Browsing Scholarly Works, Fralin Life Sciences Institute by Issue Date
Now showing items 1-20 of 542
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Towards a calculus of biological networks
(2002)In this paper we present a new framework for studying the dynamics of biological networks. A specific class of dynamical systems, Sequential Dynamical Systems (SDS), is introduced. These systems allow one to investigate ... -
Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome
(2005-01-01)The serial analysis of gene expression (SAGE) method is used to study global gene expression in cells or tissues in various experimental conditions. However, its reproducibility has not yet been definitively assessed. In ... -
Mitochondrial-encoded membrane protein transcripts are pyrimidine-rich while soluble protein transcripts and ribosomal RNA are purine-rich
(2005-09-26)Background Eukaryotic organisms contain mitochondria, organelles capable of producing large amounts of ATP by oxidative phosphorylation. Each cell contains many mitochondria with many copies of mitochondrial DNA in each ... -
The distribution of SNPs in human gene regulatory regions
(2005-10-06)Background As a result of high-throughput genotyping methods, millions of human genetic variants have been reported in recent years. To efficiently identify those with significant biological functions, a practical strategy ... -
VMD: a community annotation database for oomycetes and microbial genomes
(2006-01-01)The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae ... -
Tomato Expression Database (TED): a suite of data presentation and analysis tools
(2006-01-01)The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. ... -
The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison
(2006-04-20)Background Analysis of DNA microarray data takes as input spot intensity measurements from scanner software and returns differential expression of genes between two conditions, together with a statistical significance ... -
GenomeBlast: a web tool for small genome comparison
(2006-12-12)Background Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. ... -
A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts
(2007)Motivation: The sequence of artificial genetic constructs is composed of multiple functional fragments, or genetic parts, involved in different molecular steps of gene expression mechanisms. Biologists have deciphered ... -
Computational prediction of host-pathogen protein–protein interactions
(Oxford University Press, 2007)Motivation: Infectious diseases such as malaria result in millions of deaths each year. An important aspect of any host-pathogen system is the mechanism by which a pathogen can infect its host. One method of infection is ... -
GeneTrees: a phylogenomics resource for prokaryotes
(2007-01)The GeneTrees phylogenomics system pursues comparative genomic analyses from the perspective of gene phylogenies for individual genes. The GeneTrees project has the goal of providing detailed evolutionary models for all ... -
MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications
(2007-01)Knowledge of toxins, virulence factors and antibiotic resistance genes is essential for bio-defense applications aimed at identifying 'functional' signatures for characterizing emerging or engineered pathogens. Whereas ... -
PATRIC: The VBI PathoSystems Resource Integration Center
(2007-01)The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource ... -
Plasmids and Rickettsial Evolution: Insight from Rickettsia felis
(PLOS, 2007-03-07)Background The genome sequence of Rickettsia felis revealed a number of rickettsial genetic anomalies that likely contribute not only to a large genome size relative to other rickettsiae, but also to phenotypic oddities ... -
Bayesian estimation of genetic parameters for multivariate threshold and continuous phenotypes and molecular genetic data in simulated horse populations using Gibbs sampling
(2007-05-09)Background Requirements for successful implementation of multivariate animal threshold models including phenotypic and genotypic information are not known yet. Here simulated horse data were used to investigate the ... -
A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case
(2007-06)We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence ... -
Role of information and communication networks in malaria survival
(2007-10-10)Background Quite often symptoms of malaria go unrecognized or untreated. According to the Multilateral Initiative on Malaria, 70% of the malaria cases that are treated at home are mismanaged. Up to 82% of all malaria ... -
A virtual look at Epstein-Barr virus infection: Biological interpretations
(PLOS, 2007-10-19)The possibility of using computer simulation and mathematical modeling to gain insight into biological and other complex systems is receiving increased attention. However, it is as yet unclear to what extent these techniques ... -
Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions
(2007-11-08)Background: Schistosoma mansoni is a blood helminth parasite that causes schistosomiasis, a disease that affects 200 million people in the world. Many orthologs of known mammalian genes have been discovered in this parasite ... -
Detecting epistatic interactions contributing to human gene expression using the CEPH family data
(2007-12-18)It is believed that epistatic interactions among loci contribute to variations in quantitative traits. Several methods are available to detect epistasis using population-based data. However, methods to characterize epistasis ...
