Resource
Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- First Published August 16, 2024
Method
cis-regulatory elements" > Probabilistic association of differentially expressed genes with cis-regulatory elements
- First Published April 17, 2024
Research
Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- First Published October 18, 2023
Research
Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
- First Published April 20, 2021
Research
Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages" > Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages
- First Published November 18, 2020
Research
Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations
- First Published July 2, 2020
Resource
Dynamics of microRNA expression during mouse prenatal development
- First Published October 23, 2019
Method
A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS
- First Published April 2, 2019
Corrigendum
Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data
- First Published January 2, 2018
Resource
A genome-wide interactome of DNA-associated proteins in the human liver
- First Published October 11, 2017
Corrigendum
Corrigendum: The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2
- First Published September 1, 2017
Resource
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- First Published April 10, 2017
Research
Discovery and genotyping of structural variation from long-read haploid genome sequence data
- First Published November 28, 2016
Research
Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- First Published October 7, 2016
Research
Pangolin genomes and the evolution of mammalian scales and immunity
- First Published August 10, 2016
Method
INTEGRATE: gene fusion discovery using whole genome and transcriptome data
- First Published November 10, 2015
Research
Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites
- First Published October 20, 2015
Resource
Chlorocebus aethiops sabaeus)" > The genome of the vervet (Chlorocebus aethiops sabaeus)
- First Published September 16, 2015
Method
CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
- First Published September 9, 2015
Resource
Single haplotype assembly of the human genome from a hydatidiform mole
- First Published November 4, 2014
Resource
Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline
- First Published March 27, 2014
Method
Reconstructing complex regions of genomes using long-read sequencing technology
- First Published January 13, 2014
Method
From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
- First Published December 3, 2013
Resource
Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
- First Published October 29, 2013
Resource
Dynamic DNA methylation across diverse human cell lines and tissues
- First Published January 16, 2013
Research
Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner
- First Published September 26, 2012
Research
Widespread plasticity in CTCF occupancy linked to DNA methylation
- First Published September 5, 2012
Resource
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
- First Published September 5, 2012
Resource
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- First Published September 5, 2012
Research
The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2
- First Published March 14, 2012
Research
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
- First Published February 2, 2012
Resource
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
- First Published February 2, 2012
Research
Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee
- First Published June 17, 2011
Research
DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer
- First Published April 26, 2011
Research
Sequence features that drive human promoter function and tissue specificity
- First Published May 25, 2010
Letter
Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
- First Published January 12, 2010
Article
Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
- First Published October 2, 2009
Letter
Signals of recent positive selection in a worldwide sample of human populations
- First Published March 23, 2009
Methods
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
- First Published March 9, 2009
LETTER
Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
- First Published November 24, 2008
RESOURCE
Haplotype sorting using human fosmid clone end-sequence pairs
- First Published October 3, 2008
LETTER
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
- First Published February 7, 2008
ARTICLE
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
- First Published June 13, 2007
ARTICLE
Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
- First Published June 13, 2007
ARTICLE
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- First Published June 13, 2007
LETTER
Transcription factor binding and modified histones in human bidirectional promoters
- First Published June 13, 2007
RESOURCE
PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data
- First Published April 6, 2007
LETTER
Serum response factor binding sites differ in three human cell types
- First Published January 2, 2007
LETTER
Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
- First Published September 8, 2006
ARTICLE
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome
- First Published December 12, 2005
ARTICLE
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- First Published July 15, 2005
LETTER
Punctuated duplication seeding events during the evolution of human chromosome 2p11
- First Published June 17, 2005
Methods
Direct isolation and identification of promoters in the human genome
- First Published May 17, 2005
LETTER
Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana" > Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana
- First Published April 1, 2005
RESOURCE
EAnnot: A genome annotation tool using experimental evidence
- First Published December 1, 2004
ARTICLE
Coelacanth genome sequence reveals the evolutionary history of vertebrate genes
- First Published November 15, 2004
LETTER
Analysis of Human mRNAs With the Reference Genome Sequence Reveals Potential Errors, Polymorphisms, and RNA Editing
- First Published October 15, 2004
Chicken Special/Letters
The repetitive landscape of the chicken genome
- First Published July 15, 2004
LETTER
Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity
- First Published March 1, 2004
Methods
Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay
- First Published June 12, 2003
METHODS
Identification and Functional Analysis of Human Transcriptional Promoters
- First Published February 1, 2003
METHODS
Rapid Mapping of Zebrafish Mutations With SNPs and Oligonucleotide Microarrays
- First Published December 1, 2002
LETTER
Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters
- First Published March 1, 2001
METHODS
Theories and Applications for Sequencing Randomly Selected Clones
- First Published January 18, 2001
GENOME METHODS
A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes
- First Published May 1, 1997
EDITORIAL
The End of the Beginning: The Race to Begin Human Genome Sequencing
- First Published September 1, 1996