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---+ Xi (Steven) Chen
*<nop>Associate Professor of Biostatistics* <br /> Division of Cancer Biostatistics<br />Department of Biostatistics<br />Vanderbilt University School of Medicine<br />549 Preston Research Building<br />Nashville, TN 37232-6848

steven.chen@vanderbilt.edu <br />phone: (615) 936-2785<br />fax: (615) 936-2602</td> <td width="100"><img alt="" height="200" src="%ATTACHURLPATH%/704398.jpg" /></td> </tr> </tbody> </table>

---+++ 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

---+++ [[%ATTACHURL%/Bioinformatics_position_12_2013.pdf][ Postdoctoral Position Available]]

---+++ Education

*<nop>PhD in Statistics* <br />North Carolina State University, 2006<br />Dissertation: Characterizing the Genetic Structure of Populations <br />Advisor: Dr Bruce S Weir

*<nop>MS in Molecular Genetics* <br />North Carolina State University, 2002

---+++ Work Experience

*Associate Professor (with tenure)* 2015-present<br />Department of Biostatistics, Vanderbilt University

*Assistant Professor* 2009 - 2014<br />Department of Biostatistics, Vanderbilt University

*Assistant Staff* 2006 - 2009 <br />Department of Quantitative Health Sciences, Cleveland Clinic

---+++ Methodology Grants

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

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

---+++ Media Coverage

*Interview by Momentum*

[[http://www.vanderbilt.edu/magazines/momentum/2012/03/controlling-the-data-tsunami/][A closer look]]

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

[[http://www.mc.vanderbilt.edu/reporter/index.html?ID=12436][VUMC Reporter 2012]]

[[http://www.mc.vanderbilt.edu/reporter/index.html?ID=10945][VUMC Reporter 2011]]

[[http://journals.lww.com/oncotimesuk/Fulltext/2011/09000/Identifying_subtypes_in_triple_negative_breast.5.aspx][Oncology Times: Identifying subtypes in triple-negative breast cancer]]

[[http://www.breastcancerdeadline2020.org/event/cat-event/2011-november-leadcast.html][LEADcast, a critical appraisal of "Indentification of Human Triple-Negative Breast Cancer Subtypes and Preclinical Models for Selection of Targeted Therapies"]]

[[http://www.cancernetwork.com/breast-cancer/content/article/10165/1903520][Cancer network]]

[[http://www.ascopost.com/articles/february-15-2011/triple-negative-breast-cancer-proving-to-be-genetically-diverse/][The ASCO Post]]

*Building prediction model for colon cancer prognosis*

[[http://www.vicc.org/research/grants/pilots-awarded/pilot-projects-awarded.php][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

[[https://cbc.mc.vanderbilt.edu/tnbc/][TNBCtype: A subtyping tool for triple-negative breast cancer]]
---+++ Publications

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   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.
   1 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.
   1 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.
   1 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.
   1 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.
   1 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.
   1 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..
   1 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.
   1 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.
   1 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.
   1 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.
   1 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.
   1 *Chen X*, Ishwaran H. Pathway hunting by random survival forests. <em>Bioinformatics </em>2013; 29(1): 99-105.
   1 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. <em>Journal of Clinical Investigation. </em>2013<em>; </em>123(7):3112-3123.
   1 Tanksley JP<em>, </em> *Chen X*, Coffey RJ. <i>NEDD4L </i>is downregulated in colorectal caccer and inhibits canonical WNT signaling. _PLoS One_ 2013; 8(11): e81514.
   1 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 <em>NRAS </em>mutations. _Clinical Cancer Research_ 2013; 19:2584-2591.
   1 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.
   1 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.
   1 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.
   1 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.
   1 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.
   1 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. <em>Annals of Surgical Oncology </em>2013<em>; </em>20:1336-1340<em>.<br /></em>
   1 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.
   1 *Chen X*, Li J, Gray WH, Lehmann BD, Bauer JA, Shyr Y, Pietenpol JA. TNBCtype: A subtyping tool for triple-negative breast cancer. <em>Cancer Informatics </em>2012; 11:147-156<em>.</em>
   1 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.
   1 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.
   1 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.
   1 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. <em>Sarcoma </em>2012; Article 498472.
   1 *Chen X*, Ishwaran H. Random forests for genomic data analysis. _Genomics_ 2012; 99:323-329.
   1 Wang L, *Chen X*, Zhang B. Statistical analysis of patient-specific pathway activities via mixed models. _Journal of Biometrics & Biostatistics_ 2012; S8-001.
   1 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.
   1 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.
   1 Chmielecki J, Pietanza MC, Aftab D, Shen R, Zhao Z, *Chen X*, Hutchinson K, Viele A, Kris MG, Stout T, Miller V, Pao W. <em>EGFR </em>mutant lung adenocarcinomas treated first-line with the novel EGFR inhibitor, XL647, can subsequently retain moderate sensitivity to erlotinib. <em>Journal of Thoracic Oncology </em>2012; 7(2):434-442.
   1 *Chen X*. Adaptive elastic-net sparse principal component analysis for pathway association testing. <em>Statistical Applications in Genetics and Molecular Biology </em>2011; 10(1): Article 48.
   1 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.
   1 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. <em>Journal of Clinical Investigation </em>2011; 121(10): 4056-4069.
   1 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. <em>Bioinformatics </em>2011; 27(5): 686-692.
   1 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.
   1 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.
   1 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. <em>Journal of Clinical Investigation </em>2011; 121(7): 2750-2767.
   1 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. <em>PLoS One </em>2011; 6(5): e20454.
   1 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.
   1 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. <em>Clinical Genetics </em>2011; 80: 59-67.
   1 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.
   1 *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.
   1 *Chen X*, Wang L, Ishwaran H. An integrative pathway-based clinical-genomic model for cancer survival prediction. <em>Statistics and Probability Letters </em>2010; 80: 1313-1319.
   1 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<em>. Journal Clinical Investigation</em> 2010; 120(3): 840-849.
   1 !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. <em>Journal of Shoulder and Elbow Surgery </em>2010; 19(5): 688-696.
   1 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.
   1 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. <em>Digestive Diseases and Sciences </em>2010; 55: 3171-3180.
   1 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.
   1 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.
   1 *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.
   1 *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.
   1 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.
   1 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
   1 *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 attachments
I	Attachment	Action	Size	Date	Who	Comment
jpg	704398.jpg	manage	868.6 K	04 Jun 2009 - 20:43	StevenChen
pdf	Bioinformatics_position_12_2013.pdf	manage	33.1 K	16 Dec 2013 - 22:18	StevenChen
Topic revision: r64 - 18 Mar 2015, StevenChen
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