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[Arabidopsis] Araport/IAIC Workshop at PAG

Reddy,Anireddy via arab-gen%40net.bio.net (by Anireddy.Reddy from colostate.edu)
Fri Nov 20 20:40:36 EST 2015


Dear Dr. Town and Dr. Meyers,

My collaborators (Michael Hamilton and Dr. Asa Ben-Hur) from Computer Science Dept. have developed a new tool to detect differential intron retention. We provided a brief summary about iDiffIR below.   We think it would be a nice tool to present at the Araport workshop. Mike or Asa is willing to present this at your workshop.  Please let us know if you would be interested in including this tool in your workshop.

If you would like us to present this workshop let us know how to submit our abstract.  Thanks, Reddy



"Deep sequencing of mRNA (RNA-seq) is widely used for the study of gene expression and alternative splicing.  Intron retention (IR) is the dominant form of alternative splicing in plants and no existing tool is specifically designed to detect differential intron retention across samples.  We developed a method called iDiffIR that detects differential intron retention using an interpretable statistic; it can be used when no replicates are available thanks to the use of a novel measure of intragenic read depth variability.  We have used iDiffIR in multiple datasets from a variety of plant and animal species including Arabidopsis, and demonstrated the biological relevance of its predictions.  iDiffIR is publicly available athttps://bitbucket.org/comp_bio/idiffir and would be a useful resource for the plant research community."


On Nov 20, 2015, at 10:22 AM, Town, Christopher D. <cdtown from jcvi.org<mailto:cdtown from jcvi.org>> wrote:

The Araport/IAIC Workshop at PAG aims to focus on ongoing developments in Araport, including new data sets, new tools, apps etc.
Under the broader remit of the IAIC (which gave rise to the Araport project), it can also highlight other developments in Arabidopsis Informatics outside Araport.

At present, we have some possible speaker slots available. The workshop is 12.50-3.00 pm on Monday Jan 11, 2016 and each time slot would be 15-20 min.

If you have developed some Arabidopsis-related tool, app or widget that you would like to present, please let us know right away.

Best wishes to all ...

Chris Town and Blake Meyers


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