Hogenesch Lab

From clock genes to circadian medicine

Biological time across molecular mechanisms, temporal genomics, and human physiology.

Our work helped define core components of the mammalian circadian clock, including BMAL1 and NPAS2, map genome-scale circadian transcription across tissues, and develop widely used methods including JTK_CYCLE, MetaCycle, and CYCLOPS. The lab also developed public resources including Gene Atlas and CircaDB. Current work focuses on measuring circadian timing and amplitude in humans and translating temporal biology into physiology, pharmacology, transplantation, and medicine.

Selected Contributions Current Research Selected Publications CircaDB People and Training

Affiliations

Selected Contributions

Selected contributions

Core clock architecture

Our work helped define mammalian clock architecture through BMAL1/MOP3, NPAS2, BMAL2, and later the RORE loop.

Genome-scale circadian transcription

This work established that rhythmic transcription in mammals extends well beyond a small canonical set of clock genes.

Temporal atlases

The lab developed Gene Atlas and later circadian atlases across mouse organs and human datasets.

Methods for rhythmic biology

The lab developed or co-developed JTK_CYCLE, PSEA, MetaCycle, CYCLOPS, and CYCLOPS2.

Public scientific resources

The group built public resources including Gene Atlas, Clock Gene Wiki, and CircaDB.

Human circadian biology and medicine

This work showed that time of day can be recovered from human data at scale and used to interpret physiology and pharmacology.

Why This Lab

Why this lab

Over two decades, the lab has contributed to circadian biology from molecular mechanisms to genome-scale systems and human physiology. The same progression produced clock gene discoveries, temporal atlases, analytical methods, and public resources. That trajectory informs current work in human timing, circadian medicine, and translation.

See selected publications

Chronological timeline showing the lab's contributions across clock biology, atlases, algorithms, human ordering, and public resources. — A chronological view of the lab’s major contributions, with time as the organizing variable across molecular clock biology, atlas-scale genomics, computational methods, and public resources.

Current Research

Current work

Measuring human circadian timing and amplitude

Current work focuses on measuring circadian timing and amplitude in humans and relating those measures to physiology, pharmacology, and treatment.

Molecular output and physiology

The lab studies how clock factors regulate downstream transcription and connect molecular oscillators to physiological output.

Systems-level chronobiology

The group examines how rhythmic programs vary across tissues, cell states, and organ systems.

Methods, resources, and translation

Current work extends computational tools and reusable datasets for circadian biology, human translation, genetics, and medicine.

Public Resources

Public resources developed by the lab

Resource building has been a recurring part of the lab’s work. Gene Atlas, Clock Gene Wiki, and CircaDB were developed to make genomic and circadian data easier to use across the field.

Gene Atlas established a tissue-scale reference for mammalian gene expression.
Clock Gene Wiki organized clock components and annotations in a public framework.
CircaDB provides access to circadian expression data across tissues and datasets.

Explore CircaDB View resources

Published CircaDB query interface. — CircaDB provides direct access to circadian expression data by gene, dataset, tissue, phase, and significance threshold.

People and Training

John B. Hogenesch and the lab

John B. Hogenesch, PhD

John B. Hogenesch is a chronobiologist and genomicist whose work spans core clock biology, temporal genomics, public scientific resources, and circadian medicine.

He is Thomas F. Boat Chair at Cincinnati Children’s Hospital Medical Center, with appointments in Human Genetics, Pulmonary Medicine, and Immunobiology.

What kind of lab this is

The lab combines experimental biology, computational analysis, and clinical translation.

Current work follows directly from earlier contributions to clock genes, temporal genomics, methods, and public resources.

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Press

Selected coverage

Selected coverage of published work in the lab, including long-form reporting, science journalism, and historical context around key papers and datasets.

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