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
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
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
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- First Published July 27, 2011
Method
Genome-wide identification of conserved regulatory function in diverged sequences
- First Published May 31, 2011
Article
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- First Published November 3, 2009
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
LETTER
Thylacinus cynocephalus)" > The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)
- First Published January 12, 2009
LETTER
Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
- First Published September 25, 2008
12 | Genomes/Methods
Drosophila genomes" > Reliable prediction of regulator targets using 12 Drosophila genomes
- First Published November 7, 2007
12 | 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 | Genomes/Letter
Drosophila microRNAs" > Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
- First Published November 7, 2007
12 | Genomes/Letter
Drosophila genomes" > Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
- First Published November 7, 2007
12 | Genomes/Methods
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
- First Published November 7, 2007
RESOURCE
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
- First Published November 5, 2007
ARTICLE
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- First Published June 13, 2007
RESOURCE
A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
- First Published June 13, 2007
LETTER
Using genomic data to unravel the root of the placental mammal phylogeny
- First Published February 23, 2007
Methods
ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
- First Published October 19, 2006
LETTER
cis-regulatory modules" > Experimental validation of predicted mammalian erythroid cis-regulatory modules
- First Published October 12, 2006
RESOURCE
Galaxy: A platform for interactive large-scale genome analysis
- First Published September 16, 2005
ARTICLE
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- First Published July 15, 2005
Chicken Special/Resources
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
- First Published December 8, 2004
Chicken Special/Letters
Evolution and functional classification of vertebrate gene deserts
- First Published December 8, 2004
LETTER
Reconstructing large regions of an ancestral mammalian genome in silico
- First Published December 1, 2004
RESOURCE
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
- First Published April 1, 2004
Methods
Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
- First Published April 1, 2004
LETTER
Comparative Analysis of the α-Like Globin Clusters in Mouse, Rat, and Human Chromosomes Indicates a Mechanism Underlying Breaks in Conserved Synteny
- First Published April 1, 2004
ARTICLE
Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
- First Published April 1, 2004