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Model-based Analysis of ChIP-Seq (MACS)

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TLDR
This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
Abstract
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.

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Journal ArticleDOI

Chromatin accessibility: a window into the genome

TL;DR: The limitations and advantages of current genome-wide chromatin accessibility assays are discussed with especial attention on experimental precautions and sequence data analysis and the perspective on future improvements necessary for moving the field of chromatin profiling forward is concluded.
Journal ArticleDOI

The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming

TL;DR: It is shown in mice and humans that the histone H3 methylated Lys’27 (H3K27) demethylase Utx regulates the efficient induction, rather than maintenance, of pluripotency, and highlights the principle that molecular regulators mediating loss of repressive chromatin during in vivo germ cell reprograming can be co-opted during in vitro reprogramming towards ground state pluripOTency.
References
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Journal ArticleDOI

High-resolution profiling of histone methylations in the human genome.

TL;DR: High-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology are generated.
Journal ArticleDOI

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

TL;DR: A large-scale chromatin immunoprecipitation assay based on direct ultrahigh-throughput DNA sequencing was developed, which was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST) to 1946 locations in the human genome.
PatentDOI

Genome-wide location and function of dna binding proteins

TL;DR: In this paper, a method for identifying a set of genes where cell cycle regulator binding correlates with gene expression and identifying genomic targets of cell cycle transcription activators in living cells is also encompassed.
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