Genome Technology

From GersteinInfo

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Latest revision as of 13:55, 10 June 2010

Contents 1 Recent Publications 2 Websites 2.1 Yale Chip-seq Data Pipeline 2.2 YEP: Yale ENCODE Project 3 Software 4 Summaries of Some Softwares from Other Groups in Bioinformatics

Recent Publications

Integrating sequencing technologies in personal genomics - optimal low cost reconstruction of structural variants.

J Du, RD Bjornson, ZD Zhang, Y Kong, M Snyder, M Gerstein (2009) PLoS Computational Biology, in press.

Website

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

J Rozowsky, G Euskirchen, RK Auerbach, ZD Zhang, T Gibson, R Bjornson, N Carriero, M Snyder, MB Gerstein (2009) Nat Biotechnol 27: 66-75.

More Info

Mismatch oligonucleotides in human and yeast - guidelines for probe design on tiling microarrays.

M Seringhaus, J Rozowsky, T Royce, U Nagalakshmi, J Jee, M Snyder, M Gerstein (2008) BMC Genomics 9: 635.

More Info

Modeling ChIP sequencing in silico with applications.

ZD Zhang, J Rozowsky, M Snyder, J Chang, M Gerstein (2008) PLoS Comput Biol 4: e1000158.

More Info

Websites

Yale Chip-seq Data Pipeline

Software download

Illumina pipeline (wrapper for Illumina pipeline)

Chip-seq scoring pipeline (runs PeakSeq)

YEP: Yale ENCODE Project

``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."

-- http://encode.gersteinlab.org/

Software

PEMEr

A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.

Link: http://papers.gersteinlab.org/papers/pemer

breakptr

Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.

Link: http://papers.gersteinlab.org/papers/breakptr

BreakSeq

Link: http://sv.gersteinlab.org/breakseq

Sequencing vs Arrays

Coming soon...

Summaries of Some Softwares from Other Groups in Bioinformatics

• Aligners (labinfo link)
• SOLiD Software Tools (labinfo link)