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Bioinformatics

Selected Works

2016

Articles 1 - 20 of 20

Full-Text Articles in Life Sciences

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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Supporting Biomedical Research In The Era Of Omics And Precision Medicine, Rolando Garcia-Milian, Denise Hersey, Nathan Rupp Aug 2016

Supporting Biomedical Research In The Era Of Omics And Precision Medicine, Rolando Garcia-Milian, Denise Hersey, Nathan Rupp

Rolando Garcia-Milian


This annual report (2015-2016) provides a continuing view on the position of the Cushing/Whitney Medical Library End-user Bioinformatics Program. Besides the report on the three main areas of training, resources and tools, and consultations, it contains the results of the recent assessment “Information and Needs Assessment for Biomedical Research in the Omics Era” During this period, 741 Yale affiliates attended (out of 1240 registered) the end-user bioinformatics training and presentations organized by the Medical Library.  This year, the number of Ingenuity Pathway Analysis and MetaCore accounts continued to grow. Consequently, the number and length of research support consultations (130 researchers …

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A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im Aug 2016

A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im

Heather Wheeler

Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates ‘imputed’ gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys …

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Bringing Toxicology Into The 21st Century: A Global Call To Action, Troy Seidle, Martin Stephens Jul 2016

Bringing Toxicology Into The 21st Century: A Global Call To Action, Troy Seidle, Martin Stephens

Martin Stephens, PhD

Conventional toxicological testing methods are often decades old, costly and low-throughput, with questionable relevance to the human condition. Several of these factors have contributed to a backlog of chemicals that have been inadequately assessed for toxicity. Some authorities have responded to this challenge by implementing large-scale testing programmes. Others have concluded that a paradigm shift in toxicology is warranted. One such call came in 2007 from the United States National Research Council (NRC), which articulated a vision of ‘‘21st century toxicology” based predominantly on non-animal techniques. Potential advantages of such an approach include the capacity to examine a far greater …

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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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Genome-Wide Compensatory Changes Accompany Drug-Selected Mutations In The Plasmodium Falciparum Crt Gene, Hongying Jiang, Jigar J. Patel, Ming Yi, Jianbing Mu, Jinhui Ding, Robert Stephens, Roland A. Cooper, Michael T. Ferdig, Xin-Zhuan Su May 2016

Genome-Wide Compensatory Changes Accompany Drug-Selected Mutations In The Plasmodium Falciparum Crt Gene, Hongying Jiang, Jigar J. Patel, Ming Yi, Jianbing Mu, Jinhui Ding, Robert Stephens, Roland A. Cooper, Michael T. Ferdig, Xin-Zhuan Su

Roland A. Cooper

Mutations in PfCRT (Plasmodium falciparum chloroquine-resistant transporter), particularly the substitution at amino acid position 76, confer chloroquine (CQ) resistance in P. falciparum. Point mutations in the homolog of the mammalian multidrug resistance gene (pfmdr1) can also modulate the levels of CQ response. Moreover, parasites with the same pfcrt and pfmdr1 alleles exhibit a wide range of drug sensitivity, suggesting that additional genes contribute to levels of CQ resistance (CQR). Reemergence of CQ sensitive parasites after cessation of CQ use indicates that changes in PfCRT are deleterious to the parasite. Some CQR parasites, however, persist in the …

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Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian, John Gallagher, Janis Glover May 2016

Design, Implementation And Evaluation Of A Medical Library Program To Support Biomedical Research In The Omics Era, Rolando Garcia-Milian, John Gallagher, Janis Glover

Rolando Garcia-Milian


Objectives
Design and implement a sustainable program that supports biomedical research at Yale University. Our program responds to the challenges posed by omics (e.g. genomics, transcriptomics, proteomics, etc.) technologies, identifies the role and place of the Yale Cushing/Whitney Medical Library in the high-throughput omics research cycle, and is based on the organizational culture of the institution.

Methods
Key challenges posed by omics technologies on preclinical and clinical research are: rapidly generating high amount of diverse omics data; integrating these diverse data; exponential increase in the biomedical literature and databases; use of pathway and network-based methods to analyze and visualize information; …

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Making Sense Of Genomic Variation: Part 1 Snp Annotation, Rolando Garcia-Milian Mar 2016

Making Sense Of Genomic Variation: Part 1 Snp Annotation, Rolando Garcia-Milian

Rolando Garcia-Milian

The  specific combination of genetic variation in an individual defines not  only the external appearance but also susceptibility to diseases,  cancer, genetic disorders, drug response, etc. This explains the great  interest in discovering and cataloging these variations and using them  for disease association and functional studies, among others. In this  session we will review the most popular databases and tools to annotate,  analyze and visualize genetic variations. Some of the databases and  tools that will be discussed are:
-dbSNP
- Online Mendelian Inheritance in Man a comprehensive, authoritative compendium of human genes and genetic phenotypes.
- GWAS Catalog
-  EBI's …

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Mapping Transcriptome Profiles Of In Vitro Ipsc-Derived Cardiac Differentiation To In Utero Heart Development, Xing Li, Katherine A. Campbell, Sherri M. Biendarra, Andre Terzic, Timothy J. Nelson Feb 2016

Mapping Transcriptome Profiles Of In Vitro Ipsc-Derived Cardiac Differentiation To In Utero Heart Development, Xing Li, Katherine A. Campbell, Sherri M. Biendarra, Andre Terzic, Timothy J. Nelson

Katherine Campbell, PhD

No abstract provided.

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Distinct Cardiac Responses To Heat Stress Between Two Broiler Lines Identified By Transcriptome Analysis, Jibin Zhang, Carl J. Schmidt, Susan J. Lamont Jan 2016

Distinct Cardiac Responses To Heat Stress Between Two Broiler Lines Identified By Transcriptome Analysis, Jibin Zhang, Carl J. Schmidt, Susan J. Lamont

Jibin Zhang

Prolonged exposure to high temperature can significantly increase metabolism, depress appetite, reduce meat production and raise mortality in broilers. Because the cardiovascular system plays an important role to dissipate heat and transport oxygen, strong cardiac function is indispensable for birds to survive under heat stress. However, due to small hearts relative to body weight, modern broilers have high risk of heart failure at high temperature.
In this study, a Ross 708 line (modern broilers) and a Heritage broiler line (relaxed selection since the 1950s) were subjected to heat stress at 35℃  for 7 hours/day from 21 to 42 days posthatch …

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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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