Exploratory analysis of genomic segmentations with Segtools

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

The Genomedata format for storing large-scale functional genomics data

(2010) M. M. Hoffman et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nucleosome landscape and control of transcription in the human malaria parasite

(2010) N. Ponts et al.   GENOME RESEARCH

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

(2009) Paul G. Giresi et al.   METHODS

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS