User:Tong Zhou

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Tong Zhou
Tong Zhou, Research Assistant Professor
Department of Medicine
The University of Arizona, Tucscon, Arizona, 85721
Email: tongzhou@email.arizona.edu, Tel: 520-626-8433

Former Position

  • 2006 - 2010, Postdoc, Center for Computational Biology and Bioinformatics and Section of Integrative Biology, The University of Texas at Austin

Education

  • 2006, PhD, Southeast University, China
  • 2002, MS, Southeast University, China
  • 2000, BS, Southeast University, China

Research interests

  1. Computational Biology
  2. Bioinformatics
  3. Translational Genomics and Genetics

Publications

  • In press
  1. Zhang W., Zhou T., Ma S.F., Machado R.F., Bhorade S.M., and Garcia J.G.N., MicroRNAs implicated in dysregulation of gene expression following human lung transplantation. Transl. Respir. Med., in press.
  2. Sun X. , Dr. Ma S.F., Wade M.S., Acosta-Herrera M., Villar J., Pino-Yanes M., Zhou T., Liu B., Belvitch P., Moitra J., Han Y.J., Machado R., Noth I., Natarajan V., Dudek S.M., Jacobson J.R., Flores C., and Garcia J.G.N., Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome. Am. J. Physiol. Lung Cell Mol. Physiol., in press.
  • 2013
  1. Mathew B., Jacobson J.R., Siegler J.H., Moitra J., Blasco M., Xie L.S., Unzueta C., Zhou T., Evenoski C., Al-Sakka M., Sharma R., Huey B., Bulent A., Smith B., Sundararajan J., Reddy N.M., Reddy S.P., Dudek S.M., Natarajan V., Weichselbaum R.R., and Garcia J.G.N., Role of MIF in age-related susceptibility to radiation lung injury via Nrf2 and antioxidant regulation. Am. J. Respir. Cell Mol Biol., 49, 269-278, 2013.
  2. Gu W., Wang X., Zhai C., Zhou T.*, Xie X., Biological basis of miRNA action when their targets are located in human protein coding region. PLoS ONE, 8, e63403, 2013. (*co-corresponding author)
  3. Huang L.S., Berdyshev E., Mathew B., Fu P., Gorshkova I.A., He D., Ma W., Noth I., Ma S.F., Pendyala S., Reddy S.P., Zhou T., Zhang W., Garzon S.A., Garcia J.G.N., and Natarajan V. Targeting Sphingosine Kinase 1 attenuates bleomycin-induced pulmonary fibrosis. FASEB J., 27, 1749-1760, 2013.
  • 2012
  1. Sun X., Singleton P.A., Letsiou E., Zhao J., Belvitch P., Sammani S., Chiang E.T., Moreno-Vinasco L., Wade M.S., Zhou T., Liu B., Parastatidis I., Thomson L., Ischiropoulos H., Natarajan V., Jacobson J.R., Machado R.F., Dudek S.M., and Garcia J.G., Sphingosine-1-phosphate receptor 3 is a novel biomarker in acute lung injury. Am. J. Respir. Cell Mol. Biol., 47, 628-636, 2012.
  2. 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, 2012. (*co-first author)
  3. Zhou T., Ko E.A., Gu W., Lim I., Bang H., and Ko J.H., Non-silent story on synonymous sites in voltage-gated ion channel genes. PLoS ONE, 7, e48541, 2012.
  4. Gu W., Wang X., Zhai C., Xie X., and Zhou T., Selection on synonymous sites for increased accessibility around miRNA binding sites in plants. Mol. Biol. Evol., 29, 3037-3044, 2012.
  5. Gu W., Wang X., Zhai C., Xie X., Parinandi G., and Zhou T., Translation efficiency in upstream region of microRNA targets in Arabidopsis thaliana. Evol. Bioinform., 8, 565-574, 2012.
  6. Zhou T., Zhang W., Sweiss N.J., Chen E.S., Moller D.R., Knox K.S., Ma S.F., Wade M.S., Noth I., Machado R.F., and Garcia J.G.N., Peripheral blood gene expression as a novel genomic biomarker in complicated sarcoidosis. PLoS ONE, 7, e44818, 2012.
  7. Frank K.M., Zhou T., Moreno-Vinasco L., Hollett B., Garcia J.G.N., and Wardenburg J.B., Host response signature to Staphylococcus aureus α-hemolysin implicates pulmonary TH17 response. Infection and Immunity, 80, 3161-3169, 2012.
  8. 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. Am. J. Respir. Crit. Care. Med., 186, 359-368, 2012.
  9. Gorshkova I., Zhou T., Mathew B., Jacobson J.R., Takekoshi D., Bhattacharya P., Smith B., Aydogan B., Weichselbaum R.R., Natarajan V., Garcia J.G., and Berdyshev E.V., Inhibition of serine palmitoyltransferase delays the onset of radiation-induced pulmonary fibrosis through the negative regulation of sphingosine kinase-1 expression. J. Lipid Res., 53, 1553-1568, 2012.
  10. Mekontso Dessap A., Voiriot G., Zhou T., Marcos E., Dudek S.M., Jacobson J.R., Machado R., Adnot S., Brochard L., Maitre B., and Garcia J.G., Conflicting physiological and genomic cardiopulmonary effects of recruitment maneuvers in murine acute lung injury. Am. J. Respir. Cell Mol. Biol., 46, 541-550, 2012.
  • 2011
  1. Mathew B., Jacobson J.R., Berdyshev E., Huang Y., Sun X., Zhao Y., Gerhold L.M., Siegler J., Evenoski C., Wang T., Zhou T., Zaidi R., Moreno-Vinasco L., Bittman R., Chen C.T., Lariviere P.J., Sammani S., Lussier Y.A., Dudek S.M., Natarajan V., Weichselbaum R.R., and Garcia J.G., Role of sphingolipids in murine radiation-induced lung injury: protection by sphingosine 1-phosphate analogs. FASEB J., 25, 3388-3400, 2011.
  2. Ma S.F., Xie L., Pino-Yanes M., Sammani S., Wade M.S., Letsiou E., Siegler J., Wang T., Infusino G., Kittles R.A., Flores C., Zhou T., Prabhakar B.S., Moreno-Vinasco L., Villar J., Jacobson J.R., Dudek S.M., and Garcia J.G., Type 2 Deiodinase and host responses of sepsis and acute lung injury. Am. J. Respir. Cell Mol. Biol., 45, 1203-1211, 2011.
  3. Sammani S., Park K.S., Zaidi S.R., Mathew B., Wang T., Huang Y., Zhou T., Lussier Y.A., Husain A.N., Moreno-Vinasco L., Vigneswaran W.T., and Garcia J.G., A sphingosine 1-phosphate 1 receptor agonist modulates brain death-induced neurogenic pulmonary injury. Am. J. Respir. Cell Mol. Biol., 45, 1022-1027, 2011.
  4. 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, 2011.
  5. Zhou T. and Wilke C.O., Reduced stability of mRNA secondary-structure near the translation-initiation site in dsDNA viruses. BMC Evol. Biol., 11, 59, 2011.
  6. Zhou T., Garcia J.G.N., and Zhang W., Integrating microRNAs into a system biology approach to acute lung injury. Transl. Res., 157, 180-190, 2011. Featured in Elsevier
  • 2010
  1. 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. Am. J. Hum. Genet., 87, 829-833, 2010.
  2. 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, 2010.
  3. Zhou T., Gu W., and Wilke C.O., Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol. Biol. Evol., 27, 1912-1922, 2010.
  4. Novella I.S., Presloid J.B., Zhou T., Smith-Tsurkan S.D., Ebendick-Corpus B.E., Dutta R.N., Lust K.L., and Wilke C.O., Genomic evolution of vesicular stomatitis virus strains with differences in adaptability. Journal of Virology., 84, 4960-4968, 2010.
  5. 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 Comput. Biol., 6, e1000664, 2010. (*co-first author) Featured in GenomeWeb Daily Scan
  • Before 2010
  1. Zhou T., Weems M., and Wilke C.O., Translationally optimal codons associate with structurally sensitive sites in protein. Mol. Biol. Evol., 26, 1571-1580, 2009.
  2. Zhou T., Enyeart P.J., and Wilke C.O., Detecting clusters of mutations. PLoS ONE, 3, e3765, 2008.
  3. Zhou T., Drummond D.A., and Wilke C.O., Contact density affects protein evolutionary rate from bacteria to animals. J. Mol. Evol., 66, 395-404, 2008.
  4. 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, 2006.
  5. 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, 2006.
  6. Zhou T., Gu W., Ma J., Sun X., and Lu Z., Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. Biosystems, 81, 77-86, 2005.
  7. 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 Res., 101, 155-161, 2004.
  8. Gu W., Zhou T., Ma J., Sun X., and Lu Z., The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens. Biosystems, 73, 89-97, 2004.
  9. Gu W., Zhou T., Ma J., Sun X., and Lu Z., Folding type specific secondary structure propensities of synonymous codons. IEEE T. Nanobiosci., 2, 150-157, 2003.

Useful links

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