Research
Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources
- First Published May 14, 2026
Research
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- First Published December 5, 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
Research
High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma
- First Published June 27, 2019
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
Method
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
- First Published July 24, 2014
Method
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- First Published June 26, 2013
Method
Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
- First Published June 26, 2013
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
Extensive relationship between antisense transcription and alternative splicing in the human genome
- First Published June 30, 2011
Research
Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver
- First Published June 15, 2010
Methods
Next-generation tag sequencing for cancer gene expression profiling
- First Published June 18, 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
In-depth characterization of the microRNA transcriptome in a leukemia progression model
- First Published October 10, 2008
LETTER
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
- First Published September 11, 2008
Methods
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
- First Published February 19, 2008
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
LETTER
Caenorhabditis elegans operons" > Identification and analysis of internal promoters in Caenorhabditis elegans operons
- First Published August 21, 2007
ARTICLE
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- First Published June 13, 2007
Methods
Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines
- First Published November 29, 2006
LETTER
Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla
- First Published December 19, 2005
Methods
Simple, robust methods for high-throughput nanoliter-scale DNA sequencing
- First Published September 16, 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
Methods
Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
- First Published October 15, 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
ARTICLE
Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
- First Published April 1, 2004
RESOURCE
Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics
- First Published February 12, 2004
ARTICLE
Identification and Characterization of Multi-Species Conserved Sequences
- First Published December 1, 2003
RESOURCE
Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps
- First Published June 1, 2003