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
Resource
Precision environmental health monitoring by longitudinal exposome and multi-omics profiling
- First Published June 6, 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
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
Detection and analysis of ancient segmental duplications in mammalian genomes
- First Published May 7, 2018
Method
Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome
- First Published December 1, 2017
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
Method
Linking disease associations with regulatory information in the human genome
- First Published September 5, 2012
Resource
Annotation of functional variation in personal genomes using RegulomeDB
- 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
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
- First Published September 5, 2012
Research
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
- First Published September 5, 2012
Research
A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells
- First Published September 5, 2012
Method
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
- First Published September 5, 2012
Resource
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
- First Published February 7, 2011
Research
C. elegans" > Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
- First Published December 22, 2010
Method
C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data" > Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
- First Published December 22, 2010
Resource
Candida albicans using RNA-seq" > Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq
- First Published September 1, 2010
RESOURCE
De novo fragment assembly with short mate-paired reads: Does the read length matter?
- First Published December 3, 2008
Methods
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
- First Published November 26, 2008
LETTER
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
- First Published September 11, 2008
LETTER
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation
- First Published May 16, 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
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
- First Published June 13, 2007
ARTICLE
The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
- First Published June 13, 2007
LETTER
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
- First Published June 13, 2007
LETTER
Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- First Published June 13, 2007
LETTER
Structured RNAs in the ENCODE selected regions of the human genome
- First Published June 13, 2007
Methods
Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
- First Published June 13, 2007
Methods
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)
- First Published June 13, 2007
PERSPECTIVE
What is a gene, post-ENCODE? History and updated definition
- First Published June 13, 2007
Methods
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
- First Published November 21, 2006
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
RESOURCE
Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon
- First Published October 1, 2004