Hogenesch Lab

Research program

Hogenesch Lab

Circadian Biology • Systems Biology • Circadian Medicine

The Hogenesch Lab studies biological timing across molecular mechanisms, genome-scale transcription, and medicine. The work links core clock architecture to tissue-scale rhythmic programs and to translational questions about when physiology, disease processes, and therapies are most sensitive to time of day.

Research Selected Publications CircaDB People Join the Lab

Affiliations Cincinnati Children's Hospital Medical Center logo Scripps Research logo

Abstract clock and network graphic representing connected areas of circadian biology, systems biology, and medicine.
An abstract view of biological timing across molecular mechanisms, tissues, methods, and medicine.

Landmark Contributions

Major published contributions

  • Defining the positive loop of the mammalian circadian clock through BMAL1, CLOCK, NPAS2, and BMAL2.
  • Creation of Gene Atlas, one of the first comprehensive maps of gene expression across mammalian tissues.
  • Defining the mammalian circadian transcriptome with genome-scale temporal profiling.
  • Creation of the circadian gene expression atlas across mouse organs.
  • Development of widely used algorithms including JTK_CYCLE, PSEA, and MetaCycle.
  • Extraction of human circadian structure from unordered transcriptomic data using CYCLOPS.
  • Creation of CircaDB as a public circadian gene-expression resource.
Conceptual map showing the lab's landmark contributions across clock biology, atlases, algorithms, human ordering, and public resources.
A temporal 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.

Research Themes

Five directions of research

Molecular Circadian Clock

Mechanistic work on BMAL1, NPAS2, transcriptional feedback architecture, and clock-controlled gene regulation in mammalian systems.

Circadian Biology

Rhythmic physiology across organs, tissues, and cell systems, including the architecture and outputs of biological clocks.

Systems Biology

Genome-scale transcriptional programs, the mammalian circadian transcriptome, and atlas-level studies of time across tissues.

Computational Methods and Resources

Algorithms and public tools including JTK_CYCLE, PSEA, MetaCycle, CYCLOPS, CYCLOPS2, CircaDB, and Gene Atlas.

Circadian Medicine and Rare Disease

Human transcriptomics, chronotherapy, and published work linking circadian phenotypes to Human Genetics and rare disease, including Smith-Kingsmore syndrome.

Featured Resource

CircaDB

CircaDB is a public database of mammalian circadian gene expression profiles developed by the Hogenesch Lab in collaboration with Andrew Su. The resource allows researchers to explore rhythmic gene expression across tissues and datasets and has become a widely used tool in the circadian biology community.

Explore CircaDB

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

Pizarro et al., Nucleic Acids Research 2013. Open-access figure (CC BY-NC 3.0).

People

Experimental, computational, and translational chronobiology

Principal Investigator

John B. Hogenesch, PhD

Thomas F. Boat Chair, Cincinnati Children’s Hospital Medical Center.

The lab’s work spans molecular circadian biology, systems biology, public resources, and translational questions in circadian medicine.

Lab Community

Research in the group brings together experimental biologists, computational scientists, clinician-scientists, trainees, and collaborators around shared questions of biological timing.

View the full People page or Scientific Lineage.

Join the Lab

Students, postdoctoral fellows, and collaborators

The lab welcomes inquiries from people interested in circadian biology, systems biology, computational methods, and translational timing questions in medicine.

Join the Lab

Press

Selected coverage and image links

Selected external coverage of the lab’s published work, with links to stories and associated figure or image pages.

View In the Press