Genomics Commons^™

Development Of Functional Markers For Resistance To Smut And Identification Of Genes Differentially Expressed In Response To Brown Rust In Sugarcane, Jose David Cortes

LSU Doctoral Dissertations

Smut, caused by Sporisorium scitamineum and brown rust, caused by Puccinia melanocephala, are two of the most important diseases that affect sugarcane production in Louisiana and worldwide. Smut continues to cause losses in the breeding program in Louisiana. Therefore, a QTL analysis was conducted to identify molecular markers associated with resistance in F₁ progeny (162) of a biparental cross between susceptible cultivar L 99-233 and resistant HoCP 96-540. Using 1,574 single-dose SNP markers, a total of 253 linkage groups (LG) were obtained with a genome coverage of 24,580.15 cM. Six QTLs were localized on five LGs. The highest …

Effects Of Continuous In Situ Low-Dose Ionizing Radiation On Microorganisms, Molly E. Wintenberg

All Dissertations

Precise detection and monitoring of nuclear fuel cycle, enrichment, and weapon development activities are critical for supporting warfighter preparation in chemical, biological, radiological, nuclear, and explosives (CBRNE) operations, clandestine activities, and nuclear compliance. A biological sensing system could serve as an alternative to traditional detection methods by using organic material naturally present in the environment to discreetly detect residual trace nuclear material. Microorganisms provide an optimal platform for an alternative sensing system; however, their response to low levels of ionizing radiation is poorly characterized. Combining the power of next-generation sequencing and transcriptomic analysis, this dissertation takes an approach to obtain …

Genetic And Environmental Regulation Of Plant Growth, Kirk J-M Mackinnon

Doctoral Dissertations

Field grown crops are continually exposed to a variety of external stimuli that influence plant responses. Light, temperature, and water availability interact to affect many economically important traits including growth rate, size, and lifespan. My research is focused on the intersection of genetic and environmental factors influencing plant growth. Specifically, I am interested in elucidating the regulation of rhythmic genes in response to photo- and thermocycles and identifying novel candidate genes associated with growth and drought traits. Understanding the gene regulatory networks that mediate time-of-day signaling is vital to identifying candidate genes across the pan-genome associated with traits of interest.

Mapping Selected Polyphenols Metabolism By Gut Bacteria And Their Genes, Ermin Zhao

Doctoral Dissertations

The human gut microbiome is a huge enzyme repository for dietary polyphenols metabolism, especially considering most of the polyphenols cannot be digested in the host and their biological functions are limited. Poor bioaccessibility based on traditional pharmaceutical ADME (absorption, distribution, metabolism, and excretion) assessment is the main problem facing the widely medical application of most polyphenols. Gut bacteria have the potential to mediate a wide range of biotransformation reactions of polyphenols, which leads to the production of many bioactive metabolites. In the past decades, mounting evidence in traditional ADME study have demonstrated gut bacteria play an irreplaceable role in dietary …

Meta-Analysis Of The Alzheimer's Disease Human Brain Transcriptome And Functional Dissection In Mouse Models., Ying-Wooi Wan, Rami Al-Ouran, Carl G Mangleburg, Thanneer M Perumal, Tom V Lee, Katherine Allison, Vivek Swarup, Cory C Funk, Chris Gaiteri, Mariet Allen, Minghui Wang, Sarah M Neuner, Catherine C Kaczorowski, Vivek M Philip, Gareth R Howell, Heidi Martini-Stoica, Hui Zheng, Hongkang Mei, Xiaoyan Zhong, Jungwoo Wren Kim, Valina L Dawson, Ted M Dawson, Ping-Chieh Pao, Li-Huei Tsai, Jean-Vianney Haure-Mirande, Michelle E Ehrlich, Paramita Chakrabarty, Yona Levites, Xue Wang, Eric B Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K Sieberts, Larsson Omberg, Kristen D Dang, James A Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuss, Ayla Ergun, Phillip J Ebert, David C Airey, Sara Mostafavi, Lei Yu, Hans-Ulrich Klein, Accelerating Medicines Partnership, Alzheimer’S Disease Consortium, Gregory W Carter, David A Collier, Todd E Golde, Allan I Levey, David A Bennett, Karol Estrada, T Matthew Townsend, Bin Zhang, Eric Schadt, Philip L De Jager, Nathan D Price, Nilüfer Ertekin-Taner, Zhandong Liu, Joshua M Shulman, Lara M Mangravite, Benjamin A Logsdon

Articles, Abstracts, and Reports

We present a consensus atlas of the human brain transcriptome in Alzheimer's disease (AD), based on meta-analysis of differential gene expression in 2,114 postmortem samples. We discover 30 brain coexpression modules from seven regions as the major source of AD transcriptional perturbations. We next examine overlap with 251 brain differentially expressed gene sets from mouse models of AD and other neurodegenerative disorders. Human-mouse overlaps highlight responses to amyloid versus tau pathology and reveal age- and sex-dependent expression signatures for disease progression. Human coexpression modules enriched for neuronal and/or microglial genes broadly overlap with mouse models of AD, Huntington's disease, amyotrophic …

Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh

Department of Computer Science Publications

One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to …

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

Ray Enke Ph.D.

• view the output files of FastQC analysis
• create custom data tracks from HISAT alignment files for visualization in the UCSC Genome Browser

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

Ray Enke Ph.D.

The Determinants Of Nucleosome Patterns And The Impact Of Phosphate Starvation On Nucleosome Patterns And Gene Expression In Rice, Qi Zhang

LSU Doctoral Dissertations

In eukaryotic cells, DNA is a large molecule that must be greatly condensed to fit within the nucleus. DNA is wrapped around histone proteins to form nucleosomes, which facilitate DNA condensation, but on the other hand, may limit DNA processes. Organisms must respond to environmental stress in order to survive, and one strategy is by remodeling nucleosomes to promote changes in DNA accessibility to alter gene expression. Studies have demonstrated a clear correlation between nucleosome dynamics and transcriptional change in some eukaryotes, however factors that affect nucleosome positioning in plants are largely unknown, and the correlation between nucleosome dynamics and …

Novel Computational Methods For Sequencing Data Analysis: Mapping, Query, And Classification, Xinan Liu

Theses and Dissertations--Computer Science

Over the past decade, the evolution of next-generation sequencing technology has considerably advanced the genomics research. As a consequence, fast and accurate computational methods are needed for analyzing the large data in different applications. The research presented in this dissertation focuses on three areas: RNA-seq read mapping, large-scale data query, and metagenomics sequence classification.

A critical step of RNA-seq data analysis is to map the RNA-seq reads onto a reference genome. This dissertation presents a novel splice alignment tool, MapSplice3. It achieves high read alignment and base mapping yields and is able to detect splice junctions, gene fusions, and circular …

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

Ray Enke Ph.D.

No abstract provided.

Finding Function In The Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti

Catherine Putonti

Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.

Unravelling Organelle Genome Transcription Using Publicly Available Rna-Sequencing Data, Matheus Sanita Lima

Electronic Thesis and Dissertation Repository

The study of organelles helped forge theories of genome evolution because of their unconventional genomes and gene expression regimes. The organelle genomics field (~35 years old) has seen the development of next generation sequencing (NGS) techniques and the consequent skyrocketing of genomic and transcriptomic data. However, these data are being underused in the studies of organelle genome transcription. My thesis investigates how NGS has affected the field of organelle genomics at both the DNA and RNA levels. First, I demonstrate that although organelle genomes are being sequenced as never before, they are un-characterized as they are published mostly as “organelle …

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

Ray Enke Ph.D.

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

Ray Enke Ph.D.

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.

Sequence Annotation & Designing Gene-Specific Qpcr Primers (Computational), Ray A. Enke

Ray Enke Ph.D.

• Obtaining and annotating genomic DNA and mRNA sequence information
• Designing primers for quantitative PCR (qPCR) analysis of a cDNA library

Finding Function In The Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti

Bioinformatics Faculty Publications

Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.

Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang

Theses and Dissertations--Computer Science

The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome from short RNA-seq reads remains a challenging problem. We …

A Novel Computational Framework For Transcriptome Analysis With Rna-Seq Data, Yin Hu

Theses and Dissertations--Computer Science

The advance of high-throughput sequencing technologies and their application on mRNA transcriptome sequencing (RNA-seq) have enabled comprehensive and unbiased profiling of the landscape of transcription in a cell. In order to address the current limitation of analyzing accuracy and scalability in transcriptome analysis, a novel computational framework has been developed on large-scale RNA-seq datasets with no dependence on transcript annotations. Directly from raw reads, a probabilistic approach is first applied to infer the best transcript fragment alignments from paired-end reads. Empowered by the identification of alternative splicing modules, this framework then performs precise and efficient differential analysis at automatically detected …