John B. Hogenesch

Machine learning approaches to identify sleep genes

This study uses machine learning to predict sleep-related genes from genomic data and validates the NF-κB pathway's role in sleep duration in mice.

An in silico genome-wide screen for circadian clock strength in human samples

This paper introduces LTM, an in silico method to identify genetic influences on circadian clock function using gene expression data, and finds the cell cycle and extracellular matrix pathways are strongly associated with clock strength in human tissues.

Detailed Clinical and Functional Studies of New MTOR Variants in Smith-Kingsmore Syndrome Reveal Deficits of Circadian and Sleep Homeostasis

This study identifies new MTOR variants in Smith-Kingsmore Syndrome, reveals circadian and sleep deficits, and shows rapamycin treatment can improve symptoms.

NF-κB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1

This study shows NF-κB interacts with BMAL1 to regulate circadian clock function through transcriptional repression at E-box elements.

Ontogeny and function of the circadian clock in intestinal organoids

This study investigates circadian rhythms in human intestinal organoids, showing circadian phase-dependent necrotic cell death responses to TcdB and identifying anti-phasic gene expression between mouse and human enteroids.

Normalized coefficient of variation (nCV): a method to evaluate circadian clock robustness in population scale data

The paper introduces nCV, a method to assess circadian clock robustness in population-scale data without time labels, finding dampened oscillations in tumors.

A single-sample circadian biomarker that performs across populations and platforms

The paper develops a 12-gene circadian biomarker from epidermal samples that accurately estimates circadian phase across body sites, ages, sexes, and platforms.

CRY1-CBS binding regulates circadian clock function and metabolism

This study identifies CBS-CRY1 binding as a regulatory mechanism linking circadian rhythms and metabolism, showing that CBS modulates CRY1 activity and vice versa.

A detailed graphical and computational model of the mammalian renal circadian clock

The paper constructs a computational model of the mammalian renal circadian clock and validates it against experimental data to understand its role in blood pressure regulation.

Population level rhythms in human skin: implications for circadian medicine

The paper identifies robust circadian rhythms in human skin at the population level and develops single-sample biomarkers for circadian phase.

Systematic analysis of mouse genome reveals distinct evolutionary and functional properties among circadian and ultradian genes

The paper analyzes mouse genome data to show ultradian genes are more evolutionarily conserved and linked to dawn/dusk transitions.

An adipocyte light-Opsin 3 pathway regulates the circadian clock and energy balance.

This study identifies a light-OPN3 pathway in adipocytes that regulates circadian rhythms, energy balance, and thermogenesis in mice.

A population-based human enCYCLOPedia for circadian medicine

The paper identifies rhythmic gene expression across human tissues using computational methods and highlights implications for circadian medicine in cardiovascular disease.