Resource
An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- First Published December 5, 2024
Method
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
- First Published December 14, 2023
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
Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
- First Published April 5, 2017
Research
Pangolin genomes and the evolution of mammalian scales and immunity
- First Published August 10, 2016
Research
Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
- First Published July 20, 2015
Research
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
- First Published November 21, 2013
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
Research
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
- 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
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb
- First Published March 15, 2012
Method
Estimation of alternative splicing variability in human populations
- First Published November 23, 2011
Method
C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data" > Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
- First Published December 22, 2010
Research
Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing
- First Published October 29, 2010
Method
Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
- First Published April 29, 2010
LETTER
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
- First Published June 13, 2007
LETTER
Structured RNAs in the ENCODE selected regions of the human genome
- First Published June 13, 2007
Methods
Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
- First Published June 13, 2007
LETTER
Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- 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
ARTICLE
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
- 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
PERSPECTIVE
What is a gene, post-ENCODE? History and updated definition
- First Published June 13, 2007
Methods
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
- First Published November 21, 2006
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
RESOURCE
Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon
- First Published October 1, 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
