HughesLab:Publications

Home        Lab Members        Research        JTK_Cycle        MuscleDB        Publications        Protocols        Academic Analytics        Open Positions        Contact       

Publications

2017

• 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. In review
• Hughes, M.E., Abruzzi, K., Allada, R., Anafi, R., Arpat, A.B., Asher, G., Baldi, P., de Bekker, C., Bell-Pedersen, D., Blau, J., Brown, S., Ceriani, M.F., Chen, Z., Chiu, J.C., Cox, J., Crowell, A., DeBruyne, J., Dijk, D., DiTacchio, L., Doyle, F., Duffield, G.E., Dunlap, J., Eckel-Mahan, K., Esser, K., FitzGerald, G.A., Forger, D.B., Francey, L.J., Fu, Y., Gachon, F., Gatfield, D., de Goede, P., Golden, S.S., Green, C., Harer, J., Harmer, S., Haspel, J., Hastings, M.H., Herzel, H., Herzog, E., Hoffmann, C., Hong, C., Hughey, J., Hurley, J.M., de la Iglesia, H.O., Johnson, C., Kay, S., Koike, N., Kornacker, K., Kramer, A., Lamia, K., Leise, T., Lewis, S., Li, J., Li, X., Liu, A.C., Loros, J.J., Martino, T.A., Menet, J.S., Merrow, M., Millar, A.J., Mockler, T., Naef, F., Nagoshi, E., Nitabach, M.N., Olmedo, M., Nusinow, D.A., Ptáček, L.J., Rand, D., Reddy, A.B., Robles, M.S., Roenneberg, T., Rosbash, M., Ruben, M.D., Rund, S.S.C., Sancar, A., Sassone-Corsi, P., Sehgal, A., Sherrill-Mix, S., Skene, D.J., Storch, K., Takahashi, J.S., Ueda, H.R., Wang, H., Weitz, C., Westermark, P.O., Wijnen, H., Xu, Y., Wu, G., Yoo, S., Young, M., Zhang, E.E., Zielinski, T., and Hogenesch, J.B. (2017). Guidelines for genome-scale analysis of biological rhythms. Journal of Biological Rhythms. 32(5), 380-393.
• Hughes LD, Lewis SA, Hughes ME (2017) ExpressionDB: An open source platform for distributing genome-scale datasets. PLoS ONE 12(11): e0187457. https://doi.org/10.1371/journal.pone.0187457

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.

---

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