Bioinformatics Commons^™

How I Would Like Semantic Web To Be, For My Children., Raghava Mutharaju

Kno.e.sis Publications

Semantic Web, since its inception, has gone through lot of developments in its relatively nascent existence; right from people's perception, to the standards and to its adoption by the industry and more importantly by the scientific community. This impressive growth only seems to increase. In this paper, we project this growth to the next 10 years and highlight some of the facets on which Semantic Web could have a major impact on. We also present the challenges that Semantic Web and its community has to deal with in order to get there.

Evolution And Development In Cave Animals: From Fish To Crustaceans, Meredith E. Protas, William R. Jeffery

Collected Faculty and Staff Scholarship

Cave animals are excellent models to study the general principles of evolution as well as the mechanisms of adaptation to a novel environment: the perpetual darkness of caves. In this article, two of the major model systems used to study the evolution and development (evo–devo) of cave animals are described: the teleost fish Astyanax mexicanus and the isopod crustacean Asellus aquaticus. The ways in which these animals match the major attributes expected of an evo–devo cave animal model system are described. For both species, we enumerate the regressive and constructive troglomorphic traits that have evolved during their adaptation to cave …

An Efficient Bit Vector Approach To Semantics-Based Machine Perception In Resource-Constrained Devices, Cory Andrew Henson, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

The primary challenge of machine perception is to define efficient computational methods to derive high-level knowledge from low-level sensor observation data. Emerging solutions are using ontologies for expressive representation of concepts in the domain of sensing and perception, which enable advanced integration and interpretation of heterogeneous sensor data. The computational complexity of OWL, however, seriously limits its applicability and use within resource-constrained environments, such as mobile devices. To overcome this issue, we employ OWL to formally define the inference tasks needed for machine perception – explanation and discrimination – and then provide efficient algorithms for these tasks, using bit-vector encodings …

Iexplore: Interactive Browsing And Exploring Biomedical Knowledge, Vinh Nguyen, Olivier Bodenreider, Jagannathan Srinivasan, Todd Minning, Thomas Rindflesch, Bastien Rance, Ramakanth Kavuluru, Himi Yalamanchili, Krishnaprasad Thirunarayan, Satya S. Sahoo, Amit P. Sheth

Kno.e.sis Publications

We present iExplore, a Semantic Web based application that helps biomedical researchers study and explore biomedical knowledge interactively. iExplore uses the Biomedical Knowledge Repository (BKR), which integrates knowledge from various sources ranging from information extracted from biomedical literature (from PubMed) to many structured vocabularies in the Unified Medical Language System (UMLS). The current version of BKR provides a unified provenance representation for 12 million semantic predications (triples with a predicate connecting a subject and an object) derived from 87 vocabulary families in the UMLS and 14 million predications extracted from 21 million PubMed abstracts. To engage the domain experts in …

Inhibition Of Herpes Simplex Virus Type 1 With The Modified Green Tea Polyphenol Pamitoyl-Epigallocatechin Gallate., Aline De Oliveira, Sandra Adams, Lee Lee, Sean Murray, Stephen Hsu, Jeffrey Hammond, Douglas Dickinson, Ping Chen, Tin-Chun Chu

Tin-Chun Chu, Ph.D.

No abstract provided.

Epigallocatechin-3-Gallate Modulates Oxidative Stress In Exocrine Glands Of A Primary Sjogren’S Syndrome Mouse Model Prior To Disease Onset, Seiji Ohno, Hongfang Yu, Douglas Dickinson, Tin-Chun Chu, Kalu Ogbureke, Scott Derossi, Tetsuya Yamamoto, Stephen Hsu

Tin-Chun Chu, Ph.D.

No abstract provided.

Freq-Seq: A Rapid, Cost-Effective, Sequencing-Based Method To Determine Allele Frequencies Directly From Mixed Populations, Lon Chubiz, Ming-Chun Lee, Nigel Delaney, Christopher Marx

Biology Department Faculty Works

No abstract provided.

Naturally Selecting Solutions: The Use Of Genetic Algorithms In Bioinformatics, Timmy Manning, Roy D. Sleator, Paul Walsh

Department of Biological Sciences Publications

For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the …

How Can Pacific Island Economies Benefits From The Advent Of Ict’S – Review Of Best Practices In Education, Deogratias Harorimana Sr

Dr Deogratias Harorimana

This paper explored implementation and use of information and communication technologies in Fiji, in order to gain insight into recent government initiatives to introduce computers and other ICTs for the community of Fiji. The focus of this paper in that it provided the framework for an in-depth exploration of e-learning centers around the country and the benefits from the advent of ICT’s in e-learning community centers in Fiji. Areas concentrated on are outcome of ICT’s in formal education to students and community as a whole in areas of agriculture, health, environment and infrastructure etc. The research sought understanding from the …

A Base Composition Analysis Of Natural Patterns For The Preprocessing Of Metagenome Sequences, Oliver Bonham-Carter, Hesham Ali, Dhundy Raj Bastola

Information Systems and Quantitative Analysis Faculty Publications

Background: On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutations of bacterial restriction sites and the base composition analysis framework to measure their proportional content in sequence data. We suggest that this framework will increase the efficiency during the pre-processing stages of metagenome sequencing and assembly projects. Results: Our method is able …

Privacy Preserving Boosting In The Cloud With Secure Half-Space Queries, Shumin Guo, Keke Chen

Kno.e.sis Publications

This paper presents a preliminary study on the PerturBoost approach that aims to provide efficient and secure classifier learning in the cloud with both data and model privacy preserved.

A Study Of Cellular Calcium Dynamics In Culture Using Fluorescence Microscopy – A Statistical And Mathematical Approach, Richard Adekola Idowu

Doctoral Dissertations

Calcium in its ionic form is very dynamic, especially in excitable cells such as muscle and brain cells, moving from the high concentration exterior of the cell to much lower concentrations inside the cell, where calcium is used as a second messenger. In brain cells, and neurons especially, calcium is a key signaling ion involved in memory and learning with excitatory neurotransmitters such as glutamate turning neurons "on." Glutamate excites the neurons in part by causing large and dynamic changes in the intracellular calcium concentration. While these dynamics are essential for normal signaling in the brain, excessive and sustained elevations …

Computing Perception From Sensor Data, Payam Barnaghi, Frieder Ganz, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

This paper describes a framework for perception creation from sensor data. We propose using data abstraction techniques, in particular Symbolic Aggregate Approximation (SAX), to analyse and create patterns from sensor data. The created patterns are then linked to semantic descriptions that define thematic, spatial and temporal features, providing highly granular abstract representation of the raw sensor data. This helps to reduce the size of the data that needs to be communicated from the sensor nodes to the gateways or highlevel processing components. We then discuss a method that uses abstract patterns created by SAX method and occurrences of different observations …

Recent Advances In Integrating Owl And Rules, Matthias Knorr, David Carral Martinez, Pascal Hitzler, Adila A. Krisnadhi, Frederick Maier, Cong Wang

Computer Science and Engineering Faculty Publications

As part of the quest for a unifying logic for the Semantic Web Technology Stack, a central issue is finding suitable ways of integrating description logics based on the Web Ontology Language (OWL) with rule-based approaches based on logic programming. Such integration is difficult since naive approaches typically result in the violation of one or more desirable design principles. For example, while both OWL 2 DL and RIF Core (a dialect of the Rule Interchange Format RIF) are decidable, their naive union is not, unless carefully chosen syntactic restrictions are applied.

We report on recent advances and ongoing work by …

A Tableau Algorithm For Description Logics With Nominal Schema, Adila Krisnadhi, Pascal Hitzler

Computer Science and Engineering Faculty Publications

We present a tableau algorithm for the description logic ALCOV. This description logic is obtained by extending the description logic ALCO with the expressive nominal schema construct that enables DL-safe datalog with predicates of arbitrary arity to be covered within the description logic framework. The tableau algorithm provides a basis to implement a delayed grounding strategy which was not facilitated by earlier versions of decision procedures for satisfiability in expressive description logics with nominal schemas.

Technical Assistance, Knowledge Gatekeeping And Indigenous Knowledge: Re-Thinking The International Development Practice, Deogratias Harorimana Sr

Dr Deogratias Harorimana

This paper presents results from a multi-disciplinary conceptual analysis of development theory and practice. It reviews issues raised and proposes a shift in the epistemology of possession towards an epistemology of practice which is guided by the following aspects (1) The consideration of the learning culture of parties involved, (2) the ability and willingness for decontextualisation of the knowledge by the source and (3) the ability to embedded it by recipients (embededness ), (4) the importance that is attached to knowledge of the host country as reflected through (5) Similarity in culture, values, understanding of context and knowledge bases; (6) …

Reconciling Owl And Non-Monotonic Rules For The Semantic Web, Matthias Knorr, Pascal Hitzler, Frederick Maier

Computer Science and Engineering Faculty Publications

We propose a description logic extending SROIQ (the description logic underlying OWL 2 DL) and at the same time encompassing some of the most prominent monotonic and nonmonotonic rule languages, in particular Datalog extended with the answer set semantics. Our proposal could be considered a substantial contribution towards fulfilling the quest for a unifying logic for the Semantic Web. As a case in point, two non-monotonic extensions of description logics considered to be of distinct expressiveness until now are covered in our proposal. In contrast to earlier such proposals, our language has the 'look and feel' of a description logic …

Evolution Of Nuclear Integrations Of The Mitochondrial Genome In Great Apes And Their Potential As Molecular Markers, Ivan D. Soto-Calderon

University of New Orleans Theses and Dissertations

The mitochondrial control region (MCR) has played an important role as a population genetic marker in many taxa but sequencing of complete eukaryotic genomes has revealed that nuclear integrations of mitochondrial DNA (numts) are abundant and widespread across many taxa. If left undetected, numts can inflate mitochondrial diversity and mislead interpretation of phylogenetic relationships. Comparative analyses of complete genomes in humans, orangutans and chimpanzees, and preliminary studies in gorillas have revealed high numt prevalence in great apes, but rigorous comparative analyses across taxa have been lacking.

The present study aimed to systematically compare the evolutionary dynamics of MCR numts in …

Optimal Clustering Techniques For Metagenomic Sequencing Data, Erik T. Cameron

Electronic Thesis and Dissertation Repository

Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in the vagina, but results have been inconsistent, possibly due to methodological differences. We performed an extensive comparison of six commonly-used clustering algorithms and four distance metrics, using clinical data from 777 vaginal samples across 5 studies, and 36,000 synthetic datasets based on these clinical data. We found that centroid-based clustering algorithms (K-means and Partitioning around Medoids), with Euclidean or Manhattan distance metrics, performed well. They were best at correctly clustering …

Sulfate Reducing Communities In Aquifer Systems Can Be Reliably Stimulated By Addition Of Complex Nutrients, Matthew Bryan Scholz

Doctoral Dissertations

The disseration presented below is the summation of research into the potential roles of microbial communities associated with aquifers of Bangladesh contaminated with naturally occuring arsenic. These investigations also included experimental microcosm experiments to assess the role of nutrients supplementation of complex carbon sources (molasses), and inorganic sulfate (MgSO4), on both the solubility of arsenic to determine the feasibility of this method for the goal of performing in situ bioremediation. Community structure and functional gene profiling was performed on all samples, as well as detection of community shifts following amendments predicted to encourage the growth of sulfate reducting microorganisms (SRM). …