[ged] paper for GED next week

[Likit Preeyanon]

Hi, 

Owen is talking about this paper next week. Find the detail below. :)

Begin forwarded message:

> From: Owen Pierce <opierce at gmail.com>
> Date: March 18, 2011 2:10:45 PM EDT
> To: Likit Preeyanon <preeyano at msu.edu>
> Subject: Re: GED next week
> 
> Hey Likit,
> 
> Definitely.  I selected a paper for my presentation - Transcript assembly and quantification by rNA-seq reveals unannotated transcripts and isoform switching during cell differentiation.  You can find it here: http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html
> 
> Abstract:
> High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation1, 2, 3. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed >430 million paired 75-bp RNA-Seq reads from a mouse myoblast cell line over a differentiation time series. We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Over the time series, 330 genes showed complete switches in the dominant transcription start site (TSS) or splice isoform, and we observed more subtle shifts in 1,304 other genes. These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.
> 
> Cheers,
> 
> Owen
> 
> On Fri, Mar 18, 2011 at 1:52 PM, Likit Preeyanon <preeyano at msu.edu> wrote:
> Hi, Owen
> 
> I just got the email from Titus about the seminar about data sharing talked by Ian Dworkin next Wed. at noon.
> I think this seminar is good for all of us, especially those who work on bioinformatics.
> Would you mind if I ask you to do your presentation the week after next week so we can join the seminar?
> 
> Thanks.
> 

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