Method
Accurate sequencing of DNA motifs able to form alternative (non-B) structures
- First Published July 11, 2023
Research
Gaps and complex structurally variant loci in phased genome assemblies
- First Published May 10, 2023
Research
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- First Published December 8, 2022
Research
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
- First Published June 29, 2021
Research
Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
- First Published August 20, 2020
Resource
A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection
- First Published October 24, 2019
Research
Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
- First Published November 6, 2018
Method
Chromosome assembly of large and complex genomes using multiple references
- First Published October 19, 2018
Research
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- First Published March 21, 2018
Corrigendum
Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- First Published December 1, 2017
Method
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
- First Published October 11, 2017
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
Corrigendum
Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- First Published November 1, 2016
Corrigendum
Corrigendum: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- First Published October 3, 2016
Research
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
- First Published February 12, 2015
Research
Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals
- First Published November 13, 2014
Research
Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- First Published October 7, 2014
Research
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
- First Published September 3, 2013
Research
Extensive compensatory cis-trans regulation in the evolution of mouse gene expression
- First Published August 23, 2012
Research
Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- First Published July 10, 2012
Research
A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- First Published March 28, 2012
Research
A matter of life or death: How microsatellites emerge in and vanish from the human genome
- First Published October 12, 2011
Research
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- First Published July 27, 2011
Research
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- First Published April 29, 2010
Research
A CTCF-independent role for cohesin in tissue-specific transcription
- First Published March 10, 2010
Article
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- First Published November 3, 2009
Resource
Windshield splatter analysis with the Galaxy metagenomic pipeline
- First Published October 9, 2009
Letter
Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions
- First Published June 5, 2009
Letter
Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
- First Published April 28, 2009
Methods
Genome-wide nucleotide-level mammalian ancestor reconstruction
- First Published October 10, 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
RESOURCE
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- First Published June 24, 2008
LETTER
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
- First Published February 7, 2008
LETTER
The genome-wide determinants of human and chimpanzee microsatellite evolution
- First Published November 21, 2007
LETTER
Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
- First Published June 13, 2007
ARTICLE
The landscape of histone modifications across 1% of the human genome in five human cell lines
- 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
LETTER
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
- First Published July 15, 2005
Methods
Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
- First Published April 1, 2004
LETTER
Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents
- 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
LETTER
Leveraging the Mouse Genome for Gene Prediction in Human: From Whole-Genome Shotgun Reads to a Global Synteny Map
- First Published January 1, 2003
ARTICLE
Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution
- First Published January 1, 2003
LETTER
Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels
- First Published January 1, 2003