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

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

(2010) Houtan Noushmehr et al.   CANCER CELL

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

(2010) A. E. Teschendorff et al.   GENOME RESEARCH

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

(2010) V. K. Rakyan et al.   GENOME RESEARCH

Sequence features that drive human promoter function and tissue specificity

(2010) J. M. Landolin et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Upregulation of c-MYC in cis through a Large Chromatin Loop Linked to a Cancer Risk-Associated Single-Nucleotide Polymorphism in Colorectal Cancer Cells

(2010) J. B. Wright et al.   MOLECULAR AND CELLULAR BIOLOGY

Mutation spectrum revealed by breakpoint sequencing of human germline CNVs

(2010) Donald F Conrad et al.   NATURE GENETICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Characterization of missing human genome sequences and copy-number polymorphic insertions

(2010) Jeffrey M Kidd et al.   NATURE METHODS

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

(2010) J. Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Common Genetic Variants near the Brittle Cornea Syndrome Locus ZNF469 Influence the Blinding Disease Risk Factor Central Corneal Thickness

(2010) Yi Lu et al.   PLoS Genetics

Meta Association of Colorectal Cancer Confirms Risk Alleles at 8q24 and 18q21

(2009) K. Curtin et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Genomic Antagonism between Retinoic Acid and Estrogen Signaling in Breast Cancer

(2009) Sujun Hua et al.   CELL

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

(2009) M. J. Fullwood et al.   GENOME RESEARCH

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

(2009) A. L. Brunner et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

CCCTC-Binding Factor and the Transcription Factor T-bet Orchestrate T Helper 1 Cell-Specific Structure and Function at the Interferon-γ Locus

(2009) Masayuki Sekimata et al.   IMMUNITY

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

(2009) Paul G. Giresi et al.   METHODS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Prepublication data sharing

(2009)   NATURE

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Multiple loci on 8q24 associated with prostate cancer susceptibility

(2009) Ali Amin Al Olama et al.   NATURE GENETICS

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer

(2009) Mark M Pomerantz et al.   NATURE GENETICS

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

(2009) Sari Tuupanen et al.   NATURE GENETICS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

My5C: web tools for chromosome conformation capture studies

(2009) Bryan R Lajoie et al.   NATURE METHODS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

ENCODE whole-genome data in the UCSC Genome Browser

(2009) K. R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Ensembl's 10th year

(2009) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome

(2009) S. C. J. Parker et al.   SCIENCE

Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus

(2009) Li Jia et al.   PLoS Genetics

Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification

(2008) Jainab Khatun et al.   BIOINFORMATICS

A Range of Cancers Is Associated with the rs6983267 Marker on Chromosome 8

(2008) D. Wokolorczyk et al.   CANCER RESEARCH

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

(2008) H. M. Petrykowska et al.   GENOME RESEARCH

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

(2008) G. E. Merrihew et al.   GENOME RESEARCH

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

(2008) E. Valen et al.   GENOME RESEARCH

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

Long-range chromosomal interactions and gene regulation

(2008) Adriana Miele et al.   Molecular BioSystems

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

(2008) Ina Poser et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS