Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging

The circadian clock gene period extends healthspan in aging Drosophila melanogaster

(2016) Natraj Krishnan et al.   Aging-US

Antioxidant N-acetyl-L-cysteine ameliorates symptoms of premature aging associated with the deficiency of the circadian protein BMAL1

(2016) Roman V. Kondratov et al.   Aging-US

Gene expression changes in response to aging compared to heat stress, oxidative stress and ionizing radiation in Drosophila melanogaster

(2016) Gary Landis et al.   Aging-US

Premature aging of the hippocampal neurogenic niche in adult Bmal1‐ deficient mice

(2015) Amira A. H. Ali et al.   Aging-US

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

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

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

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

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Phosphorylation of the Transcription Activator CLOCK Regulates Progression through a ∼24-h Feedback Loop to Influence the Circadian Period inDrosophila

(2014) Guruswamy Mahesh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Circadian timekeeping and output mechanisms in animals

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

Circadian clock proteins regulate neuronal redox homeostasis and neurodegeneration

(2013) Erik S. Musiek et al.   JOURNAL OF CLINICAL INVESTIGATION

Activation of transposable elements during aging and neuronal decline in Drosophila

(2013) Wanhe Li et al.   NATURE NEUROSCIENCE

ROS Stress Resets Circadian Clocks to Coordinate Pro-Survival Signals

(2013) Teruya Tamaru et al.   PLoS One

Nascent-Seq analysis ofDrosophilacycling gene expression

(2013) Joseph Rodriguez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Old flies have a robust central oscillator but weaker behavioral rhythms that can be improved by genetic and environmental manipulations

(2012) Wenyu Luo et al.   AGING CELL

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Effects of Aging on the Molecular Circadian Oscillations inDrosophila

(2012) Kuntol Rakshit et al.   CHRONOBIOLOGY INTERNATIONAL

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Circadian Phase Has Profound Effects on Differential Expression Analysis

(2012) Polly Yingshan Hsu et al.   PLoS One

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

(2012) N. Koike et al.   SCIENCE

An integrative approach to ortholog prediction for disease-focused and other functional studies

(2011) Yanhui Hu et al.   BMC BIOINFORMATICS

The redox stress hypothesis of aging

(2011) Rajindar S. Sohal et al.   FREE RADICAL BIOLOGY AND MEDICINE

Loss of circadian clock accelerates aging in neurodegeneration-prone mutants

(2011) Natraj Krishnan et al.   NEUROBIOLOGY OF DISEASE

Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation

(2010) R. Yang et al.   BIOINFORMATICS

Circadian Rhythms and Metabolic Syndrome

(2010) Eleonore Maury et al.   CIRCULATION RESEARCH

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Hyperoxia-induced neurodegeneration as a tool to identify neuroprotective genes in Drosophila melanogaster

(2009) Christoph Gruenewald et al.   FREE RADICAL BIOLOGY AND MEDICINE

Circadian regulation of response to oxidative stress in Drosophila melanogaster

(2008) Natraj Krishnan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS