Research
Epigenetic characterization of pseudogenes across human tissues
- First Published April 15, 2026
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
Research
Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division
- First Published September 11, 2013
Research
The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes
- First Published March 11, 2013
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
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- First Published September 5, 2012
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
Resource
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
- First Published February 7, 2011
Research
C. elegans" > Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
- First Published December 22, 2010
Article
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- First Published November 3, 2009
LETTER
Thylacinus cynocephalus)" > The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)
- First Published January 12, 2009
Methods
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
- First Published November 26, 2008
LETTER
Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
- First Published September 25, 2008
LETTER
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation
- First Published May 16, 2008
LETTER
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
- First Published February 7, 2008
RESOURCE
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
- First Published November 5, 2007
RESOURCE
A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
- First Published June 13, 2007
ARTICLE
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- 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
LETTER
Assessing the limits of genomic data integration for predicting protein networks
- First Published July 5, 2005
LETTER
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
- First Published May 2, 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
Methods
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
- First Published June 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
RESOURCE
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
- First Published March 1, 2004
LETTER
Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome
- First Published December 1, 2003
RESOURCE
GALA, a Database for Genomic Sequence Alignments and Annotations
- First Published April 1, 2003
METHODS
Spectral Biclustering of Microarray Data: Coclustering Genes and Conditions
- First Published April 1, 2003
LETTER
Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels
- First Published January 1, 2003
ARTICLE
Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution
- First Published January 1, 2003
LETTER
Systematic Learning of Gene Functional Classes From DNA Array Expression Data by Using Multilayer Perceptrons
- First Published November 1, 2002