Research
Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources
- First Published May 14, 2026
Resource
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
- First Published July 1, 2024
Research
Gaps and complex structurally variant loci in phased genome assemblies
- First Published May 10, 2023
Method
A complete pedigree-based graph workflow for rare candidate variant analysis
- First Published April 28, 2022
Research
A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
- First Published March 24, 2022
Research
Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- First Published October 19, 2021
Resource
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
- First Published March 4, 2020
Resource
The full-length transcriptome of C. elegans using direct RNA sequencing
- First Published February 5, 2020
Method
Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
- First Published June 8, 2018
Method
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
- First Published February 4, 2016
Resource
Alignathon: a competitive assessment of whole-genome alignment methods
- First Published October 1, 2014
Resource
GENCODE: The reference human genome annotation for The ENCODE Project
- First Published September 5, 2012
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
Resource
Windshield splatter analysis with the Galaxy metagenomic pipeline
- First Published October 9, 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
Methods
Targeted discovery of novel human exons by comparative genomics
- First Published November 7, 2007
RESOURCE
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
- First Published November 5, 2007
LETTER
Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion
- First Published September 4, 2007
ARTICLE
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- First Published June 13, 2007
LETTER
Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
- 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
Methods
ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
- First Published October 19, 2006
LETTER
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
LETTER
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
- First Published July 15, 2005
ARTICLE
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- First Published July 15, 2005
RESOURCE
Exploring relationships and mining data with the UCSC Gene Sorter
- First Published May 2, 2005
LETTER
Reconstructing large regions of an ancestral mammalian genome in silico
- First Published December 1, 2004
LETTER
Analysis of Human mRNAs With the Reference Genome Sequence Reveals Potential Errors, Polymorphisms, and RNA Editing
- First Published October 15, 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
ARTICLE
Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
- First Published April 1, 2004
ARTICLE
Comparative Recombination Rates in the Rat, Mouse, and Human Genomes
- First Published April 1, 2004
ARTICLE
Identification and Characterization of Multi-Species Conserved Sequences
- First Published December 1, 2003
ARTICLE
Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution
- First Published January 1, 2003
METHODS
Assembly of the Working Draft of the Human Genome with GigAssembler
- First Published August 16, 2001
