Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

Major role for mRNA stability in shaping the kinetics of gene induction

(2010) Ran Elkon et al.   BMC GENOMICS

Global coordination of transcriptional control and mRNA decay during cellular differentiation

(2010) Maria J Amorim et al.   Molecular Systems Biology

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Timing of Gene Expression Responses to Environmental Changes

(2009) Gal Chechik et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Metabolic tagging and purification of nascent RNA: implications for transcriptomics

(2009) Caroline C. Friedel et al.   Molecular BioSystems

Dissection of a complex transcriptional response using genome-wide transcriptional modelling

(2009) Martino Barenco et al.   Molecular Systems Biology

The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules

(2009) Shengli Hao et al.   NATURE IMMUNOLOGY

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life

(2009) Caroline C. Friedel et al.   NUCLEIC ACIDS RESEARCH

Impact of Shifting Patterns of Pacific Ocean Warming on North Atlantic Tropical Cyclones

(2009) Hye-Mi Kim et al.   SCIENCE

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

(2008) Ophir Shalem et al.   Molecular Systems Biology

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

(2008) Gal Chechik et al.   NATURE BIOTECHNOLOGY

Direct multiplexed measurement of gene expression with color-coded probe pairs

(2008) Gary K Geiss et al.   NATURE BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

(2008) Stephen A. Ramsey et al.   PLoS Computational Biology

The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast

(2007) Vicent Pelechano et al.   YEAST