User:Tong Zhou

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

• 2010 - 2013, Research Assistant Professor, Department of Medicine, The University of Illinois at Chicago
• 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. Translational and Clinical Bioinformatics
2. Computational Genomics and Genetics
3. Molecular Evolution

Publications

• In press

1. 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, in press. doi: 10.1261/rna.044792.114
2. Letsiou E., Sammani S., Zhang W., Zhou T., Quijada H., Moreno-Vinasco L., Dudek S.M., and Garcia J.G., Pathologic mechanical stress and endotoxin exposure increases lung endothelial microparticle shedding. Am. J. Respir. Cell Mol. Biol., in press. doi: 10.1165/rcmb.2013-0347OC

• 2014

1. 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 Evol. Biol., 14, 87, 2014. doi: 10.1186/1471-2148-14-87 Highly accessed
2. Zhou T., Wang T.*, and Garcia J.G.N. Genes influenced by the non-muscle isoform of myosin light chain kinase impact human cancer prognosis. PLoS ONE, 9, e94325, 2014. (*co-first author) doi: 10.1371/journal.pone.0094325
3. Ko J.H., Gu W., Lim I., Bang H., Ko E.A., and Zhou T.*, Ion channel gene expression in lung adenocarcinoma: potential role in prognosis and diagnosis. PLoS ONE, 9, e86569, 2014. doi: 10.1371/journal.pone.0086569
4. Huang L.S., Mathew B., Li H., Zhao Y., Ma S.F., Noth I., Reddy S.P., Harijith A., Usatyuk P.V., Berdyshev E.V., Kaminski N., Zhou T., Zhang W., Zhang Y., Rehman J., Kotha S.R., Gurney T.O., Parinandi N.L., Lussier Y.A., Garcia J.G., and Natarajan V., The mitochondrial cardiolipin remodeling enzyme lysocardiolipin acyltransferase is a novel target in pulmonary fibrosis. Am. J. Respir. Crit. Care Med., 189, 1402-1415, 2014. doi: 10.1164/rccm.201310-1917OC
5. Wang T., Moreno-Vinasco L., Ma S.F., Zhou T., Shimizu Y., Sammani S., Epshtein Y., Watterson D.M., Dudek S.M., and Garcia J.G., Nonmuscle myosin light chain kinase regulates murine asthmatic inflammation. Am. J Respir. Cell Mol. Biol., 50, 1129-1135, 2014. doi: 10.1165/rcmb.2013-0434OC
6. Abraham A., Karathedath S., Kumaraswamy V., Jayavelu A.K., M S., Srivastava V.M., Zhang W., Zhou T., George B., Srivastava A., Mathews V., and Balasubramanian P., Novel NPM1 mutation in the 3'-untranslated region identified in two patients with acute myeloid leukemia. Leuk. Lymphoma, 55, 1421-1424, 2014. doi: 10.3109/10428194.2013.838235

• 2013

1. 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. Mol. Cancer, 12, 106, 2013. doi: 10.1186/1476-4598-12-106
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., 305, L467-L477, 2013. doi: 10.1152/ajplung.00010.2013
3. 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., 1, 12, 2013. doi: 10.1186/2213-0802-1-12
4. 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. doi: 10.1165/rcmb.2012-0291OC
5. 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) doi: 10.1371/journal.pone.0063403
6. 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. doi: 10.1096/fj.12-219634

• 2012

1. 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. doi: 10.1093/molbev/mss109
2. 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. doi: 10.4137/EBO.S10362
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. (*co-first author) doi: 10.1371/journal.pone.0048541
4. 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. (*co-first author) doi: 10.1371/journal.pone.0044818
5. 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) doi: 10.1371/journal.pone.0046104
6. 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. doi: 10.1165/rcmb.2012-0048OC
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. doi: 10.1128/IAI.00191-12
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. doi: 10.1164/rccm.201201-0057OC
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. doi: 10.1194/jlr.M026039
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. doi: 10.1165/rcmb.2011-0306OC

• 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. doi: 10.1096/fj.11-183970
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. doi: 10.1165/rcmb.2011-0179OC
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. doi: 10.1165/rcmb.2010-0267OC
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. doi: 10.1534/genetics.111.128025
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. doi: 10.1186/1471-2148-11-59
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. doi: 10.1016/j.trsl.2011.01.010 Featured in Elsevier

• 2010

1. 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) doi: 10.1371/journal.pcbi.1000664 Featured in GenomeWeb Daily Scan
2. 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. doi: 10.1016/j.ajhg.2010.10.018
3. 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. doi: 10.1002/pmic.201000229
4. 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. doi: 10.1093/molbev/msq077
5. 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. J. Virol., 84, 4960-4968, 2010. doi: 10.1128/JVI.00710-09

• 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. doi: 10.1093/molbev/msp070
2. Zhou T., Enyeart P.J., and Wilke C.O., Detecting clusters of mutations. PLoS ONE, 3, e3765, 2008. doi: 10.1371/journal.pone.0003765
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. doi: 10.1007/s00239-008-9094-4
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. doi: 10.1186/1471-2105-7-223
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. doi: 10.1016/j.gene.2005.10.035
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. doi: 10.1016/j.biosystems.2005.03.002
7. Zhou T., Lu Z., and Sun X., The correlation between recombination rate and codon bias in yeast mainly results from mutational bias associated with recombination rather than Hill-Robertson interference. Conf. Proc. IEEE Eng. Med. Biol. Soc., 5, 4787-4790, 2005. doi: 10.1109/IEMBS.2005.1615542
8. Song X., Zhou T., and Zhang H., Support vector regression estimation based on non-uniform lost function. Conf. Proc. IEEE Eng. Med. Biol. Soc., 2, 1127-1130, 2005. doi: 10.1109/IEMBS.2005.1616619
9. 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. doi: 10.1016/j.virusres.2004.01.006
10. 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. doi: 10.1016/j.biosystems.2003.10.001
11. 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. doi: 10.1109/TNB.2003.817024
12. Ma J., Zhou T., Gu W., Sun X., and Lu Z., Cluster analysis of the codon use frequency of MHC genes from different species. Biosystems, 65, 199-207, 2002. doi: 10.1016/S0303-2647(02)00016-3

Useful links

• Introductory tutorial
• OpenWetWare help pages