HughesLab:Publications

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Publications

2016

• 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.
• Wu, G., Anafi, R.C., Hughes, M.E., Kornacker, K., Hogenesch, J.B. (2016). MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics. 32 (21), 3351-3353.

2015

• 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
• Gong, C., Li, C., Qi, X., Song, Z., Wu, J., Hughes, M. E., Li, X. (2015). The daily rhythms of mitochondrial gene expression and oxidative stress regulation are altered by aging in the mouse liver. Chronobiology International. 32(9): 1254-1263.
• Tranel, H.R., Schroder, E.A., England, J., Black, W.S., Bush, H., Hughes, M.E., Esser, K.A. Clasey, J.L., (2015). Physical activity, and not fat mass is a primary predictor of circadian parameters in young men. Chronobiology International. 32(6): 832-841.

2014

• Kunst, M., Hughes, M.E., Barnett, G., Duah, J., Nitabach, M.N. (2014). Calcitonin gene-related peptide neurons mediate sleep-specific circadian output in Drosophila. Current Biology. 24 (22), 2652-2664.
• 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
• Anafi, R., Lee, Y., Sato, T.K., Venkataraman, A., Ramanathan, C., Kavakli, I.H., Hughes, M.E., Baggs, J.B., Growe, J., Liu, A.C., Kim, J., Hogenesch, J.B. (2014) Machine learning helps identify CHRONO as a circadian clock component. PLoS Biology. 12(4): e1001840.
• Hughes, M.E., Peeler, P., Hogenesch, J.B., Trojanowski, J.Q. (2014). The growth and impact of Alzheimer Disease Centers as measured by social network analysis. JAMA Neurology. 71(4): 412-420.

2013

• Li, M.D., Ruan, H.B., Hughes, M.E., Lee, J.S., Singh, J.P., Jones, S.P., Nitabach, M.N., and Yang X. (2013). O-GlcNAc signaling entrains the circadian clock by modulating BMAL1/CLOCK ubiquitination. Cell Metabolism. 17(2): 303-310.
  

2012

• 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.
  
• Silver, A.C., Arjona, A., Hughes, M.E., Nitabach, M.N., Fikrig, E., (2012). Circadian expression of clock genes in mouse macrophages, dendritic cells, and B cells. Brains, Behavior and Immunity. 26(3):407-13.
  

2011

• Miyazaki M., Schroder E., Edelmann S.E., Hughes M.E., Balke C.W., Esser K.A. (2011). Age-Associated Disruption of Molecular Clock Expression in Skeletal Muscle of the Spontaneously Hypertensive Rat. PLoS ONE. 6(11), e27168.
  
• Xu, K., Diangelo, J. R., Hughes, M. E., Hogenesch, J. B., and Sehgal, A. (2011). The circadian clock interacts with metabolic physiology to influence reproductive fitness. Cell Metabolism. 13, 639-654.
  

2010

• 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., Peeler, J., and Hogenesch, J. B. (2010). Network dynamics to evaluate performance of an academic institution. Science Translational Medicine. 2, 53ps49.
  
• Baggs, J. E., Hughes, M. E., and Hogenesch, J. B. (2010). The network as the target. Wiley Interdiscip. Rev. Syst. Biol. Med. 2, 127-133.
  

2009

• 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.
  

2007

• Hughes, M., Deharo, L., Pulivarthy, S. R., Gu, J., Hayes, K., Panda, S., and Hogenesch, J. B. (2007). High-resolution time course analysis of gene expression from pituitary. Cold Spring Harbor Symposia on Quantitative Biology 72, 381-386.
  
• Hughes, M. E., Bortnick, R., Tsubouchi, A., Bäumer, P., Kondo, M., Uemura, T., and Schmucker, D. (2007). Homophilic Dscam interactions control complex dendrite morphogenesis. Neuron. 54, 417-427.
  
• Kang, Y. J., Kusler, B., Otsuka, M., Hughes, M., Suzuki, N., Suzuki, S., Yeh, W.-C., Akira, S., Han, J., and Jones, P. P. (2007). Calcineurin negatively regulates TLR-mediated activation pathways. Journal of Immunology. 179, 4598-4607.
  

2005

• Watson, F. L., Püttmann-Holgado, R., Thomas, F., Lamar, D. L., Hughes, M., Kondo, M., Rebel, V. I., and Schmucker, D. (2005). Extensive diversity of Ig-superfamily proteins in the immune system of insects. Science. 309, 1874-1878.

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Hughes Lab
Pulmonary and Critical Care Medicine
Washington University School of Medicine