Research
Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources
- First Published May 14, 2026
Research
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- First Published April 10, 2025
Method
MCHelper automatically curates transposable element libraries across eukaryotic species
- First Published December 9, 2024
Method
Ultrafast genome-wide inference of pairwise coalescence times
- First Published August 10, 2023
Research
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- First Published December 8, 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
Resource
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- First Published April 10, 2017
Method
Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes
- First Published December 16, 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
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
Resource
Assemblathon 1: A competitive assessment of de novo short read assembly methods
- First Published September 16, 2011
Research
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- First Published July 27, 2011
Method
Revealing the genetic structure of a trait by sequencing a population under selection
- First Published March 21, 2011
Resource
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
- First Published October 27, 2010
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
RESOURCE
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
- First Published November 24, 2008
RESOURCE
Mapping short DNA sequencing reads and calling variants using mapping quality scores
- First Published August 19, 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
METHODS
GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming
- First Published September 1, 2002
LETTER
Alfresco—A Workbench for Comparative Genomic Sequence Analysis
- First Published August 1, 2000
METHODS
GeneWise in the Drosophila Annotation Experiment" > Using GeneWise in the Drosophila Annotation Experiment
- First Published April 1, 2000
LETTER
Comparative Analysis of Noncoding Regions of 77 Orthologous Mouse and Human Gene Pairs
- First Published September 1, 1999
