Evidence for widespread dysregulation of circadian clock progression in human cancer

Cell-intrinsic, Bmal1-dependent Circadian Regulation of Temozolomide Sensitivity in Glioblastoma

(2017) Emily A. Slat 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

The Ink4a/Arf locus operates as a regulator of the circadian clock modulating RAS activity

(2017) Rukeia El-Athman et al.   PLOS BIOLOGY

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

Circadian Homeostasis of Liver Metabolism Suppresses Hepatocarcinogenesis

(2016) Nicole M. Kettner et al.   CANCER CELL

Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis

(2016) Selma Masri et al.   CELL

Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML

(2016) Rishi V. Puram et al.   CELL

Circadian Rhythm Disruption Promotes Lung Tumorigenesis

(2016) Thales Papagiannakopoulos et al.   Cell Metabolism

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

Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture

(2016) Toru Matsu-ura et al.   MOLECULAR CELL

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

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

Circadian control of oscillations in mitochondrial rate-limiting enzymes and nutrient utilization by PERIOD proteins

(2016) Adi Neufeld-Cohen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets

(2016) Scott C. Ritchie et al.   Cell Systems

Advanced Circadian Phase in Mania and Delayed Circadian Phase in Mixed Mania and Depression Returned to Normal after Treatment of Bipolar Disorder

(2016) Joung-Ho Moon et al.   EBioMedicine

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results

(2015) Mumtahena Rahman et al.   BIOINFORMATICS

MYC Disrupts the Circadian Clock and Metabolism in Cancer Cells

(2015) Brian J. Altman et al.   Cell Metabolism

Chronically Alternating Light Cycles Increase Breast Cancer Risk in Mice

(2015) Kirsten C.G. Van Dycke et al.   CURRENT BIOLOGY

Neoangiogenesis-related genes are hallmarks of fast-growing hepatocellular carcinomas and worst survival. Results from a prospective study

(2015) Erica Villa et al.   GUT

The chondrocyte clock gene Bmal1 controls cartilage homeostasis and integrity

(2015) Michal Dudek et al.   JOURNAL OF CLINICAL INVESTIGATION

Fast and Stable Multiple Smoothing Parameter Selection in Smoothing Spline Analysis of Variance Models With Large Samples

(2015) Nathaniel E. Helwig et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Identification of Circadian Determinants of Cancer Chronotherapy through In Vitro Chronopharmacology and Mathematical Modeling

(2015) S. Dulong et al.   MOLECULAR CANCER THERAPEUTICS

Cancer/Testis Antigen PASD1 Silences the Circadian Clock

(2015) Alicia K. Michael et al.   MOLECULAR CELL

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

(2015) Ning Leng et al.   NATURE METHODS

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

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

Genetic and epigenetic regulation of gene expression in fetal and adult human livers

(2014) Marc Bonder et al.   BMC GENOMICS

Loss of circadian clock gene expression is associated with tumor progression in breast cancer

(2014) Cristina Cadenas et al.   CELL CYCLE

Time-Restricted Feeding Is a Preventative and Therapeutic Intervention against Diverse Nutritional Challenges

(2014) Amandine Chaix et al.   Cell Metabolism

Cardiomyocyte-Specific BMAL1 Plays Critical Roles in Metabolism, Signaling, and Maintenance of Contractile Function of the Heart

(2014) Martin E. Young et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells

(2014) J. Bieler et al.   Molecular Systems Biology

Loss of Connectivity in Cancer Co-Expression Networks

(2014) Roberto Anglani et al.   PLoS One

Non-Circadian Expression Masking Clock-Driven Weak Transcription Rhythms in U2OS Cells

(2014) Julia Hoffmann et al.   PLoS One

Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle

(2014) Céline Feillet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mistimed sleep disrupts circadian regulation of the human transcriptome

(2014) Simon N. Archer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Blood-Gene Expression Reveals Reduced Circadian Rhythmicity in Individuals Resistant to Sleep Deprivation

(2014) Erna S. Arnardottir et al.   SLEEP

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

Ras-Mediated Deregulation of the Circadian Clock in Cancer

(2014) Angela Relógio et al.   PLoS Genetics

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Rotating Night-Shift Work and Lung Cancer Risk Among Female Nurses in the United States

(2013) E. S. Schernhammer et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Prediction of Disease-free Survival in Hepatocellular Carcinoma by Gene Expression Profiling

(2013) Ho-Yeong Lim et al.   ANNALS OF SURGICAL ONCOLOGY

Reprogramming of the Circadian Clock by Nutritional Challenge

(2013) Kristin L. Eckel-Mahan et al.   CELL

Human Epidermal Stem Cell Function Is Regulated by Circadian Oscillations

(2013) Peggy Janich et al.   Cell Stem Cell

Circadian patterns of gene expression in the human brain and disruption in major depressive disorder

(2013) J. Z. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of insufficient sleep on circadian rhythmicity and expression amplitude of the human blood transcriptome

(2013) C. S. Moller-Levet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular architecture of the mammalian circadian clock

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

Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock

(2013) Kenneth A. Dyar et al.   Molecular Metabolism

Comparison of co-expression measures: mutual information, correlation, and model based indices

(2012) Lin Song et al.   BMC BIOINFORMATICS

Molecular Signature of Smoking in Human Lung Tissues

(2012) Y. Bosse et al.   CANCER RESEARCH

Entrainment of breast (cancer) epithelial cells detects distinct circadian oscillation patterns for clock and hormone receptor genes

(2012) Stefano Rossetti et al.   CELL CYCLE

Time-Restricted Feeding without Reducing Caloric Intake Prevents Metabolic Diseases in Mice Fed a High-Fat Diet

(2012) Megumi Hatori et al.   Cell Metabolism

Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression

(2012) S. A. Selamat et al.   GENOME RESEARCH

The Circadian Clock Modulates Renal Sodium Handling

(2012) S. Nikolaeva et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

A mechanism for robust circadian timekeeping via stoichiometric balance

(2012) Jae Kyoung Kim et al.   Molecular Systems Biology

Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β

(2012) Han Cho et al.   NATURE

Mapping cis- and trans-regulatory effects across multiple tissues in twins

(2012) Elin Grundberg et al.   NATURE GENETICS

Obesity in mice with adipocyte-specific deletion of clock component Arntl

(2012) Georgios K Paschos et al.   NATURE MEDICINE

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

Brain and muscle Arnt-like protein-1 (BMAL1) controls circadian cell proliferation and susceptibility to UVB-induced DNA damage in the epidermis

(2012) M. Geyfman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Involvement of urinary bladder Connexin43 and the circadian clock in coordination of diurnal micturition rhythm

(2012) Hiromitsu Negoro et al.   Nature Communications

Differential network entropy reveals cancer system hallmarks

(2012) James West et al.   Scientific Reports

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Predictive Genes in Adjacent Normal Tissue Are Preferentially Altered by sCNV during Tumorigenesis in Liver Cancer and May Rate Limiting

(2011) John R. Lamb et al.   PLoS One

Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue

(2011) Federico Innocenti et al.   PLoS Genetics

The Mammalian Circadian Timing System: Organization and Coordination of Central and Peripheral Clocks

(2010) Charna Dibner et al.   Annual Review of Physiology

Identification of a Novel Biomarker, SEMA5A, for Non-Small Cell Lung Carcinoma in Nonsmoking Women

(2010) T.-P. Lu et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

A Unique Metastasis Gene Signature Enables Prediction of Tumor Relapse in Early-Stage Hepatocellular Carcinoma Patients

(2010) S. Roessler et al.   CANCER RESEARCH

Poly(ADP-Ribose) Polymerase 1 Participates in the Phase Entrainment of Circadian Clocks to Feeding

(2010) Gad Asher et al.   CELL

Gene Expression-Based Classification of Non-Small Cell Lung Carcinomas and Survival Prediction

(2010) Jun Hou et al.   PLoS One

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn

(2010) Belinda Phipson et al.   Statistical Applications in Genetics and Molecular Biology

A large-scale functional RNAi screen reveals a role for CK2 in the mammalian circadian clock

(2009) B. Maier et al.   GENES & DEVELOPMENT

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

Circadian Control of the NAD+ Salvage Pathway by CLOCK-SIRT1

(2009) Y. Nakahata et al.   SCIENCE

Harmonics of Circadian Gene Transcription in Mammals

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

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Transcriptional Profiling of mRNA Expression in the Mouse Distal Colon

(2008) Willemijntje A. Hoogerwerf et al.   GASTROENTEROLOGY

Gene Expression Signature of Cigarette Smoking and Its Role in Lung Adenocarcinoma Development and Survival

(2008) Maria Teresa Landi et al.   PLoS One

A High-Throughput Assay for siRNA-Based Circadian Screens in Human U2OS Cells

(2008) Christopher Vollmers et al.   PLoS One

Mapping the Genetic Architecture of Gene Expression in Human Liver

(2008) Eric E Schadt et al.   PLOS BIOLOGY