John B. Hogenesch

faculty photo
Adjunct Professor of Pharmacology
Member, Perinatal Institute, Cincinnati Children's Hospital Medical Center
Deputy Director, Center for Chronobiology, Cincinnati Children's Hospital Medical Center
Department: Pharmacology

Contact information
240 Albert Sabin Way
Cincinnati, OH 45229
Office: 4848424232
B.A. (History)
University of Southern California, 1989.
B.S. (Biology)
University of Southern California, 1991.
Ph.D. (Neuroscience)
Northwestern University, 1999.
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Description of Research Expertise

Our laboratory studies the mammalian circadian clock using genomic and computational tools. We use these tools to discover new clock genes, learn how the clock keeps time, and how it coordinates rhythms in physiology and behavior. This clock research drives development of genomic and computational methods that we apply to other areas of biology. Finally, we recognize biological complexity and conduct this research at the network, rather than single gene, level.

Description of Itmat Expertise

Dr. Hogenesch studies the biology of circadian clocks in the mammal and the application of functional genomics tools to understanding genome function.

Selected Publications

Babb Paul L, Lahens Nicholas F, Correa-Garhwal Sandra M, Nicholson David N, Kim Eun Ji, Hogenesch John B, Kuntner Matjaž, Higgins Linden, Hayashi Cheryl Y, Agnarsson Ingi, Voight Benjamin F: The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression. Nature genetics 49(6): 895-903, Jun 2017.

Krishnaiah Saikumari Y, Wu Gang, Altman Brian J, Growe Jacqueline, Rhoades Seth D, Coldren Faith, Venkataraman Anand, Olarerin-George Anthony O, Francey Lauren J, Mukherjee Sarmistha, Girish Saiveda, Selby Christopher P, Cal Sibel, Er Ubeydullah, Sianati Bahareh, Sengupta Arjun, Anafi Ron C, Kavakli I Halil, Sancar Aziz, Baur Joseph A, Dang Chi V, Hogenesch John B, Weljie Aalim M: Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism. Cell metabolism 25(5): 1206, May 2017.

Anafi Ron C, Francey Lauren J, Hogenesch John B, Kim Junhyong: CYCLOPS reveals human transcriptional rhythms in health and disease. Proceedings of the National Academy of Sciences of the United States of America 114(20): 5312-5317, May 2017.

Love Michael I, Hogenesch John B, Irizarry Rafael A: Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nature biotechnology 34(12): 1287-1291, Dec 2016.

Wu Gang, Anafi Ron C, Hughes Michael E, Kornacker Karl, Hogenesch John B: MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics (Oxford, England) 32(21): 3351-3353, Nov 2016.

Sengupta Arjun, Krishnaiah Saikumari Y, Rhoades Seth, Growe Jacqueline, Slaff Barry, Venkataraman Anand, Olarerin-George Anthony O, Van Dang Chi, Hogenesch John B, Weljie Aalim M: Deciphering the Duality of Clock and Growth Metabolism in a Cell Autonomous System Using NMR Profiling of the Secretome. Metabolites 6(3), July 2016.

Zhang Ray, Podtelezhnikov Alexei A, Hogenesch John B, Anafi Ron C: Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA). Journal of biological rhythms 31(3): 244-57, Jun 2016.

Erion Renske, King Anna N, Wu Gang, Hogenesch John B, Sehgal Amita: Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue. eLife 5: pii: e13552, Apr 2016 Notes: doi: 10.7554/eLife.13552.

Vaquero-Garcia Jorge, Barrera Alejandro, Gazzara Matthew R, González-Vallinas Juan, Lahens Nicholas F, Hogenesch John B, Lynch Kristen W, Barash Yoseph: A new view of transcriptome complexity and regulation through the lens of local splicing variations. eLife 5: e11752, Feb 2016 Notes: doi: 10.7554/eLife.11752.

Jang Christopher, Lahens Nicholas F, Hogenesch John B, Sehgal Amita: Ribosome profiling reveals an important role for translational control in circadian gene expression. Genome research(12), 1836-47, Dec 2015.

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Last updated: 07/31/2017
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