Research
Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources
- First Published May 14, 2026
Research
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- First Published April 10, 2025
Method
MCHelper automatically curates transposable element libraries across eukaryotic species
- First Published December 9, 2024
Method
Ultrafast genome-wide inference of pairwise coalescence times
- First Published August 10, 2023
Research
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- First Published December 8, 2022
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
Resource
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- First Published April 10, 2017
Method
Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes
- First Published December 16, 2016
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
Resource
Assemblathon 1: A competitive assessment of de novo short read assembly methods
- First Published September 16, 2011
Method
Unamplified cap analysis of gene expression on a single-molecule sequencer
- First Published May 19, 2011
Method
Revealing the genetic structure of a trait by sequencing a population under selection
- First Published March 21, 2011
Research
Drosophila melanogaster" > Genome-wide analysis of promoter architecture in Drosophila melanogaster
- First Published December 22, 2010
Resource
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
- First Published October 27, 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
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
Methods
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
- First Published December 11, 2008
RESOURCE
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
- First Published November 24, 2008
RESOURCE
Mapping short DNA sequencing reads and calling variants using mapping quality scores
- First Published August 19, 2008
ARTICLE
Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
- 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
LETTER
Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage
- First Published June 2, 2003
METHODS
GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming
- First Published September 1, 2002
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
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
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
LETTER
Alfresco—A Workbench for Comparative Genomic Sequence Analysis
- First Published August 1, 2000
METHODS
GeneWise in the Drosophila Annotation Experiment" > Using GeneWise in the Drosophila Annotation Experiment
- First Published April 1, 2000
LETTER
Comparative Analysis of Noncoding Regions of 77 Orthologous Mouse and Human Gene Pairs
- First Published September 1, 1999
LETTER
Automated Filtration-Based High-Throughput Plasmid Preparation System
- First Published May 1, 1999
