Graduate Group in Genomics and Computational Biology

John B. Hogenesch, Ph.D.

faculty photo
Adjunct Professor of Pharmacology
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.

Selected Publications

Anafi et al.,: "CYCLOPS reveals human transcriptional rhythms in health and disease" PNAS In Press, 2017.

Krishnaiah et al.,: "Clock regulation of metabolites reveals coupling between transcription and metabolism" Cell Metabolism In Press, 2017.

Babb et al.,: "The Nephila clavipes genome reveals greater diversity of spider silk genes and the complexity of their expression" Nature Genetics In Press, 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.

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.

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) Jul 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, Apr 2016.

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, Feb 2016.

Ma Di, Liu Tongyu, Chang Lin, Rui Crystal, Xiao Yuanyuan, Li Siming, Hogenesch John B, Chen Y Eugene, Lin Jiandie D: The Liver Clock Controls Cholesterol Homeostasis through Trib1 Protein-mediated Regulation of PCSK9/Low Density Lipoprotein Receptor (LDLR) Axis. The Journal of biological chemistry 290(52): 31003-12, Dec 2015.

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Last updated: 03/21/2017
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