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Ray Enke Ph.D.

Articles 1 - 27 of 27

Full-Text Articles in Bioinformatics

Cure-All- Large Scale Implementation Of Authentic Dna Barcoding Research Into First-Year Biology Curriculum, Oliver Hyman, Elizabeth Doyle, Joseph Harsh, Joanna Mott, Andrea Pesce, Bejan Rasoul, Kyle Seifert, Ray A. Enke Dec 2018

Cure-All- Large Scale Implementation Of Authentic Dna Barcoding Research Into First-Year Biology Curriculum, Oliver Hyman, Elizabeth Doyle, Joseph Harsh, Joanna Mott, Andrea Pesce, Bejan Rasoul, Kyle Seifert, Ray A. Enke

Ray Enke Ph.D.

Growing calls in science education reform have emphasized wide-scale engagement of first-year undergraduate students in authentic research experiences; however, large course enrollments, inadequate student experience, limited resources and departmental inertia often create obstacles to reaching this goal. To help overcome these obstacles, the Department of Biology at James Madison University (JMU) has developed a cost-effective, scalable, and transferable semester-long (14- week) course-based undergraduate research experience (CURE) designed for large enrollment introductory biology labs. In this series of labs, first-year students use DNA barcoding to engage in authentic research practices drawn from the fields of ecology, molecular biology, and bioinformatics. These …

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Intro To Rna-Sequencing Lecture Slides, Ray A. Enke Dec 2018

Intro To Rna-Sequencing Lecture Slides, Ray A. Enke

Ray Enke Ph.D.

Introductory lecture slides on eukaryotic RNA-sequencing analysis

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Rna-Seq Bioinformatics Analysis Using Cyverse Discovery Environment, Ray A. Enke Dec 2018

Rna-Seq Bioinformatics Analysis Using Cyverse Discovery Environment, Ray A. Enke

Ray Enke Ph.D.

This slide deck gives an overview of FastQC and Kallisto psudoalignment RNA-seq analysis using the CyVerse Discovery Environment cyberinfrastructure platform.

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Saccharomyces Genome Database & Uniprot Bioinformatics Analysis, Ray A. Enke Dec 2018

Saccharomyces Genome Database & Uniprot Bioinformatics Analysis, Ray A. Enke

Ray Enke Ph.D.

This in class activity introduces basic bioinformatics analysis using the Saccharomyces Genome Database (SGD) and the UniProt Database. The yeast URA3 gene is studied in this activity, however, any other yeast gene can be substituted. This activity is designed for novice instructors and students for implementation into core biology lecture or lab courses.

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Dna Subway Purple Line Metagenome Analysis, Ray A. Enke Nov 2018

Dna Subway Purple Line Metagenome Analysis, Ray A. Enke

Ray Enke Ph.D.

This in class walkthrough demonstrates how to use the DNA Subway Purple Line for metagenomics analysis of 16S microbiome Illumina sequencing reads.

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Fastqc Analysis & Hisat Alignments Using Cyverse (Part 2), Ray A. Enke Oct 2018

Fastqc Analysis & Hisat Alignments Using Cyverse (Part 2), Ray A. Enke

Ray Enke Ph.D.

Part 2 of this in class exercise uses CyVerse Discovery Environment (DE) for the following:
  • view the output files of FastQC analysis
  • create custom data tracks from HISAT alignment files for visualization in the UCSC Genome Browser

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Fastqc Analysis & Hisat Alignments Using Cyverse (Part 1), Ray A. Enke Oct 2018

Fastqc Analysis & Hisat Alignments Using Cyverse (Part 1), Ray A. Enke

Ray Enke Ph.D.

This in class exercise demonstrates the basic features of the CyVerse Discovery Environment (DE) cyberinfrastructure and also provides a tutorial for setting up FastQC analysis of next generation sequencing reads as well as HISAT alignment of eukaryotic RNA-seq FASTQ files.

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Intro To Command Line Coding (Fastqe & Fastp), Ray A. Enke Oct 2018

Intro To Command Line Coding (Fastqe & Fastp), Ray A. Enke

Ray Enke Ph.D.

This in class activity is designed for novices as an introduction to command line coding. The activity uses the programs FASTQE and FASTP to analyze the quality and trim Illumina FASTQ sequencing data.

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Transcripity Split: Course-Based Rna-Seq Analysis Using The Ultrafast Kallisto-Sleuth Pipeline, Ray A. Enke Dec 2017

Transcripity Split: Course-Based Rna-Seq Analysis Using The Ultrafast Kallisto-Sleuth Pipeline, Ray A. Enke

Ray Enke Ph.D.

No abstract provided.

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Uploading Data To The Ncbi Sra Database, Ray A. Enke Jun 2017

Uploading Data To The Ncbi Sra Database, Ray A. Enke

Ray Enke Ph.D.

This in class exercise focuses on uploading FASTQ files sequencing data to the NCBI SRA database

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Using Rstudio For Manipulating And Visualizing Data (Updated 11/17), Ray A. Enke, Bejan A. Rasoul Dec 2016

Using Rstudio For Manipulating And Visualizing Data (Updated 11/17), Ray A. Enke, Bejan A. Rasoul

Ray Enke Ph.D.

This in class exercise is designed to teach novices about the basic features of R and RStudio using a non-biological data set called Gapminder. It is a modified version of a Data Carpentry Workshop that I use to teach programming to beginners.

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Genomics Rna-Seq Analysis Part 1-Cyverse De, Fastqc, Trimmomatic (Updated 11/17), Ray A. Enke, Melika Rahmani-Mofrad Dec 2016

Genomics Rna-Seq Analysis Part 1-Cyverse De, Fastqc, Trimmomatic (Updated 11/17), Ray A. Enke, Melika Rahmani-Mofrad

Ray Enke Ph.D.

This in class exercise is designed to teach students about the basic features of CyVerse Discovery Environment (DE) as well as how to run FastQC and Trimmomatic steps of a general eukaryotic RNA-seq analysis pipeline using CyVerse DE apps.

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Genomics Rna-Seq Analysis Part 2_ Kallisto Indexing And Quantification (Updated 11/17), Ray A. Enke, Melika Rahmani-Mofrad Dec 2016

Genomics Rna-Seq Analysis Part 2_ Kallisto Indexing And Quantification (Updated 11/17), Ray A. Enke, Melika Rahmani-Mofrad

Ray Enke Ph.D.

This in class exercise is a hands on activity designed to teach students about how to run Kallisto indexing quantification using CyVerse DE apps as part of a eukaryotic RNA-seq analysis pipeline.

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Genomics Rna-Seq Analysis Part 3-Sleuth Data Visualization (Updated 11/17), Ray A. Enke, Scott Schumacker Dec 2016

Genomics Rna-Seq Analysis Part 3-Sleuth Data Visualization (Updated 11/17), Ray A. Enke, Scott Schumacker

Ray Enke Ph.D.

This in class exercise is a hands on activity designed to teach students about how to run Sleuth statistical modeling and RStudio data visualization package using Kallisto pseudoalignment output files as part of a eukaryotic RNA-seq analysis pipeline.

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Heat Map Analysis Of Rna-Seq Data Using Rstudio, Ray A. Enke, Ashton Holub Nov 2016

Heat Map Analysis Of Rna-Seq Data Using Rstudio, Ray A. Enke, Ashton Holub

Ray Enke Ph.D.

This in class exercise focuses on using the CummeRbund package in RStudio to create heat maps for analyzing differential gene expression output generated by Cuffdiff in DNA Subway Green Line

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Rna Sequencing Analysis Of The Developing Chicken Retina, Christophe Langouet-Astrie*, Annamarie Meinsen*, Emily R. Grunwald*, Stephen Turner, Raymond A. Enke Nov 2016

Rna Sequencing Analysis Of The Developing Chicken Retina, Christophe Langouet-Astrie*, Annamarie Meinsen*, Emily R. Grunwald*, Stephen Turner, Raymond A. Enke

Ray Enke Ph.D.

RNA sequencing transcriptome analysis using massively parallel next generation sequencing technology provides the capability to understand global changes in gene expression throughout a range of tissue samples. Development of the vertebrate retina requires complex temporal orchestration of transcriptional activation and repression. The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology and retinogenesis. Existing retinal transcriptome projects have been critical to the vision research community for studying aspects of murine and human retinogenesis, however, there are currently no publicly available data sets describing the developing chicken retinal transcriptome. Here we used Illumina RNA sequencing …

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Intro To Rstudio, Ray A. Enke, Ashton Holub Nov 2016

Intro To Rstudio, Ray A. Enke, Ashton Holub

Ray Enke Ph.D.

This in class exercise is designed to teach novices about the basic features of R and RStudio using a non-biological data set called Gapminder. It is a modified version of a Data Carpentry Workshop that I use to teach programming to beginners.

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Connecting Common Genetic Polymorphisms To Protein Function: A Modular Project Sequence For Lecture Or Lab, Christopher E. Berndsen, Byron H. Young, Quinlin Mccormick*, Raymond A. Enke Oct 2016

Connecting Common Genetic Polymorphisms To Protein Function: A Modular Project Sequence For Lecture Or Lab, Christopher E. Berndsen, Byron H. Young, Quinlin Mccormick*, Raymond A. Enke

Ray Enke Ph.D.

Single nucleotide polymorphisms (SNPs) in DNA can result in phenotypes where the biochemical basis may not be clear due to the lack of protein structures. With the growing number of modeling and simulation software available on the internet, students can now participate in determining how small changes in genetic information impact cellular protein structure and function. We have developed a modular series of activities to engage lab or lecture students in examining the basis for common phenotypes. The activities range from basic phenotype test- ing/observation to DNA sequencing and simulation of protein structure and dynamics. We provide as an exam- …

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Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Ray A. Enke Oct 2016

Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Ray A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • analyzing qPCR standard curve data to determine primer efficiency
  • analyzing differential gene expression experimental qPCR data
  • applying KEGG pathway analysis of selected candidates genes

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Research & Course-Based Applicatons Of The Ucsc Genome Browser, Ray A. Enke Jun 2016

Research & Course-Based Applicatons Of The Ucsc Genome Browser, Ray A. Enke

Ray Enke Ph.D.

No abstract provided.

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Approaches To Teaching Rna-Seq In Undergraduate Lecture & Lab Courses, Ray A. Enke May 2016

Approaches To Teaching Rna-Seq In Undergraduate Lecture & Lab Courses, Ray A. Enke

Ray Enke Ph.D.

No abstract provided.

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Pathway Analysis Of Differentially Expressed Genes (Computational), Raymond A. Enke May 2016

Pathway Analysis Of Differentially Expressed Genes (Computational), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Conduct gene ontology (GO) pathway analysis of statistically and biologically significant differentially expressed genes (DEGs)
  • Sort and organize lists of DEGs in MS Excel spreadsheets based on biological function

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Analysis Of Rna-Seq Alignments Using Dna Subway Green Line (Computational), Raymond A. Enke May 2016

Analysis Of Rna-Seq Alignments Using Dna Subway Green Line (Computational), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Review basic steps of RNA-Seq bioinformatics analysis in DNA Subway Green Line
  • View and run basic analytics of RNA-Seq data set in DNA Subway Green Line

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Bitter Taste Receptor Genotype/Phenotype Lab: A Modular Project Sequence For Lecture Or Lab, Raymond A. Enke May 2016

Bitter Taste Receptor Genotype/Phenotype Lab: A Modular Project Sequence For Lecture Or Lab, Raymond A. Enke

Ray Enke Ph.D.


Single nucleotide polymorphisms (SNPs) in DNA can result in phenotypes where the biochemical basis may not be clear due to the lack of protein structures. With the growing number of modeling and simulation software available on the internet, students can now participate in determining how small changes in genetic information impact cellular protein structure and function. We have developed a modular series of activities to engage lab or lecture students in examining the basis for common phenotypes.  The activities range from basic phenotype testing/observation to DNA sequencing and simulation of protein structure and dynamics. We provide as an example study …

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Creating Custom Rna-Seq Data Tracks In The Ucsc Genome Browser (Computational), Raymond A. Enke May 2016

Creating Custom Rna-Seq Data Tracks In The Ucsc Genome Browser (Computational), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Create your own custom data tracks in the UCSC Genome Browser
  • Visualize RNA-Seq TopHat alignment data as custom tracks in the UCSC Genome Browser
  • Integrate RNA-Seq alignment data with other genome-wide data sets

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Integration Of Rna-Seq Data Analysis Into Undergraduate Lab Teaching Modules, Raymond A. Enke Jan 2016

Integration Of Rna-Seq Data Analysis Into Undergraduate Lab Teaching Modules, Raymond A. Enke

Ray Enke Ph.D.


Undergraduate students learn about Next Generation Sequencing (NGS) platforms in courses, but often have difficulty understanding the impact of these techniques without hands-on experience analyzing actual NGS datasets.  The NSF-supported Infrastructure & Training to Bring NGS Analysis Into Undergraduate Education project focuses on streamlining RNA-sequencing (RNA-seq) data analysis using a combination of bioinformatics and wet lab workflows tailored for implementation into diverse undergraduate laboratory classroom settings. These modular workflows can be applied to a variety of novel or publicly available RNA-seq datasets.
 
To create a course-based undergraduate research experience focusing on NGS that complements my research program, I …

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Jmu 4-Va Grant: Gene Expression Analysis In The Developing Vertebrate Retina Using Next Generation Sequencing, Raymond A. Enke Mar 2014

Jmu 4-Va Grant: Gene Expression Analysis In The Developing Vertebrate Retina Using Next Generation Sequencing, Raymond A. Enke

Ray Enke Ph.D.

4-VA Funded Research Grant: Gene expression analysis in the developing vertebrate retina using next generation sequencing



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