Michael Hughes, Ph.D.

Assistant Professor
Internal Medicine
Pulmonary & Critical Care

Molecular Genetics and Genomics Program
Computational and Systems Biology Program
Neurosciences Program

Research Abstract:

Our laboratory is interested in the function and mechanism of tissue-specific gene expression. This leads us to study many different biological phenomena, including circadian clock outputs, specialization of skeletal muscle, and pathological changes in pulmonary disease. We study the specialization of both mRNA and small ncRNA expression, as well as the functional consequences of their manipulation. We use a combination of functional genomics, bioinformatics, and molecular biology approaches.

Selected Publications:

Erin E. Terry, Xiping Zhang, Christy Hoffmann, Laura D. Hughes, Scott A. Lewis, Jiajia Li, Lance Riley, Nicholas F. Lahens, Ming Gong, Francisco Andrade, Karyn A. Esser, Michael E. Hughes. (2017).Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues. BioRxiv.

Laura D Hughes, Scott A Lewis, and Michael E Hughes. (2017) ExpressionDB: An open-source platform for distributing genome-scale datasets. PLoS ONE.

Li, J., Terry, E.E., Fejer, E., Gamba, D., Hartmann, N., Logsdon, J., Michalski, D., Rois, L.E., Scuderi, M.J., Kunst, M., Hughes, M.E. (2016). Achilles is a circadian clock-controlled gene that regulates immune function in Drosophila. Brain, Behavior, and Immunity. doi: 10.1016/j.bbi.2016.11.012.

Li, J., Grant, G., Hogenesch, J.B., Hughes, M.E. (2015). Considerations for RNA-seq analysis of circadian rhythms. Methods in Enzymology. doi: 10.1016/bs.mie.2014.10.020

Zhang, R., Lahens, N., Ballance, H., Hughes, M.E., Hogenesch, J.B. (2014). A circadian gene expression atlas in mammals: implications for biology and medicine. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1408886111

Hughes, M.E., Hong, H.K., Chong, J.L., Indacochea, A.A., Lee, S.S., Han, M., Takahashi, J.S., and Hogenesch, J.B. (2012). Brain-specific rescue of Clock reveals system-driven transcriptional rhythms in peripheral tissue. PLoS Genetics. 8(7): e1002835.

Hughes, M.E., Grant, G., Pacquin, C., and Nitabach, M. (2012). Deep sequencing the circadian transcriptome of Drosophila brain. Genome Research. 22: 1266-1281.

Hughes, M. E., Hogenesch, J. B., and Kornacker, K. (2010). JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. Journal of Biological Rhythms. 25, 372-380.

Hughes, M. E., DiTacchio, L., Hayes, K. R., Vollmers, C., Pulivarthy, S., Baggs, J. E., Panda, S., and Hogenesch, J. B. (2009). Harmonics of circadian gene transcription in mammals. PLoS Genetics. 5, e1000442.

Last Updated: 1/19/2018 11:18:07 AM

Extraordinary diversity of gene expression in skeletal muscle tissues
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