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
Method
Analyzing rare mutations in metagenomes assembled using long and accurate reads
- First Published November 23, 2022
Method
Fast and accurate mapping of long reads to complete genome assemblies with VerityMap
- First Published November 15, 2022
Method
Variations in antibody repertoires correlate with vaccine responses
- First Published March 31, 2022
Research
V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s
- First Published September 18, 2020
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
Method
BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs
- First Published June 3, 2019
Method
Plasmid detection and assembly in genomic and metagenomic data sets
- First Published May 2, 2019
Method
Chromosome assembly of large and complex genomes using multiple references
- First Published October 19, 2018
Method
Detection and analysis of ancient segmental duplications in mammalian genomes
- First Published May 7, 2018
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
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
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
Research
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
- First Published February 12, 2015
Research
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers
- First Published February 2, 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
Method
Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform" > Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
- First Published April 5, 2013
Research
cis-trans regulation in the evolution of mouse gene expression" > Extensive compensatory cis-trans regulation in the evolution of mouse gene expression
- First Published August 23, 2012
Research
cis-regulatory modules" > Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- First Published July 10, 2012
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
Letter
Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
- First Published April 28, 2009
RESOURCE
De novo fragment assembly with short mate-paired reads: Does the read length matter?
- First Published December 3, 2008
Methods
Genome-wide nucleotide-level mammalian ancestor reconstruction
- First Published October 10, 2008
RESOURCE
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- First Published June 24, 2008
Methods
Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
- First Published April 21, 2008
LETTER
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
- First Published February 7, 2008
Methods
Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
- First Published August 9, 2007
ARTICLE
The landscape of histone modifications across 1% of the human genome in five human cell lines
- First Published June 13, 2007
Forum
The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
- First Published March 1, 2006
Chicken Special/Letters
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
- First Published December 8, 2004
LETTER
Alu repeat elements reveals complex evolutionary history" > Whole-genome analysis of Alu repeat elements reveals complex evolutionary history
- First Published November 1, 2004
ARTICLE
Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat 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
LETTER
Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species
- First Published January 1, 2002
METHODS
Efficiency of Database Search for Identification of Mutated and Modified Proteins via Mass Spectrometry
- First Published February 1, 2001