Search Results - "Shanahan, Hugh P."

Intra-Exon Motif Correlations as a Proxy Measure for Mean Per-Tile Sequence Quality Data in RNA-Seq by Alnasir, Jamie J, Shanahan, Hugh P

“…Given the wide variability in the quality of next-generation sequencing data submitted to public repositories, it is essential to identify methods that can…”
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Bioinformatics on the cloud computing platform Azure by Shanahan, Hugh P, Owen, Anne M, Harrison, Andrew P

“…We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its…”
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A Novel Method to Detect Bias in Short Read NGS Data by Alnasir, Jamie, Shanahan, Hugh P.

“…Detecting sources of bias in transcriptomic data is essential to determine signals of Biological significance. We outline a novel method to detect sequence…”
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The application of Hadoop in structural bioinformatics by Alnasir, Jamie J, Shanahan, Hugh P

“…Abstract The paper reviews the use of the Hadoop platform in structural bioinformatics applications. For structural bioinformatics, Hadoop provides a new…”
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Investigation into the annotation of protocol sequencing steps in the sequence read archive by Alnasir, Jamie, Shanahan, Hugh P

“…The workflow for the production of high-throughput sequencing data from nucleic acid samples is complex. There are a series of protocol steps to be followed in…”
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Dissecting the chromatin interactome of microRNA genes by Chen, Dijun, Fu, Liang-Yu, Zhang, Zhao, Li, Guoliang, Zhang, Hang, Jiang, Li, Harrison, Andrew P, Shanahan, Hugh P, Klukas, Christian, Zhang, Hong-Yu, Ruan, Yijun, Chen, Ling-Ling, Chen, Ming

“…Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes (MIRs) is evolving rapidly. Here we investigate the effect of…”
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Using electrostatic potentials to predict DNA‐binding sites on DNA‐binding proteins by Jones, Susan, Shanahan, Hugh P., Berman, Helen M., Thornton, Janet M.

“…A method to detect DNA‐binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue…”
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Normalized Affymetrix expression data are biased by G-quadruplex formation by Shanahan, Hugh P, Memon, Farhat N, Upton, Graham J G, Harrison, Andrew P

“…Probes with runs of four or more guanines (G-stacks) in their sequences can exhibit a level of hybridization that is unrelated to the expression levels of the…”
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Identifying DNA-binding proteins using structural motifs and the electrostatic potential by Shanahan, Hugh P., Garcia, Mario A., Jones, Susan, Thornton, Janet M.

“…Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for…”
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Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins by Jones, Susan, Shanahan, Hugh P, Berman, Helen M, Thornton, Janet M

“…A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue…”
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How many extant pinniped species remain to be described? by Woodley, Michael A., Naish, Darren, Shanahan, Hugh P.

“…Large extant marine vertebrates continue to be discovered and described: during the late twentieth and early twenty-first century, several cetaceans and…”
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HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif by Ferrer-Costa, C., Shanahan, H. P., Jones, S., Thornton, J. M.

“…HTHquery is a web-based service to determine if a protein structure has a helix-turn-helix structural motif which could bind to DNA. It is based on a…”
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Lattice calculations in heavy hadron physics by Shanahan, Hugh P

“…The simulation of heavy hadrons using lattice field theory is outlined. Heavy Quark Effective Theory (HQET) is reviewed and is applied in determining an…”
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