https://info.gersteinlab.org/index.php?action=history&feed=atom&title=Genome_TechnologyGenome Technology - Revision history2026-05-14T06:30:24ZRevision history for this page on the wikiMediaWiki 1.42.6https://info.gersteinlab.org/index.php?title=Genome_Technology&diff=94&oldid=prevInfoadmin: Created page with '== Recent Publications == ;'''Integrating sequencing technologies in personal genomics - optimal low cost reconstruction of structural variants.''' :J Du, RD Bjornson, ZD Zhang,…'2010-06-10T13:55:45Z<p>Created page with '== Recent Publications == ;'''Integrating sequencing technologies in personal genomics - optimal low cost reconstruction of structural variants.''' :J Du, RD Bjornson, ZD Zhang,…'</p>
<p><b>New page</b></p><div>== Recent Publications ==<br />
<br />
;'''Integrating sequencing technologies in personal genomics - optimal low cost reconstruction of structural variants.'''<br />
:J Du, RD Bjornson, ZD Zhang, Y Kong, M Snyder, M Gerstein (2009) PLoS Computational Biology, in press.<br />
:[http://archive.gersteinlab.org/proj/ReSeqSim/ Website]<br />
<br />
;'''PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.'''<br />
:J Rozowsky, G Euskirchen, RK Auerbach, ZD Zhang, T Gibson, R Bjornson, N Carriero, M Snyder, MB Gerstein (2009) ''Nat Biotechnol'' 27: 66-75.<br />
:[http://papers.gersteinlab.org/papers/PeakSeq/index-all.html More Info]<br />
<br />
;'''Mismatch oligonucleotides in human and yeast - guidelines for probe design on tiling microarrays.'''<br />
:M Seringhaus, J Rozowsky, T Royce, U Nagalakshmi, J Jee, M Snyder, M Gerstein (2008) ''BMC Genomics'' 9: 635.<br />
:[http://papers.gersteinlab.org/papers/mismatch/index-all.html More Info]<br />
<br />
;'''Modeling ChIP sequencing in silico with applications.'''<br />
:ZD Zhang, J Rozowsky, M Snyder, J Chang, M Gerstein (2008) ''PLoS Comput Biol'' 4: e1000158. <br />
:[http://papers.gersteinlab.org/papers/chip-seq-simu/index-all.html More Info]<br />
<br />
== Websites ==<br />
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=== Yale Chip-seq Data Pipeline ===<br />
Software download <br />
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[http://array.mbb.yale.edu/pipeline/illumina.html Illumina pipeline] (wrapper for Illumina pipeline)<br />
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[http://array.mbb.yale.edu/pipeline/scoring.html Chip-seq scoring pipeline] (runs PeakSeq)<br />
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=== YEP: Yale ENCODE Project ===<br />
<br />
<blockquote><br />
<p> <br />
``The Yale Encode Project (YEP) is a member of the NIH/NHGRI Encode Consortium. The goal of the consortium is to obtain a coordinated and comprehensive picture of the transcribed regions and factors that regulate or affect transcriptional activity over the genomic regions selected as part of the ENCODE (ENCyclopedia Of DNA Elements) project."<br />
</p><br />
<p><br />
-- http://encode.gersteinlab.org/<br />
</p><br />
</blockquote><br />
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<br />
==Software==<br />
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'''PEMEr'''<br />
<br />
A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.<br />
<br />
Link: http://papers.gersteinlab.org/papers/pemer<br />
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<br />
'''breakptr'''<br />
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Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.<br />
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Link: http://papers.gersteinlab.org/papers/breakptr<br />
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'''BreakSeq'''<br />
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Link: http://sv.gersteinlab.org/breakseq<br />
<br />
<br />
<br />
'''Sequencing vs Arrays'''<br />
<br />
Coming soon...<br />
<br />
== Summaries of Some Softwares from Other Groups in Bioinformatics ==<br />
* [http://wiki.gersteinlab.org/labinfo/Aligners Aligners] (labinfo link)<br />
* [http://wiki.gersteinlab.org/labinfo/SOLiD_Software_Tools SOLiD Software Tools] (labinfo link)</div>Infoadmin