Method
Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- First Published August 12, 2022
Research
Embryonic LTR retrotransposons supply promoter modules to somatic tissues
- First Published October 21, 2021
Research
Antisense RNAs during early vertebrate development are divided in groups with distinct features
- First Published April 1, 2021
Corrigendum
Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping
- First Published September 14, 2020
Resource
Functional annotation of human long noncoding RNAs via molecular phenotyping
- First Published July 27, 2020
Corrigendum
Corrigendum: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
- First Published January 9, 2020
Resource
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
- First Published February 13, 2019
Method
SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
- First Published November 7, 2018
Research
CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
- First Published October 28, 2015
Research
The frequent evolutionary birth and death of functional promoters in mouse and human
- First Published July 30, 2015
Resource
D. melanogaster modENCODE transcriptome annotation" > Comparative validation of the D. melanogaster modENCODE transcriptome annotation
- First Published July 1, 2014
Resource
Digital expression profiling of the compartmentalized translatome of Purkinje neurons
- First Published June 5, 2014
Method
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
- First Published March 27, 2014
Resource
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
- First Published September 3, 2013
Research
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
- 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
Method
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
- First Published August 30, 2012
Research
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- First Published July 27, 2011
Method
Genome-wide identification of conserved regulatory function in diverged sequences
- First Published May 31, 2011
Method
Unamplified cap analysis of gene expression on a single-molecule sequencer
- First Published May 19, 2011
Research
Drosophila melanogaster" > Genome-wide analysis of promoter architecture in Drosophila melanogaster
- First Published December 22, 2010
Research
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- First Published April 29, 2010
Methods
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
- First Published January 5, 2010
Article
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- First Published November 3, 2009
LETTER
Thylacinus cynocephalus)" > The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)
- First Published January 12, 2009
Methods
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
- First Published December 11, 2008
LETTER
Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
- First Published September 25, 2008
RESOURCE
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
- First Published November 5, 2007
ARTICLE
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- First Published June 13, 2007
RESOURCE
A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
- First Published June 13, 2007
LETTER
Using genomic data to unravel the root of the placental mammal phylogeny
- First Published February 23, 2007
Methods
ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
- First Published October 19, 2006
LETTER
cis-regulatory modules" > Experimental validation of predicted mammalian erythroid cis-regulatory modules
- First Published October 12, 2006
RESOURCE
Galaxy: A platform for interactive large-scale genome analysis
- First Published September 16, 2005
ARTICLE
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- First Published July 15, 2005
Chicken Special/Resources
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
- First Published December 8, 2004
Chicken Special/Letters
Evolution and functional classification of vertebrate gene deserts
- First Published December 8, 2004
LETTER
Reconstructing large regions of an ancestral mammalian genome in silico
- First Published December 1, 2004
RESOURCE
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
- First Published April 1, 2004
Methods
Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
- First Published April 1, 2004
LETTER
Comparative Analysis of the α-Like Globin Clusters in Mouse, Rat, and Human Chromosomes Indicates a Mechanism Underlying Breaks in Conserved Synteny
- First Published April 1, 2004
ARTICLE
Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
- First Published April 1, 2004
RESOURCE
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
- First Published March 1, 2004
LETTER
Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage
- First Published June 2, 2003
LETTER
Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System
- First Published June 2, 2003
ARTICLE
Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
- First Published June 2, 2003
RESOURCE
GALA, a Database for Genomic Sequence Alignments and Annotations
- First Published April 1, 2003
ARTICLE
Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution
- First Published January 1, 2003
LETTER
Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels
- First Published January 1, 2003
RESOURCE
Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data
- First Published July 19, 2002
METHODS
A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs
- First Published June 18, 2002
REPORT
3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome " > Generation and Comparative Analysis of ∼3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome
- First Published January 1, 2002
METHODS
Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library
- First Published January 18, 2001
LETTER
RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer
- First Published November 1, 2000
ARTICLE
Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain
- First Published November 1, 2000
METHODS
Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes
- First Published October 1, 2000
REPORT
Naip Gene Array" > Genomic Sequence Analysis of the Mouse Naip Gene Array
- First Published August 1, 2000
LETTER
Automated Filtration-Based High-Throughput Plasmid Preparation System
- First Published May 1, 1999
LETTER
mnd2 Region of Chromosome 2p13" > Comparative Sequence of Human and Mouse BAC Clones from the mnd2 Region of Chromosome 2p13
- First Published January 1, 1999
GENOME METHODS
Analysis of the Quality and Utility of Random Shotgun Sequencing at Low Redundancies
- First Published October 1, 1998
GENOME METHODS
A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence
- First Published September 1, 1998
RESEARCH
Comparative Sequence Analysis of a Gene-Rich Cluster at Human Chromosome 12p13 and its Syntenic Region in Mouse Chromosome 6
- First Published January 1, 1998
PERSPECTIVE
Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome
- First Published October 1, 1997
RESEARCH
Large-Scale Comparative Sequence Analysis of the Human and Murine Bruton’s Tyrosine Kinase Loci Reveals Conserved Regulatory Domains
- First Published April 1, 1997