Seems I can't go a week without finding a paper describing a new ChIP-Seq analytical tool, so I thought it would be helpful to put together a list of a few of the most interesting papers in this area.
For those not familiar with ChIP-Seq, it involves massively parallel sequencing of nucleic acids recovered from a chromatin-immunoprecipitation (ChIP). ChIP uses an antibody to capture protein that has been previously crosslinked to DNA in its native state. Thus, ChIP-Seq allows sequencing of all DNA that a specific protein physically interacts with within the cell.
There are quite a few studies recently which describe either a software tool, and/or an analytical framework for working with this type of data. The difficulty and thus the plethora of approaches is using the read density information to "call peaks" or more precisely, statistically significant ChIP-Seq binding sites.
Recent papers I have found helpful are below, in reverse chronological order. Please accept my apologies in advance if I've missed your favorite tool.
November
October
September
August
Hopefully those are useful. I'll post up my experiences with some of these tools soon, and would love to hear yours.
For those not familiar with ChIP-Seq, it involves massively parallel sequencing of nucleic acids recovered from a chromatin-immunoprecipitation (ChIP). ChIP uses an antibody to capture protein that has been previously crosslinked to DNA in its native state. Thus, ChIP-Seq allows sequencing of all DNA that a specific protein physically interacts with within the cell.
There are quite a few studies recently which describe either a software tool, and/or an analytical framework for working with this type of data. The difficulty and thus the plethora of approaches is using the read density information to "call peaks" or more precisely, statistically significant ChIP-Seq binding sites.
Recent papers I have found helpful are below, in reverse chronological order. Please accept my apologies in advance if I've missed your favorite tool.
November
- F-Seq: a feature density estimator for high-throughput sequence tags., Duke University. F-Seq Project Homepage
- CisGenome: An integrated software system for analyzing ChIP-chip and ChIP-seq data., Johns Hopkins. CisGenome homepage
October
- ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome., UC San Diego. ChromaSig homepage
- An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data., Genome Institute of Singapore. ChiPDiff Homepage
September
- Model-based Analysis of ChIP-Seq (MACS)., Dana-Farber Cancer Institute and Harvard School of Public Health. MACS Homepage
- A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology., Indiana University School of Medicine
- Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data., NHLBI, NIH. SISSRs Homepage
August
- Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data., Stanford University Medical Center (woohoo!), QuEST Homepage
- FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology., BCGSC (First author is our very own apfejes!). Vancouver Short Read Analysis Package Homepage. Version 3.2 is out.
Hopefully those are useful. I'll post up my experiences with some of these tools soon, and would love to hear yours.
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