Loraine AE

RNA-Seq of Arabidopsis Pollen Uncovers Novel Transcription and Alternative Splicing

June 07, 2013

RNA-Seq of Arabidopsis Pollen Uncovers Novel Transcription and Alternative Splicing. Plant Physiology. June 2013. Loraine AE, McCormick S, Estrada A, Patel K, Qin P. Department of Bioinformatics and Genomics, University of North Carolina, Kannapolis. Abstract Pollen grains of Arabidopsis (Arabidopsis thaliana) contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the […]

Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.

March 22, 2013

Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis. Plant Physiology. May 2013. Epub Mar 22, 2013. Bhargava A, Clabaugh I, To JP, Maxwell BB, Chiang YH, Schaller GE, Loraine A (UNC Charlotte at the NC Research Campus), Kieber JJ. Department of Biology, University of North Carolina, Chapel Hill, North Carolina. Abstract Cytokinins […]

Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a.

February 11, 2012

Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a. American Journal of Botany, February 2012. Gulledge AA, Roberts AD, Vora H, Patel K, Loraine AE. Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus. Abstract PREMISE OF THE STUDY: […]

Prevalence of alternative splicing choices in Arabidopsis

March 19, 2010

English A, Patel K, Loraine AE. Prevalence of alternative splicing choices in Arabidopsis. BMC Plant Biology. BMC Plant Biology 2010, 10:102.PubMed.ArabiTag-alternative splicing data-mining tool. Abstract BACKGROUND: Around 14% of protein-coding genes of Arabidopsis thaliana genes from the TAIR9 genome release are annotated as producing multiple transcript variants through alternative splicing. However, for most alternatively spliced […]

Consistency analysis of redundant probe sets on Affymetrix three-prime expression arrays and applications to differential mRNA processing

March 19, 2009

Cui X, Loraine AE. 2009. Consistency analysis of redundant probe sets on Affymetrix three-prime expression arrays and applications to differential mRNA processing. PLoSOne. 2009;4(1):e4229. Epub 2009 Jan 23. PubMed Abstract Affymetrix three-prime expression microarrays contain thousands of redundant probe sets that interrogate different regions of the same gene. Differential expression analysis methods rarely consider probe […]

The Integrated Genome Browser: Free software for distribution and exploration of genome-scale data sets.

March 19, 2009

Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE. The Integrated Genome Browser: Free software for distribution and exploration of genome-scale data sets. Bioinformatics. 2009 October 15; 25(20):27302. Article Abstract Experimental techniques that survey an entire genome demand flexible, highly interactive visualization tools that can display new data alongside foundation datasets, such as reference […]

The Genoviz Software Development Kit: A Java toolkitfor building genomics visualization applications.

March 19, 2009

Helt GA, Nicol JW, Blossom E, Blanchard S, Chervitz SA, Harmon C, LoraineAE. The Genoviz Software Development Kit: A Java toolkitfor building genomics visualization applications. BMC Bioinformatics. 2009, 10:266. Abstract BACKGROUND: Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. RESULTS: The Genoviz Software Development Kit (SDK) is an open […]

Large-Scale Transposon Mutagenesis of Mycoplasma pulmonis

March 19, 2008

French CT, Lao P, Loraine AE, Matthews BT, Yu H, Dybvig K. Large-Scale Transposon Mutagenesis of Mycoplasma pulmonis. Mol Microbiol. Mol Microbiol. 2008 Jul;69(1):67-76. Epub 2008 Apr 28. Abstract To obtain mutants for the study of the basic biology and pathogenic mechanisms of mycoplasmas, the insertion site of transposon Tn4001T was determined for 1700 members […]

The Genome of Mycoplasma arthritidis

March 19, 2008

Dybvig K, Zuhua C, Lao P, Jordan DS, French CT, Tu AH, Loraine AE. The Genome of Mycoplasma arthritidis. Infect Immun. 2008 Jun 23. Abstract The genomes of several species of mycoplasma have been sequenced. Most of these species rely on the glycolytic pathway for energy production, with the one exception of Ureaplasma, a species […]

CressExpress: A tool for large-scale mining of expression data from Arabidopsis thaliana.

March 19, 2008

Srinivasasainagendra V, Page G, Mehta T, Coulibaly I, Loraine AE. CressExpress: A tool for large-scale mining of expression data from Arabidopsis thaliana. Plant Physiology. 2008 Jul;147(3):1004-16. Abstract CressExpress is a user-friendly, online, coexpression analysis tool for Arabidopsis (Arabidopsis thaliana) microarray expression data that computes patterns of correlated expression between user-entered query genes and the rest […]