Perspective
The Topological Regulatory Logic of noncoding RNA–mediated gene expression
- First Published June 17, 2026
Resource
A limited set of transcriptional programs define major cell types
- First Published July 29, 2020
Resource
Dynamics of microRNA expression during mouse prenatal development
- First Published October 23, 2019
Method
Read clouds uncover variation in complex regions of the human genome
- First Published August 18, 2015
Method
Discovery of recurrent structural variants in nasopharyngeal carcinoma
- First Published November 8, 2013
Research
De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
- First Published June 28, 2013
Research
The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes
- First Published March 11, 2013
Method
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
- First Published September 5, 2012
Research
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
- First Published September 5, 2012
Resource
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- First Published September 5, 2012
Resource
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
- 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
Method
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
- First Published August 30, 2012
Resource
Drosophila cell lines" > The transcriptional diversity of 25 Drosophila cell lines
- First Published December 22, 2010
Letter
Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
- First Published January 12, 2010
Resource
ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses
- First Published October 21, 2009
LETTER
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
- First Published February 7, 2008
LETTER
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
- First Published January 29, 2008
LETTER
Structured RNAs in the ENCODE selected regions 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
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
ARTICLE
De novo discovery of a tissue-specific gene regulatory module in a chordate
- First Published September 16, 2005
Methods
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
- First Published July 5, 2005
ARTICLE
Distribution and intensity of constraint in mammalian genomic sequence
- First Published June 17, 2005
Methods
Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
- First Published June 17, 2005
Methods
Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human
- First Published April 1, 2004
LETTER
Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes
- First Published April 1, 2004
ARTICLE
Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22
- First Published March 1, 2004
LETTER
Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes
- First Published May 1, 2003
METHODS
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
- First Published March 12, 2003
LETTER
Partitioning of Tissue Expression Accompanies Multiple Duplications of the Na+/K+ ATPase α Subunit Gene
- First Published September 20, 2001
METHODS
Flexible Use of High-Density Oligonucleotide Arrays for Single-Nucleotide Polymorphism Discovery and Validation
- First Published July 12, 2001
LETTER
Mycobacterium tuberculosis " > Comparing Genomes within the Species Mycobacterium tuberculosis
- First Published April 1, 2001
METHODS
Detection of Deleted Genomic DNA Using a Semiautomated Computational Analysis of GeneChip Data
- First Published November 21, 2000
