Brian E. Howard

Works (4)

Updated: July 5th, 2023 15:56

2013 journal article

High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants

PLOS ONE, 8(10).

By: B. Howard n, Q. Hu  n, A. Babaoglu n, M. Chandra n, M. Borghi n, X. Tan  n, L. He n, H. Winter-Sederoff ...

Contributors: B. Howard n, Q. Hu  n, A. Babaoglu n, M. Chandra n, M. Borghi n, X. Tan  n, L. He n, H. Winter-Sederoff ...

MeSH headings : Alternative Splicing / genetics; Arabidopsis / microbiology; Exons / genetics; Gene Expression Profiling; Genomics; High-Throughput Nucleotide Sequencing; Introns / genetics; Pseudomonas syringae / genetics; Pseudomonas syringae / physiology; RNA Splice Sites / genetics; Sequence Analysis, RNA; Transcription, Genetic / genetics
TL;DR: A genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato finds several genes previously known to be alternatively spliced or expressed during the defense response may serve as a pool of candidate genes for regulated alternative splicing with possible biological relevance for thedefense response against invasive pathogens. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018

2010 article

Towards reliable isoform quantification using RNA-SEQ data

BMC BIOINFORMATICS, Vol. 11.

By: B. Howard n & S. Heber n 

MeSH headings : Algorithms; Alternative Splicing / genetics; Arabidopsis / genetics; Base Sequence; Chi-Square Distribution; Computational Biology / methods; Computer Simulation; Databases, Nucleic Acid; Gene Expression Regulation, Plant; Genes, Plant; Linear Models; Models, Genetic; Molecular Sequence Data; Protein Isoforms / analysis; Protein Isoforms / genetics; Sequence Analysis, RNA / methods; Stress, Physiological
TL;DR: This research investigates the use of RNA sequencing datasets to address the isoform quantification problem and identifies several alternatively-spliced genes with switch-like, on/off expression properties, as well as a number of other genes that varied more subtly in isoform expression. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2009 journal article

Unsupervised assessment of microarray data quality using a Gaussian mixture model

BMC BIOINFORMATICS, 10.

By: B. Howard n, B. Sick * & S. Heber n 

MeSH headings : Algorithms; Computational Biology / methods; Gene Expression Profiling / methods; Normal Distribution; Oligonucleotide Array Sequence Analysis / methods
TL;DR: This research illustrates the efficacy of an unsupervised classification approach for the purpose of automated microarray data quality assessment, which requires only unannotated training data and is easy to customize and to keep up-to-date as technology evolves. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2006 journal article

Accessible proteomics space and its implications for peak capacity for zero-, one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry

JOURNAL OF MASS SPECTROMETRY, 41(3), 281–288.

By: J. Frahm n, B. Howard n, S. Heber n  & D. Muddiman n 

MeSH headings : Biotechnology / instrumentation; Biotechnology / methods; Electrophoresis, Gel, Two-Dimensional; Fourier Analysis; Mass Spectrometry; Peptides / analysis; Proteomics / instrumentation; Proteomics / methods
TL;DR: The results indicate that reverse-phase-nanoHPLC (RP-nHPLC) separation coupled with FT-ICR MS offers an order of magnitude improvement in peak capacity over RP- nHPLC separation coupling with TOF MS, and the addition of an orthogonal separation method, strong cation exchange (SCX), for 2D LC-MS demonstrates an additional 10-fold improvement inpeak capacity over 1D LC -MS methods. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

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