium tuberculosis isolates shows the attenuation of the human tubercle bacillus for cattle. 2018
RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus). 2018
Comparative ’omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli. 2018
Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis. 2016
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data. 2016
High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants 2015
Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. 2015
RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli. 2015
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data 2016
Comparative functional genomics and the bovine macrophage response to strains of the mycobacterium genus. 2014
RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis. 2014
Shields Group (2010)
This publication arose from a summer internship in the group of Prof. Denis Shields, under the supervision of Dr. Nora Khaldi.