LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data

Diurnal transcriptome atlas of a primate across major neural and peripheral tissues

(2018) Ludovic S. Mure et al.   SCIENCE

Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data

(2018) Alan L. Hutchison et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Guidelines for Genome-Scale Analysis of Biological Rhythms

(2017) Michael E. Hughes et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

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

Machine learning identifies a compact gene set for monitoring the circadian clock in human blood

(2017) Jacob J. Hughey   Genome Medicine

Blood transcriptome based biomarkers for human circadian phase

(2017) Emma E Laing et al.   eLife

Differential rhythmicity: detecting altered rhythmicity in biological data

(2016) Paul F. Thaben et al.   BIOINFORMATICS

MetaCycle: an integrated R package to evaluate periodicity in large scale data

(2016) Gang Wu et al.   BIOINFORMATICS

Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis

(2016) Selma Masri et al.   CELL

Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans

(2016) Jacob J. Hughey et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA)

(2016) Ray Zhang et al.   JOURNAL OF BIOLOGICAL RHYTHMS

ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system

(2016) Jacob J. Hughey et al.   NUCLEIC ACIDS RESEARCH

Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals

(2016) Alexandra Montagner et al.   Scientific Reports

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

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

Robust meta-analysis of gene expression using the elastic net

(2015) Jacob J. Hughey et al.   NUCLEIC ACIDS RESEARCH

Effects of aging on circadian patterns of gene expression in the human prefrontal cortex

(2015) Cho-Yi Chen 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

Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data

(2015) Alan L. Hutchison et al.   PLoS Computational Biology

Temporal transcriptomics suggest that twin-peaking genes reset the clock

(2015) William G Pembroke et al.   eLife

Detecting Rhythms in Time Series with RAIN

(2014) Paul F. Thaben et al.   JOURNAL OF BIOLOGICAL RHYTHMS

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

(2014) Aaron T.L. Lun 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

Cosinor-based rhythmometry

(2014) Germaine Cornelissen   Theoretical Biology and Medical Modelling

Circadian rhythm reprogramming during lung inflammation

(2014) Jeffrey A. Haspel et al.   Nature Communications

Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

(2014) Sarah Lück et al.   Cell Reports

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

Circadian Phase Has Profound Effects on Differential Expression Analysis

(2012) Polly Yingshan Hsu et al.   PLoS One

Kruppel-like factor 9 is a circadian transcription factor in human epidermis that controls proliferation of keratinocytes

(2012) F. Sporl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

(2012) Jovana Maksimovic et al.   GENOME BIOLOGY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets

(2010) Michael E. Hughes et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Harmonics of Circadian Gene Transcription in Mammals

(2009) Michael E. Hughes et al.   PLoS Genetics

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

(2008) Mi-Youn Brusniak et al.   BMC BIOINFORMATICS

Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development

(2008) Michael F Covington et al.   GENOME BIOLOGY