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
We 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.
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.
Collaborative project: Sequencing and annotating a highbush blueberry genome
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:
- IGB Quickload site for the blueberry genome (contains genome sequence, processed RNA-Seq data, gene model annotations)
- Public git repository containing data analysis code used in the blueberry genome paper Gupta et al (2015). Also contains Gene Ontology annotations and gene model annotations
- Gupta et al (2015) 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. PubMed
- Slides from RNA-Seq analysis of blueberry fruit identifies candidate genes involved in ripening and secondary metabolism, presented at the Plant Animal Genome Conference in 2014
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
Working 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:
- Abstract for NSF Plant Genome award (PI Joe Kieber) Genomic approaches to understanding cytokinin signaling and function in rice
- Abstract for NSF Arabidopsis 2010 award (PI Joe Kieber) Analysis of the cytokinin-regulated transcriptional network