Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

(2017) Jonathan Aryeh Sobel et al.   PLOS BIOLOGY

Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein geneCirbp

(2016) Ivana Gotic et al.   GENES & DEVELOPMENT

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

(2016) P. Eser et al.   Molecular Systems Biology

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

(2016) Jérôme Mermet et al.   Cold Spring Harbor Perspectives in Biology

Perfect timing: splicing and transcription rates in living cells

(2016) Tara Alpert et al.   Wiley Interdisciplinary Reviews-RNA

INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments

(2015) Stefano de Pretis et al.   BIOINFORMATICS

Circadian timing of metabolism in animal models and humans

(2015) C. Dibner et al.   JOURNAL OF INTERNAL MEDICINE

Rhythmic control of mRNA stability modulates circadian amplitude of mousePeriod3mRNA

(2015) Sung-Hoon Kim et al.   JOURNAL OF NEUROCHEMISTRY

Bursty Gene Expression in the Intact Mammalian Liver

(2015) Keren Bahar Halpern et al.   MOLECULAR CELL

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

The RNA binding protein FXR1 is a new driver in the 3q26-29 amplicon and predicts poor prognosis in human cancers

(2015) Jun Qian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

(2015) Florian Atger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian Clocks and Feeding Time Regulate the Oscillations and Levels of Hepatic Triglycerides

(2014) Yaarit Adamovich et al.   Cell Metabolism

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

(2014) Sarah Lück et al.   Cell Reports

MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale

(2014) Ngoc-Hien Du et al.   eLife

Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response

(2014) Kate Sidaway-Lee et al.   GENOME BIOLOGY

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver

(2013) D. Mauvoisin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response

(2013) Kaspar Burger et al.   RNA Biology

Molecular architecture of the mammalian circadian clock

(2013) Carrie L. Partch et al.   TRENDS IN CELL BIOLOGY

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

(2013) Robert M. Martin et al.   Cell Reports

Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression

(2012) S. Kojima et al.   GENES & DEVELOPMENT

RNA-binding protein nucleolin in disease

(2012) Kotb Abdelmohsen et al.   RNA Biology

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

(2012) N. Koike et al.   SCIENCE

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

(2012) Gwendal Le Martelot et al.   PLOS BIOLOGY

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

(2012) Jerome S Menet et al.   eLife

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli

(2011) A. Zeisel et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

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

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

hnRNP Q mediates a phase-dependent translation-coupled mRNA decay of mouse Period3

(2011) Do-Yeon Kim et al.   NUCLEIC ACIDS RESEARCH

Matrin 3 Binds and Stabilizes mRNA

(2011) Maayan Salton et al.   PLoS One

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   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

MicroRNA-122 Modulates the Rhythmic Expression Profile of the Circadian Deadenylase Nocturnin in Mouse Liver

(2010) Shihoko Kojima et al.   PLoS One

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

(2009) A. Raue et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

Rates of in situ transcription and splicing in large human genes

(2009) Jarnail Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

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

Control of c-myc mRNA stability by IGF2BP1-associated cytoplasmic RNPs

(2008) D. Weidensdorfer et al.   RNA

The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast

(2007) Vicent Pelechano et al.   YEAST