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Charlie Johnson

Director Genomics and bioinformatics (Medical biotechnology not elsewhere classified)

College Station, Texas

Publications

  • https://scholar.google.com/citations?user=VUv9TbEAAAAJ&hl=en
  • Computational considerations in transcriptome assemblies and their evaluation, using high quality human RNA-Seq data
  • Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112
  • Promoter scanning during transcription initiation inSaccharomyces cerevisiae: Pol II in the “shooting gallery”
  • CBGSE_presentation 3Short.pptx
  • HiMMe: using genetic patterns as a proxy for genome assembly reliability assessment
  • A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction.
  • Jobs Posts up to April 19th 2016
  • Jobs Posts up to April 19th 2016
  • Bioinformatics education needs
  • Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
  • 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
  • Additional file 3: Table S3. of Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
  • Additional file 5: Figure S1. of Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
  • Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells.
  • Developing KASP Markers on a Major Stripe Rust Resistance QTL in a Popular Wheat TAM 111 Using 90K Array and Genotyping-by-Sequencing SNPs
  • Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes
  • Functional RNAs in Stallion Sperm: Potential Indicators of Sperm Quality and Contributors to Fertility
  • What are the most influencing factors in reconstructing a reliable transcriptome assembly?
  • Jobs Posts up to September 30th 2017
  • Jobs Posts up to September 30th 2017
  • Jobs Posts up to October 10th 2016
  • Jobs Posts up to September 30th 2017
  • Low cost, fast and accurate high throughput genotyping
  • CBGSE_presentation 3Short.pptx
  • Jobs Posts up to April 19th 2016
  • Jobs Posts up to April 19th 2016
  • Jobs Posts up to April 19th 2016
  • Jobs Posts up to April 19th 2016
  • Jobs Posts up to April 19th 2016
  • Jobs Posts up to April 19th 2016
  • Bioinformatic Jobs
  • Data from: Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy
  • Bobwhite Mitogenome Alignment_IDs
  • Data from: Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy
  • Bobwhite Mitogenome Reads-Illumina_PE
  • Bobwhite Mitogenome Reads-Illumina_PE
  • Bobwhite Mitogenome Reads-Illumina_PE
  • Bobwhite Mitogenome Reads-Illumina_PE
  • Data from: Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy
  • Bobwhite Mitogenome Reads-Illumina_PE
  • Bobwhite Mitogenome Reads-Illumina_PE
  • Bobwhite Mitogenome Alignment_IDs
  • Bioinformatics education needs
  • Additional file 1: Figure S1. of A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction
  • Additional file 2: of A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction
  • Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
  • Bobwhite Mitogenome Alignment - SUPERSEDED - DELETE AT CURATION
  • Additional file 1: Table S1. of Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
  • Additional file 2: Table S2. of Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
  • Additional file 4: Table S4. of Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing
  • OBGene: Optimal barcode generator for NGS experiments
  • miR-10 Regulated Genes and Pathways as Targets for Therapeutic Intervention
  • Modulation of RNA Polymerase II Phosphorylation Downstream of Pathogen Perception Orchestrates Plant Immunity
  • Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture
  • Whole-Genome Sequencing and Genetic Variant Analysis of a Quarter Horse Mare
  • Fast DNA Barcode Generating Algorithm Using Radix Coding Method
  • Short papers and notes
  • Jobs Posts up to April 19th 2016
  • Jobs Posts up to April 19th 2016
  • De novo transcriptome assemblies and annotation for pacifie whiteleg shrimp
  • Mir-143 regulated genes and pathways as targets for therapeutic intervention
  • FUNCTIONS AND TARGETS OF LET-7 MICRO RNAS
  • miR-200 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION
  • Comparison of High-Density Short Oligonucleotide Microarray Platforms
  • MIR-15, MIR-26, MIR-31, MIR-145, MIR-147, MIR-188, MIR-215, MIR-216 MIR-331, MMU-MIR-292-3P REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION
  • Amplicon Based 16S Ribosomal RNA Sequencing and Genus Identification - Mixed Species
  • mir-21 Regulated genes and pathways as targets for therapeutic intervention
  • Identification and Analysis of the First 2009 Pandemic H1N1 Influenza Virus from US Feral Swine
  • FUNCTIONS AND TARGETS OF LET-7 MICRO RNAS
  • Whole-genome Analysis of a Quarter Horse Mare
  • Mir-16 regulated genes and pathways as targets for therapeutic intervention
  • OBGene: Optimal Barcode Generator for NGS Experiments
  • Mir-34 regulated genes and pathways as targets for therapeutic intervention
  • A Global View of miRNA Expression Using a Microarray Platform Featuring Probes for More than 15,000 Putative and Validated miRNAs
  • Functions and targets of let-7 micro rnas
  • A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
  • Identification of Pandemic H1N1 Influenza Virus in Feral Swine
  • FUNCTIONS AND TARGETS OF LET-7 MICRO RNAS
  • Mir-20 regulated genes and pathways as targets for therapeutic intervention
  • miR-126 REGULATED GENES AND PATHWAYS AS TARGETS FOR THERAPEUTIC INTERVENTION
  • Quail Mitogenome Alignment For RAxML Tree
  • Quail Mitogenome Alignment For RAxML Tree
  • A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene
  • Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy
  • Jobs Posts up to October 10th 2016
  • Modeling the next generation sequencing sample processing pipeline for the purposes of classification
  • Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline
  • Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens
  • The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
  • Jobs Posts up to October 10th 2016
  • Scaled Quail Mitogenome Reads-Illumina_PE
  • Jobs Posts up to October 10th 2016
  • Three gene combinations to predict the behavior of selected target genes
  • Quail Mitogenome Alignment For RAxML Tree
  • Insight into redox-regulated gene networks in vascular cells-1
  • Insight into redox-regulated gene networks in vascular cells-1
  • Three gene combinations to predict the behavior of selected target genes
  • Scaled Quail Mitogenome Reads-Illumina_PE
  • Scaled Quail Mitogenome Reads-Illumina_PE
  • Jobs Posts up to October 10th 2016
  • Genomic profiles and predictive biological networks in oxidant-induced atherogenesis
  • Clustering: Revealing intrinsic dependencies in microarray data
  • In vitro models to evaluate acute and chronic injury to the heart and vascular systems
  • Neural crest and mesoderm lineage-dependent gene expression in orofacial development
  • Genome-scale microRNA and small interfering RNA screens identify small RNA modulators of TRAIL-induced apoptosis pathway
  • Toxicogenomic profile of 2,3,7,8-tetrachlorodibenzo-p-dioxin in the murine fetal heart: Modulation of cell cycle and extracellular matrix genes
  • Using RNA sample titrations to assess microarray platform performance and normalization techniques
  • NITROGEN AND POTASSIUM FERTILITY OF JALAPENO PEPPER DURING PLANT DEVELOPMENT AFFECTS PLANT GROWTH AND FRUIT YIELD AND PUNGENCY
  • The let-7 microRNA represses cell proliferation pathways in human cells
  • The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
  • Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction
  • Insight into redox-regulated gene networks in vascular cells.
  • Differential response in cell proliferation to beta estradiol in coronary arterial vascular smooth muscle cells obtained from mature female versus male animals
  • Global microRNA profiles from archived colorectal cancer tumors
  • By TIMOTHY S. DAVISON, CHARLES D. JOHNSON, and
  • In vitro models to evaluate acute and chronic injury to the heart and vascular systems
  • Nitrogen and potassium nutrition of Jalapeno pepper
  • Improved microarray sensitivity using whole blood RNA samples
  • Increase Signal and Detect More Genes on Affymetrix® Arrays
  • Exploration of microRNA Expression Profiling in Fixed Archived Tissues: Lung Cancer Pilot Study
  • Dioxin induces growth arrest and reduces cell cycle gene expression in the fetal murine heart.
  • Application of clustering methodologies to the analysis of altered cellular phenotypes induced by oxidative stress.
  • Habanero Pepper: World’s Hottest Pepper Comes to South Carolina
  • Cash In On New Markets For Collards
  • Clustering: revealing intrinsic dependencies in microarray data
  • Synthesize High Yields of Biotinylated aRNA
  • microRNAs in the Treatment of Cancer
  • Chemical disruption of global gene expression during nephrogenesis: Role of aryl hydrocarbon receptor.
  • From" omics" to insight: The use of a novel computational approach to study genegene interactions.
  • GROWTH HORMONE: AN EARLY EMBRYONIC PARACRINE?
  • Neural crest and mesoderm lineage-dependent gene expression in orofacial development
  • Insight into redox-regulated gene networks in vascular cells
  • Genomic profiles and predictive biological networks in oxidant-induced atherogenesis
  • Novel genomic targets in oxidant-induced vascular injury
  • Toxicogenomic profile of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin in the murine fetal heart: modulation of cell cycle and extracellular matrix genes
  • A high-density MicroRNA array for analyzing the expression of 15,090 verified and predicted small, non-coding RNAs.
  • Genomic and immunofluorescence analysis of interactive gene networks in oxidant induced atherogenesis.
  • PowerAssist™: A Microarray QC Tool
  • Two Zesty Alternatives to Bell Pepper
  • Nitrogen Fertility and Cultivar Influence Collard Yield and Leaf Nitrogen Content
  • Analyzing Micro-RNA Expression Using Microarrays
  • Genome-scale microRNA and small interfering RNA screens identify small RNA modulators of TRAIL-induced apoptosis pathway
  • Leptin and pubertal development in heifers: relationship of ob gene expression to circulating leptin as measured by heterologous radioimmunoassay
  • Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor
  • [2] Analyzing Micro‐RNA Expression Using Microarrays
  • Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor
  • Unraveling Gene-Gene Interactions Regulated by Ligands of the Aryl Hydrocarbon Receptor*
  • Nitrogen and potassium fertility affects Jalapeno pepper plant growth, pod yield, and pungency
  • Novel genomic targets in oxidant-induced vascular injury.
  • Transcriptome Analysis of Developing Grains from Wheat Cultivars TAM 111 and TAM 112 Reveal Cultivar-Specific Regulatory Networks
  • Horn fly transcriptome data of ten populations from the southern United States with varying degrees and molecular mechanisms of pesticide resistance
  • Mapping QTL for Yield and Its Component Traits Using Wheat (Triticum aestivum L.) RIL Mapping Population from TAM 113 × Gallagher

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