CirGRDB: a database for the genome-wide deciphering circadian genes and regulators

The aging clock: circadian rhythms and later life

(2017) Suzanne Hood et al.   JOURNAL OF CLINICAL INVESTIGATION

A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation

(2017) Zenghua Fan et al.   NUCLEIC ACIDS RESEARCH

CYCLOPS reveals human transcriptional rhythms in health and disease

(2017) Ron C. Anafi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional architecture of the mammalian circadian clock

(2016) Joseph S. Takahashi   NATURE REVIEWS GENETICS

Distinct Roles of HDAC3 in the Core Circadian Negative Feedback Loop Are Critical for Clock Function

(2016) Guangsen Shi et al.   Cell Reports

CLOCKWORK ORANGE Enhances PERIOD Mediated Rhythms in Transcriptional Repression by Antagonizing E-box Binding by CLOCK-CYCLE

(2016) Jian Zhou et al.   PLoS Genetics

Comparative Circadian Metabolomics Reveal Differential Effects of Nutritional Challenge in the Serum and Liver

(2015) Serena Abbondante et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Genetics and epigenetics of circadian rhythms and their potential roles in neuropsychiatric disorders

(2015) Chunyu Liu et al.   Neuroscience Bulletin

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

Circadian regulation of gene expression: at the crossroads of transcriptional and post-transcriptional regulatory networks

(2014) Esteban J Beckwith et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data

(2014) Daogang Guan et al.   NUCLEIC ACIDS RESEARCH

The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations

(2014) Yuanbin Ru et al.   NUCLEIC ACIDS 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

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Circadian Disruption Leads to Insulin Resistance and Obesity

(2013) Shu-qun Shi et al.   CURRENT BIOLOGY

Circadian timekeeping and output mechanisms in animals

(2013) Paul E Hardin et al.   CURRENT OPINION IN NEUROBIOLOGY

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Cold-induced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation

(2013) Yuting Liu et al.   Scientific Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Circadian Oscillations of Protein-Coding and Regulatory RNAs in a Highly Dynamic Mammalian Liver Epigenome

(2012) Christopher Vollmers et al.   Cell Metabolism

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Aberrant light directly impairs mood and learning through melanopsin-expressing neurons

(2012) Tara A. LeGates et al.   NATURE

CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics

(2012) Vishal R Patel et al.   NATURE METHODS

Cold-Inducible RNA-Binding Protein Modulates Circadian Gene Expression Posttranscriptionally

(2012) J. Morf et al.   SCIENCE

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

(2012) N. Koike et al.   SCIENCE

LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data

(2011) Rendong Yang et al.   BIOINFORMATICS

Understanding systems-level properties: timely stories from the study of clocks

(2011) John B. Hogenesch et al.   NATURE REVIEWS GENETICS

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

(2011) Guillaume Rey et al.   PLOS BIOLOGY

A framework for oligonucleotide microarray preprocessing

(2010) Benilton S. Carvalho et al.   BIOINFORMATICS

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

(2010) Mali Salmon-Divon et al.   BMC BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Clocks not winding down: unravelling circadian networks

(2010) Eric E. Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Circadian Integration of Metabolism and Energetics

(2010) J. Bass et al.   SCIENCE

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

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

The Meter of Metabolism

(2008) Carla B. Green et al.   CELL

The genetics of mammalian circadian order and disorder: implications for physiology and disease

(2008) Joseph S. Takahashi et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY