nucleosome positioning

PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads

We introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing tools. In contrast to other approaches that …

Computational Methods for Exploring Nucleosome Dynamics

Nucleosomes are the basic elements of DNA chromatin structure. Not only they control DNA packaging but also play a critical role in gene regulation by allowing physical access to transcription factors. In addition to providing the positions of …

DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum.

In eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors. The human malaria parasite Plasmodium falciparum encodes relatively few transcription factors, while …

NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model

**Motivation:** Nucleosomes are the basic elements of chromatin structure. They control the packaging of DNA and play a critical role in gene regulation by allowing physical access to transcription factors. The advent of second-generation sequencing …