Before 2020

Before 2011

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
 
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
 
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
 
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
 
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
 
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

2011

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
Shi J., Zhou T.*, and Chen Q.*, Exploring the expanding universe of small RNAs. Nat. Cell Biol., 24, 415-423, 2022. (*co-corresponding author) doi:10.1038/s41556-022-00880-5
 
Meng Z., Hernandez R., Liu J., Gwag T., Lu W., Hsiai T.K., Kaul M., Zhou T., and Zhou C., HIV Protein Tat Induces Macrophage Dysfunction and Atherosclerosis Development in Low-Density Lipoprotein Receptor-Deficient Mice. Cardiovasc. Drugs Ther., 36, 201-215, 2022. doi:10.1007/s10557-021-07141-x
 
Satta S., Meng Z., Hernandez R., Cavallero S., Zhou T., Hsiai T.K., and Zhou C., An engineered nano-liposome-human ACE2 decoy neutralizes SARS-CoV-2 Spike protein-induced inflammation in both murine and human macrophages. Theranostics, 12, 2639-2657, 2022. doi:10.7150/thno.66831
Gu W.*, Shi J., Liu H., Zhang X, Zhou J.J., Li M., Zhou D., Li R., Lv J., Wen G., Zhu S., Qi T., Li W., Wang X., Wang Z., Zhu H., Zhou C., Knox, K.S., Wang T., Chen Q.*, Qian Z.*, and Zhou T.*, Peripheral blood non-canonical small non-coding RNAs as novel biomarkers in lung cancer. Mol. Cancer, 19, 159, 2020. (*co-corresponding author)  doi:10.1186/s12943-020-01280-9
 
Ko E.A., Lee H., Sanders K.M., Koh S.D.*, and Zhou T.*, Expression of alpha-type platelet-derived growth factor receptor influenced genes predicts clinical outcome in glioma. Transl. Oncol., 13, 233-240, 2020. (*co-corresponding author) doi:10.1016/j.tranon.2019.10.002
 
Zhang X., Trebak F., Souza L.A.C., Shi J., Zhou T., Kehoe P.G., Chen Q., and Earley Y.F., Small RNA modifications in Alzheimer's disease. Neurobiol. Dis., 145, 105058, 2020. doi:10.1016/j.nbd.2020.105058
 
Sui Y., Meng Z., Park S.H., Lu W., Livelo C., Chen Q., Zhou T., and Zhou C., Myeloid-specific deficiency of pregnane X receptor decreases atherosclerosis in LDL receptor-deficient mice. J. Lipid Res., 61, 696-706, 2020. doi:10.1194/jlr.RA119000122
 
Evans L., Bender A., Burnett L., Godoy L., Shen Y., Staten D., Zhou T., Angermann J., Ferguson B., Emodin and emodin-rich rhubarb inhibits histone deacetylase (HDAC) activity and cardiac myocyte hypertrophy. J. Nutr. Biochem., 79, 108339, 2020.  doi:10.1016/j.jnutbio.2019.108339
 
Wang J., Xie X., Shi J., He W., Chen Q., Chen L.*, Gu W.*, and Zhou T.*, Denoising autoencoder, a deep learning algorithm, aids the identification of a novel molecular signature of lung adenocarcinoma . Genomics, Proteomics & Bioinformatics, 18, 468-480, 2020. (*co-corresponding author)  doi:10.1016/j.gpb.2019.02.003
Chen Q.*, Zhang X., Shi J., Yan M., and Zhou T.*, Origins and evolving functionalities of tRNA-derived small RNAs. Trends Biochem. Sci., 46, 790-804, 2021. (*co-corresponding author) doi:10.1016/j.tibs.2021.05.001
 
Shi J., Zhang Y., Tan D., Zhang X., Yan M., Zhang Y., Franklin R., Shahbazi M., Mackinlay K., Liu S., Kuhle B., James E.R., Zhang L., Qu Y., Zhai Q., Zhao W., Zhao L., Zhou C., Gu W., Murn J., Guo J., Carrell D.T., Wang Y., Chen X., Cairns B.R., Yang X.L., Schimmel P., Zernicka-Goetz M., Cheloufi S.*, Zhang Y.*, Zhou T.*, and Chen Q.*, PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat. Cell Biol., 23, 424-436, 2021. (*co-corresponding author) doi:10.1038/s41556-021-00652-7
 
Gupta A., Fei Y.D., Kim T.Y., Xie A., Batai K., Greener I., Tang H., Ciftci-Yilmaz S., Juneman E.B., Indik J.H., Shi G., Christensen J., Gupta G., Hillery C.A., Kansal M., Parikh D.S., Zhou T., Yuan J.X., Kanthi Y., Bronk P., Koren G., Kittles R., Duarte J., Garcia J.G.N., Machado R.F., Dudley S.C., Choi B.R., and Desai A.A., IL-18 mediates sickle cell cardiomyopathy and ventricular arrhythmias. Blood, 137, 1208–1218, 2021.  doi:10.1182/blood.2020005944
 
Casanova N.G.*, Zhou T.*, Gonzalez-Garay M., Lussier Y.A., Sweiss N., Ma S.F., Noth I., Knox K.S., and Garcia J.G.N., MicroRNA and Protein-Coding Gene Expression Analysis in Idiopathic Pulmonary Fibrosis Yields Novel Biomarker Signatures Associated to Survival. Transl. Res., 228, 1-12, 2021. (*co-first author)  doi:10.1016/j.trsl.2020.07.009
 
Wen G.,Zhou T.*, and Gu W.*, The potential of using blood circular RNA as liquid biopsy biomarker for human diseases. Protein & Cell, 12, 911-946, 2021. (*co-corresponding author) doi:10.1007/s13238-020-00799-3
 
Kim Y.W., Ko E.A., Jung S.C., Lee D., Seo Y., Kim S., Kim J.H., Bang H., Zhou T.*, and Ko J.H.*, Transcriptomic insight into the translational value of two murine models in human atopic dermatitis.  Sci. Rep., 11, 6616, 2021. (*co-corresponding author)  doi:10.1038/s41598-021-86049-w
 
Evans L., Shen Y., Bender A., Burnett L.E., Li M., Habibian J.S., Zhou T., and Ferguson B.S., Divergent and Overlapping Roles for Selected Phytochemicals in the Regulation of Pathological Cardiac Hypertrophy. Molecules, 26, 1210, 2021.  doi:10.3390/molecules26051210

2020-2022

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
 
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
 
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

Shi J., Zhang Y., Zhou T.*, and Chen Q.*, tsRNAs: The Swiss Army Knife for Translational Regulation. Trends Biochem. Sci., 44, 185-189, 2019. (*co-corresponding author) doi:10.1016/j.tibs.2018.09.007

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 Biol. Evol., 7, 2929-2940, 2015. doi:10.1093/gbe/evv191
 
Wang T.*, Zhou T.*, Saadat L., and Garcia J.G.N., A MYLK variant regulates asthmatic inflammation via alterations in mRNA secondary structure. Eur. J. Hum. Genet., 23, 874–876, 2015. (*co-first author) doi:10.1038/ejhg.2014.201
Wang J., Wang L., Feng G., Wang Y., Li Y., Li X, Liu C., Jiao G., Huang C., Shi J., Zhou T., Chen Q., Liu Z., Li W., and Zhou Q., Asymmetric Expression of LincGET Biases Cell Fate in Two-Cell Mouse Embryos. Cell, 175, 1887-1901, 2018. doi:10.1016/j.cell.2018.11.039.
 
Zhou T.*, Xie X., Li M., Shi J., Zhou J.J., Knox K.S., Wang T. Chen Q., and Gu W.*, Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages. RNA, 24, 1443-1456. (*co-corresponding author) doi:10.1261/rna.067132.118
 
Shi J.*, Ko E.A., Sanders K.M., Chen Q.*, and Zhou T.*, SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA- and tRNA- derived small RNAs. Genomics, Proteomics & Bioinformatics, 16, 144-151, 2018. (*co-corresponding author) doi:10.1016/j.gpb.2018.04.004
 
Zhang Y., Zhang X., Shi J., Tuorto F., Li X., Liu Y., Liebers R., Zhang L., Qu Y., Qian J., Pahima M., Liu Y., Yan M., Cao Z., Lei X., Cao Y., Peng H., Liu S., Wang Y., Zheng H., Woolsey R., Quilici D., Zhai Q., Li L., Zhou T., Yan W., Lyko F., Zhang Y., Zhou Q., Duan E., and Chen Q., Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nat. Cell Biol., 20, 535-540, 2018. doi:10.1038/s41556-018-0087-2
 
Bime C., Pouladi N., Sammani S., Batai K., Casanova N., Zhou T., Kempf C.L., Sun X., Camp S.M., Wang T., Kittles R.A., Lussier Y.A., Jones T.K., Reilly J.P., Meyer N.J., Christie J.D., Karnes J., Gonzalez-Garay M., Christiani D.C., Yates C.R., Wurfel M.M., Meduri G.U., and Garcia J.G.N., Genome wide association study in African Americans with acute respiratory distress syndrome identifies the Selectin P Ligand gene as a risk factor. Am. J. Respir. Crit. Care Med., 197, 1421-1432, 2018. doi:10.1164/rccm.201705-0961OC

Ko E.A., Sanders K., and Zhou T., A transcriptomic insight into the impacts of mast cells in lung, breast, and colon cancers. OncoImmunology, e1360457, 2017. doi:10.1080/2162402X.2017.1360457

 
Li M., Xie X., Zhou J., Sheng M., Yin X., Ko E.A., Zhou T.*, and Gu W.*, Quantifying circular RNA expression from RNA-seq data using model-based framework. Bioinformatics, 33, 2131-2139, 2017. (*co-correspinding author) doi:10.1093/bioinformatics/btx129
 
Huang Y., Ma S.F., Espindola M.S., Vij R., Oldham J.M., Huffnagle G.B., Erb-Downward J.R., Flaherty K.R., Moore B.B., White E.S., Zhou T., Li J., Lussier Y.A., Han M.K., Kaminski N., Garcia J.G., Hogaboam C.M., Martinez F.J., and Noth I., Microbes associate with host innate immune response in idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med., 196, 208-219, 2017. doi:10.1164/rccm.201607-1525OC
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, 1369-1375, 2014. doi:10.1261/rna.044792.114
 
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
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
 
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
 
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
 
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