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Statistical Genetics

genetics
bayesian
computational
Statistical modelling of population genomics, local ancestry inference, polygenic risk, and evolutionary adaptation.

Our work in statistical genetics develops probabilistic and computational models to uncover demographic history, recombination patterns, natural selection, and complex trait architecture from high-dimensional genomic data. A central contribution is MOSAIC, a two-layer Hidden Markov Model for multiway local ancestry inference that reconstructs historical admixture events without requiring direct surrogate reference populations.

Recent and ongoing collaborations span human biobank cohorts (quantifying group-structure effects on polygenic risk scores in the UK Biobank and mitonuclear discordance in Parkinson’s disease), livestock and equine functional genomics (mitonuclear coadaptation and trypanotolerance in hybrid African cattle; imputation and exercise genomics in Thoroughbred horses), and bacterial comparative genomics.

Project Publications

Feng, Mian, Thomas J Hall, John F O’Grady, Kseniia Maksimova, Michael Salter-Townshend, John A Browne, David E MacHugh, Lisa M Katz, Beatrice A McGivney, and Emmeline W Hill. 2026. “Integrative Genomic and Transcriptomic Analyses Identify Functionally Relevant Causal Genes for Exercise in a Large Animal Model.”
Mahoney, Catherine F, Michael Salter-Townshend, Darren J Fitzpatrick, and Denis C Shields. 2026. “Detecting Genomic Regions Enriched for Reciprocal Recombination in Autism Spectrum Disorder.” bioRxiv. https://doi.org/10.1101/2026.05.26.727863.
McHugo, Gillian P, James A Ward, Said Ismael Ng’ang’a, Laurent AF Frantz, John A Browne, Michael Salter-Townshend, Grace M O’Gorman, et al. 2026. “Integrative Genomics Identifies Candidate Genes Underlying Trypanotolerance in Hybrid African Cattle.” Evolutionary Applications 19 (6): e70274. https://doi.org/10.1111/eva.70274.
McHugo, Gillian P, James A Ward, Said Ismael Ng’ang’a, Laurent AF Frantz, Michael Salter-Townshend, Emmeline W Hill, Grace M O’Gorman, Kieran G Meade, Thomas J Hall, and David E MacHugh. 2025. “Genome-Wide Local Ancestry and the Functional Consequences of Admixture in African and European Cattle Populations.” Heredity 134 (1): 49–63. https://doi.org/10.1038/s41437-024-00734-w.
Maksimova, Kseniia, Emmeline W Hill, Beatrice A McGivney, David E MacHugh, and Michael Salter-Townshend. 2024. “Exploring Genetic Diversity and Identifying Key Contributors in the Thoroughbred Horse Population for Development of an Imputation Reference Panel.”
Ward, James A, Said I Ng’ang’a, Imtiaz AS Randhawa, Gillian P McHugo, John F O’Grady, Julio M Flórez, John A Browne, et al. 2024. “Genomic Insights into the Population History and Adaptive Traits of Latin American Criollo Cattle.” Royal Society Open Science 11 (3): 231388.
Zhao, Jinbo, Adrian O’Hagan, and Michael Salter-Townshend. 2024. “How Group Structure Impacts the Numbers at Risk for Coronary Artery Disease: Polygenic Risk Scores and Nongenetic Risk Factors in the UK Biobank Cohort.” Genetics 227 (3): iyae086. https://doi.org/10.1093/genetics/iyae086.
Zhao, Jinbo, Michael Salter-Townshend, and Adrian O’Hagan. 2023. “A Simulation Study for Multifactorial Genetic Disorders to Quantify the Impact of Polygenic Risk Scores on Critical Illness Insurance.” European Actuarial Journal 13 (2): 775–813. https://doi.org/10.1007/s13385-023-00345-5.
Ward, James A, Gillian P McHugo, Michael J Dover, Thomas J Hall, Said Ismael Ng’ang’a, Tad S Sonstegard, Daniel G Bradley, Laurent AF Frantz, Michael Salter-Townshend, and David E MacHugh. 2022. “Genome-Wide Local Ancestry and Evidence for Mitonuclear Coadaptation in African Hybrid Cattle Populations.” iScience 25 (7): 104672. https://doi.org/10.1016/j.isci.2022.104672.
Zhao, Jinbo, Adrian O’Hagan, and Michael Salter-Townshend. 2022. “Polygenic Risk Scores for Determining Number at Risk.” In Irish Journal of Medical Science, 191:S70. Suppl 3. Springer.
Cotroneo, Chiara E, Isobel Claire Gormley, Denis C Shields, and Michael Salter-Townshend. 2021. “Computational Modelling of Chromosomally Clustering Protein Domains in Bacteria.” BMC Bioinformatics 22 (1): 593. https://doi.org/10.1186/s12859-021-04512-x.
Salter-Townshend, Michael, and Simon Myers. 2019a. “Fine-Scale Inference of Ancestry Segments Without Prior Knowledge of Admixing Groups.” Genetics 212 (3): 869–89. https://doi.org/10.1534/genetics.119.302139.
Salter-Townshend, Michael, and Simon Myers. 2019b. “Local Ancestry Inference in Non-Model Organisms.” In Human Heredity (European Meeting on Mathematical Genetics), 83:244. 5. Karger.