Jen-Tsan Ashley Chi, MD, PhD – Publications

Associate Professor
Center for Genomic and Computational Biology

research • biography lab members • publications • alumni • lab website

Google Scholar Profile 

Representative Publications

 Chang, H.Y., Chi, J.T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D. and Brown, P. O. (2002) Diversity, topographic differentiation, and positional memory in human fibroblasts. Proceeding of National Academy of Science USA 99:12877-12882.

Chi, J.T., Chang, H.Y., Wang, N.N., Chang, D.S., Dunphy, N. and Brown, P.O. (2003) Genomewide view of gene silencing by small interfering RNAs. Proceeding of National Academy of Science USA 100:6343-6346.

Chi, J.T., Chang, H.Y., Haraldsen, G., Jahnsen, F.L., Troyanskaya, O.G., Chang, D.S., Wang, Z., Rockson, S.G., van de Rijn, M., Botstein, D. and Brown, P.O. (2003) Endothelial cell diversity revealed by global expression profiling. Proceeding of National Academy of Science USA 100:10623-10628.

Whitfield, M.L., Finlay, D., Murray, J.I., Troyanskaya, O.,Chi, J.T., Brown, P.O., Botstein, D. and Connolly, M.K. (2003) Patterns of gene expression in scleroderma. Proceeding of National Academy of Science USA100:12319-12324.

Chang, H.Y., Sneddon, J.B., Alizadeh, A.A., Sood R., West, R.B., Montgomery, K., Chi, J. T., van de Rijn, M., Botstein, D. and Brown, P.O. (2004) Gene expression signature of fibroblast serum response predicts human cancer progression–similarities between tumors and wounds. PLoS Biology 2:e7.

Chi, J.T., Wang, Z., Nuyten, D.S.A., Rodriguez, E.H., Schaner, M.E., Salim, A., Wang, Y., Kristensen, G.B., Helland, A., Børresen-Dale, A., Giaccia, A., Longaker, M.T., Hastie, T., Yang, Y.P., van de Vijver, M.J. and Brown, P.O. (2006) Gene expression programs in response to hypoxia; cell type specificity and prognostic significance in human cancers. PLoS Medicine 3:e47.

Erler, J.T., Bennewith, K.L., Nicolau, M., Dornhofer, N., Kong, C., Le, Q.T., Chi, J.T., Jeffrey, S.S., Giaccia, A.J. (2006) Lysyl oxidase is essential for hypoxia-induced metastasis. Nature 440:1222-1226.

Myers, J.W., Chi, J.T., Gong, D, Schaner, M.E., Brown, P.O., Ferrell, J.E. (2006) Minimizing off target effects by using diced siRNAs for RNA interference. Journal of RNAi and Gene Silencing 2:181-194.

Moon, E.J., Brizel, D.M., Chi, J.T. and Dewhirst, M.W. (2007) The potential role of intrinsic hypoxia markers as prognostic variables in cancer. Antioxidants & Redox Signaling 9:1237-1294.

Chi, J.T., Rodriguez, E.H., Wang, Z., Nuyten, D., Mukherjee, S., van de Rijn, M., Vijver, M.J., Hastie, T. and Brown, P. O. (2007) Gene expression programs of human smooth muscle cells: Tissue-specific differentiation and prognostic significance in breast cancers. PLoS Genetics 3:e164.

Gottwein, E., Mukherjee, N., Sachse, C., Frenzel, C., Majoros, W.H., Chi, J.T., Braich, R., Manoharan, M., Soutschek, J., Ohler, U. and Cullen, B. (2007) A viral microRNA functions as an ortholog of cellular miR-155. Nature 450:1096-1099.

Edelman, E., Guinney, J., Chi, J.T., Febbo, P.G., Mukherjee, S. (2008) Modeling cancer progression via pathway dependencies. PLoS Computational Biology 4:e28.

Chen, S.Y., Wang, Y., Telen, M.J., Chi, J.T. (2008) The genomic analysis of erythrocyte microRNAs expression in sickle cell diseases. PLoS ONE 3:e2360.

Nuyten, D.S., Hastie, T., Chi, J.T., Chang, H.Y., Vijver, M.J. (2008) Combining biological gene expression signatures in predicting outcome in breast cancer: An alternative to supervised classification. European Journal of Cancer 44: 2319-2329.

Chen, J.L., Lucase, J.E., Schroede,r T., Mori, S., Nevins, J.R., Dewhirst, M.W., West, M., Chi, J.T. (2008) Genomic analysis of lactic acidosis and acidosis response in human cancers. PLoS Genetics 4:e1000293.

Lucas, J.E., Carvalho, C.M., Chen, J.L., Chi, J.T. and West, M. (2009) Cross-study projections of Genomic biomarkers: An evaluation in cancer genomics. PLoS One 4:e4523.

Chan, A.S., Kawahara, T.L., Sutphin, P.D., Change, H.Y., Chi, J.T., Giaccia, A. (2009) Tumor vasculature is regulated by PHD2- mediated angiogenesis and bone marrow-derived cell recruitment. Cancer Cell 5:527-538.

Merl, D., Chen, J.L., Chi, J.T. and West, M. (2009) An integrative analysis of cancer gene expression studies using Bayesian latent factor modeling. Annals of Applied Statistics 3:1675-1694.

Pogozelski, A.R., Geng, T., Li, P., Yin, X., Lira, V.A., Zhang, M., Chi, J.T., and Yan, Z. (2009) p38gamma mitogen-activated protein kinase is a key regulator in skeletal muscle metabolic adaptation in mice. PLoS One 4:e7934.

Himburg, H.A. Muramoto, G.G., Daher, P., Meadows, S.K., Russell, J.L., Doan, P., Chi, J.T., Salter, A.B., Lento, W.E., Reya, T., Chao, N.J., and Chute, J.P. (2010) Pleiotrophin regulates the expansion and regeneration of hematopoietic stem cells. Nature Medicine 16:475-482.

Lindsay, R.G. and Chi, J.T. (2010) Contact lens management of infantile aphakia. Clinical and Experimental Optometry 93:3-14. Review

Chen, J.L, Merl, D., Peterson, C., Wu, J, Liu, P, Ayer, D, West M, and Chi, J.T. (2010) Lactic acidosis triggers starvation response with paradoxical induction of TXNIP through MondoA. PLOS Genetics 6:e1001093.

Sangokoya, C., Telen, M. J., Chi, J. T. (2010) MicroRNA miR-144 modulates oxidative stress tolerance and associates with anemia severity in sickle cell disease. Blood 116: 4338-4348.

Lucas J.E., Kung H.N., Chi J.T. (2010) Latent factor analysis to discover pathway-associated putative segmental aneuploidies in human cancers. PLoS Computational Biology 6:e1000920.

Sangokoya C., Lamonte G., Chi J.T. (2010) Isolation and Characterization of MicroRNAs of Human Mature Erythrocytes Methods. Molecular Biology 667:193-203.

Chi J.T. #, Thrall D.E., Jiang C., Snyder S., Fels D., Landon C., McCall L., Lan L., Hauck M., MacFall J.R., Viglianti B.L. and Dewhirst M.W. Comparison of genomics and functional imaging from canine sarcomas treated with thermoradiotherapy predicts therapeutic response and identifies combination therapeutics. Clinical Cancer Research 17:2549-60, 2011 PMCID: PMC3078971 #Corresponding author.

Gatza M.L., Kung H.N., Blackwell K.L., Dewhirst M.W., Marks J.R., Chi J.T. Analysis of tumor environmental response and oncogenic pathway activation identifies distinct basal and luminal features in HER2-related breast tumor subtypes. Breast Cancer Research 13: R62. 2011 “Highly Accessed” PMCID: PMC3218951

Lacsina J.R., LaMonte G., Nicchitta, C.V., and Chi J.T. Polysome profiling of the malaria parasite Plasmodium falciparum. Molecular & Biochemical Parasitology 179:42-6. Epub 2011 May 13. PMCID: PMC3135974

Akslen L.A., Straume O., Geisler S., Sorlie T., Chi J.T., Aas T., Børresen-Dale A.L., Lønning P.E. Glomeruloid microvascular proliferation is associated with lack of response to chemotherapy in breast cancer. British Journal of Cancer 105:9-12, 2011. PMCID: PMC3137417

Lewis D.A., Stashenko G.J., Akay O.M., Price L.I., Owzar K., Ginsburg G.S., Chi J.T., and Ortel T.L. Whole blood gene expression analyses in patients with single versus recurrent venous thromboembolism. Thrombosis Research 128:536-40, 2011.

Chan D.A., Sutphin P.D., Nguyen P., Turcotte S., Lai E.W., Banh A., Reynolds G.E., Chi J.T., Wu J., Solow-Cordero D.E., Bonnet M., Flanagan J.U., Bouley D.M., Graves E.E., Denny W.A., Hay M.P., and Giaccia A.J. Targeting GLUT1 and the Warburg effect in renal cell carcinoma by chemical synthetic lethality. Scientific Translational Medicine 3:94ra70, 2011.

Kung H.N., Marks J.R., and Chi J.T. Glutamine synthetase is a genetic determinant of cell type-specific glutamine independence in breast epithelia. PLoS Genetics 7(8):e1002229, 2011. PMCID: PMC3154963.