Genome Technology
From GersteinInfo
Contents |
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."
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)
