Computer Sciences Commons^™

15. Pharmacy, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

18. Statistics, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.

Towards Personalized Medicine Using Systems Biology And Machine Learning, Calin Voichita

Wayne State University Dissertations

The rate of acquiring biological data has greatly surpassed our ability to interpret it. At the same time, we have started to understand that evolution of many diseases such as cancer, are the results of the interplay between the disease itself and the immune system of the host. It is now well accepted that cancer is not a single disease, but a “complex collection of distinct genetic diseases united by common hallmarks”. Understanding the differences between such disease subtypes is key not only in providing adequate treatments for known subtypes but also identifying new ones. These unforeseen disease subtypes are …

A Hybrid Approach To Finding Relevant Social Media Content For Complex Domain Specific Information Needs, Delroy H. Cameron, Amit P. Sheth, Nishita Jaykumar, Gaurish Anand, Krishnaprasad Thirunarayan, Gary Alan Smith

Kno.e.sis Publications

While contemporary semantic search systems offer to improve classical keyword-based search, they are not always adequate for complex, domain specific information needs. Some complex search situations require knowledge of both ontological concepts as well as 'intelligible constructs' not typically modeled in ontologies. Intelligible constructs convey essential information, which may be important to the holistic information needs of information seekers. Such constructs may include notions of intensity, frequency, interval, dosage, emotion, sentiment, equivalence, synonymy, negation, parts-of-speech, etc. However, few search systems utilize both structured background knowledge (ontologies) and the aforementioned knowledge for query interpretation in domain specific searches. Instead, there is …

Traffic Analytics Using Probabilistic Graphical Models Enhanced With Knowledge Bases, Pramod Anantharam, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

Graphical models have been successfully used to deal with uncertainty, incompleteness, and dynamism within many domains. These models built from data often ignore preexisting declarative knowledge about the domain in the form of ontologies and Linked Open Data (LOD) that is increasingly available on the web. In this paper, we present an approach to leverage such 'top-down' domain knowledge to enhance 'bottom-up' building of graphical models. Specifically, we propose three operations on the graphical model structure to enrich it with nodes, edges, and edge directions. We illustrate the enrichment process using traffic data from 511.org and declarative knowledge from ConceptNet. …

Advancing Data Reuse In Phyloinformatics Using An Ontology-Driven Semantic Web Approach, Maryam Panahiazar, Amit P. Sheth, Ajith Harshana Ranabahu, Rutger Vos, Jim Leebens-Mack

Kno.e.sis Publications

Phylogenetic analyses can resolve historical relationships among genes, organisms or higher taxa. Understanding such relationships can elucidate a wide range of biological phenomena, including, for example, the importance of gene and genome duplications in the evolution of gene function, the role of adaptation as a driver of diversification, or the evolutionary consequences of biogeographic shifts. Phyloinformaticists are developing data standards, databases and communication protocols (e.g. Application Programming Interfaces, APIs) to extend the accessibility of gene trees, species trees, and the metadata necessary to interpret these trees, thus enabling researchers across the life sciences to reuse phylogenetic knowledge. Specifically, Semantic Web …

Twitris: Socially Influenced Browsing, Ashutosh Sopan Jadhav, Wenbo Wang, Raghava Mutharaju, Pramod Anantharam, Vinh Nguyen, Amit P. Sheth, Karthik Gomadam, Meenakshi Nagarajan, Ajith Harshana Ranabahu

Kno.e.sis Publications

In this paper, we present Twitris, a semantic Web application that facilitates browsing for news and information, using social perceptions as the fulcrum. In doing so we address challenges in large scale crawling, processing of real time information, and preserving spatio-temporal-thematic properties central to observations pertaining to real time events. We extract metadata about events from Twitter and bring related news and Wikipedia articles to the user. In developing Twitris, we have used the DBPedia ontology.

Adaptive Semantic Annotation Of Entity And Concept Mentions In Text, Pablo N. Mendes

Kno.e.sis Publications

The recent years have seen an increase in interest for knowledge repositories that are useful across applications, in contrast to the creation of ad hoc or application-specific databases.
These knowledge repositories figure as a central provider of unambiguous identifiers and semantic relationships between entities. As such, these shared entity descriptions serve as a common vocabulary to exchange and organize information in different formats and for different purposes. Therefore, there has been remarkable interest in systems that are able to automatically tag textual documents with identifiers from shared knowledge repositories so that the content in those documents is described in a …

On Identifying And Analyzing Significant Nodes In Protein-­Protein Interaction Networks, Rohan Khazanchi, Kathryn Dempsey Cooper, Ishwor Thapa, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Network theory has been used for modeling biological data as well as social networks, transportation logistics, business transcripts, and many other types of data sets. Identifying important features/parts of these networks for a multitude of applications is becoming increasingly significant as the need for big data analysis techniques grows. When analyzing a network of protein-protein interactions (PPIs), identifying nodes of significant importance can direct the user toward biologically relevant network features. In this work, we propose that a node of structural importance in a network model can correspond to a biologically vital or significant property. This relationship between topological and …

On Mining Biological Signals Using Correlation Networks, Kathryn Dempsey Cooper, Ishwor Thapa, Claudia Cortes, Zack Eriksen, Dhundy Raj Bastola, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks have been used in biological networks to analyze and model high-throughput biological data, such as gene expression from microarray or RNA-seq assays. Typically in biological network modeling, structures can be mined from these networks that represent biological functions; for example, a cluster of proteins in an interactome can represent a protein complex. In correlation networks built from high-throughput gene expression data, it has often been speculated or even assumed that clusters represent sets of genes that are coregulated. This research aims to validate this concept using network systems biology and data mining by identification of correlation network clusters …

Disulfide By Design 2.0: A Web-Based Tool For Disulfide Engineering In Proteins, Douglas B. Craig, Alan A. Dombkowski

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Disulfide engineering is an important biotechnological tool that has advanced a wide range of research. The introduction of novel disulfide bonds into proteins has been used extensively to improve protein stability, modify functional characteristics, and to assist in the study of protein dynamics. Successful use of this technology is greatly enhanced by software that can predict pairs of residues that will likely form a disulfide bond if mutated to cysteines.

Results

We had previously developed and distributed software for this purpose: Disulfide by Design (DbD). The original DbD program has been widely used; however, it has a number …

Logical Linked Data Compression, Amit Krishna Joshi, Pascal Hitzler, Guozhu Dong

Computer Science and Engineering Faculty Publications

Linked data has experienced accelerated growth in recent years. With the continuing proliferation of structured data, demand for RDF compression is becoming increasingly important. In this study, we introduce a novel lossless compression technique for RDF datasets, called Rule Based Compression (RB Compression) that compresses datasets by generating a set of new logical rules from the dataset and removing triples that can be inferred from these rules. Unlike other compression techniques, our approach not only takes advantage of syntactic verbosity and data redundancy but also utilizes semantic associations present in the RDF graph. Depending on the nature of the dataset, …

A Parallel Template For Implementing Filters For Biological Correlation Networks, Kathryn Dempsey Cooper, Vladimir Ufimtsev, Sanjukta Bhowmick, Hesham Ali

Interdisciplinary Informatics Faculty Publications

High throughput biological experiments are critical for their role in systems biology – the ability to survey the state of cellular mechanisms on the broad scale opens possibilities for the scientific researcher to understand how multiple components come together, and what goes wrong in disease states. However, the data returned from these experiments is massive and heterogeneous, and requires intuitive and clever computational algorithms for analysis. The correlation network model has been proposed as a tool for modeling and analysis of this high throughput data; structures within the model identified by graph theory have been found to represent key players …

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 …

Improved Efficiency Of Rna Secondary Structure Prediction Using Distributed Computing, Gerardo A. Cardenas

Open Access Theses & Dissertations

The rapidly growing amounts of available biomolecular sequence data, which may represent information from small gene fragments to large complete genomes, have led to the a great need for powerful computational resources for data analysis and storage. With the decoding of the human and other genomes, RNA secondary structure prediction has become an important area of interest in biology and medicine because they help in understanding the mechanisms of many biological processes such as gene regulation and viral replication, and in designing RNA-based therapies to treat various diseases. Due to the complexity of their algorithms, many existing and upcoming computational …

Biodiversity Heritage Library, Smithsonian Institution Libraries, Deanna Marcum

Copyright, Fair Use, Scholarly Communication, etc.

The Biodiversity Heritage Library (BHL), created in 2006, is the result of a collaboration of ten natural history museum and botanical garden libraries seeking to digitize core taxonomic literature and to make it free and openly available throughout the world. Today, the BHL includes fifteen member institutions whose efforts have shaped a collection of over 60,000 titles. It is supported through a combination of membership dues, in-kind support from member institutions, contributions from the user community, and direct support from the Smithsonian Institution Libraries, and it reaches tens of thousands of users each year. While managing the complex partnership has …

Computational Approaches For Structure Based Drug Design And Protein Structure-Function Prediction, Sai Lakshmana Kumar Vankayala

USF Tampa Graduate Theses and Dissertations

This dissertation thesis consists of a series of chapters that are interwoven by solving interesting biological problems, employing various computational methodologies. These techniques provide meaningful physical insights to promote the scientific fields of interest. Focus of chapter 1 concerns, the importance of computational tools like docking studies in advancing structure based drug design processes. This chapter also addresses the prime concerns like scoring functions, sampling algorithms and flexible docking studies that hamper the docking successes. Information about the different kinds of flexible dockings in terms of accuracy, time limitations and success studies are presented. Later the importance of Induced fit …

Estimating Loop Length From Cryoem Images At Medium Resolutions, Andrew Mcknight, Dong Si, Kamal Al Nasr, Andrey Chemikov, Nikos Chrisochoides, Jing He

Computer Science Faculty Publications

Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein.

Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was …

Image-Level And Group-Level Models For Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment …

Computational Genetic Neuroanatomy Of The Developing Mouse Brain: Dimensionality Reduction, Visualization, And Clustering, Shuiwang Ji

Computer Science Faculty Publications

Background: The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development.

Results: In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in …

A Mesh Generation And Machine Learning Framework For Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, Shuiwang Ji

Computer Science Faculty Publications

Background: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide …

Conformational Sampling In Template Free Protein Loop Structure Modeling: An Overview, Yaohang Li

Computer Science Faculty Publications

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the …

Intensity-Based Skeletonization Of Cryoem Gray-Scale Images Using A True Segmentation-Free Algorithm, Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the …

Mining Climate Data For Shire Level Wheat Yield Predictions In Western Australia, Yunous Vagh

Theses: Doctorates and Masters

Climate change and the reduction of available agricultural land are two of the most important factors that affect global food production especially in terms of wheat stores. An ever increasing world population places a huge demand on these resources. Consequently, there is a dire need to optimise food production.

Estimations of crop yield for the South West agricultural region of Western Australia have usually been based on statistical analyses by the Department of Agriculture and Food in Western Australia. Their estimations involve a system of crop planting recommendations and yield prediction tools based on crop variety trials. However, many crop …

Application Of Web Mashup Technology To Oyster Information Services, Christian Chuindja Ngniah

LSU New Orleans Theses and Dissertations

Web mashup is a lightweight technology used to integrate data from remote sources without direct access to their databases. As a data consumer, a Web mashup application creates new contents by retrieving data through the Web application programming interface (API) provided by the external sources. As a data provider, the service program publishes its Web API and implements the specified functions.

In the project reported by this thesis, we have implemented two Web mashup applications to enhance the Web site oystersentinel.org: the Perkinsus marinus model and the Oil Spill model. Each model overlay geospatial data from a local database …

Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller

Life Sciences Faculty Research

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …

Contour Extraction Of Drosophila Embryos Using Active Contours In Scale Space, Soujanya Siddavaram Ananta

Masters Theses & Specialist Projects

Contour extraction of Drosophila embryos is an important step to build a computational system for pattern matching of embryonic images which aids in the discovery of genes. Automatic contour extraction of embryos is challenging due to several image variations such as size, shape, orientation and neigh- boring embryos such as touching and non-touching embryos. In this thesis, we introduce a framework for contour extraction based on the connected components in the gaussian scale space of an embryonic image. The active contour model is applied on the images to refine embryo contours. Data cleaning methods are applied to smooth the jaggy …

User Taglines: Alternative Presentations Of Expertise And Interest In Social Media, Hemant Purohit, Alex Dow, Omar Alonso, Lei Duan, Kevin Haas

Kno.e.sis Publications

Web applications are increasingly showing recommended users from social media along with some descriptions, an attempt to show relevancy - why they are being shown. For example, Twitter search for a topical keyword shows expert twitterers on the side for 'whom to follow'. Google+ and Facebook also recommend users to follow or add to friend circle. Popular Internet newspaper- The Huffington Post shows Twitter influencers/ experts on the side of an article for authoritative relevant tweets. The state of the art shows user profile bios as summary for Twitter experts, but it has issues with length constraint imposed by user …

Are Twitter Users Equal In Predicting Elections? A Study Of User Groups In Predicting 2012 U.S. Republican Primaries, Lu Chen, Wenbo Wang, Amit P. Sheth

Kno.e.sis Publications

Existing studies on predicting election results are under the assumption that all the users should be treated equally. However, recent work [14] shows that social media users from different groups (e.g., “silent majority” vs. “vocal minority”) have significant differences in the generated content and tweeting behavior. The effect of these differences on predicting election results has not been exploited yet. In this paper, we study the spectrum of Twitter users who participate in the on-line discussion of 2012 U.S. Republican Presidential Primaries, and examine the predictive power of different user groups (e.g., highly engaged users vs. lowly engaged users, right-leaning …

The Ssn Ontology Of The W3c Semantic Sensor Network Incubator Group, Michael Compton, Payam Barnaghi, Luis Bermudez, Raul Garcia-Castro, Oscar Corcho, Simon Cox, John Graybeal, Manfred Hauswirth, Cory Andrew Henson, Arthur Herzog, Vincent Huang, Krzysztof Janowicz, W. David Kelsey, Danh Le Phuoc, Laurent Lefort, Myriam Leggieri, Holger Neuhaus, Andriy Nikolov, Kevin Page, Alexandre Passant, Amit P. Sheth, Kerry Taylor

Kno.e.sis Publications

The W3C Semantic Sensor Network Incubator group (the SSN-XG) produced an OWL 2 ontology to describe sensors and observations — the SSN ontology, available at http://purl.oclc.org/NET/ssnx/ssn. The SSN ontology can describe sensors in terms of capabilities, measurement processes, observations and deployments. This article describes the SSN ontology. It further gives an example and describes the use of the ontology in recent research projects.