BSc MSc MRes PhD (Cantab.)
Advanced Research Fellow
- About
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- Office Address
- School/Department
- School of Medicine, Medical Sciences and Nutrition
Biography
My research centres on the early detection of neurodegenerative diseases and the understanding of disease heterogeneity to inform precision-prevention and precision-medicine approaches aimed at improving clinical outcomes for patients and individuals at risk of neurodegenerative conditions. My research is particularly focused on the basic and comparative aetiology and pathobiology of ALS/MND, FTD, Alzheimer’s disease, and Parkinson’s disease.
This work spans peripheral and systemic signatures of neurodegenerative disease, biomarker discovery and development (esp. aptamers), non-motor and systemic disease manifestations—including the role of the gut—co-pathologies and multiproteinopathies, the role of the immune system, and the synthesis of epidemiological and biological data to better understand disease heterogeneity.
I am also interested in the application of artificial intelligence and meta-analytical approaches to integrate complex biological, clinical, and population-level datasets, to support data-driven discovery, and translate complex research findings into clinically meaningful insights.
My research adopts an integrative, multidisciplinary approach informed by a broad range of research and training in classical and evolutionary genetics, genomics, data analytics and modelling, bioinformatics, molecular biology, experimental biology, neuroscience and immunity.
A central aim of my research is to translate discoveries into practical tools, resources and insights that can be used in clinical care and research, enabling preventive or disease-modifying therapies, improving clinical trial design, and ultimately improving outcomes for people with, or at risk of, neurodegenerative diseases.
Qualifications
- BSc Zoology2003 - National University of Ireland, Galway
- MRes Zoology2006 - National University of Ireland, Galway
- MSc Evolutionary Genetics and Genome Analysis2008 - University of Edinburgh
- PhD Evolutionary Genetics2013 - University of Cambridge
Internal Memberships
The Genetics Society
The Pathological Society of Great Britain and Ireland
Latest Publications
Machine learning identifies routine blood tests as accurate predictive measures of pollution-dependent poor cognitive function
Scientific ReportsContributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/s41598-026-64389-9
Theragnostic potential of aptamers in neurodegenerative diseases: A protocol for a sytematic review and meta-analysis v1
Other Contributions: Other ContributionsProtein misfolding enteropathy predicts and prognosticates neurodegenerative disease years before symptom onset
GastroenterologyContributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1053/j.gastro.2026.04.003
- [ONLINE] View publication in Scopus
Metabolic signatures of ferritin and TDP-43 co-pathology provide a mechanistic basis for stratified therapeutic approaches in ALS
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.64898/2026.03.13.711539
Genotype-specific interferon signatures in amyotrophic lateral sclerosis relate to disease severity
Brain, vol. 149, no. 2, pp. 489-501Contributions to Journals: Articles
- Research
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Funding and Grants
Statistical frameworks for the evaluation of undiagnosed gut proteinopathies as early indicators of neurological disease (PI): £19,930 | 2025 | Grant | NHS Grampian
A Laboratory Model for Antiviral Immunity in Molluscs (co-writer); £201,732 | 2018-06 to 2021-10 | Grant | The Leverhulme Trust (London, GB)
Establishment of a Laboratory Model for Antiviral Immunity in Molluscs (co-writer); £44,364 | 2017-04 to 2017-12 | Grant | Wellcome Trust ISSF (London, GB)
Antiviral immune expression in the mollusc Lymnaea stagnalis (co-writer); £1,791 | 2017-02 to 2017-06 | Grant | University of Edinburgh Moray Endowement Fund (Edinburgh, GB)
Next Generation Sequencing workshop hosted by the Vienna Graduate School of Population Genetics Registration and Travel Award; €1,000 | 2011-05 to 2011-06 | AwardEuropean Science Foundation (Strasbourg, FR)
St. John’s College, Cambridge Learning and Research Fund; £1,000 | 2010-06 to 2010-07 | Award | St. John's College, University of Cambridge (Cambridge, GB)
Summer Institute in Statistics and Modelling in Infectious Diseases workshop hosted by The University of Washington Registration and Travel Award; $4,000 | 2010-06 to 2010-07 | Award | National Institutes of Health (Bethesda, Maryland, US)
Marie Curie Early Stage Research Fellowship; £24,055 | 2007-09 to 2008-08 | Salary award | Marie Curie (London, GB)
Embark Initiative Thermadapt Programme Research Fellowship; €38,012 | 2003-09 to 2005-08 | Salary award | Irish Research Council (Dublin, IE)
- Publications
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Page 1 of 1 Results 1 to 49 of 49
Machine learning identifies routine blood tests as accurate predictive measures of pollution-dependent poor cognitive function
Scientific ReportsContributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/s41598-026-64389-9
Theragnostic potential of aptamers in neurodegenerative diseases: A protocol for a sytematic review and meta-analysis v1
Other Contributions: Other ContributionsProtein misfolding enteropathy predicts and prognosticates neurodegenerative disease years before symptom onset
GastroenterologyContributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1053/j.gastro.2026.04.003
- [ONLINE] View publication in Scopus
Metabolic signatures of ferritin and TDP-43 co-pathology provide a mechanistic basis for stratified therapeutic approaches in ALS
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.64898/2026.03.13.711539
Genotype-specific interferon signatures in amyotrophic lateral sclerosis relate to disease severity
Brain, vol. 149, no. 2, pp. 489-501Contributions to Journals: ArticlesAmygdala TDP-43 pathology is associated with behavioural dysfunction and ferritin accumulation in amyotrophic lateral sclerosis
Brain Communications, vol. 8, no. 2, fcag104Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1093/braincomms/fcag104
- [OPEN ACCESS] https://aura.abdn.ac.uk/bitstreams/026d5004-b64a-43b0-b54a-5f4d1cd66c3e/download
- [ONLINE] View publication in Scopus
Quantitative Profiling of Nanoscopic Protein Aggregates Reveals Specific Fingerprint of TDP-43-Positive Assemblies in Motor Neuron Disease
Advanced Science, vol. 12, no. 44, e05484Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1002/advs.202505484
- [OPEN ACCESS] https://aura.abdn.ac.uk/bitstreams/28a77c8f-b5b9-4d75-96d4-db231ef9d41d/download
- [ONLINE] View publication in Scopus
Protein misfolding in the gastrointestinal tract predicts and prognosticates neurodegenerative disease years before symptom onset
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2025.10.13.25337884
Brain Iron as a Surrogate Biomarker of Pathological TDP-43 Identifies Brain Region-Specific Signatures in Ageing, Alzheimer’s Disease and Amyotrophic Lateral Sclerosis
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2025.10.02.680028
Skin TDP-43 pathology as a candidate biomarker for predicting amyotrophic lateral sclerosis decades prior to motor symptom onset
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2025.04.10.648122
FUS mislocalization rewires a cortical gene network to drive cognitive and behavioral impairment in ALS
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2025.06.16.25329673
Computationally Designed RNA Aptamers Enable Selective Detection of FUS Pathology in ALS
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2025.04.30.651570
Fingerprinting disease-derived protein aggregates reveals unique signature of Motor Neuron Disease
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.5281/zenodo.14960397
Improving ALS detection and cognitive impairment stratification with attention-enhanced deep learning models
Scientific Reports, vol. 15, no. 1, 7045Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1038/s41598-025-90881-9
- [OPEN ACCESS] https://aura.abdn.ac.uk/bitstreams/eeb78e48-3c62-40f6-bd7d-3cd12b732c1b/download
- [ONLINE] View publication in Scopus
Organellomics: AI-driven deep organellar phenotyping reveals novel ALS mechanisms in human neurons
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2024.01.31.572110
Machine learning identifies routine blood tests as accurate predictive measures of pollution-dependent poor cognitive function
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2025.01.10.632396
Clinicopathological analysis of NEK1 variants in amyotrophic lateral sclerosis
Brain Pathology, vol. 35, no. 1, e13287Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1111/bpa.13287
- [OPEN ACCESS] https://aura.abdn.ac.uk/bitstreams/7f5fe087-34e9-4a35-9b2b-5f98b51bdde2/download
- [ONLINE] View publication in Scopus
Integrating Transfer Learning and Attention Mechanisms for Accurate ALS Diagnosis and Cognitive Impairment Detection
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2024.09.22.24313406
An adaptable protocol for antibody & TDP-43 RNA aptamer dual immunohistochemical staining for FFPE-preserved human tissue: with SOP and tick-sheet
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.17504/protocols.io.yxmvm97k6l3p/v1
Antibody and TDP-43 RNA aptamer dual staining to detect patterns of co-pathology in FFPE-preserved human tissue, as described in Rifai et al., 2024 (Brain Pathology): A SOP and tick-sheet. V1
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.17504/protocols.io.14egn6wnml5d/v1
Understanding the influence of altered lipid metabolism on TDP-43 pathology: a protocol for a systematic review and meta-analysis v1
protocols.io.Other Contributions: Other Contributions- [ONLINE] DOI: https://doi.org/10.17504/protocols.io.8epv5xk75g1b/v1
Amygdala TDP-43 pathology is associated with behavioural dysfunction and ferritin accumulation in amyotrophic lateral sclerosis
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2024.06.01.596819
RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides with STMN-2 cryptic splicing and precedes clinical manifestation in ALS
Acta Neuropathologica, vol. 147, 50Contributions to Journals: ArticlesSOP and tick-sheet for using TDP-43 RNA aptamer (TDP-43APT) to detect pathological TDP-43 in FFPE-preserved human tissue, as described in Spence and Waldron et al., 2024 (Acta Neuropathologica) v1
protocols.io.Other Contributions: Other Contributions- [ONLINE] DOI: https://doi.org/10.17504/protocols.io.eq2lyjo4mlx9/v1
TDP-43 RNA aptamer staining to detect pathological TDP-43 in FFPE human tissue, as described in Spence and Waldron et al., 2024 (Acta Neuropathologica):: A SOP and tick-sheet. v2
protocols.io (article).Other Contributions: Other Contributions- [ONLINE] DOI: https://doi.org/10.17504/protocols.io.eq2lyjo4mlx9/v2
Distinct neuroinflammatory signatures exist across genetic and sporadic amyotrophic lateral sclerosis cohorts
Brain, vol. 146, no. 12, pp. 5124-5138Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1093/brain/awad243
- [OPEN ACCESS] https://aura.abdn.ac.uk/bitstreams/6097d076-80e6-4054-8a3d-a249a7809a32/download
- [ONLINE] View publication in Scopus
RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides withSTMN-2cryptic splicing and precedes clinical manifestation in ALS
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2023.10.24.563701
Systematic, comprehensive, evidence-based approach to identify neuroprotective interventions for motor neuron disease: Using systematic reviews to inform expert consensus
BMJ Open, vol. 13, no. 2, e064169Contributions to Journals: ArticlesALS and the Gut-Brain Axis: A protocol for a systematic review and meta-analysis assessing the relationship between amyotrophic lateral sclerosis, the gut and its microbiome.
protocols.io.Other Contributions: Other Contributions- [ONLINE] DOI: https://doi.org/10.17504/protocols.io.5qpvorqpzv4o/v1
Distinct neuroinflammatory signatures exist across genetic and sporadic ALS cohorts
Working Papers: Preprint PaperspTDP-43 aggregates accumulate in non-central nervous system tissues prior to symptom onset in amyotrophic lateral sclerosis: a case series linking archival surgical biopsies with clinical phenotypic data
Journal of Pathology: Clinical Research, vol. 9, no. 1, pp. 44-55Contributions to Journals: Articles- [ONLINE] DOI: https://doi.org/10.1002/cjp2.297
- [OPEN ACCESS] https://aura.abdn.ac.uk/bitstreams/258f0f88-25fe-4b06-a2d0-be007dbd630b/download
- [ONLINE] View publication in Scopus
A Systematic Approach to Identify Neuroprotective Interventions for Motor Neuron Disease
Working Papers: Preprint PapersInterferon signalling as a potentional therapeutic target in amyotrophic lateral sclerosis and frontotemporal dementia – protocol for a systematic review and meta-analysis
protocols.io.Other Contributions: Other ContributionspTDP-43 aggregates accumulate in the gut and other non-central nervous system tissues prior to symptom onset in amyotrophic lateral sclerosis
Working Papers: Preprint PapersBuilding a Systematic Online Living Evidence Summary of COVID-19 Research
Journal of EAHIL, vol. 17, no. 2, pp. 21-26Contributions to Journals: ArticlesTesting evolutionary explanations for the lifespan benefit of dietary restriction in fruit flies (Drosophila melanogaster)
Evolution, vol. 75, no. 2, pp. 450-463Contributions to Journals: Articles- [ONLINE] https://doi.org/10.5061/dryad.80gb5mkq2
- [ONLINE] DOI: https://doi.org/10.1111/evo.14146
- [OPEN ACCESS] https://aura.abdn.ac.uk/bitstreams/5381676f-2eda-4ca7-8511-73b8c3605033/download
- [ONLINE] View publication in Scopus
Unlocking Spatial Molecular & Cellular Relationships of SARS-CoV-2 in Archived Human Tissue
protocols.io.Other Contributions: Other ContributionsTesting evolutionary explanations for the lifespan benefit of dietary restriction in Drosophila melanogaster
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/2020.06.18.159731
- [ONLINE] http://europepmc.org/abstract/PPR/PPR178319
Therapeutic Targeting of Proteostasis in Amyotrophic Lateral Sclerosis: a Systematic Review and Meta-Analysis of Preclinical Research
Frontiers in Neuroscience, vol. 14, no. 2020, 511Contributions to Journals: ArticlesCorrection: Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes
PLoS Genetics, vol. 16, no. 3, e1008679Contributions to Journals: ArticlesTargeting mitochondrial dysfunction in amyotrophic lateral sclerosis: a systematic review and meta-analysis
Brain Communications, vol. 1, no. 1, fcz009Contributions to Journals: ArticlesCreation and maintenance of Ashworth outcrossed DGRP population V.1
protocols.io.Other Contributions: Other Contributions- [ONLINE] DOI: https://doi.org/10.17504/protocols.io.zbuf2nw
Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes.
PLoS Genetics, vol. 14, no. 7, e1008679Contributions to Journals: ArticlesThe virome of Drosophila suzukii, an invasive pest of soft fruit
Virus Evolution, vol. 4, no. 1, vey009Contributions to Journals: ArticlesThe virome of Drosophila suzukii, an invasive pest of soft fruit
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/190322
Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes
Working Papers: Preprint Papers- [ONLINE] DOI: https://doi.org/10.1101/166488
- [ONLINE] http://dx.doi.org/10.1101/166488
Protocol for a systematic review and meta-analysis of experimental models of amyotrophic lateral sclerosis
Evidence-based Preclinical Medicine, vol. 3, no. 2, pp. 17-19Contributions to Journals: ArticlesThe Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster
PLoS Biology, vol. 13, no. 7, e1002210Contributions to Journals: ArticlesElevated levels of expression associated with regions of the Drosophila genome that lack crossing over
Biology Letters, vol. 4, no. 6, pp. 758-761Contributions to Journals: Articles