Charlie Johnson

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
• Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1
• Late-life dietary folate restriction reduces biosynthesis without compromising healthspan in mice
• A Streamlined Approach to Genotyping with Low-Pass WGS
• A Streamlined Approach to Genotyping with Low-Pass WGS