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A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed 2015 Western Michigan University

A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

With the advent of high-throughput next-generation sequencing (NGS) techniques, the amount of data being generated represents challenges including storage, analysis and transport of huge datasets. One solution to storage and transmission of data is compression using specialized compression algorithms. However, these specialized algorithms suffer from poor scalability with increasing size of the datasets and best available solutions can take hours to compress gigabytes of data. In this paper we introduce paraDSRC, a parallel implementation of DSRC algorithm using a message passing model that presents reduction of the compression time complexity by a factor of O(1/p ). Our experimental results ...


Ferret: A Sentence-Based Literature Scanning System, Padmini Srinivasan, Xiao-Ning Zhang, Roxane Bouten, Caren Chang 2015 University of Iowa

Ferret: A Sentence-Based Literature Scanning System, Padmini Srinivasan, Xiao-Ning Zhang, Roxane Bouten, Caren Chang

Department of Computer Science Publications

Background

The rapid pace of bioscience research makes it very challenging to track relevant articles in one’s area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year. Thus it is not surprising to see active research in building new document retrieval and sentence retrieval systems. We present Ferret, a prototype retrieval system, designed to retrieve and rank sentences (and their documents) conveying gene-centric relationships of interest to a scientist. The prototype has several features. For example, it is designed to handle ...


"Time For Dabs": Analyzing Twitter Data On Butane Hash Oil Use, Raminta Daniulaityte, Robert G. Carlson, Farahnaz Golroo, Sanjaya Wijeratne, Edward W. Boyer, Silvia S. Martins, Ramzi W. Nahhas, Amit P. Sheth 2015 Wright State University - Main Campus

"Time For Dabs": Analyzing Twitter Data On Butane Hash Oil Use, Raminta Daniulaityte, Robert G. Carlson, Farahnaz Golroo, Sanjaya Wijeratne, Edward W. Boyer, Silvia S. Martins, Ramzi W. Nahhas, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.


Three-Dimensional Ideal Gas Reference State Based Energy Function, Avdesh Mishra 2015 University of New Orleans

Three-Dimensional Ideal Gas Reference State Based Energy Function, Avdesh Mishra

University of New Orleans Theses and Dissertations

Energy functions are found to be a key of protein structure prediction. In this work, we propose a novel 3-dimensional energy function based on hydrophobic-hydrophilic properties of amino acid where we consider at least three different possible interaction of amino acid in a 3-dimensional sphere categorized as hydrophilic versus hydrophilic, hydrophobic versus hydrophobic and hydrophobic versus hydrophilic. Each of these interactions are governed by a 3-dimensional parameter alpha used to model the interaction and 3-dimensional parameter beta used to model weight of contribution. We use Genetic Algorithm (GA) to optimize the value of alpha, beta and Z-score. We obtain three ...


Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner 2015 Bowling Green State University - Main Campus

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species4. RNA-seq analysis showed that one gene, PPTG_16698 has the 5th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of the ...


A Hierarchical Graph For Nucleotide Binding Domain 2, Samuel Kakraba 2015 East Tennessee State University

A Hierarchical Graph For Nucleotide Binding Domain 2, Samuel Kakraba

Electronic Theses and Dissertations

One of the most prevalent inherited diseases is cystic fibrosis. This disease is caused by a mutation in a membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is known to function as a chloride channel that regulates the viscosity of mucus that lines the ducts of a number of organs. Generally, most of the prevalent mutations of CFTR are located in one of two nucleotide binding domains, namely, the nucleotide binding domain 1 (NBD1). However, some mutations in nucleotide binding domain 2 (NBD2) can equally cause cystic fibrosis. In this work, a hierarchical graph is built for NBD2 ...


Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel 2015 University of Nebraska-Lincoln

Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel

Dissertations, Theses, and Student Research Papers in Mathematics

The exact evolutionary history of any set of biological sequences is unknown, and all phylogenetic reconstructions are approximations. The problem becomes harder when one must consider a mix of vertical and lateral phylogenetic signals. In this dissertation we propose a game-theoretic approach to clustering biological sequences and analyzing their evolutionary histories. In this context we use the term evolution as a broad descriptor for the entire set of mechanisms driving the inherited characteristics of a population. The key assumption in our development is that evolution tries to accommodate the competing forces of selection, of which the conservation force seeks to ...


A Dynamic Behavioral Biometric Approach To Authenticate Users Employing Their Fingers To Interact With Touchscreen Devices, Arturo Ponce 2015 Nova Southeastern University

A Dynamic Behavioral Biometric Approach To Authenticate Users Employing Their Fingers To Interact With Touchscreen Devices, Arturo Ponce

GSCIS ETDs

The use of mobile devices has extended to all areas of human life and has changed the way people work and socialize. Mobile devices are susceptible to getting lost, stolen, or compromised. Several approaches have been adopted to protect the information stored on these devices. One of these approaches is user authentication. The two most popular methods of user authentication are knowledge based and token based methods but they present different kinds of problems.

Biometric authentication methods have emerged in recent years as a way to deal with these problems. They use an individual’s unique characteristics for identification and ...


Analyzing The Social Media Footprint Of Street Gangs, Sanjaya Wijeratne, Derek Doran, Amit P. Sheth, Jack Dustin 2015 Wright State University - Main Campus

Analyzing The Social Media Footprint Of Street Gangs, Sanjaya Wijeratne, Derek Doran, Amit P. Sheth, Jack Dustin

Kno.e.sis Publications

Gangs utilize social media as a way to maintain threatening virtual presences, to communicate about their activities, and to intimidate others. Such usage has gained the attention of many justice service agencies that wish to create better crime prevention and judicial services. However, these agencies use analysis methods that are labor intensive and only lead to basic, qualitative data interpretations. This paper presents the architecture of a modern platform to discover the structure, function, and operation of gangs through the lens of social media. Preliminary analysis of social media posts shared in the greater Chicago, IL region demonstrate the platform ...


Big Data And Smart Cities, Amit P. Sheth 2015 Wright State University - Main Campus

Big Data And Smart Cities, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.


Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University 2015 Eastern Illinois University

Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University

Darwin Core Archive Download

ZIP file contains occurrences.csv, identivications.csv, and images.csv. The meta.xml document describes the content. Fields within the occurrences.csv file are defined by the Darwin Core exchange standard.


Isolation And Genomic Analysis Of Cluster O Mycobacteriophage Vorrps, Leslie Ann Sterling, Rahul Ramaswamy, Madeleine Mullon, Peeti Sithiyopasakul 2015 Washington University in St Louis

Isolation And Genomic Analysis Of Cluster O Mycobacteriophage Vorrps, Leslie Ann Sterling, Rahul Ramaswamy, Madeleine Mullon, Peeti Sithiyopasakul

Undergraduate Research Symposium Posters & Abstracts

Mycobacteriophage Vorrps was isolated in 2014 from soil on the Washington University campus. The phage was isolated and purified by repeatedly infecting host Mycobacterium smegmatis. Vorrps produces small, circular, clear plaques approximately 1 mm in diameter, indicating that it is a lytic phage. Electron microscopy reveals that Vorrps has an unusual prolate head and a long tail characteristic of cluster O mycobacteriophage. Vorrps is very similar to the five analyzed O cluster phages Corndog, Catdawg, YungJamal, Firecracker and Dylan, as well as cluster O phage Mori, another phage isolated and analyzed by Washington University students this year. Vorrps and Mori ...


Isolation And Comparative Genomic Analysis Of Mycobacteriophage Enkatz, Thomas Van Horn, Micah Rickles-Young, Shaarada Srivasta, Tina Zudock 2015 Washington University in St Louis

Isolation And Comparative Genomic Analysis Of Mycobacteriophage Enkatz, Thomas Van Horn, Micah Rickles-Young, Shaarada Srivasta, Tina Zudock

Thomas Van Horn

Phage Enkatz is a temperate mycobacteriophage isolated from an un-enriched soil sample collected from the South Forty housing area of the Washington University in St. Louis campus. Enkatz displays unequally sized plaques with a clear center that become cloudier with radial distance from the center. Genome analysis indicates that Enkatz is a cluster A1 mycobacteriophage with a genome size of 49,738 bases and 82 identified genes, 33 of which have been assigned functions. This analysis reveals that the majority of the genes in the positive strand code for structural proteins, while the majority of the genes in the negative ...


The Deaf Cyborg: Analyzing Technoscience, Gender, And Ability, Callahan Roan 2015 Georgia State University

The Deaf Cyborg: Analyzing Technoscience, Gender, And Ability, Callahan Roan

Georgia State Undergraduate Research Conference

Gsurc 2015


Characterizing Orphan Gpcrs In Molluscan Neurons Through Bioinformatics, Preetham Ganupuru 2015 Georgia State University

Characterizing Orphan Gpcrs In Molluscan Neurons Through Bioinformatics, Preetham Ganupuru

Georgia State Undergraduate Research Conference

No abstract provided.


Integrating External Resources Into Health Informatics And Computing Instruction: Emerging Roles For Librarians And Information Professionals, Daina R. Bouquin, Michael E. Bales 2015 Weill Cornell Medical College of Cornell University

Integrating External Resources Into Health Informatics And Computing Instruction: Emerging Roles For Librarians And Information Professionals, Daina R. Bouquin, Michael E. Bales

University of Massachusetts and New England Area Librarian e-Science Symposium

Background: In informatics courses, instructors often present materials in a didactic, module-by-module fashion; however, they may not readily integrate outside materials to facilitate learning. This may be due to a lack of time or expertise in identifying appropriate external resources. Librarians are uniquely suited to address this gap.

Setting/Participants: A librarian (D.B.) and a digital curation fellow (M.B.) taught a graduate level course on computational methods in health informatics. Students were mainly from basic science and informatics programs and had varying levels of computational experience.

Purpose: The objective of the course was to promote critical thinking about ...


Creation Of A Computational Pipeline To Extract Genes From Quantitative Trait Loci For Diabetes And Obesity, Joseph Fox 2015 Marquette University

Creation Of A Computational Pipeline To Extract Genes From Quantitative Trait Loci For Diabetes And Obesity, Joseph Fox

Master's Theses (2009 -)

Type 2 Diabetes is a disease of relative insulin deficiency resulting from a combination of insulin resistance and decreased beta-cell function. Over the past several years, over 60 genes have been identified for Type 2 Diabetes in human genome-wide association studies (GWAS). It is important to understand the genetics involved with Type 2 diabetes in order to improve treatment and understand underlying molecular mechanisms. Heterogeneous stock (HS) rats are derived from 8 inbred founder strains and are powerful tools for genetic studies because they provide a basis for high resolution mapping of quantitative trait loci (QTL) in a relatively short ...


Mir-10b-5p Expression In Huntington's Disease Brain Relates To Age Of Onset And The Extent Of Striatal Involvement, Andrew G. Hoss, Adam Labadorf, Jeanne C. Latourelle, Vinay K. Kartha, Tiffany C. Hadzi, James F. Gusella, Marcy E. MacDonald, Jiang-Fan Chen, Schahram Akbarian, Zhiping Weng, Jean Paul Vonsattel, Richard H. Myers 2015 Boston University

Mir-10b-5p Expression In Huntington's Disease Brain Relates To Age Of Onset And The Extent Of Striatal Involvement, Andrew G. Hoss, Adam Labadorf, Jeanne C. Latourelle, Vinay K. Kartha, Tiffany C. Hadzi, James F. Gusella, Marcy E. Macdonald, Jiang-Fan Chen, Schahram Akbarian, Zhiping Weng, Jean Paul Vonsattel, Richard H. Myers

Program in Bioinformatics and Integrative Biology Publications and Presentations

BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that recognize sites of complementarity of target messenger RNAs, resulting in transcriptional regulation and translational repression of target genes. In Huntington's disease (HD), a neurodegenerative disease caused by a trinucleotide repeat expansion, miRNA dyregulation has been reported, which may impact gene expression and modify the progression and severity of HD.

METHODS: We performed next-generation miRNA sequence analysis in prefrontal cortex (Brodmann Area 9) from 26 HD, 2 HD gene positive, and 36 control brains. Neuropathological information was available for all HD brains, including age at disease onset, CAG-repeat size, Vonsattel grade, and ...


A Bioinformatics Approach To Revealing The Genetic Basis For Host Range Specificity, Hayley A. Norian 2015 James Madison University

A Bioinformatics Approach To Revealing The Genetic Basis For Host Range Specificity, Hayley A. Norian

James Madison Undergraduate Research Journal

Bacteriophages, or phages, are viruses that infect bacteria. Mycobacteriophages are bacteriophages that specifically infect the genus Mycobacterium. This genus of bacteria includes human pathogens such as Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium ulcerans, which cause tuberculosis, leprosy and Buruli ulcer, respectively. The full genome sequences of 654 mycobacteriophages are currently available. Collectively, these 654 phages encode 69,581 genes. Only 20.25% of these genes have at least one known homologue in NCBI, the National Center for Biotechnology Information, leaving roughly 80% of all known mycobacteriophage genes without even a predicted function. Bacteriophages are highly host-specific and typically only infect ...


G-Quadruplex Dna Structures And Site Specific Genetic Instability, Jonathan David Williams 2015 Illinois State University

G-Quadruplex Dna Structures And Site Specific Genetic Instability, Jonathan David Williams

Theses and Dissertations

Repetitive DNA comprises a majority of the human genome yet functions and overall impacts on site-specific genetic instability are not fully defined. Repetitive G-rich sequences have the propensity to form G-quadruplex (G4), which are stable non-B form DNA structures. G4 structures are conspicuously found at regions of site-specific instability. Even so, human genomic loci capable of forming this structure and their connection to DNA rearrangements are just beginning to be elucidated. My dissertation focuses on G4 structures and their capacity to promote site-specific changes in the human genome, particularly at oncogenes. I identified and investigated new biologically relevant G4 loci ...


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