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Bioinformatics

Selected Works

2018

Articles 1 - 10 of 10

Full-Text Articles in Life Sciences

Confold2: Improved Contact-Driven Ab Initio Protein Structure Modeling, Badri Adhikari, Jianlin Cheng Nov 2018

Confold2: Improved Contact-Driven Ab Initio Protein Structure Modeling, Badri Adhikari, Jianlin Cheng

Badri Adhikari

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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Mapping Molecular Datasets Back To The Brain Regions They Are Extracted From: Remembering The Native Countries Of Hypothalamic Expatriates And Refugees, Arshad M. Khan, Alice H. Grant, Anais Martinez, Gully Apc Burns, Brendan S. Thatcher, Vishwanath T. Anekonda, Benjamin W. Thompson, Zachary S. Roberts, Daniel H. Moralejo, James E. Blevins Jun 2018

Mapping Molecular Datasets Back To The Brain Regions They Are Extracted From: Remembering The Native Countries Of Hypothalamic Expatriates And Refugees, Arshad M. Khan, Alice H. Grant, Anais Martinez, Gully Apc Burns, Brendan S. Thatcher, Vishwanath T. Anekonda, Benjamin W. Thompson, Zachary S. Roberts, Daniel H. Moralejo, James E. Blevins

Arshad M. Khan, Ph.D.

This article, which includes novel unpublished data along with commentary and analysis,
focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined from
brain tissue to the original locations within the brain that they are derived from using digital atlas
mapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomic
analyses conducted in the mammalian hypothalamus. Following a brief historical overview, we
highlight studies that have mined biochemical and molecular information from the hypothalamus
and then lay out a strategy for how these data can be linked spatially to the mapped locations in a
canonical brain atlas …

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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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Fast And Space-Efficient Location Of Heavy Or Dense Segments In Run-Length Encoded Sequences, Ronald I. Greenberg Jan 2018

Fast And Space-Efficient Location Of Heavy Or Dense Segments In Run-Length Encoded Sequences, Ronald I. Greenberg

Ronald Greenberg

This paper considers several variations of an optimization problem with potential applications in such areas as biomolecular sequence analysis and image processing. Given a sequence of items, each with a weight and a length, the goal is to find a subsequence of consecutive items of optimal value, where value is either total weight or total weight divided by total length. There may also be a specified lower and/or upper bound on the acceptable length of subsequences. This paper shows that all the variations of the problem are solvable in linear time and space even with non-uniform item lengths and divisible …

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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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