Browsing Faculty Works, Fralin Life Sciences Institute by Issue Date

Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome

Dinel, S; Bolduc, C; Belleau, P; Boivin, A; Yoshioka, M; Calvo, E; Piedboeuf, B; Snyder, EE; Labrie, F; St-Amand, J (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

Bradshaw, Patrick C; Rathi, Anand; Samuels, David C (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

Guo, Yongjian; Jamison, D Curtis (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 ...

Tomato Expression Database (TED): a suite of data presentation and analysis tools

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James (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. ...

VMD: a community annotation database for oomycetes and microbial genomes

Tripathy, Sucheta; Pandey, Varun N.; Fang, Bing; Salas, Fidel; Tyler, Brett M. (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 ...

The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison

Sioson, Allan A; Mane, Shrinivasrao P; Li, Pinghua; Sha, Wei; Heath, Lenwood S.; Bohnert, Hans J; Grene, Ruth (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

Lu, Guoqing; Jiang, Liying; Helikar, Resa MK; Rowley, Thaine W; Zhang, Luwen; Chen, Xianfeng; Moriyama, Etsuko N (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

Cai, Y; Hartnett, B; Gustafsson, C; Peccoud, J (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 ...

GeneTrees: a phylogenomics resource for prokaryotes

Tian, Yuying; Dickerman, Allan W. (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 ...

PATRIC: The VBI PathoSystems Resource Integration Center

Snyder, E. E.; Kampanya, N.; Lu, J.; Nordberg, E. K.; Karur, H. R.; Shukla, M.; Soneja, J.; Tian, Y.; Xue, T.; Yoo, H.; Zhang, F.; Dharmanolla, C.; Dongre, N. V.; Gillespie, J. J.; Hamelius, J.; Hance, M.; Huntington, K. I.; Jukneliene, D.; Koziski, J.; Mackasmiel, L.; Mane, S. P.; Nguyen, V.; Purkayastha, A.; Shallom, J.; Yu, G.; Guo, Y.; Gabbard, J.; Hix, D.; Azad, A. F.; Baker, S. C.; Boyle, S. M.; Khudyakov, Y.; Meng, X. J.; Rupprecht, C.; Vinje, J.; Crasta, O. R.; Czar, M. J.; Dickerman, A.; Eckart, J. D.; Kenyon, R.; Will, R.; Setubal, J. C.; Sobral, B. W. S. (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 ...

MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications

Zhou, C. E.; Smith, J.; Lam, M.; Zemla, A.; Dyer, M. D.; Slezak, T. (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 ...

Plasmids and Rickettsial Evolution: Insight from Rickettsia felis

Gillespie, Joseph J.; Beier, Magda S.; Rahman, M. Sayeedur; Ammerman, Nicole C.; Shallom, Joshua M.; Purkayastha, Anjan; Sobral, Bruno S.; Azad, Abdu F. (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

Stock, Kathrin F; Distl, Ottmar; Hoeschele, Ina (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 properties ...

A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case

Yu, G. X.; Snyder, E. E.; Boyle, S. M.; Crasta, O. R.; Czar, M.; Mane, S. P.; Purkayastha, A.; Sobral, B.; Setubal, J. C. (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 ...