[ged] Canceled: We have journal club tomorrow at noon.

[Tasneem Pierce]

Hi all,

Owen is sick today and can't do journal club today.  I think we should
cancel it.

-neem

On Wed, Mar 30, 2011 at 12:36 AM, Likit Preeyanon <preeyano at msu.edu> wrote:

> Please meet at noon at 2228 BPS. Owen is talking about the paper below.
>
> cheers.
>
> Begin forwarded message:
>
> *From: *Likit Preeyanon <preeyano at msu.edu>
> *Date: *March 25, 2011 11:05:33 AM EDT
> *To: *ged-jclub at lists.idyll.org
> *Subject: **[ged] paper for GED next week*
>
> 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<http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html#ref1>,
> 2 <http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html#ref2>, 3<http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html#ref3>.
> 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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