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A photo of John Hogenesch.

Professor, UC Department of Pediatrics


Biography & Affiliation


Dr. Hogenesch is an Ohio Eminent Scholar and professor of Pediatrics at Cincinnati Children's Hospital Medical Center in the Divisions of Human Genetics and Immunobiology within the UC Department of Pediatrics. His lab studies genome biology with a focus on the molecular mechanisms of circadian rhythms in mammals. Dr. Hogenesch discovered several new bHLH-PAS transcription factors, including the hypoxia inducible factors, as well as the core clock components, Npas2, Bmal2, Rora, and Bmal1, the only required component of the mammalian circadian clock. Dr. Hogenesch also pioneered the discovery of clock regulated gene expression in plants, flies, mice, and man. As a genome biologist, Dr. Hogenesch's lab applies and integrates various disciplines including bioinformatics, genomics, molecular and cellular biology, and genetics.

Before moving to Cincinnati, Dr. Hogenesch was professor and vice chair of Pharmacology at the University of Pennsylvania Perelman School of Medicine. He did his PhD in Neuroscience at Northwestern University. Currently, Dr. Hogenesch is a Penn Fellow, sits or has sat on the Scientific Advisory Boards of Qiagen, Mimetics, Bio-Rad, the Ryan Licht Sang Foundation Medical Committee, and the Gene Ontology (GO) consortium, and is an advisor to several National Institutes of Health, NIDDK, NCI, NHLBI, and the Environmental Protection Agency (EPA).

Academic Affiliation

Professor, UC Department of Pediatrics


Human Genetics, Immunobiology


Postdoctoral Training: Genomics, Novartis, Basel, Switzerland.

PhD: Neuroscience, Northwestern University, Evanston, IL, 1999.

BA: History, University of Southern California, Los Angeles, CA, 1989.

BS: Biology, University of Southern California, Los Angeles, CA, 1991.


Selected Publication

CYCLOPS reveals human transcriptional rhythms in health and disease. Anafi, RC; Francey, LJ; Hogenesch, JB; Kim, J. Proceedings of the National Academy of Sciences of USA. 2017; 114:5312-5317.

Circadian Rhythms: Move Over Neurons - Astrocytes Mediate SCN Clock Function. Ruben, MD; Hogenesch, JB. Current Biology. 2017; 27:R350-R352.

Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism. Krishnaiah, SY; Wu, G; Altman, BJ; Growe, J; Rhoades, SD; Coldren, F; Venkataraman, A; Olarerin-George, AO; Francey, LJ; Mukherjee, S; et al. Cell Metabolism. 2017; 25:961-974.e4.

MetaCycle: an integrated R package to evaluate periodicity in large scale data. Wu, G; Anafi, RC; Hughes, ME; Kornacker, K; Hogenesch, JB. Bioinformatics. 2016; 32:3351-3353.

Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA). Zhang, R; Podtelezhnikov, AA; Hogenesch, JB; Anafi, RC. Journal of Biological Rhythms. 2016; 31:244-257.

KPNB1 mediates PER/CRY nuclear translocation and circadian clock function. Lee, Y; Jang, AR; Francey, LJ; Sehgal, A; Hogenesch, JB. eLife. 2015; 4.

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive. Olarerin-George, AO; Hogenesch, JB. Nucleic Acids Research. 2015; 43:2535-2542.

A circadian gene expression atlas in mammals: Implications for biology and medicine. Zhang, R; Lahens, NF; Ballance, HI; Hughes, ME; Hogenesch, JB. Proceedings of the National Academy of Sciences of USA. 2014; 111:16219-16224.

IVT-seq reveals extreme bias in RNA sequencing. Lahens, NF; Kavakli, IH; Zhang, R; Hayer, K; Black, MB; Dueck, H; Pizarro, A; Kim, J; Irizarry, R; Thomas, RS; et al. Genome Biology: biology for the post-genomic era. 2014; 15:R86-R86.

Machine Learning Helps Identify CHRONO as a Circadian Clock Component. Anafi, RC; Lee, Y; Sato, TK; Venkataraman, A; Ramanathan, C; Kavakli, IH; Hughes, ME; Baggs, JE; Growe, J; Liu, AC; et al. PLoS Biology. 2014; 12:e1001840-e1001840.