Core clock architecture
Our work helped define mammalian clock architecture through BMAL1/MOP3, NPAS2, BMAL2, and later the RORE loop.
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 human circadian timing and translating temporal biology into physiology, pharmacology, transplantation, and medicine.
Affiliations
Scientific Record
Selected contributions
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.
Scientific Trajectory
From mechanism to medicine
The program moved from defining clock components to measuring temporal biology across genomes and tissues, then to methods that recover biological time from human data. That progression provides the experimental and computational basis for current work in circadian medicine and human genetics.
Current Research
Current work
Measuring human circadian timing
Current work focuses on measuring circadian timing in humans and relating biological time 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.
Human genetics and rare disease
Published work connects circadian and sleep phenotypes to MTOR variants in Smith-Kingsmore syndrome and to a patient-derived model of DLG4-related SHINE syndrome.
Public Resources
Data and methods built for reuse
Gene Atlas, Clock Gene Wiki, CircaDB, and the lab’s analytical methods make genomic and circadian data available for reuse across the field.
People and Training
John B. Hogenesch and the lab
John B. Hogenesch, PhD
John B. Hogenesch is a circadian and genome biologist 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.
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.