Bioinformatics Commons^™

Semantics Of Perception: Towards A Semantic Web Approach To Machine Perception, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

The acts of observation and perception provide the building blocks for all human knowledge (Locke, 1690); they are the processes from which all ideas are born; and the sole bond connecting ourselves to the world around us. Now, with the advent of sensor networks capable of observation, this world may be directly accessible to machines. Missing from this vision, however, is the ability of machines to glean semantics from observation; to apprehend entities from detected qualities; to perceive. The systematic automation of this ability is the focus of machine perception -- the ability of computing machines to sense and interpret …

Extracting Diverse Sentiment Expressions With Target-Dependent Polarity From Twitter, Lu Chen, Wenbo Wang, Meenakshi Nagarajan, Shaojun Wang, Amit P. Sheth

Kno.e.sis Publications

This study focuses on automatic extraction of sentiment expressions associated with given targets from Twitter. It addresses one of the key challenges in this work: Wide diversity and informal nature of sentiment expressions that cannot be trivially enumerated or captured using predefined lexical patterns.

On The Role Of Social Identity And Cohesion In Characterizing Online Social Communities, Hemant Purohit, Yiye Ruan, David Fuhry, Srinivasan Parthasarathy, Amit P. Sheth

Kno.e.sis Publications

Two prevailing theories for explaining social group or community structure are cohesion and identity. The social cohesion approach posits that social groups arise out of an aggregation of individuals that have mutual interpersonal attraction as they share common characteristics. These characteristics can range from common interests to kinship ties and from social values to ethnic backgrounds. In contrast, the social identity approach posits that an individual is likely to join a group based on an intrinsic self-evaluation at a cognitive or perceptual level. In other words group members typically share an awareness of a common category membership. In this work …

Towards Cloud Mobile Hybrid Application Generation Using Semantically Enriched Domain Specific Languages, Ajith Harshana Ranabahu, Amit P. Sheth, Ashwin Manjunatha, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The advancements in computing have resulted in a boom of cheap, ubiquitous, connected mobile devices as well as seemingly unlimited, utility style, pay as you go computing resources, commonly referred to as Cloud computing. Taking advantage of this computing landscape, however, has been hampered by the many heterogeneities that exist in the mobile space as well as the Cloud space.

This research attempts to introduce a disciplined methodology to develop Cloud-mobile hybrid applications by using a Domain Specific Language (DSL) centric approach to generate applications. A Cloud-mobile hybrid is an application that is split between a Cloud based back-end and …

Alignment-Based Querying Of Linked Open Data, Amit Krishna Joshi, Prateek Jain, Pascal Hitzler, Peter Z. Yeh, Kunal Verma, Amit P. Sheth, Mariana Damova

Kno.e.sis Publications

The Linked Open Data (LOD) cloud is rapidly becoming the largest interconnected source of structured data on diverse domains. The potential of the LOD cloud is enormous, ranging from solving challenging AI issues such as open domain question answering to automated knowledge discovery. However, due to an inherent distributed nature of LOD and a growing number of ontologies and vocabularies used in LOD datasets, querying over multiple datasets and retrieving LOD data remains a challenging task. In this paper, we propose a novel approach to querying linked data by using alignments for processing queries whose constituent data come from heterogeneous …

Semantics And Ontologies For Earthcube, Gary Berg-Cross, Isabel F. Cruz, Michael Dean, Timothy Finin, Mark Gahegan, Pascal Hitzler, Hook Hau, Krzysztof Janowicz, Naicong Li, Philip Murphy, Bryce Nordgren, Leo Obrst, Mark Schildhauer, Amit P. Sheth, Krishna Sinha, Anne Thessen, Nancy Wiegand, Ilya Zaslavasky

Kno.e.sis Publications

Semantic technologies and ontologies play an increasing role in scientific workflow systems and knowledge infrastructures. While ontologies are mostly used for the semantic annotation of metadata, semantic technologies enable searching metadata catalogs beyond simple keywords, with some early evidence of semantics used for data translation. However, the next generation of distributed and interdisciplinary knowledge infrastructures will require capabilities beyond simple subsumption reasoning over subclass relations. In this work, we report from the EarthCube Semantics Community by highlighting which role semantics and ontologies should play in the EarthCube knowledge infrastructure. We target the interested domain scientist and, thus, introduce the value …

The Ontology For Parasite Lifecycle (Opl): Towards A Consistent Vocabulary Of Lifecycle Stages In Parasitic Organisms, Priti Parikh, Jie Zheng, Flora J. Logan-Klumpler, Christian J. Stoeckert, Pantelis Topalis, Anna Protasio, Amit P. Sheth, Mark Carrington, Matthew Berriman, Satya S. Sahoo

Kno.e.sis Publications

Background

Genome sequencing of many eukaryotic pathogens and the volume of data available on public resources have created a clear requirement for a consistent vocabulary to describe the range of developmental forms of parasites. Consistent labeling of experimental data and external data, in databases and the literature, is essential for integration, cross database comparison, and knowledge discovery. The primary objective of this work was to develop a dynamic and controlled vocabulary that can be used for various parasites. The paper describes the Ontology for Parasite Lifecycle (OPL) and discusses its application in parasite research.

Results

The OPL is based on …

An Efficient And Scalable Graph Modeling Approach For Capturing Information At Different Levels In Next Generation Sequencing Reads, Julia Warnke, Hesham Ali

Information Systems and Quantitative Analysis Faculty Publications

Background: Next generation sequencing technologies have greatly advanced many research areas of the biomedical sciences through their capability to generate massive amounts of genetic information at unprecedented rates. The advent of next generation sequencing has led to the development of numerous computational tools to analyze and assemble the millions to billions of short sequencing reads produced by these technologies. While these tools filled an important gap, current approaches for storing, processing, and analyzing short read datasets generally have remained simple and lack the complexity needed to efficiently model the produced reads and assemble them correctly.

Results: Previously, we presented an …

Open And Transparent: The Review Process Of The Semantic Web Journal, Krzysztof Janowicz, Pascal Hitzler

Computer Science and Engineering Faculty Publications

While open access is established in the world of academic publishing, open reviews are rare. The Semantic Web journal goes further than just open review by implementing an open and transparent review process in which reviews are publicly available, and the assigned editors and reviewers are known by name, and are published together with accepted manuscripts. In this article we introduce the steps to realize such a process from the conceptual design, over the implementation, a overview of the results so far, and up to lessons learned.

Miip: The Monomer Identification And Isolation Program, Christopher Bun, William Ziccardi, Jeffrey Doering, Catherine Putonti

Bioinformatics Faculty Publications

Repetitive elements within genomic DNA are both functionally and evolutionarily informative. Discovering these sequences ab initio is computationally challenging, compounded by the fact that selection on these repeats is often relaxed; thus sequence identity between repetitive elements can vary significantly. Here we present a new application, the Monomer Identification and Isolation Program (MiIP), which provides functionality to both search for a particular repeat as well as discover repetitive elements within a larger genomic sequence. To compare MiIP’s performance with other repeat detection tools, analysis was conducted for synthetic sequences as well as several α21-II clones and HC21 BAC sequences. The …

Cbdb: The Codon Bias Database, Adam Hilterbrand, Joseph Saelens, Catherine Putonti

Bioinformatics Faculty Publications

Background

In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mutational bias and drift. Furthermore, correlations between codon usage within host genomes and their viral pathogens have been observed for a myriad of host-virus systems. As such, numerous studies have investigated codon usage and codon bias in an effort to better understand how species evolve. Numerous metrics have been developed to identify biases in codon usage. In addition, a few data repositories of codon bias data are available, …

Age Composition And Distribution Of Red Drum (Sciaenops Ocellatus) In Offshore Waters Of The North Central Gulf Of Mexico: An Evaluation Of A Stock Under A Federal Harvest Moratorium, Sean P. Powers, Crystal Hightower, J. Marcus Drymon, Matthew W. Johnson

University Faculty and Staff Publications

Because of a lack of fishery- dependent data, assessment of the recovery of fish stocks that undergo the most aggressive form of management, namely harvest moratoriums, remains a challenge. Large schools of red drum (Sclaenops ocellatus) were common along the northern Gulf of Mexico until the late 1980s when increased fishing effort quickly depleted the stock. After 24 years of harvest moratorium on red drum in federal waters, the stock is in need of reassessment; however, fishery dependent data are not available in federal waters and fishery-independent data are limited. We document the distribution, age composition, growth, and condition of …

Phylogenetic Utility Of Mitochondrial And Nuclear Genes: A Case Study In The Diptera (True Flies), Jason Caravas

Wayne State University Dissertations

The value of mitochondrial versus nuclear gene sequence data in phylogenetic analysis has received much attention without yielding definitive conclusions. Theoretical arguments and empirical data suggest a lower phylogenetic utility than equivalent nuclear gene sequences, but there are also many examples of important progress made using mitochondrial sequences. We therefore undertook a systematic performance analysis of mitochondrial and nuclear sequence partitions taken from a representative sample of dipteran species. For phylogenetic tree reconstruction, mitochondrial genes performed generally inferior to nuclear genes. However, the mitochondrial genes resolved branches for which nuclear genes failed. Moreover, the combined use of mitochondrial and nuclear …

Differential Modeling For Cancer Microarray Data, Omar Odibat

Wayne State University Dissertations

Capturing the changes between two biological phenotypes is a crucial task in understanding the mechanisms of various diseases. Most of the existing computational approaches depend on testing the changes in the expression levels of each single gene individually. In this work, we proposed novel computational approaches to identify the differential genes between two phenotypes. These approaches aim to quantitatively characterize the differences between two phenotypes and can provide better insights and understanding of various diseases. The purpose of this thesis is three-fold. Firstly, we review the state-of-the-art approaches for differential analysis of gene expression data.

Secondly, we propose a novel …

A Proposal To Test The Effects Of Factor Ecat1 On Pluripotency, From Reprogramming To Differentiation Of Human Somatic Cells, Vritti R. Goel

CMC Senior Theses

The field of stem cell research has been growing more because of the interest in using stem cells to cure diseases and heal injuries. Human embryonic stem cells, because of the controversy surrounding them—and subsequently the difficulties in acquiring samples of the existing aging cell lines—can only be used in limited capacities. While the development of induced pluripotent stem cells in the last decade has allowed the field to progress closer to medical treatments, the low efficiency of reprogramming a somatic cell to a pluripotent state, and the vast molecular and genomic differences between human embryonic stem cells and human …

Minimalist Ensemble Algorithms For Genome-Wide Protein Localization Prediction, J.-R. Lin, A. M. Mondal, R. Liu, Jianjun Hu

Faculty Publications

Background

Computational prediction of protein subcellular localization can greatly help to elucidate its functions. Despite the existence of dozens of protein localization prediction algorithms, the prediction accuracy and coverage are still low. Several ensemble algorithms have been proposed to improve the prediction performance, which usually include as many as 10 or more individual localization algorithms. However, their performance is still limited by the running complexity and redundancy among individual prediction algorithms.

Results

This paper proposed a novel method for rational design of minimalist ensemble algorithms for practical genome-wide protein subcellular localization prediction. The algorithm is based on combining a feature …

Effects Of Single-Nucleotide Polymorphisms In The Human Holocarboxylase Synthetase Gene On Enzyme Catalysis, Sridhar Malkaram, Shingo Esaki, Janos Zempleni

Sridhar A Malkaram

No abstract provided.

Incorporating Network Structure In Integrative Analysis Of Cancer Prognosis Data, Shuangge Ma

Shuangge Ma

In high-throughput cancer genomic studies, markers identified from the analysis of single datasets may have unsatisfactory properties because of low sample sizes. Integrative analysis pools and analyzes raw data from multiple studies, and can effectively increase sample size and lead to improved marker identification results. In this study, we consider the integrative analysis of multiple high-throughput cancer prognosis studies. In the existing integrative analysis studies, the interplay among genes, which can be described using the network structure, has not been effectively accounted for. In network analysis, tightly-connected nodes (genes) are more likely to have related biological functions and similar regression …

Risk Factors Of Follicular Lymphoma, Shuangge Ma

Shuangge Ma

No abstract provided.

Health Insurance Coverage And Impact: A Survey In Three Cities In China, Shuangge Ma

Shuangge Ma

No abstract provided.