Assessing & Filtering Illumina Short Read Ngs Data Using Galaxy, 2018 Selected Works
Assessing & Filtering Illumina Short Read Ngs Data Using Galaxy, Ray A. Enke
Ray Enke Ph.D.
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
Computational Analysis Of Papionini Evolution Using Alu Insertions, 2018 Louisiana State University and Agricultural and Mechanical College
Computational Analysis Of Papionini Evolution Using Alu Insertions, Vallmer Edward Jordan Ii
LSU Doctoral Dissertations
Alu elements are primate specific retrotransposons that have remained active throughout the course of primate evolution. As a result of this sustained mobilization. Alu elements are present in greater copy number in primate genomes than any other transposable element. An average of over one million Alu elements has been identified in every sequenced haplorrhine genome to date. These characteristics qualify Alu elements as ideal characters for studying evolutionary relationship among primates.
The increasing availability of whole genome sequencing data presents novel challenges and opportunities for comparative genomic analyses. Genomic data is now publicly available for most primate species. Such an ...
Draft Genome Sequence Of Bifidobacterium Longum Uma026, Isolated From Holstein Dairy Cow Feces, 2018 University of Massachusetts Amherst
Draft Genome Sequence Of Bifidobacterium Longum Uma026, Isolated From Holstein Dairy Cow Feces, Korin Albert, David Sela
Open Access Articles
The draft genome sequence of an isolate identified as Bifidobacterium longum is communicated herein. This strain was isolated from the feces of a 1-week-old Holstein dairy cow. The draft genome of this Bifidobacterium longum isolate is 2.39 Mb in length, with a G+C content of 60.1%.
Complete Genome Sequences Of Paenibacillus Larvae Phages Bn12, Dragolir, Kiel007, Leyra, Likha, Pagassa, Pbl1c, And Tadhana, 2018 Brigham Young University
Complete Genome Sequences Of Paenibacillus Larvae Phages Bn12, Dragolir, Kiel007, Leyra, Likha, Pagassa, Pbl1c, And Tadhana, Jamison K. Walker, Bryan D. Merrill, Jordan A. Berg, Aziza Dhalai, Douglas W. Dingman, Chris P. Fajardo, Kiel Graves, Hunter L. Hill, Jared A. Hilton, Cameron Imahara, Bradley K. Knabe, James Mangohig, Josh Monk, Heejin Mun, Ashley M. Payne, Alicia Salisbury, Casey Stamereilers, Kathie Velez, Andy T. Ward, Donald P. Breakwell, Julianne H. Grose, Sandra Hope, Philippos K. Tsourkas
Life Sciences Faculty Publications
We present here the complete genomes of eight phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. Phage PBL1c was originally isolated in 1984 from a P. larvae lysogen, while the remaining phages were isolated in 2014 from bee debris, honeycomb, and lysogens from three states in the USA.
Evolutionary And Population Dynamics Of Crustaceans In The Gulf Of Mexico, 2018 Florida International University
Evolutionary And Population Dynamics Of Crustaceans In The Gulf Of Mexico, Laura Timm
FIU Electronic Theses and Dissertations
Evolution occurs and can be conceptualized along a spectrum, bounded on one extreme by the relationships between deep lineages – such as phyla, classes, and orders – and on the other by the molecular dynamics of operational taxonomic units within a species, defined as population genetics. The purpose of this dissertation was to better understand the evolutionary and population dynamics of crustaceans within the Gulf of Mexico. In the second chapter of my dissertation, I provide a guide to best phylogenetic practice while reviewing infraordinal relationships within Decapoda, including the promise held by next-generation sequencing (NGS) approaches such as Anchored Hybrid Enrichment ...
A Systems Biology Approach For Studying Heterotopic Ossification: Proteomic Analysis Of Clinical Serum And Tissue Samples, Erin Crowgey, Jennifer Wyffels, Patrick Osborn, Thomas Wood, Laura Edsberg
Heterotopic ossification (HO) refers to the abnormal formation of bone in soft tissue. Although some of the underlying processes of HO have been described, there are currently no clinical tests using validated biomarkers for predicting HO formation. As such, the diagnosis is made radiographically after HO has formed. To identify potential and novel biomarkers for HO, we used isobaric tags for relative and absolute quantitation (iTRAQ) and high-throughput antibody arrays to produce a semi-quantitative proteomics survey of serum and tissue from subjects with (HO+) and without (HO−) heterotopic ossification. The resulting data were then analyzed using a systems biology approach ...
Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, 2018 Tianjin University,
Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam Mcdermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma
CSE Journal Articles
Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to ...
Fine Grained Compositional Analysis Of Port Everglades Inlet Microbiome Using High Throughput Dna Sequencing, 2018 Nova Southeastern University
Fine Grained Compositional Analysis Of Port Everglades Inlet Microbiome Using High Throughput Dna Sequencing, Lauren M. O'Connell, Song Gao, Donald S. Mccorquodale Jr., Jay M. Fleisher, Jose Lopez
Marine & Environmental Sciences Faculty Articles
Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis.
Methods & Results
Surface water samples were collected every week for one year. A total of four samples per ...
Investigating Invasion In Ductal Carcinoma In Situ With Topographical Single Cell Genome Sequencing, 2018 The University of Texas M D Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Investigating Invasion In Ductal Carcinoma In Situ With Topographical Single Cell Genome Sequencing, Anna Casasent, Anna Casasent
UT GSBS Dissertations and Theses (Open Access)
Synchronous Ductal Carcinoma in situ (DCIS-IDC) is an early stage breast cancer invasion in which it is possible to delineate genomic evolution during invasion because of the presence of both in situ and invasive regions within the same sample. While laser capture microdissection studies of DCIS-IDC examined the relationship between the paired in situ (DCIS) and invasive (IDC) regions, these studies were either confounded by bulk tissue or limited to a small set of genes or markers. To overcome these challenges, we developed Topographic Single Cell Sequencing (TSCS), which combines laser-catapulting with single cell DNA sequencing to measure genomic copy ...
Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, 2018 Augustana College, Rock Island Illinois
Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Mourin Azar, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants ...
Response To Persistent Er Stress In Plants: A Multiphasic Process That Transitions Cells From Prosurvival Activities To Cell Death, Renu Srivastava, Zhaoxia Li, Giulia Russo, Jie Tang, Ran Bi, Usha Muppirala, Sivanandan Chudalayandi, Andrew J. Severin, Mingze He, Samuel I. Vaitkevicius, Carolyn J. Lawrence-Dill, Peng Liu, Ann E. Stapleton, Diane C. Bassham, Federica Brandizzi, Stephen H. Howell
Office of Biotechnology Publications
The unfolded protein response (UPR) is a highly conserved response that protects plants from adverse environmental conditions. The UPR is elicited by endoplasmic reticulum (ER) stress, in which unfolded and misfolded proteins accumulate within the ER. Here, we induced the UPR in maize (Zea mays) seedlings to characterize the molecular events that occur over time during persistent ER stress. We found that a multiphasic program of gene expression was interwoven among other cellular events, including the induction of autophagy. One of the earliest phases involved the degradation by regulated IRE1-dependent RNA degradation (RIDD) of RNA transcripts derived from a family ...
Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, 2018 University of Connecticut
Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty
Honors Scholar Theses
The relationship between the fungus-growing ant Trachymyrmex septentrionalis, its symbiotic cultivar fungus, and the transient and residential community of microorganisms is a diverse and complex symbiosis that has evolved over space and time. The fungus garden, comprised primarily of the cultivar fungus belonging to the family Leucocoprineae,provides an environment that hosts many bacteria, which may also play an important role in this symbiosis. Although it is known that Pseudonocardia bacteria defend the ant host against fungal pathogens, other species of bacteria that are present in these fungus gardens also likely contribute to this symbiosis. Previous studies of this system ...
Bayesian Network Modeling And Inference Of Gwas Catalog, 2018 University of Arkansas, Fayetteville
Bayesian Network Modeling And Inference Of Gwas Catalog, Qiuping Pan
Theses and Dissertations
Genome-wide association studies (GWASs) have received an increasing attention to understand genotype-phenotype relationships. The Bayesian network has been proposed as a powerful tool for modeling single-nucleotide polymorphism (SNP)-trait associations due to its advantage in addressing the high computational complex and high dimensional problems. Most current works learn the interactions among genotypes and phenotypes from the raw genotype data. However, due to the privacy issue, genotype information is sensitive and should be handled by complying with specific restrictions. In this work, we aim to build Bayesian networks from publicly released GWAS statistics to explicitly reveal the conditional dependency between SNPs ...
Involvement Of The Ino80 Complex In Chromosome Segregation, 2018 University of Arkansas, Fayetteville
Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno
Theses and Dissertations
Chromatin remodeling complexes are multi-protein complexes that regulate the dynamics of the nucleosomes in the genome. The INO80 chromatin remodeling complex participates in varied biological processes such as: transcription, DNA repair, DNA replication and chromosome integrity. It catalyzes the eviction of the H2A.Z variant histone as well as whole nucleosome eviction. This complex is comprised of 15 subunits and the contribution of each to chromosome segregations remains unknown. To evaluate the contribution of each subunit to chromosome segregation, we tested deletion mutants of the non-essential subunits for DNA content and benomyl sensitivity. Also, we assessed members of the SWR1 ...
Effects Of Mitochondrial Nadp+-Dependent Isocitrate Dehydrogenase Deficiency On Fructose-Induced Obesity In Mice, 2018 University of Arkansas, Fayetteville
Effects Of Mitochondrial Nadp+-Dependent Isocitrate Dehydrogenase Deficiency On Fructose-Induced Obesity In Mice, Allison Michelle Montalbano, Kaleigh Elizabeth Beane
Human Nutrition and Hospitality Innovation Undergraduate Honors Theses
Obesity prevalence in the United States continues to increase and is associated with health consequences such as type 2 diabetes, hypertension, atherosclerosis, and hyperlipidemia. Among many contributing factors to obesity, fructose may be one of the major reasons as it disrupts the antioxidant system thereby resulting in an accumulation of reactive oxidative species and leading to obese conditions. The enzyme, isocitrate dehydrogenase 2 (IDH2), reduces nicotinamide adenine dinucleotide phosphate from the TCA Cycle, hence might be implicated with not only energy metabolism but also cellular redox homeostasis. Therefore, the hypothesis was that IDH2 deficiency in mice would exacerbate hepatic lipid ...
A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, 2018 University of Washington
A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, Maxwell Wing Libbrecht, Oscar Rodriguez, Zhiping Weng, Michael Hoffman, Jeffrey A. Bilmes, William Stafford Noble
University of Massachusetts Medical School Faculty Publications
Semi-automated genome annotation methods such as Segway enable understanding of chromatin activity. Here we present chromatin state annotations of 164 human cell types using 1,615 genomics data sets. To produce these annotations, we developed a fully-automated annotation strategy in which we train separate unsupervised annotation models on each cell type and use a machine learning classifier to automate the state interpretation step. Using these annotations, we developed a measure of the functional importance of each genomic position called the "functionality score," which allows us to aggregate information across cell types into a multi-cell type view. This score provides a ...
Genomic Insights Into The Mitochondria Of 11 Eastern North American Species Of Cladonia, 2018 University of Colorado, Boulder
Genomic Insights Into The Mitochondria Of 11 Eastern North American Species Of Cladonia, Laurel M. Brigham, Luis M. Allende, Benjamin R. Shipley, Kayla C. Boyd, Tanya J. Higgins, Nicholas Kelly, Carly R. Anderson-Stewart, Kyle Keepers, Cloe S. Pogoda, James C. Lendemer, Erin A. Tripp, Nolan C. Kane
University Libraries Open Access Fund Supported Publications
Cladonia is among the most species-rich genera of lichens globally. Species in this lineage, commonly referred to as reindeer lichens, are ecologically important in numerous regions worldwide. In some locations, species of Cladonia can comprise the dominant groundcover, and are a major food source for caribou and other mammals. Additionally, many species are known to produce substances with antimicrobial properties or other characteristics with potentially important medical applications. This exceptional morphological and ecological variation contrasts sharply with the limited molecular divergence often observed among species. As a new resource to facilitate ongoing and future studies of these important species, we ...
Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, 2018 Yale University
Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks
Yale Day of Data
Through targeted genetic manipulations guided by network modeling, we will create a flexible, cyanobacteria-based platform for the production of biofuel-precursors and valuable chemical products. To build gene-metabolite predictive models, we have characterized Synecococcus elongatus sp. UTEX 2973’s (henceforth, UTEX 2973) gene expression and metabolite production under a number of environmental conditions.
Viper: Visualization Pipeline For Rna-Seq, A Snakemake Workflow For Efficient And Complete Rna-Seq Analysis, 2018 Dana-Farber Cancer Institute
Viper: Visualization Pipeline For Rna-Seq, A Snakemake Workflow For Efficient And Complete Rna-Seq Analysis, Macintosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Koster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X Shirley Liu, Henry W. Long
Open Access Articles
BACKGROUND: RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.
RESULTS: Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis ...