Perspective
The impact of long-read sequencing on human population-scale genomics
- First Published April 14, 2025
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
Research
Gaps and complex structurally variant loci in phased genome assemblies
- First Published May 10, 2023
Resource
A high-resolution map of small-scale inversions in the gibbon genome
- First Published September 30, 2022
Research
Somatic structural variant formation is guided by and influences genome architecture
- First Published February 17, 2022
Resource
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- First Published September 19, 2019
Research
An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
- First Published January 3, 2019
Method
Co-expression networks reveal the tissue-specific regulation of transcription and splicing
- First Published October 11, 2017
Research
Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation
- First Published March 20, 2017
Resource
D. melanogaster modENCODE transcriptome annotation" > Comparative validation of the D. melanogaster modENCODE transcriptome annotation
- First Published July 1, 2014
Resource
Drosophila melanogaster" > Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
- First Published July 1, 2014
Research
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
- First Published January 15, 2014
Method
Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
- First Published December 5, 2013
Resource
Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
- First Published October 29, 2013
Method
Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
- First Published May 2, 2013
Research
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
- First Published April 17, 2013
Research
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
- First Published March 19, 2013
Resource
Drosophila melanogaster based on population-scale sequencing" > Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
- First Published December 6, 2012
Research
Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence
- First Published November 2, 2012
Resource
GENCODE: The reference human genome annotation for The ENCODE Project
- First Published September 5, 2012
Resource
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- First Published September 5, 2012
Method
Unified modeling of gene duplication, loss, and coalescence using a locus tree
- First Published January 23, 2012
Research
Drosophila and other metazoa" > Evidence of abundant stop codon readthrough in Drosophila and other metazoa
- First Published October 12, 2011
Method
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- First Published October 12, 2011
Method
New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes
- First Published October 12, 2011
Research
Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
- First Published August 23, 2011
Research
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- First Published July 27, 2011
Resource
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
- First Published June 4, 2009
Methods
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
- First Published November 26, 2008
12 Drosophila Genomes/Methods
Drosophila genomes" > Reliable prediction of regulator targets using 12 Drosophila genomes
- First Published November 7, 2007
12 Drosophila Genomes/Letter
Drosophila melanogaster using 12 fly genomes" > Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
- First Published November 7, 2007
12 Drosophila Genomes/Letter
Drosophila microRNAs" > Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
- First Published November 7, 2007
12 Drosophila Genomes/Letter
Drosophila genomes" > Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
- First Published November 7, 2007
12 Drosophila Genomes/Methods
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
- First Published November 7, 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
Structured RNAs in the ENCODE selected regions of the human genome
- First Published June 13, 2007
PERSPECTIVE
What is a gene, post-ENCODE? History and updated definition
- First Published June 13, 2007