Method
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- First Published April 10, 2025
Method
Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- First Published August 12, 2022
Research
Sequence determinants of polyadenylation-mediated regulation
- First Published September 17, 2019
Corrigendum
Corrigendum: Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
- First Published March 1, 2017
Research
Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
- First Published December 13, 2016
Corrigendum
Corrigendum: Unraveling determinants of transcription factor binding outside the core binding site
- First Published September 1, 2015
Research
The frequent evolutionary birth and death of functional promoters in mouse and human
- First Published July 30, 2015
Research
Core promoter sequence in yeast is a major determinant of expression level
- First Published May 12, 2015
Method
Unraveling determinants of transcription factor binding outside the core binding site
- First Published March 11, 2015
Research
Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
- First Published October 7, 2014
Method
Probing the effect of promoters on noise in gene expression using thousands of designed sequences
- First Published July 16, 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
Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
- First Published August 15, 2013
Research
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise
- First Published February 12, 2013
Research
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters
- First Published October 18, 2011
Method
Unamplified cap analysis of gene expression on a single-molecule sequencer
- First Published May 19, 2011
Research
C. elegans" > High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
- First Published December 22, 2010
Research
A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness
- First Published August 18, 2010
Research
p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy
- First Published August 17, 2010
Methods
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
- First Published January 5, 2010
Methods
Incorporating nucleosomes into thermodynamic models of transcription regulation
- First Published May 18, 2009
Methods
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
- First Published December 11, 2008
Methods
cis-regulatory motifs in human core promoters" > Systematic functional characterization of cis-regulatory motifs in human core promoters
- First Published February 6, 2008
ARTICLE
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
- First Published December 12, 2005
ARTICLE
Disclosing hidden transcripts: Mouse natural sense–antisense transcripts tend to be poly(A) negative and nuclear localized
- First Published March 21, 2005
LETTER
The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment
- 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
Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling
- First Published June 2, 2003
RESOURCE
The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer
- First Published June 2, 2003
RESOURCE
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation 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
ARTICLE
Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome
- First Published June 2, 2003
ARTICLE
Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection
- First Published June 2, 2003
LETTER
Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays
- First Published June 2, 2003
LETTER
Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation
- First Published June 2, 2003
LETTER
Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome
- First Published June 2, 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
LETTER
Exploration of Novel Motifs Derived from Mouse cDNA Sequences
- First Published February 15, 2002
METHODS
Protein–Protein Interaction Panel Using Mouse Full-Length cDNAs
- First Published September 20, 2001
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
RESOURCE
Bacterial Artificial Chromosome Libraries for Mouse Sequencing and Functional Analysis
- First Published January 1, 2000
LETTER
Automated Filtration-Based High-Throughput Plasmid Preparation System
- First Published May 1, 1999