Graduate Group in Genomics and Computational Biology

John B. Hogenesch, Ph.D.

faculty photo
Adjunct Professor of Pharmacology
Department: Pharmacology

Contact information
T5.478
240 Albert Sabin Way
Cincinnati, OH 45229
Office: 4848424232
Education:
B.A. (History)
University of Southern California, 1989.
B.S. (Biology)
University of Southern California, 1991.
Ph.D. (Neuroscience)
Northwestern University, 1999.
Permanent link
 

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

Giovannone Adrian J, Winterstein Christine, Bhattaram Pallavi, Reales Elena, Low Seng Hui, Baggs Julie E, Xu Mimi, Lalli Matthew A, Hogenesch John B, Weimbs Thomas: Soluble syntaxin 3 functions as a transcriptional regulator. The Journal of biological chemistry Feb 2018.

Hughes Michael E, Abruzzi Katherine C, Allada Ravi, Anafi Ron, Arpat Alaaddin Bulak, Asher Gad, Baldi Pierre, de Bekker Charissa, Bell-Pedersen Deborah, Blau Justin, Brown Steve, Ceriani M Fernanda, Chen Zheng, Chiu Joanna C, Cox Juergen, Crowell Alexander M, DeBruyne Jason P, Dijk Derk-Jan, DiTacchio Luciano, Doyle Francis J, Duffield Giles E, Dunlap Jay C, Eckel-Mahan Kristin, Esser Karyn A, FitzGerald Garret A, Forger Daniel B, Francey Lauren J, Fu Ying-Hui, Gachon Frédéric, Gatfield David, de Goede Paul, Golden Susan S, Green Carla, Harer John, Harmer Stacey, Haspel Jeff, Hastings Michael H, Herzel Hanspeter, Herzog Erik D, Hoffmann Christy, Hong Christian, Hughey Jacob J, Hurley Jennifer M, de la Iglesia Horacio O, Johnson Carl, Kay Steve A, Koike Nobuya, Kornacker Karl, Kramer Achim, Lamia Katja, Leise Tanya, Lewis Scott A, Li Jiajia, Li Xiaodong, Liu Andrew C, Loros Jennifer J, Martino Tami A, Menet Jerome S, Merrow Martha, Millar Andrew J, Mockler Todd, Naef Felix, Nagoshi Emi, Nitabach Michael N, Olmedo Maria, Nusinow Dmitri A, Ptáček Louis J, Rand David, Reddy Akhilesh B, Robles Maria S, Roenneberg Till, Rosbash Michael, Ruben Marc D, Rund Samuel S C, Sancar Aziz, Sassone-Corsi Paolo, Sehgal Amita, Sherrill-Mix Scott, Skene Debra J, Storch Kai-Florian, Takahashi Joseph S, Ueda Hiroki R, Wang Han, Weitz Charles, Westermark Pål O, Wijnen Herman, Xu Ying, Wu Gang, Yoo Seung-Hee, Young Michael, Zhang Eric Erquan, Zielinski Tomasz, Hogenesch John B: Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of biological rhythms 32(5): 380-393, Oct 2017.

Stern David L, Clemens Jan, Coen Philip, Calhoun Adam J, Hogenesch John B, Arthur Ben J, Murthy Mala: Experimental and statistical reevaluation provides no evidence forcourtship song rhythms. Proceedings of the National Academy of Sciences of the United States of America 114(37): 9978-9983, Sep 2017.

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.

back to top
Last updated: 03/09/2018
The Trustees of the University of Pennsylvania