Search results | J. Murrey Atkins Library

Title: A comparison of transgenic and wild type soybean seeds : analysis of transcriptome profiles using RNA-Seq
Author: Loraine, Ann, Lambirth, Kevin C., Whaley, Adam M., Piller, Kenneth J.
Date Created: 2015
Subjects--Topical: Gene expression, Biotechnology
Description: Background: Soybean (Glycine max) has been bred for thousands of years to produce seeds rich in protein for human and animal consumption, making them an appealing bioreactor for producing valuable recombinant proteins at high levels. However, the ...

Title: Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR
Author: Loraine, Ann, Estrada, April, Freese, Nowlan H., Blakley, Ivory
Date Created: 2015
Subjects--Topical: Bioinformatics, Pollen, Nucleic acids
Description: Alternative splicing enables a single gene to produce multiple mRNA isoforms by varying splice site selection. In animals, alternative splicing of mRNA isoforms between cell types is widespread and supports cellular differentiation. In plants, at ...

Title: Arabidopsis bioinformatics resources : the current state, challenges, and priorities for the future
Author: Loraine, Ann, Doherty, Colleen, Friesner, Joanna, Gregory, Brian
Date Created: 2019
Subjects--Topical: Bioinformatics, Arabidopsis thaliana
Description: Effective research, education, and outreach efforts by the Arabidopsis thaliana community, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly-shared resources. These resour...

Title: Characterization of the cytokinin-responsive transcriptome in rice
Author: Loraine, Ann, Raines, Tracy, Blakley, Ivory, Kieber, Joseph J.
Date Created: 2016
Subjects--Topical: Gene expression, Cytokinins
Description: Background: Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant...

Title: Commonality of functional annotation : a method for prioritization of candidate genes from genome-wide linkage studies
Author: Loraine, Ann, Shriner, Daniel, Baye, Tesfaye M., Padilla, Miguel A.
Date Created: 2008
Subjects--Topical: Gene expression, Alzheimer's disease
Description: Linkage studies of complex traits frequently yield multiple linkage regions covering hundreds of genes. Testing each candidate gene from every region is prohibitively expensive and computational methods that simplify this process would benefit gen...

Title: Consistency analysis of redundant probe sets on Affymetrix three-prime expression arrays and applications to differential mRNA processing
Author: Loraine, Ann, Cui, Xiangqin
Date Created: 2009
Subjects--Topical: Gene expression, Nucleic acids
Description: 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 redundancy, which can lead to inaccurate in...

Title: Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient
Author: Loraine, Ann, Yao, Jianchao, Chang, Chunqi, Roux, Stanley J.
Date Created: 2008
Subjects--Topical: Genomics, Bioinformatics
Description: Background: Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD)-weighted correlat...

Title: Genoviz Software Development Kit : Java tool kit for building genomics visualization applications
Author: Loraine, Ann, Helt, Gregg A., Nicol, John W., Erwin, Ed
Date Created: 2009
Subjects--Topical: Genomics, Software
Description: 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 source, Java-based framework designed for rapid assembly ...

Title: Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing
Author: Loraine, Ann, Freese, Nowlan H., Estrada, April, Blakley, Ivory
Date Created: 2019
Subjects--Topical: Gene expression
Description: Alternatively spliced genes produce multiple spliced isoforms, called transcript variants. In differential alternative splicing, transcript variant abundance differs across sample types. Differential alternative splicing is common in animal system...

Title: Prevalence of alternative splicing choices in Arabidopsis thaliana
Author: Loraine, Ann, English, Adam C., Patel, Ketan S.
Date Created: 2010
Subjects--Topical: Gene expression, Nucleic acids
Description: 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 genes in Arabi...

Title: RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing
Author: Loraine, Ann, Gupta, Vikas, Estrada, April, Blakley, Ivory
Date Created: 2015
Subjects--Topical: Genomics, Antioxidants
Description: Background: Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable the breeding of berry varieties with enhanced he...

Title: Revisiting the use of graph centrality models in biological pathway analysis
Author: Loraine, Ann, Mostafavi, M. Taghi, Yeganeh, Pourya Naderi, Richardson, Christine
Date Created: 2020
Subjects--Topical: Biological systems, Graph theory
Description: The use of graph theory models is widespread in biological pathway analyses as it is often desired to evaluate the position of genes and proteins in their interaction networks of the biological systems. In this article, we argue that the common st...

Title: Salt tolerance response revealed by RNA-Seq in a diploid halophytic wild relative of sweet potato
Author: Loraine, Ann, Luo, Yan, Reid, Robert, Song, Bao-Hua
Date Created: 2017
Subjects--Topical: Genomics, Crop improvement
Description: Crop wild relatives harbor exotic and novel genetic resources, which hold great potential for crop improvement. Ipomoea imperati is a wild diploid relative of sweet potato with the capability of high salinity tolerance. We compared the transcripto...