<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Sorry for re-sending this. I'm not sure if all of you get my email because I used the wrong email to send it for the first time.</div><div><br></div><div>We will have a journal club tomorrow at noon at 2228 BPS.</div><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Owen Pierce <<a href="mailto:opierce@gmail.com">opierce@gmail.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">March 18, 2011 2:10:45 PM EDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Likit Preeyanon <<a href="mailto:preeyano@msu.edu">preeyano@msu.edu</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: GED next week</b><br></span></div><br>Hey Likit,<br><br>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: <a href="http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html">http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html</a><br>
<br>Abstract:<br>High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation<sup><a href="http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html#ref1" title="Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613-619 (2008)." id="ref-link-1">1</a>, <a href="http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html#ref2" title="Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008)." id="ref-link-2">2</a>, <a href="http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html#ref3" title="Nagalakshmi, U., Wang, Z., Waern, K., Shou, C. & Raha, D. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-1349 (2008)." id="ref-link-3">3</a></sup>.
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.<br><br>Cheers,<br><br>Owen<br><br><div class="gmail_quote">On Fri, Mar 18, 2011 at 1:52 PM, Likit Preeyanon <span dir="ltr"><<a href="mailto:preeyano@msu.edu">preeyano@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi, Owen<br>
<br>
I just got the email from Titus about the seminar about data sharing talked by Ian Dworkin next Wed. at noon.<br>
I think this seminar is good for all of us, especially those who work on bioinformatics.<br>
Would you mind if I ask you to do your presentation the week after next week so we can join the seminar?<br>
<br>
Thanks.</blockquote></div><br><div style="visibility: hidden; left: -5000px;" id="avg_ls_inline_popup"></div><style type="text/css">#avg_ls_inline_popup{position: absolute;z-index: 9999;padding: 0px 0px;margin-left: 0px;margin-top: 0px;overflow: hidden;word-wrap: break-word;color: black;font-size: 10px;text-align: left;line-height: 130%;}</style>
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