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Full-Text Articles in Life Sciences

Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao Apr 2019

Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao

Master's Theses

Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid methods, such as Resnik’s and Wang’s methods. Moreover, GOGO is relatively fast and does not need to calculate information content (IC) from a large gene annotation corpus but still has the advantage of using IC. This is achieved by considering the number of children nodes in the GO directed acyclic graphs when calculating the semantic contribution of an ...


Gene Ontology-Guided Force-Directed Visualization Of Protein Interaction Networks, James Lowell King Jan 2019

Gene Ontology-Guided Force-Directed Visualization Of Protein Interaction Networks, James Lowell King

CCE Theses and Dissertations

Protein interaction data is being generated at unprecedented rates thanks to advancements made in high throughput techniques such as mass spectrometry and DNA microarrays. Biomedical researchers, operating under budgetary constraints, have found it difficult to scale their efforts to keep up with the ever-increasing amount of available data. They often lack the resources and manpower required to analyze the data using existing methodologies. These research deficiencies impede our ability to understand diseases, delay the advancement of clinical therapeutics, and ultimately costs lives.

One of the most commonly used techniques to analyze protein interaction data is the construction and visualization of ...


Fedrr: Fast, Exhaustive Detection Of Redundant Hierarchical Relations For Quality Improvement Of Large Biomedical Ontologies, Guangming Xing, Guo-Qiang Zhang, Licong Cui Oct 2016

Fedrr: Fast, Exhaustive Detection Of Redundant Hierarchical Relations For Quality Improvement Of Large Biomedical Ontologies, Guangming Xing, Guo-Qiang Zhang, Licong Cui

Institute of Biomedical Informatics Faculty Publications

Background: Redundant hierarchical relations refer to such patterns as two paths from one concept to another, one with length one (direct) and the other with length greater than one (indirect). Each redundant relation represents a possibly unintended defect that needs to be corrected in the ontology quality assurance process. Detecting and eliminating redundant relations would help improve the results of all methods relying on the relevant ontological systems as knowledge source, such as the computation of semantic distance between concepts and for ontology matching and alignment.

Results: This paper introduces a novel and scalable approach, called FEDRR – Fast, Exhaustive Detection ...


Computational Labeling, Partitioning, And Balancing Of Molecular Networks, Biaobin Jiang Aug 2016

Computational Labeling, Partitioning, And Balancing Of Molecular Networks, Biaobin Jiang

Open Access Dissertations

Recent advances in high throughput techniques enable large-scale molecular quantification with high accuracy, including mRNAs, proteins and metabolites. Differential expression of these molecules in case and control samples provides a way to select phenotype-associated molecules with statistically significant changes. However, given the significance ranking list of molecular changes, how those molecules work together to drive phenotype formation is still unclear. In particular, the changes in molecular quantities are insufficient to interpret the changes in their functional behavior. My study is aimed at answering this question by integrating molecular network data to systematically model and estimate the changes of molecular functional ...


Metviz: An Online Visualization Tool For Regulons, Genes And Gene Ontology, Achyuthan Vasanth Jan 2012

Metviz: An Online Visualization Tool For Regulons, Genes And Gene Ontology, Achyuthan Vasanth

Graduate Theses and Dissertations

Background

Interpretation of large volumes of data that has information about genes, regulons, gene ontology and probes are important for the identification of the functionality of individual genes and their role with respect to the organism. Many software tools are available today, but they become difficult to interpret when visualizing large volumes of data and representing relationships between them.

Results

MetViz is an interactive web-based tool that uses novel visualization techniques to represent regulons, genes and the gene ontology hierarchy. The tool provides easier accessibility by making it available as a website requiring no download. Instead of displaying all data ...


Quail Genomics: A Knowledgebase For Northern Bobwhite, Arun Rawat, Kurt A. Gust, Mohamed O. Elasri, Edward J. Perkins Oct 2010

Quail Genomics: A Knowledgebase For Northern Bobwhite, Arun Rawat, Kurt A. Gust, Mohamed O. Elasri, Edward J. Perkins

Faculty Publications

Background

The Quail Genomics knowledgebase (http://www.quailgenomics.info) has been initiated to share and develop functional genomic data for Northern bobwhite (Colinus virginianus). This web-based platform has been designed to allow researchers to perform analysis and curate genomic information for this non-model species that has little supporting information in GenBank.

Description

A multi-tissue, normalized cDNA library generated for Northern bobwhite was sequenced using 454 Life Sciences next generation sequencing. The Quail Genomics knowledgebase represents the 478,142 raw ESTs generated from the sequencing effort in addition to assembled nucleotide and protein sequences including 21,980 unigenes annotated with meta-data ...


Cloning, Analysis And Functional Annotation Of Expressed Sequence Tags From The Earthworm Eisenia Fetida, Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng Nov 2007

Cloning, Analysis And Functional Annotation Of Expressed Sequence Tags From The Earthworm Eisenia Fetida, Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng

Faculty Publications

Background

Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR.

Results

A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363–EH672369 and EL515444–EL515580) were obtained from the raw ...


Bi-Level Clustering Of Mixed Categorical And Numerical Biomedical Data, Bill Andreopoulos, Aijun An, Xiaogang Wang Jun 2006

Bi-Level Clustering Of Mixed Categorical And Numerical Biomedical Data, Bill Andreopoulos, Aijun An, Xiaogang Wang

William B. Andreopoulos

Biomedical data sets often have mixed categorical and numerical types, where the former represent semantic information on the objects and the latter represent experimental results. We present the BILCOM algorithm for |Bi-Level Clustering of Mixed categorical and numerical data types|. BILCOM performs a pseudo-Bayesian process, where the prior is categorical clustering. BILCOM partitions biomedical data sets of mixed types, such as hepatitis, thyroid disease and yeast gene expression data with Gene Ontology annotations, more accurately than if using one type alone.