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Resource

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

  • First Published September 5, 2012
Research

Widespread plasticity in CTCF occupancy linked to DNA methylation

  • First Published September 5, 2012
Perspective

What does our genome encode?

  • First Published September 5, 2012
Method

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

  • First Published September 5, 2012
Method

Predicting cell-type–specific gene expression from regions of open chromatin

  • First Published September 5, 2012
Research

RNA editing in the human ENCODE RNA-seq data

  • First Published September 5, 2012
Method

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

  • First Published September 5, 2012
Resource

GENCODE: The reference human genome annotation for The ENCODE Project

  • First Published September 5, 2012
Method

Sequence and chromatin determinants of cell-type–specific transcription factor binding

  • First Published September 5, 2012
Research

A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells

  • First Published September 5, 2012
Research

Discovery of hundreds of mirtrons in mouse and human small RNA data

  • First Published September 5, 2012
Research

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

  • First Published September 5, 2012
Research

Long noncoding RNAs are rarely translated in two human cell lines

  • First Published September 5, 2012
Resource

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

  • First Published September 5, 2012
Method

Linking disease associations with regulatory information in the human genome

  • First Published September 5, 2012
Commentary

Decoding the human genome

  • First Published September 5, 2012
Resource

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

  • First Published September 5, 2012
Research

Personal and population genomics of human regulatory variation

  • First Published September 5, 2012
Research

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

  • First Published September 5, 2012
Research

Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors

  • First Published September 4, 2012
Research

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations

  • First Published September 4, 2012
Research

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

  • First Published August 30, 2012
Method

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

  • First Published August 30, 2012
Research

Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans

  • First Published August 23, 2012
Research

cis-trans regulation in the evolution of mouse gene expression" > Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

  • First Published August 23, 2012
Research

Wolbachia genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis" > Analysis of gene expression from the Wolbachia genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis

  • First Published August 23, 2012
Research

IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation" > A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation

  • First Published August 16, 2012
Resource

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

  • First Published August 14, 2012
Research

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

  • First Published August 9, 2012
Method

Copy-number-aware differential analysis of quantitative DNA sequencing data

  • First Published August 9, 2012
Research

Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant

  • First Published July 26, 2012
Research

Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq

  • First Published July 26, 2012
Method

Finished bacterial genomes from shotgun sequence data

  • First Published July 24, 2012
Resource

A fine scale phenotype–genotype virulence map of a bacterial pathogen

  • First Published July 23, 2012
Research

A functional methylome map of ulcerative colitis

  • First Published July 23, 2012
Research

Noise–mean relationship in mutated promoters

  • First Published July 20, 2012
Research

Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth

  • First Published July 18, 2012
Method

Paired-end sequencing of Fosmid libraries by Illumina

  • First Published July 16, 2012
Research

Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence

  • First Published July 16, 2012
Resource

Incorporating RNA-seq data into the zebrafish Ensembl genebuild

  • First Published July 12, 2012
Research

cis-regulatory modules" > Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

  • First Published July 10, 2012
Resource

C. briggsae transcriptome" > RNA-seq analysis of the C. briggsae transcriptome

  • First Published July 6, 2012
Method

Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease

  • First Published July 5, 2012
Research

Drosophila genome" > Nature and function of insulator protein binding sites in the Drosophila genome

  • First Published July 5, 2012
Research

Conservation of replication timing reveals global and local regulation of replication origin activity

  • First Published July 5, 2012
Method

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

  • First Published July 3, 2012
Resource

MuSiC: Identifying mutational significance in cancer genomes

  • First Published July 3, 2012
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