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Yuan Ji, Ph.D.

Present Title & Affiliation

Primary Appointment

Associate Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX

Dual/Joint/Adjunct Appointment

Associate Professor, Statistics, Rice University, Houston, TX

Bio Statement

My research focuses on statistical methodologies and applications in two main areas:

1. Bayesian models for complex, high-throughput, genomics and proteomics data, such as microarrays, reverse phase protein arrays, and next-generation sequencing data.

2. Bayesian adaptive designs for early-phase clinical trials.

While the two research directions are mostly parallel, I am optimistic that the two paths will cross. For example, there are many trials now based on biomarkers. Also, the rapid progress in genomics research has hinted on personalized medicine.

My Lab page can be found at http://odin.mdacc.tmc.edu/~yuanj/index3.html

Education & Training

Degree-Granting Education

2003 University of Wisconsin-Madison, Madison, WI, PHD, Statistics
1999 University of Minnesota, Twin Cities, MN, MS, Biostatistics
1997 Fudan University, Shanghai, China, BA, Mathematics

Honors and Awards

2003 ENAR Student Award, International Biometric Society's Eastern North American Region (ENAR), Florida
2002 Merck Foundation Fellowship, Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison
2002 NSF Young Researcher Travel Grant, National Science Foundation
2002 Student Travel Award and the Charles Sampson Award, The 25th annual Midwest Biopharmaceutical Statistics Workshop, Muncie, Indiana
2002 Vilas Travel Fellowship, University of Wisconsin-Madison, Madison, Wisconsin
1996 International Mathematical Modeling Contest, Department of Mathematics, Fudan University, China
1995 National Mathematical Modeling Contest, Department of Mathematics, Fudan University, China

Selected Publications

Peer-Reviewed Original Research Articles
1. Nieto-Barajas L, Mueller P, Ji Y, Lu Y, Mills, G. A Time-Series DDP for Functional Proteomics Profiles. Biometrics. In Press.
2. Cai G, Li H, Lu Y, Lee JH, Mueller P, Ji Y, Liang S. Accuracy of RNA-Seq and its dependence on sequencing depth. BMC Bioinformatics. In Press.
3. Ji, Y, Xu, Y, Zhang, Q, Tsui, K-W, Yuan, Y, Liang, S, Liang, H. BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data. Biometrics. In Press.
4. Lee JH, Ji Y*, Liang S, Cai G, Mueller P*. On Differential Gene Expression Using RNA-Seq Data. Cancer Informatics. In Press.
5. Younes A, Oki Y, Bociek GR, Kuruvilla J, Fanale M, Neelapu S, Copeland A, Buglio D, Galal A, Besterman J, Li Z, Drouin M, Patterson T, Ward MR, Paulus JK, Ji Y, Medeiros LJ, and Martell, RE. Phase II Study of Mocetinostat (MGCD0103) In Patients with Relapsed and Refractory Classical Hodgkin Lymphoma. Lancet Oncology. In Press.
6. Ji Y, Liu P, Li Y, Bekele BN. A modified toxicity probability interval method for dose-finding trials. Clin Trials 7(6):653-63, 12/2010. e-Pub 10/8/2010. PMID: 20935021.
7. Baladandayuthapani V, Ji Y, Talluri R, Nieto-Barajas LE, Morris JS. Bayesian Random Segmentation Models to Identify Shared Copy Number Aberrations for Array CGH Data. J Am Stat Assoc 105(492):1358-1375, 12/2010. PMCID: PMC3079218.
8. Zhou X, Teegala S, Huen A, Ji Y, Fayad L, Hagemeister FB, Gladish G, Vadhan-Raj S. Incidence and Risk Factors of Venous Thromboembolic Events in Lymphoma. Am J Med 123(10):935-41, 10/2010. PMID: 20920696.
9. Hu B, Bekele BN, Ji Y. Adaptive Dose Insertion in Early Phase Clinical Trials. Clin Trials. e-Pub 9/2010. PMID: 20819841.
10. Bekele BN, Li Y, Ji Y. Risk-group-specific dose finding based on an average toxicity score. Biometrics 66(2):541-8, 6/2010. e-Pub 7/23/2009. PMID: 19645698.
11. Wang M, Oki Y, Pro B, Romaguera JE, Rodriguez MA, Samaniego F, McLaughlin P, Hagemeister F, Neelapu S, Copeland A, Samuels BI, Loyer EM, Ji Y, Younes A. Phase II Study of Yttrium-90-Ibritumomab Tiuxetan in Patients With Relapsed or Refractory Mantle Cell Lymphoma. J Clin Oncol 27(31):5213-8, 11/2009. e-Pub 9/2009. PMID: 19770379.
12. Ji Y, Bekele BN. Adaptive randomization for multi-arm comparative clinical trials based on joint efficacy/toxicity outcomes. Biometrics 65(3):876-84, 9/2009. e-Pub 1/2009. PMID: 19173694.
13. Berkova Z, Wang S, Wise JF, Maeng H, Ji Y, Samaniego F. Mechanism of Fas signaling regulation by human herpesvirus 8 K1 oncoprotein. J Natl Cancer Inst 101(6):399-411, 3/18/2009. e-Pub 3/10/2009. PMCID: PMC2720696.
14. Hu B, Ji Y, Tsui KW. Bayesian estimation of inverse dose-response. Biometrics 64(4):1223-30, 12/2008. e-Pub 3/19/2008. PMID: 18355383.
15. Li Y, Bekele BN, Ji Y, Cook JD. Dose-schedule finding in phase I/II clinical trials using a Bayesian isotonic transformation. Stat Med 27(24):4895-4913, 10/30/2008. PMID: 18563789.
16. Miyazaki K, Yamaguchi M, Suguro M, Choi W, Ji Y, Xiao L, Zhang W, Ogawa S, Katayama N, Shiku H, Kobayashi T. Gene Expression Profiling of Diffuse Large B-cell Lymphoma Supervised by CD21 Expression. Br J Haematol 142(4):562-570, 8/2008. e-Pub 6/2008. PMID: 18537973.
17. Bekele BN, Ji Y, Shen Y, Thall PF. Monitoring late-onset toxicities in phase I trials using predicted risks. Biostatistics 9(3):442-57, 7/2008. e-Pub 12/14/2007. PMID: 18084008.
18. Ji Y, Lu Y, Mills GB. Bayesian models based on test statistics for multiple hypothesis testing problems. Bioinformatics 24(7):943-949, 4/1/2008. e-Pub 2/1/2008. PMID: 18245123.
19. Sun M, Estrov Z, Ji Y, Coombes KR, Harris DH, Kurzrock R. "Curcumin (Diferuloylmethane) Alters the Expression Profiles of MicroRNAs in Human Pancreatic Cancer Cells.". Mol Cancer Ther 7(3):464-473, 3/2008. PMID: 18347134.
20. Fanale M, Fayad L, Pro B, Samaniego F, Zachariah G, Nunez C, Ji Y, Younes A. A phase I evaluation of bortezomib in combination with ice (BICE) as treatment for relapsed/refractory classical Hodgkin lymphoma. Annals of Oncology 19:236-236, 2008.
21. Zhang J, Ji Y, Zhang L. Extracting three-way gene interactions from microarray data. Bioinformatics 23(21):2903-2909, 11/1/2007. e-Pub 10/5/2007. PMID: 17921496.
22. Zhu R, Ji Y, Xiao L, Matin A. Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain. Mamm Genome 18(8):584-595, 8/2007. e-Pub 8/2/2007. PMCID: PMC2647748.
23. Ji Y, Li Y, Yin G. Bayesian dose-finding designs for phase I clinical trials. Statistica Sinica 17:531-47, 2007.
24. Ji Y, Yin G, Tsui K-W, Kolonin M, Sun J, Arap W, Pasqualini R, Do K-A. Bayesian mixture models for complex high-dimension count data. Applied Statistics 56:139-152, 2007.
25. Ji Y, Li Y, Nebiyou Bekele B. Dose-finding in phase I clinical trials based on toxicity probability intervals. Clin Trials 4(3):235-44, 2007. PMID: 17715248.
26. Yin G, Li Y, Ji Y. Bayesian dose-finding in phase I/II clinical trials using toxicity and efficacy odds ratios. Biometrics 62(3):777-84, 9/2006. PMID: 16984320.
27. Kolonin MG, Sun J, Do KA, Vidal CI, Ji Y, Baggerly KA, Pasqualini R, Arap W. Synchronous selection of homing peptides for multiple tissues by in vivo phage display. FASEB J 20(7):979-81, 5/2006. e-Pub 3/31/2006. PMID: 16581960.
28. Ji Y, Tsui K-W, Kim KM. A two-stage empirical Bayes method for identifying differentially expressed genes. Computational Statistics and Data Analysis. 50:3592-604, 2006.
29. Ji Y, Coombes K, Zhang J, Wen S, Mitchell J, Pusztai L, Symmans WF, Wang J. RefSeq refinements of UniGene-based gene matching improve the correlation of expression measurements between two microarray platforms. Appl Bioinformatics 5(2):89-98, 2006. PMID: 16722773.
30. Ji Y, Wu C, Liu P, Wang J, Coombes KR. Applications of beta-mixture models in bioinformatics. Bioinformatics 21(9):2118-22, 5/1/2005. e-Pub 2/15/2005. PMID: 15713737.
31. Ji Y, Tsui KW, Kim K. A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples. Bioinformatics 21(7):1055-61, 4/2005. e-Pub 10/2004. PMID: 15514000.
32. Talluri R, Baladandayuthapani V, Mallick BK, Ji Y, Coombes KR, Hennessey BT, Davies M. Bayesian Sparse Graphical Models for Classification with Application to Protein Expression Data. JASA. Submitted.

Grant & Contract Support

Title: Identifying biomarkers of response and resistance to ECP in patients with MF/SS
Funding Source: Therakos, Inc.
Role: Co-Investigator
Principal Investigator: Xiao Ni
Duration: 11/1/2010 - 11/30/2012
 
Title: UT M. D. Anderson Cancer Center Lymphoma SPORE - (PC-D)
Funding Source: NIH/NCI
Role: Co-Core Leader
Principal Investigator: Anas Younes
Duration: 9/1/2009 - 8/31/2012
 
Title: Chemotherapy Resistance in Hispanic and African American Patients
Funding Source: Komen for the Cure
Role: Co-Investigator
Principal Investigator: Ana Gonzalez-Angulo
Duration: 7/29/2009 - 7/28/2012
 
Title: Bayesian models for cancer prognosis by integrating diverse types of data
Funding Source: NIH/NCI
Role: Principal Investigator
Duration: 9/15/2008 - 7/31/2013
 
Title: SPORE in Brain Cancer (PP-2A)
Funding Source: NIH/NCI
Role: Co-Investigator
Principal Investigator: W K Alfred Yung
Duration: 9/1/2008 - 8/31/2013
 
Title: Translational Development of Novel Vaccine Therapies (PC-A)
Funding Source: Leukemia and Lymphoma Society
Role: Co-Investigator
Principal Investigator: Larry Kwak
Duration: 10/1/2007 - 9/30/2012
 
Title: Cancer Center Support Grant - Biostatistics Resource (PP-SR21)
Funding Source: NIH/NCI
Role: Biostatistician
Principal Investigator: Rondald Depinho
Duration: 7/1/2003 - 6/30/2013

Last updated: 11/9/2011