Method
Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
- First Published May 24, 2022
Research
Enhancers with tissue-specific activity are enriched in intronic regions
- First Published July 21, 2021
Corrigendum
Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping
- First Published September 14, 2020
Resource
A limited set of transcriptional programs define major cell types
- First Published July 29, 2020
Resource
Functional annotation of human long noncoding RNAs via molecular phenotyping
- First Published July 27, 2020
Resource
Dynamics of microRNA expression during mouse prenatal development
- First Published October 23, 2019
Research
Drosophila regeneration" > Damage-responsive elements in Drosophila regeneration
- First Published November 20, 2018
Research
Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
- First Published August 10, 2018
Corrigendum
Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- First Published December 1, 2017
Research
Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha
- First Published April 6, 2017
Corrigendum
Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- First Published November 1, 2016
Research
Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
- First Published July 20, 2015
Research
Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
- First Published May 29, 2015
Research
Genome accessibility is widely preserved and locally modulated during mitosis
- First Published November 4, 2014
Research
Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- First Published October 7, 2014
Research
Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape
- First Published June 24, 2014
Research
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
- First Published November 21, 2013
Research
DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
- First Published May 8, 2013
Research
A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity
- First Published April 1, 2013
Research
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
- First Published March 12, 2013
Resource
Dynamic DNA methylation across diverse human cell lines and tissues
- First Published January 16, 2013
Resource
GENCODE: The reference human genome annotation for The ENCODE Project
- 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
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
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
- First Published September 5, 2012
Method
Predicting cell-type–specific gene expression from regions of open chromatin
- 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
Research
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
- First Published February 2, 2012
Method
Estimation of alternative splicing variability in human populations
- First Published November 23, 2011
Resource
High-resolution mapping of open chromatin in the rice genome
- First Published November 22, 2011
Research
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
- First Published November 16, 2011
Research
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- First Published July 27, 2011
Resource
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
- First Published July 12, 2011
Method
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
- First Published November 24, 2010
Letter
Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns
- First Published February 27, 2009
ARTICLE
Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
- First Published June 13, 2007
ARTICLE
The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
- First Published June 13, 2007
LETTER
Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- First Published June 13, 2007
LETTER
Structured RNAs in the ENCODE selected regions of the human genome
- First Published June 13, 2007
Methods
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
- First Published December 12, 2005
LETTER
Tandem chimerism as a means to increase protein complexity in the human genome
- First Published December 12, 2005
Chicken Special/Letters
Comparison of splice sites in mammals and chicken
- First Published December 8, 2004
LETTER
Comparative Analysis of Amino Acid Repeats in Rodents and Humans
- First Published April 1, 2004
METHODS
SGP-1: Prediction and Validation of Homologous Genes Based on Sequence Alignments
- First Published September 1, 2001
LETTER
Kua, a Newly Identified Gene" > Fusion of the Human Gene for the Polyubiquitination Coeffector UEV1 with Kua, a Newly Identified Gene
- First Published November 8, 2000
METHODS
An Assessment of Gene Prediction Accuracy in Large DNA Sequences
- First Published October 1, 2000