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	<title>Olivier Elemento's weblog</title>
	<link>http://oelemento.wordpress.com</link>
	<description>Olivier's science weblog</description>
	<lastBuildDate>Sun, 26 Jul 2009 23:02:43 +0000</lastBuildDate>
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	<language>en</language>
	
	<item>
		<title>ChIPseeqer</title>
		<description><![CDATA[We have just released Version 1.0 of ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data. ChIPseeqer contains a very fast and accurate ChIP-seq peak detection program, as well as several others tools to facilitate regulatory element discovery using FIRE, pathway analysis using iPAGE and conservation analyses.
http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml
       <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=125&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/07/26/chipseeqer/</link>
			</item>
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		<title>Rice Genome now supported in FIRE</title>
		<description><![CDATA[Following a request from somebody at Virginia Tech, we have added Rice to the list of organisms supported by FIRE. We used the following gene identifiers:
LOC_Os11g37320
LOC_Os01g12410
LOC_Os01g25110
LOC_Os02g07360
LOC_Os11g45360
etc.
To analyze Rice expression data, you&#8217;ll need to download FIRE, then download the rice_data.zip file. The download site is http://tavazoielab.princeton.edu/FIRE/
       <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=122&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/07/26/rice-genome-now-supported-in-fire/</link>
			</item>
	<item>
		<title>Large Scale Analysis of Transcription Factors Recognition Sites</title>
		<description><![CDATA[In an amazing paper published in Science Express, Bulyk, Hughes and colleagues haved used protein-binding microarrays to determine the DNA-binding specificities of 104 mouse transcription factors.
The most interesting finding of the study is that nearly half of all TF seem to be able to bind two distinct types of sequences. For example, Hnf4a appears to [...]<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=116&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/05/19/large-scale-analysis-of-transcription-factors-recognition-sites/</link>
			</item>
	<item>
		<title>The BCL6 transcriptional program features repression of multiple oncogenes in primary B-cells and is deregulated in DLBCL</title>
		<description><![CDATA[This is the title of our latest paper in Blood, which is also my first one at Weill Cornell and my first one as (joint) corresponding author.
http://bloodjournal.hematologylibrary.org/cgi/content/abstract/blood-2008-12-193037v1
       <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=109&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/03/23/the-bcl6-transcriptional-program-features-repression-of-multiple-oncogenes-in-primary-b-cells-and-is-deregulated-in-dlbcl/</link>
			</item>
	<item>
		<title>Mining the Deep Web</title>
		<description><![CDATA[There&#8217;s a pretty interesting article in the NY Times about the Deep Web, that is, the data that is stored in databases and available through web interfaces. The article mentions some of the strategies that scientists (and web search companies) use to mine the Deep Web. Essentially, these strategies involve making a first few queries [...]<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=105&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/02/23/mining-the-deep-web/</link>
			</item>
	<item>
		<title>Poplar genome now supported in FIRE</title>
		<description><![CDATA[My lab doesn&#8217;t work on plants, but following a request from somebody in Malcom Campbell&#8217;s lab at U of Toronto, I&#8217;ve just added the Poplar to the list of organisms supported by FIRE.
The genome data comes from http://genome.jgi-psf.org/Poptr1_1/
To analyze Poplar expression data, you&#8217;ll need to download FIRE, then download the poplar_data.zip file from http://tavazoielab.princeton.edu/FIRE/
I tested [...]<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=96&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/02/05/poplar-genome-now-supported-by-fire/</link>
			</item>
	<item>
		<title>The US Senate wants to increase NIH funding</title>
		<description><![CDATA[Update Feb 18th. Here is more information about how the stimulus money is going to be spent, from Nature :
&#8220;National Institutes of Health:  $7.4 billion divided among the agency&#8217;s scientific institutes and centres will fund grants from a backlog of 14,000 investigator-initiated &#8216;R01&#8242; grants already reviewed and categorized as &#8220;highly meritorious&#8221;. It will also [...]<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=94&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/02/04/the-us-senate-wants-to-increase-nih-funding/</link>
			</item>
	<item>
		<title>New Journal: Genome Medicine</title>
		<description><![CDATA[The very first issue of this exciting new journal is out:
http://genomemedicine.com/
       <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=90&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/01/29/new-journal-genome-medicine/</link>
			</item>
	<item>
		<title>Seminars in Computational and Systems Biomedicine at the ICB</title>
		<description><![CDATA[I am co-organizing the new Seminars in Computational and Systems Medicine. David Botstein was our inaugural speaker and both talking to him and hearing his seminar about the coordination of growth rate, cell cycle, stress response and metabolic activity in yeast  has been a fantastic experience (his seminar was much more thought-provoking than it sounds).
We [...]<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=86&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/01/25/seminars-in-computational-and-systems-biomedicine-at-the-icb/</link>
			</item>
	<item>
		<title>Discovering gene fusions in cancer using deep sequencing</title>
		<description><![CDATA[Chinnaiyan and colleagues have combined 454 and Solexa sequencing to identify transcripts resulting from gene fusion, both in cancer cell lines and primary tumors. The approach relies on deep sequencing the cancer transcriptome and looking for reads that show partial alignment to exon boundaries from different genes. When applied to prostate cancer cell lines and [...]<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=oelemento.wordpress.com&blog=22851&post=82&subd=oelemento&ref=&feed=1" />]]></description>
		<link>http://oelemento.wordpress.com/2009/01/15/discovering-gene-fusions-in-cancer-using-deep-sequencing/</link>
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