John B. Hogenesch

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Professor of Pharmacology
Associate Director, Penn Genome Frontiers Institute, University of Pennsylvania School of Medicine
Member, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine
Interim Director, Institute for Biomedical Informatics
Department: Pharmacology

Contact information
Smilow Translational Research Center 10-124
3400 Civic Center Blvd., Bldg. 421
Philadelphia, PA 19104-5158
Office: 484-842-4232
Education:
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

Zhang Ray, Lahens Nicholas F, Ballance Heather I, Hughes Michael E, Hogenesch John B: A circadian gene expression atlas in mammals: Implications for biology and medicine. Proceedings of the National Academy of Sciences of the United States of America 111(45): 16219-24, Nov 2014.

Perez-Santángelo Soledad, Mancini Estefanía, Francey Lauren J, Schlaen Ruben Gustavo, Chernomoretz Ariel, Hogenesch John B, Yanovsky Marcelo J: Role for LSM genes in the regulation of circadian rhythms. Proceedings of the National Academy of Sciences of the United States of America 111(42): 15166-71, Oct 2014.

Pellegrino Renata, Kavakli Ibrahim Halil, Goel Namni, Cardinale Christopher J, Dinges David F, Kuna Samuel T, Maislin Greg, Van Dongen Hans P A, Tufik Sergio, Hogenesch John B, Hakonarson Hakon, Pack Allan I: A Novel BHLHE41 Variant is Associated with Short Sleep and Resistance to Sleep Deprivation in Humans. Sleep 37(8): 1327-36, August 2014.

Lahens Nicholas F, Kavakli Ibrahim Halil, Zhang Ray, Hayer Katharina, Black Michael B, Dueck Hannah, Pizarro Angel, Kim Junhyong, Irizarry Rafael, Thomas Russell S, Grant Gregory R, Hogenesch John B: IVT-seq reveals extreme bias in RNA-sequencing. Genome biology 15(6): R86, Jun 2014.

Ramanathan Chidambaram, Xu Haiyan, Khan Sanjoy K, Shen Yang, Gitis Paula J, Welsh David K, Hogenesch John B, Liu Andrew C: Cell type-specific functions of period genes revealed by novel adipocyte and hepatocyte circadian clock models. PLoS Genetics 10(4): e1004244, Apr 2014.

Anafi Ron C, Lee Yool, Sato Trey K, Venkataraman Anand, Ramanathan Chidambaram, Kavakli Ibrahim H, Hughes Michael E, Baggs Julie E, Growe Jacqueline, Liu Andrew C, Kim Junhyong, Hogenesch John B: Machine Learning Helps Identify CHRONO as a Circadian Clock Component. PLoS biology 12(4): e1001840, Apr 2014.

Hughes Michael E, Peeler John, Hogenesch John B, Trojanowski John Q: The Growth and Impact of Alzheimer Disease Centers as Measured by Social Network Analysis. JAMA neurology Feb 2014.

Toung Jonathan M, Lahens Nicholas, Hogenesch John B, Grant Gregory: Detection Theory in Identification of RNA-DNA Sequence Differences Using RNA-Sequencing. PloS one 9(11): e112040, 2014.

Musiek Erik S, Lim Miranda M, Yang Guangrui, Bauer Adam Q, Qi Laura, Lee Yool, Roh Jee Hoon, Ortiz-Gonzalez Xilma, Dearborn Joshua T, Culver Joseph P, Herzog Erik D, Hogenesch John B, Wozniak David F, Dikranian Krikor, Giasson Benoit I, Weaver David R, Holtzman David M, Fitzgerald Garret A: Circadian clock proteins regulate neuronal redox homeostasis and neurodegeneration. The Journal of clinical investigation 123(12): 5389-400, Dec 2013.

Deckard Anastasia, Anafi Ron C, Hogenesch John B, Haase Steven B, Harer John: Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. Bioinformatics (Oxford, England) Oct 2013.

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Last updated: 11/20/2014
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