Patrick K ONeill
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Explore the profile of Patrick K ONeill including associated specialties, affiliations and a list of published articles.
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7
Citations
30
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Recent Articles
1.
ONeill P, Erill I
BMC Bioinformatics
. 2016 Oct;
17(1):406.
PMID: 27716039
Background: Biological sequence motifs drive the specific interactions of proteins and nucleic acids. Accordingly, the effective computational discovery and analysis of such motifs is a central theme in bioinformatics. Many...
2.
Hobbs E, Pereira T, ONeill P, Erill I
Algorithms Mol Biol
. 2016 Jul;
11:19.
PMID: 27398089
Background: Metagenomics enables the analysis of bacterial population composition and the study of emergent population features, such as shared metabolic pathways. Recently, we have shown that metagenomics datasets can be...
3.
Boelen L, ONeill P, Quigley K, Reynolds C, Maillere B, Robinson J, et al.
PLoS Comput Biol
. 2016 Mar;
12(3):e1004796.
PMID: 26953935
Activation of CD4+ T cells requires the recognition of peptides that are presented by HLA class II molecules and can be assessed experimentally using the ELISpot assay. However, even given...
4.
Hagemann I, ONeill P, Erill I, Pfeifer J
Cancer Genet
. 2015 Aug;
208(9):441-7.
PMID: 26227479
The information-theoretic concept of Shannon entropy can be used to quantify the information provided by a diagnostic test. We hypothesized that in tumor types with stereotyped mutational profiles, the results...
5.
ONeill P, Forder R, Erill I
J Comput Biol
. 2014 Apr;
21(5):373-84.
PMID: 24689750
Transcription factors (TFs) regulate transcription by binding to specific sites in promoter regions. Information theory provides a useful mathematical framework to analyze the binding motifs associated with TFs but imposes...
6.
Cornish J, Sanchez-Alberola N, ONeill P, OKeefe R, Gheba J, Erill I
Bioinformatics
. 2014 Jan;
30(9):1193-7.
PMID: 24407225
Motivation: Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks...
7.
ONeill P, Or M, Erill I
PLoS One
. 2013 Oct;
8(10):e76177.
PMID: 24116094
Codon usage bias (CUB) results from the complex interplay between translational selection and mutational biases. Current methods for CUB analysis apply heuristics to integrate both components, limiting the depth and...