Research
Gaps and complex structurally variant loci in phased genome assemblies
- First Published May 10, 2023
Research
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- First Published December 8, 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
Research
Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
- First Published August 20, 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
A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection
- First Published October 24, 2019
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
Method
Chromosome assembly of large and complex genomes using multiple references
- First Published October 19, 2018
Research
Mus caroli and Mus pahari genomes" > Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- First Published March 21, 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
Method
Co-expression networks reveal the tissue-specific regulation of transcription and splicing
- First Published October 11, 2017
Resource
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- First Published April 10, 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
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
- First Published February 12, 2015
Research
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers
- First Published February 2, 2015
Research
Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals
- First Published November 13, 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
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
- First Published November 21, 2013
Research
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
- First Published September 3, 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
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
- First Published September 5, 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
cis-regulatory modules" > Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- First Published July 10, 2012
Method
Estimation of alternative splicing variability in human populations
- First Published November 23, 2011
Research
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- First Published April 29, 2010
Research
A CTCF-independent role for cohesin in tissue-specific transcription
- First Published March 10, 2010
Letter
Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
- First Published April 28, 2009
Methods
Genome-wide nucleotide-level mammalian ancestor reconstruction
- First Published October 10, 2008
RESOURCE
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- First Published June 24, 2008
LETTER
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
- First Published February 7, 2008
ARTICLE
The landscape of histone modifications across 1% of the human genome in five human cell lines
- First Published June 13, 2007
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
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
LETTER
Leveraging the Mouse Genome for Gene Prediction in Human: From Whole-Genome Shotgun Reads to a Global Synteny Map
- First Published January 1, 2003
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
