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Genomics

Selected Works

2018

Articles 1 - 11 of 11

Full-Text Articles in Life Sciences

Dmk_Dissertation_11.19.18.Pdf, Dana King Dec 2018

Dmk_Dissertation_11.19.18.Pdf, Dana King

Dana King

No abstract provided.

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Dmk_Dissertation_11.19.18.Pdf, Dana King Dec 2018

Dmk_Dissertation_11.19.18.Pdf, Dana King

Dana King

No abstract provided.

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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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Assessing & Filtering Illumina Short Read Ngs Data Using Galaxy, Ray A. Enke Jun 2018

Assessing & Filtering Illumina Short Read Ngs Data Using Galaxy, Ray A. Enke

Ray Enke Ph.D.

This walkthrough focuses on analyzing and filtering raw Next Generation Sequencing FASTQ file data using FastQC and Trimmomatic software in the Galaxy bioinformatics platform.

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Tissue-Specific Transcriptome For Poeciliopsis Prolifica Reveals Evidence For Genetic Adaptation Related To The Evolution Of A Placental Fish, Nathaniel K. Jue, Robert J. Foley, David N. Reznick, Rachel J. O'Neill, Michael J. O'Neill Jun 2018

Tissue-Specific Transcriptome For Poeciliopsis Prolifica Reveals Evidence For Genetic Adaptation Related To The Evolution Of A Placental Fish, Nathaniel K. Jue, Robert J. Foley, David N. Reznick, Rachel J. O'Neill, Michael J. O'Neill

Nathaniel Jue

The evolution of the placenta is an excellent model to examine the evolutionary processes underlying adaptive complexity due to the recent, independent derivation of placentation in divergent animal lineages. In fishes, the family Poeciliidae offers the opportunity to study placental evolution with respect to variation in degree of post-fertilization maternal provisioning among closely related sister species. In this study, we present a detailed examination of a new reference transcriptome sequence for the live-bearing, matrotrophic fish, Poeciliopsis prolifica, from multiple-tissue RNA-seq data. We describe the genetic components active in liver, brain, late-stage embryo, and the maternal placental/ovarian complex, as well as …

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De-Identified Interviews For The Study: Data Challenges Of Biomedical Researchers In The Age Of Omics, Rolando Garcia-Milian, Denise Hersey, Milica Vukmirovic Jan 2018

De-Identified Interviews For The Study: Data Challenges Of Biomedical Researchers In The Age Of Omics, Rolando Garcia-Milian, Denise Hersey, Milica Vukmirovic

Rolando Garcia-Milian


Background: High-throughput technologies are rapidly generating large amounts of diverse omics data. Although this offers a great opportunity, it also poses great challenges as data analysis becomes more complex. The purpose of this study was to identify the main challenges researchers face in analyzing data, and how academic libraries can support them in this endeavor.
Methods: A multimodal needs assessment analysis, combined an online survey of 860 Yale-affiliated researchers and 15 in-depth one-on-one semi-structured interviews. Interviews were recorded, transcribed, and analyzed using NVivo 10® software according to the thematic analysis approach.
Results: The survey response rate was …

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Landscape Genomics: Natural Selection Drives The Evolution Of Mitogenome In Penguins, Barbara Ramos, Daniel González-Acuña, David E. Loyola, Warren E. Johnson, Patricia G. Parker, Melanie Massaro, Gisele P. M. Dantas, Marcelo D. Miranda, Juliana A. Vianna Jan 2018

Landscape Genomics: Natural Selection Drives The Evolution Of Mitogenome In Penguins, Barbara Ramos, Daniel González-Acuña, David E. Loyola, Warren E. Johnson, Patricia G. Parker, Melanie Massaro, Gisele P. M. Dantas, Marcelo D. Miranda, Juliana A. Vianna

Patricia Parker

Background
Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera (Spheniscus, Pygoscelis, Eudyptula, Eudyptes …

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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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