Tong Zhou Ph.D.: Experience/Publications

Assistant Professor

Department of Physiology and Cell Biology

Selected publications

In Press

  • Zhou T., Casanova N., Pouladi N., Wang T., Lussier Y., Knox K., and Garcia J.G.N.,. In Press. Identification of Jak-STAT signaling involvement in sarcoidosis severity via a novel microRNA-regulated peripheral blood mononuclear cell gene signature. Scientific Reports.
  • Li M., Xie X., Zhou J., Sheng M., Yin X., Ko E.A., Zhou T.*, and Gu W.*. In Press. Quantifying circular RNA expression from RNA-seq data using model-based framework. Bioinformatics, in press. (*co-corresponding author).

2016

  • Qian Z., Lv J., Kelly G.T., Wang H., Zhang X., Gu W., Yin X., Wang T., and Zhou T. . Expression of nuclear factor, erythroid 2-like 2-mediated genes differentiates tuberculosis. Tuberculosis, 99, 56-62.

2015

  • Wang T.*, Zhou T.*, Saadat L., and Garcia J.G.N. . A MYLK variant regulates asthmatic inflammation via alterations in mRNA secondary structure. European Journal of Human Genetics, 23, 874–876.
  • Gu W., Gurguis C.I., Zhou J.J., Zhu Y., Ko E.A., Ko J.H., Wang T., and Zhou T. . Functional and structural consequence of rare exonic single nucleotide polymorphisms: one story, two tales. Genome Biology and Evolution, 7, 2929-2940.
  • Casanova N.*, Zhou T.*, Knox K.S., and Garcia J.G. . Identifying novel biomarkers in sarcoidosis using genome-based approaches. Clinics in Chest Medicine, 36, 621-630 (*co-first author).

2014

  • Zhou T., Wang T., and Garcia J.G. . Expression of nicotinamide phosphoribosyltransferase mediated genes predicts recurrence-free survival in lung and breast cancers. Scientific Reports, 4, 6107.
  • Gu W., Li M., Xu Y., Wang T., Ko J.H., and Zhou T. . The impact of RNA structure on coding sequence evolution in both bacteria and eukaryotes. BMC Evolutionary Biology, 14, 87.
  • Gu W., Xu Y., Xie X., Wang T., Ko J.H., and Zhou T. . The role of RNA structure at 5'-untranslated region in microRNA-mediated gene regulation. RNA, 20, 1369-75.

2013

  • Ko J.H., Ko E.A., Gu W., Lim I., Bang H., and Zhou T. . Expression profiling of ion channel genes predicts clinical outcome in breast cancer. Molecular Cancer, 12, 106.

2012

  • Desai A.A., Zhou T., Ahmad H., Zhang W., Mu W., Trevino S., Wade M.S., Raghavachari N., Kato G.J., Peters-Lawrence M., Thiruvoipati T., Turner K., Artz N., Huang Y., Patel A.R., Yuan J.X., Gordeuk V.R., Lang R.M., Garcia J.G.N., and Machado R.F. . A novel molecular signature for elevated tricuspid regurgitation velocity in sickle cell disease. American Journal of Respiratory and Critical Care Medicine, 186, 359-368.
  • Frank K.M., Zhou T., Moreno-Vinasco L., Hollett B., Garcia J.G.N., and Wardenburg J.B. . Host response signature to Staphylococcus aureus a-hemolysin implicates pulmonary TH17 response. Infection and Immunity, 80, 3161-3169.
  • Gu W., Wang X., Zhai C., Xie X., and Zhou T. . Selection on synonymous sites for increased accessibility around miRNA binding sites in plants. Molecular Biology and Evolution, 29, 3037-3044.
  • Pitroda S.P.*, Zhou T.*, Sweis R.F., Filippo M., Labay E., Beckett M.A., Mauceri H.J., Liang H., Darga T.E., Perakis S., Khan S.A., Sutton H.G., Zhang W., Khodarev N.N., Garcia J.G.N., and Weichselbaum R.R. . Tumor endothelial inflammation predicts clinical outcome in diverse human cancers. PLoS ONE, 7, e46104 (*co-first author).

2011

  • Zhou T., Garcia J.G.N., and Zhang W. . Integrating microRNAs into a system biology approach to acute lung injury. Translational Research, 157, 180-190.
  • Zhou T. and Wilke C.O. . Reduced stability of mRNA secondary-structure near the translation-initiation site in dsDNA viruses. BMC Evolutionary Biology, 11, 59.
  • Ramsey D.C., Scherrer M.P., Zhou T., and Wilke C.O. . The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics, 188, 479-488.

2010

  • Gu W.*, Zhou T.*, and Wilke C.O. . A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLOS Computational Biology, 6, e1000664 (*co-first author).
  • Zhou T., Gu W., and Wilke C.O. . Detecting positive and purifying selection at synonymous sites in yeast and worm. Molecular Biology and Evolution, 27, 1912-1922.
  • Stark A.L., Zhang W., Zhou T., O’Donnell P.H., Beiswanger C.M.,Huang R.S., Cox N.J., and Dolan M.E. . Population differences in rate of proliferation of international HapMap cell lines. The American Journal of Human Genetics, 87, 829-833.
  • Lee Y., Zhou T., Tartaglia G.G., Vendruscolo M., and Wilke C.O. . Translationally optimal codons associate with aggregation-prone sites in proteins. Proteomics, 10, 4163-4171.

2009

  • Zhou T., Weems M., and Wilke C.O. . Translationally optimal codons associate with structurally sensitive sites in protein. Molecular Biology and Evolution, 26, 1571-1580.

2008

  • Zhou T., Drummond D.A., and Wilke C.O. . Contact density affects protein evolutionary rate from bacteria to animals. Journal of Molecular Evolution, 66, 395-404.
  • Zhou T., Enyeart P.J., and Wilke C.O. . Detecting clusters of mutations. PLoS ONE, 3, e3765.

2006

  • Zhou T., Weng J., Sun X., and Lu Z. . Support vector machine for classification of recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon composition. BMC Bioinformatics, 7, 223.
  • Zhou T., Sun X., and Lu Z. . Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae. Gene, 368, 117-125.

2004

  • Gu W., Zhou T., Ma J., Sun X., and Lu Z. . Analysis of synonymous codon usage in SARS coronavirus and other viruses in the Nidovirales. Virus Research, 101, 155-161.

2003

  • Gu W., Zhou T., Ma J., Sun X., and Lu Z. . Folding type specific secondary structure propensities of synonymous codons. IEEE Transactions on NanoBioscience, 2, 150-157.

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