An Interactive Analysis and Exploration Tool for Epigenomic Data

StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization

(2012) A. Lex et al.   COMPUTER GRAPHICS FORUM

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ENCODE whole-genome data in the UCSC Genome Browser: update 2012

(2011) K. R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

Pathline: A Tool For Comparative Functional Genomics

(2010) M. Meyer et al.   COMPUTER GRAPHICS FORUM

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

(2010) B. G. Hoffman et al.   GENOME RESEARCH

MulteeSum: A Tool for Comparative Spatial and Temporal Gene Expression Data

(2010) M Meyer et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Color coding

(2010) Bang Wong   NATURE METHODS

Visualizing genomes: techniques and challenges

(2010) Cydney B Nielsen et al.   NATURE METHODS

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The History of the Cluster Heat Map

(2009) Leland Wilkinson et al.   AMERICAN STATISTICIAN

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

(2008) Gary Hon et al.   PLoS Computational Biology