Open Access. Powered by Scholars. Published by Universities.®

Bioinformatics Commons

Open Access. Powered by Scholars. Published by Universities.®

1,308 Full-Text Articles 1,981 Authors 174,233 Downloads 78 Institutions

All Articles in Bioinformatics

Faceted Search

1,308 full-text articles. Page 1 of 35.

Big Data Proteogenomics And High Performance Computing: Challenges And Opportunities, Fahad Saeed 2015 Western Michigan University

Big Data Proteogenomics And High Performance Computing: Challenges And Opportunities, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

Proteogenomics is an emerging field of systems biology research at the intersection of proteomics and genomics. Two high-throughput technologies, Mass Spectrometry (MS) for proteomics and Next Generation Sequencing (NGS) machines for genomics are required to conduct proteogenomics studies. Independently both MS and NGS technologies are inflicted with data deluge which creates problems of storage, transfer, analysis and visualization. Integrating these big data sets (NGS+MS) for proteogenomics studies compounds all of the associated computational problems. Existing sequential algorithms for these proteogenomics datasets analysis are inadequate for big data and high performance computing (HPC) solutions are almost non-existent. The purpose of ...


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 ...


Collecting Diverse Microorganisms From Rover Spacecraft, Jennifer I. Jacobs, Arianna Jefferson, Heidi Aronson, James Tan, Wayne Schubert, Parag Vaishampayan 2015 Chicago State University

Collecting Diverse Microorganisms From Rover Spacecraft, Jennifer I. Jacobs, Arianna Jefferson, Heidi Aronson, James Tan, Wayne Schubert, Parag Vaishampayan

STAR (STEM Teacher and Researcher) Program Posters

. The Planetary Protection discipline at NASA’s Jet Propulsion Laboratory develops and implements procedures to prevent both forward and backward contamination between the Earth and solar system bodies. However, there will always be some microorganisms that will be resistant to the strictest of sterilization methods. In order understand the microorganisms found on spacecraft during assembly, and to rapidly identify them, a mass spectrometry approach was developed. As an experimental approach, a custom database was created for a subset of microorganisms in the Planetary Protection Archive. In order to make the database as accurate and efficient as possible, several different procedures ...


Development Of A Comprehensive Massively Parallel Sequencing Panel Of Single Nucleotide Polymorphism And Short Tandem Repeat Markers For Human Identification, David H. Warshauer B.S., M.S. 2015 University of North Texas Health Science Center at Fort Worth

Development Of A Comprehensive Massively Parallel Sequencing Panel Of Single Nucleotide Polymorphism And Short Tandem Repeat Markers For Human Identification, David H. Warshauer B.S., M.S.

Theses and Dissertations

Massively parallel sequencing (MPS) technologies allow for the detection of an unparalleled amount of genetic information with unprecedented speed and relative ease. These qualities make the technology desirable for generating DNA profiles that may be uploaded into forensic offender, arrestee, and family reference database files. This doctoral dissertation research was conducted under the hypothesis that MPS, with its exquisitely high throughput, can provide a system whereby reference samples can be typed for a large battery of markers, providing more discrimination power for forensic DNA typing and offering increased opportunities to develop investigative leads. The design and implementation of large marker ...


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.


Domain Specific Document Retrieval Framework For Real-Time Social Health Data, Swapnil Soni 2015 Wright State University - Main Campus

Domain Specific Document Retrieval Framework For Real-Time Social Health Data, Swapnil Soni

Kno.e.sis Publications

With the advent of the web search and microblogging, the percentage of Online Health Information Seekers (OHIS) using these online services to share and seek health real-time information has in- creased exponentially. OHIS use web search engines or microblogging search services to seek out latest, relevant as well as reliable health in- formation. When OHIS turn to microblogging search services to search real-time content, trends and breaking news, etc. the search results are not promising. Two major challenges exist in the current microblogging search engines are keyword based techniques and results do not contain real-time information. To address these challenges ...


Evaluating A Potential Commercial Tool For Healthcare Application For People With Dementia, Tanvi Banerjee, Pramod Anantharam, William L. Romine, Larry Wayne Lawhorne 2015 Wright State University - Main Campus

Evaluating A Potential Commercial Tool For Healthcare Application For People With Dementia, Tanvi Banerjee, Pramod Anantharam, William L. Romine, Larry Wayne Lawhorne

Kno.e.sis Publications

The widespread use of smartphones and sensors has made physiology, environment, and public health notifications amenable to continuous monitoring. Personalized digital health and patient empowerment can become a reality only if the complex multisensory and multimodal data is processed within the patient context, converting relevant medical knowledge into actionable information for better and timely decisions. We apply these principles in the healthcare domain of dementia. Specifically, in this study we validate one of our sensor platforms to ascertain whether it will be suitable for detecting physiological changes that may help us detect changes in people with dementia. This study shows ...


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.


Library Support For Biomedical Research In The Omics Era: 2014- 2015 Report, Rolando Garcia-Milian 2015 Yale University

Library Support For Biomedical Research In The Omics Era: 2014- 2015 Report, Rolando Garcia-Milian

Rolando Garcia-Milian

The decreased cost of high-throughput technologies has enabled its use as the main research methods to study biological processes and disorders. In order to understand the relevance of the data generated by these methods, the researcher needs mining and integrating the enormous amount of biomedical information and knowledge contained in the text of the scientific literature and biomedical databases. Accordingly, the ability to access and examine molecular data should not be restricted to bioinformaticians or those with exceptional computer skills. In May 2014, the Cushing/Whitney Medical Library began to provide end-user bioinformatics support to the biomedical researchers of the ...


Secretion Of Heat-Labile Enterotoxin By Porcine-Origin Enterotoxigenic Escherichia Coli And Relation To Virulence, Prageeth R. Wijemanne 2015 University of Nebraska-Lincoln

Secretion Of Heat-Labile Enterotoxin By Porcine-Origin Enterotoxigenic Escherichia Coli And Relation To Virulence, Prageeth R. Wijemanne

Dissertations & Theses in Veterinary and Biomedical Science

Heat-labile enterotoxin (LT) is an important virulence factor secreted by some strains of porcine-origin enterotoxigenic Escherichia coli (pETEC). The prototypic human-origin strain H10407 secretes LT via a type II secretion system (T2SS), but its presence or importance in pETEC has not been established. Exposure of pETEC to glucose has been shown to result in different secretion levels of LT. Furthermore, the relationship between the level of LT secreted and the virulence potential of the respective pETEC strain has not been established. To determine the relationship between the capacity to secrete LT and virulence in wild-type (WT) pETEC, 16 strains isolated ...


Entity Recommendations Using Hierarchical Knowledge Bases, Siva Kumar Cheekula, Pavan Kapanipathi, Derek Doran, Prateek Jain, Amit P. Sheth 2015 Wright State University - Main Campus

Entity Recommendations Using Hierarchical Knowledge Bases, Siva Kumar Cheekula, Pavan Kapanipathi, Derek Doran, Prateek Jain, Amit P. Sheth

Kno.e.sis Publications

Recent developments in recommendation algorithms have focused on integrating Linked Open Data to augment traditional algorithms with background knowledge. These developments recognize that the integration of Linked Open Data may or better performance, particularly in cold start cases. In this paper, we explore if and how a specific type of Linked Open Data, namely hierarchical knowledge, may be utilized for recommendation systems. We propose a content-based recommendation approaches that adapts a spreading activation algorithm over the DBpedia category structure to identify entities of interest to the user. Evaluation of the algorithm over the Movielens dataset demonstrates that our method yields ...


Tailor: A Computational Framework For Detecting Non-Templated Tailing Of Small Silencing Rnas, Min-Te Chou, Bo W. Han, Chiung-Po Hsiao, Phillip D. Zamore, Zhiping Weng, Jui-Hung Hung 2015 National Chiao Tung University

Tailor: A Computational Framework For Detecting Non-Templated Tailing Of Small Silencing Rnas, Min-Te Chou, Bo W. Han, Chiung-Po Hsiao, Phillip D. Zamore, Zhiping Weng, Jui-Hung Hung

GSBS Student Publications

Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3' end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short ...


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 ...


Detext: A Database For Evaluating Text Extraction From Biomedical Literature Figures, Xu-Cheng Yin, Chun Yang, Wei-Yi Pei, Haixia Man, Jun Zhang, Erik Learned-Miller, Hong Yu 2015 University of Science and Technology Beijing

Detext: A Database For Evaluating Text Extraction From Biomedical Literature Figures, Xu-Cheng Yin, Chun Yang, Wei-Yi Pei, Haixia Man, Jun Zhang, Erik Learned-Miller, Hong Yu

Open Access Articles

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. Since text is a rich source of information in figures, automatically extracting such text may assist in the task of mining figure information. A high-quality ground truth standard can greatly facilitate the development of an automated system. This article describes DeTEXT: A database for evaluating text extraction from biomedical literature figures. It is the first publicly available, human-annotated, high quality, and large-scale figure-text dataset with 288 full-text articles, 500 biomedical figures, and 9308 text regions. This article describes how figures were selected from open-access full-text ...


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 ...


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 ...


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

CEC 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 ...


Scattering Correction Methods Of Infrared Spectra Using Graphics Processing Units, Asher Imtiaz 2015 University of Wisconsin-Milwaukee

Scattering Correction Methods Of Infrared Spectra Using Graphics Processing Units, Asher Imtiaz

Theses and Dissertations

Fourier transform infrared (FTIR) microspectroscopy has been used for many years as a technique that provides distinctive structure-specific infrared spectra for a wide range of materials (e.g., biological (tissues, cells, bacteria, viruses), polymers, energy related, composites, minerals). The mid-infrared radiation can strongly scatter from distinct particles, with diameters ranging between 2-20 micrometer. Transmission measurements of samples (approximately 100 micrometers x 100 micrometers x 10 micrometers) with distinct particles. will be dominated by this scattering (Mie scattering). The scattering distorts the measured spectra, and the absorption spectra appear different from pure absorbance spectra. This thesis presents development and implementation of ...


Digital Commons powered by bepress