Xi (Steven) Chen

Associate Professor of Biostatistics
Division of Cancer Biostatistics
Department of Biostatistics
Vanderbilt University School of Medicine
549 Preston Research Building
Nashville, TN 37232-6848

steven.chen@vanderbilt.edu
phone: (615) 936-2785
fax: (615) 936-2602

Research Interests

  • Statistical Methods for Genomic Data
  • Next generation sequencing data analysis
  • Systems Biology
  • Statistical Learning and Data Mining
  • Statistical Genetics
  • Cancer Prognosis
  • Cancer Subtypes Identification

Postdoctoral Position Available

Education

PhD in Statistics
North Carolina State University, 2006
Dissertation: Characterizing the Genetic Structure of Populations
Advisor: Dr Bruce S Weir

MS in Molecular Genetics
North Carolina State University, 2002

Work Experience

Associate Professor (with tenure) 2015-present
Department of Biostatistics, Vanderbilt University

Assistant Professor 2009 - 2014
Department of Biostatistics, Vanderbilt University

Assistant Staff 2006 - 2009
Department of Quantitative Health Sciences, Cleveland Clinic

Methodology Grants

1R01 CA158472-01A1 Integrative prediction models for metastasis risk in colon cancer 2012 - 2017
Total cost: $2,322,322
Role: PI

Vanderbilt-Ingram Cancer Center Support Grant (Pilot and Feasibility Project Grants 2010) 2010 - 2011
Role: PI

Media Coverage

Interview by Momentum

A closer look

Identifying subtypes of triple negative breast cancer (collaboration with Dr Pietenpol)

VUMC Reporter 2012

VUMC Reporter 2011

Oncology Times: Identifying subtypes in triple-negative breast cancer

LEADcast, a critical appraisal of "Indentification of Human Triple-Negative Breast Cancer Subtypes and Preclinical Models for Selection of Targeted Therapies"

Cancer network

The ASCO Post

Building prediction model for colon cancer prognosis

Vanderbilt-Ingram Cancer Center Support Grant

Patent

"Triple Negative Breast Cancer Diagnostic for Personalized Medicine", Jennifer Pietenpol, Brian Lehmann, Josh Bauer, Xi Chen, VU12047.

Software

TNBCtype: A subtyping tool for triple-negative breast cancer

Publications

  1. BHat AA, Pope JL, Smith JJ, Ahmad R, Chen X, Washington MK, Beauchamp RD, Singh AB, Dhawan P. Claudin-7 expression induces mesenchymal to epithelial transformation (MET) to inhibit colon tumorigenesis. Oncogene. In press.
  2. Meador CB, Jin H, de Stachina E, Nebhan CA, Pirazzoli V, Wang L, Lu P, Vuong H, Hutchinson KE, Jia P, Chen X, Eisenberg R, Ladanyi M, Politi K, Zhan Z, Lovly CM, Cross DAE, Pao W. Optimizing the sequence of anto-EGFR targeted therapy in EGFR-mutant lung cancer. Molecular Cancer Therapeutics In press.
  3. Lovly CM, McDonald NT, Chen H, Ortiz-Cuaran S, Heukamp LC, Yang Y, Florin A, Ozretic L, Lim D, Wang L, Chen Z, Chen X, Lu P, Pail PK, Shen R, Jin H, Buettner R, Ansen S, Perner S, Brockman M, Bos M, Wolf J, Gardizi M, Wright GM, Soloman B, Russell PA, Rogers TM, Suehara Y, Red-Brewer M, Tieu R, Stanchina ED, Wang Q, Zhan Z, Johnson D, Horn L, Wong KK, Thomas RK, Ladanyi M, Pao W. Rationale for co-targeting IGF-1R and ALK in ALK fusion positive lung cancer. Nature Medicine 2014; 20:1027-1034.
  4. Lehmann BD, Bauer JA, Schafer JM, Pendleton CS, Tang L, Johmson KC, Chen X, Balko JM, Gomez H, Arteaga CL, Mills GB, Sanders ME, Pietenpol JA. PIK3CA mutations in androgen receptor-positive triple negative breast cancer confer sensitivity to the combination of PI3K and androgen receptor inhibitors. Breast Cancer Research 2014; 16:406.
  5. Tripath MK, Deane NG, Zhu J, An H, Mima S, Wang X, Padmanabhan S, Shi Z, Prodduturi N, Ciombor KK, Chen X, Washington MK, Zhang B, Beauchamp RD. NFAT transcriptional activity is associated with metastatic capacity in colon cancer. Cancer Research 2014; 74(23):6947-6957.
  6. Sheng Q, Shyr Y, Chen X. Dupchecker: a Bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. BMC Bioinformatics 2014; 15(1): 323.
  7. Grieb BC, Chen X, Eischen CM. MTBP is over-expressed in triple negative breast cancer and contribute to its growth and survival. Molecular Cancer Research. 2014; 12(9):1216-1224..
  8. Grieb BC, Gramling MW, Arrate MP, Chen X, Beauparlant SL, Haines DS, Xiao H, Eischen CM. Oncogenic protein MTBP interacts with MYC to promote tumorigenesis. Cancer Research. 2014; 74:3591-3602.
  9. Nagathihalli NS, Beesetty Y, Lee W, Washington MK, Chen X, Lockhart AC, Merchant NB. Novel mechanistic insights into ectodomain shedding of EGFR ligands amphiregulin and TGF-alpha: impact in gastrointestinal cancers driven by secondary bile acids. Cancer Research. 2014; 74:2062-2072.
  10. Smith S, Tripathi R, Goodings C, Cleveland S, Mathias E, Hardaway JA, Elliott N, Yi Y, Chen X, Dowing J, Mullighan C, Swing DA, Tessarolla L, Li L, Love P, Jenkins NA, Copeland NG, Thompson MA Du Y, Dave UP. Lim Domain Only-2 (LMO2) induces T-cell leukemia by two distinct pathways. PLoS One. 2014; 9(1): e85883.
  11. Smith JJ, Patel R, Chen X, Tarpley MJ, Terhune KP. Does intentional support of degree programs in general surgery residency affect research productivity or pursuit of academic surgery? Journal of Surgical Education. 2014; 71(4):486-491.
  12. Kiernan CM, Du L, Chen X, Broome JT, Shi C, Peters MF, Solorzano CC. Predictors of hemodynamic instability during surgery for pheochromocytoma. Annals of Surgical Oncology. 2014; 21(12):3865-3871.
  13. Chen X, Ishwaran H. Pathway hunting by random survival forests. Bioinformatics 2013; 29(1): 99-105.
  14. Summers AR, Fischer MA, Stengel KR, Zhao Y, Kaiser JF, Wells CE, Hunt A, Bhaskara S, Luzwick JW, Simpathi S, Chen X, Thompson MA, Cortez D, Hiebert SW. Hdac3 is essential for DNA replication and differentiation of hematopoietic stem and progenitor cells. Journal of Clinical Investigation. 2013; 123(7):3112-3123.
  15. Tanksley JP, Chen X, Coffey RJ. NEDD4L is downregulated in colorectal caccer and inhibits canonical WNT signaling. PLoS One 2013; 8(11): e81514.
  16. Ohashi K, Sequist LV, Arcila ME, Lovy, CM, Chen X, Rudin CM, Moran T, Camidge DR, Vnencak-Jones CL, Berry L, Pan Y, Sasaki H, Engelman JA, Garon EB, Dubinett SM, Franklin WA, Riely GJ, Sos ML, Kris MG, Dias-Santagata D, Ladanyi M, Bunn PA, Pao W. Characteristics of lung cancers harboring NRAS mutations. Clinical Cancer Research 2013; 19:2584-2591.
  17. Yu KD, Zhu R, Zhan M, Rodriguez AA, Yang W, Wong S, Makris A, Lehmann BD, Chen X, Mayer I, Pietenpol JA, Shao ZM, Symmans F, Chang JC. Identification of prognosis-relevant subgroups in patients with chemoresistant triple negative breast cancer. Clinical Cancer Research 2013; 19:2723-2733.
  18. Cleveland SM, Smith S, Tripathi R, Mathias EM, Goodings C, Elliott N, Peng D, El-Rifai W, Yi D, Chen X, Li L, Mullighan C, Downing JR, Love P, Dave UP. Lmo2 induces hematopoietic stem cell like features in T-cell progenitor cells prior to leukemia. Stem Cells 2013; 31(5): 882-894.
  19. Smith JJ, Chen X, Schneider D, Broome JT, Sippel R, Chen H, Solorzano CC. Cancer after thyroidectomy: a multi-institutional experience with 1,523 patients. Journal of American College of Surgeons. 2013; 216(4): 571-577.
  20. Qiu Q, Lu P, Xiang Y, Shyr Y, Chen X, Lehmann BD, Viox DJ, George AL, Yi Y. A data similarity based strategy for meta-analysis of transcriptional profiles in cancer. PLoS One 2013; 8(1): e54979.
  21. Barrett CW, Ning W, Chen X, Smith JJ, Washington MK, Hill K, Peek R, Coburn LA, Chaturvedi R, Wilson KT, Burk RF, Williams CS. Tumor suppressor function of the plasma glutathione peroxidase Gpx3 in colitis-associated carcinoma. Cancer Research 2013; 73:1245-1255.
  22. Smith JJ, Chen X, Schneider DF, Nookala R, Broome JT, Sippel RS, Chen H, Solorzano CC. Toxic nodular goiter and cancer: A compelling case for thyroidectomy. Annals of Surgical Oncology 2013; 20:1336-1340.
  23. Williams CS, Bradley A, Chaturvedi R, Singh K, Piazuelo MB, Chen X, McDonough EM, Schwartz DA, Brown C, Allaman MM, Coburn LA, Horst SN, Beaulieu D, Choksi Y, Washington MK, Williams AD, Fisher MA, Zinkel SS, Peek RM, Wilson KT, Hiebert SW. MTG16 contributes to colonic epithelial integrity in experimental colitis. Gut 2013; 62: 1446-1455.
  24. Chen X, Li J, Gray WH, Lehmann BD, Bauer JA, Shyr Y, Pietenpol JA. TNBCtype: A subtyping tool for triple-negative breast cancer. Cancer Informatics 2012; 11:147-156.
  25. Barrett CW, Smith JJ, Lu LC, Markham N, Stengel KR, Short SP, Zhang B, Hunt AA, Fingleton BM, Carnahan RH, Engel ME, Chen X, Beauchamp RD, Wilson KT, Hiebert SW, Reynolds AB, Williams CS. Kaiso directs the transcriptional corepressor MTG16 to the Kaiso binding site in target promoters. PLoS One 2012; 7(12): e51205.
  26. Lin Z, Hegarty JP, Yu W, Cappel JA, Chen X, Faber PW, Wang Y, Poritz LS, Fan JB, Koltun WA. Identification of disease-associated DNA methylation in B cells from Crohn’s disease and ulcerative colitis patients. Digestive Diseases and Sciences 2012; 57:3145-3153.
  27. Su PF, Chen X, Chen H, Shyr Yu. Statistical aspects of omics data analysis using the compound covariate. BMC Systems Biology 2012; 6(Suppl 3):S11.
  28. Patel N, Black J, Chen X, Marcondes AM, Grady WM, Lawlor E, Borinstein S. DNA methylation and gene expression profiling of ewing sarcoma primary tumors reveal genes that are potential target of epigenetic inactivation. Sarcoma 2012; Article 498472.
  29. Chen X, Ishwaran H. Random forests for genomic data analysis. Genomics 2012; 99:323-329.
  30. Wang L, Chen X, Zhang B. Statistical analysis of patient-specific pathway activities via mixed models. Journal of Biometrics & Biostatistics 2012; S8-001.
  31. Tanner JF, Smith JJ, Chen X, Washington MK, Roland JT, Means AL, Eschrich SA, Yeatman TJ, Deane NG, Beauchamp RD. Smad4-mediated signaling inhibits intestinal neoplasia by inhibiting beta-catenin gene expression. Gastroenterology 2012; 142(3):562-571.
  32. Yu W, Lin Z, Hegarty JP, Chen X, Kelly AA, Wang Y, Poritz LS, Koltun WA. Genes differentially regulated by NKX2-3 in B cells between ulcerative colitis and Crohn’s disease patients and possible involvement of EGR1. Inflammation 2012; 35(3):889-899.
  33. Chmielecki J, Pietanza MC, Aftab D, Shen R, Zhao Z, Chen X, Hutchinson K, Viele A, Kris MG, Stout T, Miller V, Pao W. EGFR mutant lung adenocarcinomas treated first-line with the novel EGFR inhibitor, XL647, can subsequently retain moderate sensitivity to erlotinib. Journal of Thoracic Oncology 2012; 7(2):434-442.
  34. Chen X. Adaptive elastic-net sparse principal component analysis for pathway association testing. Statistical Applications in Genetics and Molecular Biology 2011; 10(1): Article 48.
  35. Singh AB, Sharma A, Krishnan M, Smith JJ, Chen X, Eschrich S, Yeatman T, Beauchamp RD, Dhawan P. Claudin-1 up regulates the repressor ZEB-1 to inhibit E-cadherin expression in colon cancer cells. Gastroenterology 2011; 141(6): 2140-2153.
  36. Williams CS, Zhang B, Smith JJ, Jayagopal A, Barrett CW, Pino C, Russ P, Presley S, Peng D, Rosenblatt DO, Haselton R, Yang JL, Washington MK, Chen X, Eschrich S, Yeatman T, El-Rifai W, Beauchamp RD, Chang MS. BVES regulates EMT in human corneal and colon cancer cells and is silenced via promoter methylation in human colorectal carcinoma. Journal of Clinical Investigation 2011; 121(10): 4056-4069.
  37. Wang L, Jia P, Wolfinger RD, Chen X, Grayson BL, Aune TM, Zhao Z. An efficient hierarchical generalized linear mixed model for testing disease association with biological pathways in genome-wide association studies. Bioinformatics 2011; 27(5): 686-692.
  38. Wang L, Jia P, Wolfinger RD, Chen X, Zhao Z. Pathway analysis of genome-wide association studies: methodological issues and perspectives Genomics 2011; 98:1-8.
  39. Dhawan P, Ahmad R, Chaturvedi R, Smith JJ, Midha R, Mittal M, Krishnan M, Chen X, Eschrich S, Yeatman T, Harris RC, Washington MK, Wilson KT, Beauchamp RD, Singh AB. Claudin-2 expression increases tumorigenicity of colon cancer cells: role of epidermal growth factor receptor activation. Oncogene 2011; 30: 3234-3247.
  40. Lehmann BD, Bauer JA, Chen X, Sander ME, Chakravarthy B, Shyr Y, Pietenpol JA. Identification of triple negative breast cancer subtypes and preclinical models for selection of targeted therapies. Journal of Clinical Investigation 2011; 121(7): 2750-2767.
  41. Yu W, Hegarty JP, Berg A, Chen X, West G, Kelly A, Wang Y, Poritz L, Koltun W, Lin Z. Nkx2-3 transcriptional regulation of Endothelin-1 and VEGF signaling in human intestinal microvascular endothelial cells. PLoS One 2011; 6(5): e20454.
  42. Ganapathi A, MaCarron JA, Chen X, Iannotti JP. Predicting normal glenoid version from the pathologic scapula: a comparison of 4 methods in 2- and 3-dimensional models. Journal of Shoulder and Elbow Surgery 2011; 20(2): 234-244.
  43. Lin Z, Hegarty JP, Cappel JA, Yu W, Chen X, Faber P, Wang Y, Kelly AA, Poritz LS, Peterson BZ, Schreiber S, Fan JB, Koltun WA. Identification of disease-associated DNA methylation in intestinal tissues from patients with inflammatory bowel disease. Clinical Genetics 2011; 80: 59-67.
  44. Ishwaran H, Kogalur UB, Chen X, Minn AJ. Random survival forests for high-dimensional data. Statistical Analysis and Data Mining 2011; 4(1): 115-132.
  45. Chen X, Wang L, Hu B, Guo M, Barnard J, Zhu X. Pathway-based analysis for genome-wide association studies using supervised principal components. Genetic Epidemiology 2010; 34:716-724.
  46. Chen X, Wang L, Ishwaran H. An integrative pathway-based clinical-genomic model for cancer survival prediction. Statistics and Probability Letters 2010; 80: 1313-1319.
  47. Nam KT, Lee HJ, Smith JJ, Lapierre LA, Kamath V, Chen X, Aronow BJ, Yeatman TJ, Bhartur SG, Calhoun BC, Condie B, Manley NR, Beauchamp RD, Coffey RJ, Gondenring JR. Loss of Rab25 promotes the development of intestinal neoplasia. Journal Clinical Investigation 2010; 120(3): 840-849.
  48. McCarron JA, Milks RA, Chen X, Iannotti JP, Derwin KA. Improved time-zero biomechanical properties using PLLA graft augmentation in a cadaveric rotator cuff repair model. Journal of Shoulder and Elbow Surgery 2010; 19(5): 688-696.
  49. Yu W, Lin Z, Hegarty JP, John G, Chen X, Faber PW, Kelly AA, Wang Y, Poritz LS, Schreiber S, Koltun WA. Genes regulated by Nkx2-3 in siRNA-mediated knockdown B cell: implication in endothelin-1 regulation in Crohn’s disease patients. Molecular Genetics and Metabolism 2010; 100:88-95.
  50. Yu W, Lin Z, Pastor DM, Hegarty JP, Chen X, Kelley AA, Wang Y, Poritz LS, Koltun WA. Genes regulated by Nkx2-3 in sporadic and inflammatory bowel disease-associated colorectal cancer cell lines. Digestive Diseases and Sciences 2010; 55: 3171-3180.
  51. Krishnan M, Singh AB, Smith JJ, Sharma A, Chen X, Eschrich S, Yeatman TJ, Beauchamp RD, Dhawan P. HDAC inhibitors regulate claudin-1 expression in colon cancer cells through modulation of mRNA stability. Oncogene 2010; 29:305-312.
  52. Wang L, Chen X, Wolfinger RD, Franklin JL, Coffey RJ, Zhang B. A unified mixed effects model for gene set analysis of time course microarray experiments. Statistical Applications in Genetics and Molecular Biology 2009; 8(1): Article 47.
  53. Chen X, Wang L. Integrating biological knowledge with gene expression profiles for survival prediction of cancer. Journal of Computational Biology 2009; 16(2): 265-278.
  54. Chen X, Wang L, Smith JD, Zhang B. Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics 2008; 24:2474-2481.
  55. Wang L, Zhang B, Wolfinger RD, Chen X. An integrated approach for the analysis of biological pathways using mixed models. PLoS Genetics 2008; 4(7): e1000115.
  56. Bhasin JM, Charkrabarti E, Peng D, Kulkarni A, Chen X, Smith JD. Sex specific gene regulation and expression qtls in mouse macrophages from a strain intercross. PLoS One 2008; 3(1):e1435
  57. Chen X, Yang WQ, Sivamani E, Bruneau AH, Wang BH, Qu RD. Selective elimination of perennial ryegrass by activation of a pro-herbicide through engineering E-coli argE gene. Molecular Breeding 2005; 15(4): 339-347.
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Topic revision: r64 - 18 Mar 2015, StevenChen
 

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