Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

Post-transcriptional regulatory networks play a key role in noise reduction that is conserved from micro-organisms to mammals

(2012) Anagha Joshi et al.   FEBS Journal

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain

(2012) M. E. Hughes et al.   GENOME RESEARCH

Nascent-Seq Indicates Widespread Cotranscriptional RNA Editing in Drosophila

(2012) Joseph Rodriguez et al.   MOLECULAR CELL

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

(2012) Y. L. Khodor et al.   RNA

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

(2012) N. Koike et al.   SCIENCE

Promoter Elements Regulate Cytoplasmic mRNA Decay

(2011) Almog Bregman et al.   CELL

Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast

(2011) Tatjana Trcek et al.   CELL

Delay in Feedback Repression by Cryptochrome 1 Is Required for Circadian Clock Function

(2011) Maki Ukai-Tadenuma et al.   CELL

Posttranscriptional mechanisms in controlling eukaryotic circadian rhythms

(2011) Lin Zhang et al.   FEBS LETTERS

Drosophila CLOCK target gene characterization: implications for circadian tissue-specific gene expression

(2011) K. C. Abruzzi et al.   GENES & DEVELOPMENT

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila

(2011) Y. L. Khodor et al.   GENES & DEVELOPMENT

Post-transcriptional control of circadian rhythms

(2011) S. Kojima et al.   JOURNAL OF CELL SCIENCE

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism

(2011) D. Feng et al.   SCIENCE

RNA-based regulation in the plant circadian clock

(2011) Dorothee Staiger et al.   TRENDS IN PLANT SCIENCE

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

(2011) Guillaume Rey et al.   PLOS BIOLOGY

Spotlight on post-transcriptional control in the circadian system

(2010) Dorothee Staiger et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

(2010) Fernando Carrillo Oesterreich et al.   MOLECULAR CELL

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Integration of microRNA miR-122 in hepatic circadian gene expression

(2009) D. Gatfield et al.   GENES & DEVELOPMENT

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Circadian Amplitude of Cryptochrome 1 Is Modulated by mRNA Stability Regulation via Cytoplasmic hnRNP D Oscillation

(2009) K.-C. Woo et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2009) Shengli Hao et al.   NATURE IMMUNOLOGY

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression

(2009) Christopher Vollmers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genetic Signatures of Noncoding RNAs

(2009) John S. Mattick   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

Mouse period 2 mRNA circadian oscillation is modulated by PTB–mediated rhythmic mRNA degradation

(2008) Kyung-Chul Woo et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY