Method
Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
- First Published April 8, 2026
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
Method
An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization
- First Published October 27, 2016
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
Research
Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence
- First Published November 2, 2012
Research
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
- First Published September 5, 2012
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
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
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- First Published July 27, 2011
Research
Transcriptional consequences of genomic structural aberrations in breast cancer
- First Published April 5, 2011
Research
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
- First Published April 5, 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
Next-Generation DNA Sequencing/Review
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- First Published April 1, 2009
LETTER
Evolution of the mammalian transcription factor binding repertoire via transposable elements
- First Published August 5, 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
LETTER
Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
- First Published June 13, 2007
LETTER
Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- 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