Visualizing genomes

IGB-start-screenScientists need software to explore and analyze genome data. To meet this need, we develop and maintain Integrated Genome Browser, a desktop visualization application (written in Java) used by thousands of researchers worldwide.

Originally developed in the early 2000s at Affymetrix for visualizing  tiling array data, IGB is now open source, free software you can use to visually analyze many other kinds of data, especially data from RNA-Seq, ChIP-Seq, and other *Seq experiments.

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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. It will also help us better understand and counteract negative effects of global warming on agriculture.

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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 Understanding the genetic basis for heat stress resilience during pollination

Pollination is the process by a which a pollen grain lands on the female part of a flower, germinates, and then transmits the male gametes (sperm) to the female gamete (the egg) via tube-like structure called a pollen tube. Once the pollen tube reaches the egg, it bursts, releasing sperm cells to fuse with the egg and another cell called a central cell. If the temperature is too hot, the pollen tube bursts too soon, and fertilization fails. If fertilization fails, the flower stays a flower forever and never develops into something edible –  a grain, fruit, or vegetable. Nearly every kind of plant product we consume comes from fertilization.

We are working with collaborators at Brown University, Wake Forest University, Arizona State University, and UNC Charlotte to understand why certain varieties of tomato can withstand high temperatures during pollination while others cannot. Our work thus far indicates that flavonoid compounds play a role, but there are likely many such pathways involved. Our goal is to identify and document these pathways and mechanisms that help pollination occur under adverse, high temperature conditions.

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Regulation of floral growth and patterning in Arabidopsis thaliana

We are working with Beth Krizek of University of South Carolina to understand the other end of fertilization – the flower.

Nearly every plant-based agricultural product – from grains to fruits and vegetables – originate as flowers. We are studying the basic science underlying how flowers develop.

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