C
Charles D. Johnson
Researcher at Texas A&M University
Publications - 28
Citations - 5852
Charles D. Johnson is an academic researcher from Texas A&M University. The author has contributed to research in topics: Deep sequencing & Transcriptome. The author has an hindex of 19, co-authored 26 publications receiving 5483 citations. Previous affiliations of Charles D. Johnson include Texas AgriLife Research & University of Louisville.
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Journal ArticleDOI
Modeling the next generation sequencing sample processing pipeline for the purposes of classification
Noushin Ghaffari,Mohammadmahdi R. Yousefi,Charles D. Johnson,Ivan Ivanov,Edward R. Dougherty,Edward R. Dougherty +5 more
TL;DR: In this article, the effects of different factors are considered and NGS-based classification is compared to SAGEbased classification and classification directly on the raw expression data, which is represented by a very high-dimensional model previously developed for gene expression.
Journal ArticleDOI
Annotated Draft Genome Assemblies for the Northern Bobwhite ( Colinus virginianus ) and the Scaled Quail ( Callipepla squamata ) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size.
David L. Oldeschulte,Yvette A. Halley,Miranda L. Wilson,Eric K. Bhattarai,Wesley A. Brashear,Joshua Hill,Richard P. Metz,Charles D. Johnson,Dale Rollins,Markus J. Peterson,Derek M. Bickhart,Jared E. Decker,John F. Sewell,Christopher M. Seabury +13 more
TL;DR: Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail populations have suffered precipitous declines across most of their US ranges and large-scale declines were predicted for both species beginning ∼15–20 KYA.
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Identification and analysis of the first 2009 pandemic H1N1 influenza virus from U.S. feral swine.
A. Clavijo,Amir Nikooienejad,Mohammad Shahrokh Esfahani,Richard P. Metz,Scott Schwartz,Esmaeli Atashpaz-Gargari,Thomas J. DeLiberto,Mark W. Lutman,Kerri Pedersen,L. R. Bazan,L. G. Koster,Melinda Jenkins-Moore,Sabrina L. Swenson,M. Zhang,T. Beckham,Charles D. Johnson,Mohammad Bounpheng +16 more
TL;DR: The first pH1N1 isolate in feral swine in the United States is identified and an easy unbiased linear amplification method is demonstrated for deep sequencing of multiple samples to demonstrate the feasibility of using an unbiased whole‐genome linear target amplification method.
Modeling the next generation sequencing sample processing pipeline for the purposes of
TL;DR: Having high numbers of reads can mitigate the degradation in classification performance resulting from the effects of NGS technologies, and when performing a RNA-Seq analysis, using the highest possible coverage of the genome is recommended for the purposes of classification.
Journal ArticleDOI
Nfatc2 and Tob1 have non-overlapping function in T cell negative regulation and tumorigenesis.
Sarah L. May,Qing Zhou,Mitzi Lewellen,Cristan M. Carter,Cristan M. Carter,David C. Coffey,David C. Coffey,Steven L. Highfill,Christoph Bucher,Ilze Matise,Herbert C. Morse,M. Gerard O'Sullivan,Melissa M. Schutten,Charles D. Johnson,Donald Bellgrau,Donald Bellgrau,Bruce R. Blazar,Jaime F. Modiano +17 more
TL;DR: The data support the prevailing hypothesis that Nfatc2 and Tob1 are non-redundant regulators of lymphocyte homeostasis and develop a previously uncharacterized increase in B-cell malignancies.