Research
3C sites in poly(A) RNA" > Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA
- First Published October 30, 2025
Research
Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
- First Published May 18, 2021
Research
Long-read sequencing for non-small-cell lung cancer genomes
- First Published September 4, 2020
Method
Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates
- First Published August 25, 2020
Resource
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- First Published September 19, 2019
Research
An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
- First Published January 3, 2019
Corrigendum
Plasmodium falciparum" > Corrigendum: Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum
- First Published August 1, 2018
Method
Co-expression networks reveal the tissue-specific regulation of transcription and splicing
- First Published October 11, 2017
Research
Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
- First Published May 18, 2017
Research
A GC-rich sequence feature in the 3′ UTR directs UPF1-dependent mRNA decay in mammalian cells
- First Published December 9, 2016
Resource
Ciona intestinalis" > Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
- First Published December 14, 2015
Research
Plasmodium falciparum" > Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum
- First Published August 4, 2014
Resource
D. melanogaster modENCODE transcriptome annotation" > Comparative validation of the D. melanogaster modENCODE transcriptome annotation
- First Published July 1, 2014
Resource
Drosophila melanogaster" > Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
- First Published July 1, 2014
Research
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
- First Published January 15, 2014
Method
Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
- First Published December 5, 2013
Resource
Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
- First Published October 29, 2013
Resource
Coelacanth genomes reveal signatures for evolutionary transition from water to land
- First Published July 22, 2013
Method
Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
- First Published May 2, 2013
Research
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
- First Published April 17, 2013
Research
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
- First Published March 19, 2013
Research
High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice
- First Published February 14, 2013
Research
Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence
- First Published November 2, 2012
Resource
GENCODE: The reference human genome annotation for The ENCODE Project
- First Published September 5, 2012
Resource
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- First Published September 5, 2012
Research
Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns
- First Published June 11, 2012
Method
Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals
- First Published February 27, 2012
Method
Unified modeling of gene duplication, loss, and coalescence using a locus tree
- First Published January 23, 2012
Research
Drosophila and other metazoa" > Evidence of abundant stop codon readthrough in Drosophila and other metazoa
- First Published October 12, 2011
Method
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- First Published October 12, 2011
Method
New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes
- First Published October 12, 2011
Research
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- First Published July 27, 2011
Resource
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
- First Published March 3, 2011
Research
Nucleotide composition-linked divergence of vertebrate core promoter architecture
- First Published January 10, 2011
Resource
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
- First Published June 4, 2009
12 Drosophila Genomes/Methods
Drosophila genomes" > Reliable prediction of regulator targets using 12 Drosophila genomes
- First Published November 7, 2007
12 Drosophila Genomes/Letter
Drosophila melanogaster using 12 fly genomes" > Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
- First Published November 7, 2007
12 Drosophila Genomes/Letter
Drosophila microRNAs" > Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
- First Published November 7, 2007
12 Drosophila Genomes/Letter
Drosophila genomes" > Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
- First Published November 7, 2007
12 Drosophila Genomes/Methods
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
- First Published November 7, 2007
LETTER
Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes
- First Published June 13, 2007
LETTER
Toxoplasma gondii" > Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii
- First Published August 10, 2006
LETTER
Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
- First Published December 12, 2005
LETTER
Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs
- First Published October 15, 2004
LETTER
Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions
- First Published September 1, 2004
RESOURCE
Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation" > Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation
- First Published January 1, 2003
REPORT
Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes
- First Published April 11, 2001