Publications
You will find a more extensive and up-to-date list of my articles on my Google Scholar profile which does not rely on me manually adding them.
Selected Publications
Published in Nature Communications, 2024
Enformer Celltyping outperforms current best-in-class approaches and generalises across cell types and biological regions. Moreover, we propose a framework for evaluating models on genetic variant effect prediction using regulatory quantitative trait loci mapping studies, highlighting current limitations in genomic deep learning models. Despite this, Enformer Celltyping can also be used to study cell type-specific genetic enrichment of complex traits.
Recommended citation: Murphy, A.E., Beardall, W., Rei, M. et al. Nat. Commun. 15, 9951 (2024)
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Published in eLife, 2023
Reanalysis reveals the impact of quality control and differential analysis methods on the discovery of disease-associated genes on the first Alzheimers disease single nucleus RNA-seq dataset.
Recommended citation: Murphy, A. E., Fancy, N. & Skene, N. G. eLife 12:RP90214 (2023)
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Published in Nature Communications, 2022
Based on our findings, we recommend the use of pseudobulk approaches for differential expression in single-cell RNA-sequencing analyses.
Recommended citation: Murphy, A. E. & Skene, N. G. Nat. Commun. 37, 7851 (2022)
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Published in Bioinformatics, 2021
we have developed MungeSumstats, a Bioconductor R package for the standardization and quality control of GWAS summary statistics. MungeSumstats can handle the most common summary statistic formats, including variant call format (VCF) producing a reformatted, standardized, tabular summary statistic file, VCF or R native data object.
Recommended citation: Murphy, A. E., Schilder, B. M. & Skene, N. G. Bioinformatics 37, 4593–4596 (2021)
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