GilsonTipBoxWe use computational and experimental methods to investigate gene expression and stress tolerance, using Arabidopsis thaliana as an experimental system.

We also collaborate with other groups, typically contributing bioinformatics and data analysis expertise.

The following sections describe research happening primarily in the Loraine Lab or in collaboration with other groups, as indicated.

Loraine Lab focus: Visualizing genomes

CoolGraphicWe develop software for research scientists to explore vast genomic data sets. Since 2008, we’ve been developing and maintaining Integrated Genome Browser, a desktop visualization application (written in Java) that more than 10,000 scientists worldwide have used to visualize their data.

Originally developed at Affymetrix for visual analysis of tiling array data, IGB is now freely available, open source software for visual analysis of data from from RNA-Seq, ChIP-Seq, and other *Seq experiments.

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Loraine Lab focus: Splicing under stress

Plants live their entire lives in one location and must acclimate to daily and seasonal fluctuations in temperature, water availability, and sunlight. Studying how cellular processes in plants adapt to environmental challenges will increase knowledge of how these processes function in all organisms, including humans.

We are studying how plants maintain and regulate pre-mRNA splicing, an essential process in both plants and animals, in the face of environmental stress.

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Collaborative project: Sequencing and annotating a highbush blueberry genome

blueberrybush-stressedWe worked with a consortium of researchers at the North Carolina Research Campus in Kannapolis to sequence, assemble, and annotate a diploid blueberry genome sequence.

All resources we created are published and freely available, including genome sequence data, gene model annotations, and an RNA-Seq experiment that profiled gene expression dynamics during berry fruit development and ripening.

Our role in the project is largely complete, but we continue to provide advice and support for researchers who want to use blueberry genomic resources in their experiments.

To get started using blueberry genome resources in your research, see:

Collaborative project: Regulation of floral growth and patterning in Arabidopsis thaliana

We are working with Beth Krizek of University of South Carolina, Lead Principal Investigator of NSF award titled Regulation of floral growth and patterning in Arabidopsis thaliana.

We are studying how a small family of related DNA-binding proteins control where and when flower organs form. By comparing data from RNA-Seq, ChIP-Seq, and genetic studies, we hope to identify target genes important in flower development.

For more information, see:

  • Krizek et al (2016) RNA-Seq links AINTEGUMENTA and AINTEGUMENTA-LIKE6 to cell wall remodeling and plant defense pathways in Arabidopsis

Collaborative project: Cytokinin signaling in Arabidopsis and rice

ZeatinWorking with lead Principal Investigator Joe Kieber at UNC Chapel Hill and C-PI Eric Schaller at Dartmouth University, we are investigating how cytokinin hormones regulate plant cell growth and differentiation.

Our most recent work focuses on cytokinin function in rice, focusing on how cytokinin influences panicle architecture, flower number, and thus grain production in this important staple crop.

For more information, see: