Alan E Murphy
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Explore the profile of Alan E Murphy including associated specialties, affiliations and a list of published articles.
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9
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83
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Recent Articles
1.
Murphy A, Askarova A, Lenhard B, Skene N, Marzi S
Nucleic Acids Res
. 2024 Dec;
53(4).
PMID: 39660643
To understand the complex relationship between histone mark activity and gene expression, recent advances have used in silico predictions based on large-scale machine learning models. However, these approaches have omitted...
2.
Murphy A, Beardall W, Rei M, Phuycharoen M, Skene N
Nat Commun
. 2024 Nov;
15(1):9951.
PMID: 39550354
Understanding how genetic variants affect the epigenome is key to interpreting GWAS, yet profiling these effects across the non-coding genome remains challenging due to experimental scalability. This necessitates accurate computational...
3.
Schilder B, Murphy A, Skene N
Nat Commun
. 2024 Jan;
15(1):149.
PMID: 38167858
Despite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards...
4.
Murphy A, Fancy N, Skene N
Elife
. 2023 Dec;
12.
PMID: 38047913
Mathys et al. conducted the first single-nucleus RNA-seq (snRNA-seq) study of Alzheimer's disease (AD) (Mathys et al., 2019). With bulk RNA-seq, changes in gene expression across cell types can be...
5.
Choi S, Schilder B, Abbasova L, Murphy A, Skene N
Bioinform Adv
. 2023 May;
3(1):vbad049.
PMID: 37250110
Summary: EpiCompare combines a variety of downstream analysis tools to compare, quality control and benchmark different epigenomic datasets. The package requires minimal input from users, can be run with just...
6.
7.
Wahedi A, Soondram C, Murphy A, Skene N, Rahman S
J Inherit Metab Dis
. 2022 Dec;
46(2):243-260.
PMID: 36502462
Leigh syndrome is a rare, inherited, complex neurometabolic disorder with genetic and clinical heterogeneity. Features present in affected patients range from classical stepwise developmental regression to ataxia, seizures, tremor, and...
8.
Andrews B, Murphy A, Stofella M, Maslen S, Almeida-Souza L, Skehel J, et al.
Mol Cell Proteomics
. 2022 Jan;
21(2):100192.
PMID: 34979241
The amount of any given protein in the brain is determined by the rates of its synthesis and destruction, which are regulated by different cellular mechanisms. Here, we combine metabolic...
9.
Murphy A, Schilder B, Skene N
Bioinformatics
. 2021 Oct;
37(23):4593-4596.
PMID: 34601555
Motivation: Genome-wide association studies (GWAS) summary statistics have popularized and accelerated genetic research. However, a lack of standardization of the file formats used has proven problematic when running secondary analysis...