Cheng Cheng, PhD

Cheng Cheng, PhD

Member, St. Jude Faculty



Contact Information

Cheng Cheng, PhD
MS 768, Room R6035
St. Jude Children's Research Hospital
262 Danny Thomas Place
Memphis, TN 38105-3678
Phone: (901) 595-2935
FAX: (901) 595-8843


BS - Beijing Computer Institute, China (1984)
PhD - Texas A & M University (1993)

Research Interests

I collaborate with St. Jude investigators in the areas of hematological malignancies, pharmaceutical sciences, molecular pathology, bioinformatics, and computational biology. I am interested in statistics methodological research in several areas with applications to biomedical sciences.

Selected Publications

Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, Loh ML, Devidas M, Wood B, Winter S, Dunsmore KP, Fulton RS, Fulton LL, Hong X, Harris CC, Dooling DJ, Ochoa K, Johnson KJ, Obenauer JC, Evans WE, Pui CH, Naeve CW, Ley TJ, Mardis ER, Wilson RK, Downing JR, Mullighan CG. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481(7380):157-63, 2012.

Diouf B, Cheng Q, Krynetskaia NF, Yang W, Cheok M, Pei D, Fan Y, Cheng C, Krynetskiy EY, Chen S, Thierfelder WE, Mullighah CG, Downing JR, Hsieh P, Pui C-H, Relling MV, Evans, WE. Somatic deletions of genes regulating MSH2 protein stability cause DNA mismatch repair deficiency and drug resistance in human leukemia cells. Nature Medicine 17:1298-1303, 2011.

Yang J, Cheng C, Devidas M, Cao X, Fan Y, Campana D, Yang W, Neale G, Cox N, Scheet P, Borowitz MJ, Winick NJ, Martin PL, Willman CL, Bowman WP, Camitta BM, Carroll A, Reaman GH, Carroll WL, Loh M, Hunger SP, Pui C-H, Evans WE, Relling MV. Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia. Nature Genetics 43:237-241, 2011.

Cheng C. Integration of diverse statistical evidence of gene-trait association in systems biology Studies. Invited paper for a special issue of Chemistry and Biodiversity 2011 (in press).

Cheng C, Wu J. Interval estimation of quantile ratios applied to anti-cancer drug screening by xenograft experiments. Statistics in Medicine 29:2669-2678, 2010.

Wu S, Wang J, Zhao W, Pounds S, Cheng C. ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data. Theoretical Biology and Medical Modeling 7:18, 2010.

Pounds S, Cheng C, Cao X, Crews KR, Plunkett W, Gandhi V, Rubnitz J, Raul C. Ribeiro RC, Downing JR, Lamba J. PROMISE: A Tool to Identify Genomic Features with a Specific Biologically Interesting Pattern of Correlations with Multiple Endpoint Variables. Bioinformatics 25:2013-2019, 2009.

Pui C-H, Campana D, Pei D, Bowman PW, Sandlund JT, Kaste SC, Ribeiro RC, Rubnitz JE, Raimondi SC, Onciu M, Coustan-Smith E, Kun LE, Jeha S, Cheng C, Howard SC, Simmons V, Bayles A, Metzger ML, Boyett JM, Leung W, Downing JR, Evans WE, Relling MV. Treatment of childhood acute lymphoblastic leukemia without prophylactic cranial irradiation. New England Journal of Medicine 360(26):2730-2741, 2009.

Pounds S, Cheng C, Mullighan CG, Raimondi, SC, Shurtleff S, and Downing, JR. Reference alignment of SNP microarray signals for copy number analysis of tumors. Bioinformatics 25:315-321, 2009.

Mullighan CG, Su X, Zhang J, Radtke I, Phillips LAA, Miller CB, Ma J, Liu W, Cheng C, Schulman BA, Harvey RC, Chen I-M, Clifford RJ, Carroll WL, Reaman G, Bowman PW, Devidas M, Gerhard DS, Yang W, Relling MV, Shurtleff  SA, Campana D, Borowitz MJ, Pui C-H, Smith M, Hunger SP, Willman CL, Downing JR, and the Children's Oncology Group. Deletion of IKZF1 (IKSROS) is associated with poor prognosis in acute lymphoblastic leukemia. New England Journal of Medicine 360:470-480, 2009.

Yang J, Cheng C, Yang W, Pei D, Cao X, Fan Y, Pounds S, Trevino LR, French D, Campana D, Evans WE, Piu C-H, Devidas M, Bowman WP, Camitta BM, Willman C, Davies SM, Borowitz MJ, Carroll WL, Hunger SP, Relling MV. Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia. Journal of American Medical Association 301(4):393-403, 2009.

Cheng C. Internal validation inferences of significant genomic features in genome-wide screening. Computational Statistics and Data Analysis 53:788-800, 2009.

Hunt DL, Cheng C, and Pounds S. The Beta-Binomial distribution for estimating the number of false rejections in microarray gene expression studies. Computational Statistics and Data Analysis 53:1688–1700, 2009.

Cheng C, Pounds S. False discovery rate paradigms for analysis of microarray gene expression data. Bioinformation 1(10): 436-446, 2007. Invited paper

Pounds S, Cheng C, Onar A. Statistical Inference for Microarray Studies. Handbook of Statistical Genetics, Third Edition (David Balding et al. Eds.) 1:231-266, 2007. Invited paper

Kishi S, Cheng C, French D, Pei D, DasS, Cook EH, Hijiya N, Pui CH, Relling MV. Ancestry and pharmacogenetics of antileukemic drug toxicity. Blood 109:4151-4157, 2007.

Pounds S, Cheng C. Robust estimation of the false discovery rate. Bioinformatics 22:1979-1987, 2006.

Cheng C. An adaptive significance threshold criterion for massive multiple hypothesis testing. In Optimality: The Second Erich L. Lehmann Symposium, Institute of Mathematical Statistics, Beachwood, OH, USA; 49:51-76, 2006.

Bogni A, Cheng C, Liu W, Yang W, Pfeffer J, Mukatira S, French D, Downing JR, Pui C-H, and Relling MV. Genome-Wide Approach to Identify Risk Factors for Therapy-Related Myeloid Leukemia. Leukemia 20:239-246, 2006.

Cheng Q, Cheng C, Crews KR, Ribeiro RC, Pui C-G, Relling MV, Evans WE. Epigenetic regulate of human g-glutamyl hydrolase activity in acute lymphoblastic leukemia cells. American Journal of Human Genetics, 79:264-274, 2006.

Flotho C, Coustan-Smith E, Pei D, Iwamoto S, Song G, Cheng C, Pui C-H, Downing JR, Campana D. Genes contributing to minimal residual disease in childhood acute lymphoblastic leukemia: prognostic significance of CASP8AP2. Blood 108:1050-1067, 2006.

Lugthart S, Cheok MH, den Boer ML, Yang W, Holleman A, Cheng C, Pui C-H, Relling MV, Janka-Schaub GE, Pieters R, Evans WE Identification of genes associated with chemotherapy crossresistance and treatment response in childhood acute lymphoblastic leukemia. Cancer Cell 7(4):375-386, 2005.

Marshall DR, Olivas E, Andreansky S, La Gruta NL, Neale GA, Gutierrez A, Wichlan DG, Wingo S, Cheng C, Doherty PC, Tuner SJ. Effector CD8+ T cells recovered from an influenza pneumonia differentiate to a state of focused gene expression. Proceedings of National Academy of Sciences 102(17): 6074-9, 2005.

Rocha JC, Cheng C, Liu W, Kishi S, Das S, Cook EH, Sandlund JT, Rubnitz JE, Ribeiro RC, Pui C-H, Evans WE, Relling MV. Pharmacogenetics of outcome in children with acute lymphoblastic leukemia. Blood 105(12):4752-58, 2005.

Pounds S, Cheng C. Statistical development and evaluation of microarray gene expression data filters. Journal of Computational Biology 12:482-495, 2005.

Cheng C, Pounds S, Boyett JM, Pei D, Kuo M-L, Roussel MF. Statistical significance threshold criteria for analysis of microarray gene expression data. Statistical Applications in Genetics and Molecular Biology 3(1): Article 36, 2004.

Holleman A, Cheok MH, den Boer ML, Yang W, Veerman AJP, Kazemire KM, Cheng C, Pui CH, Relling MV, Janka-Schaub GE, Pieters R, Evans WE. Gene expression patterns in drug- resistant acute lymphoblastic leukemia cells and response to treatment. New England Journal of Medicine 351(6):533-42, 2004.

Li C-S, Cheng C. Stable classification in the analysis of microarray data. Computational Statistics and Data Analysis 47:599-609 2004.

Pounds S, Cheng C. An adaptive p-value distribution estimator for estimating error rates in microarray studies. Bioinformatics 20(11):1737-45, 2004.

Pui C-H, Cheng C, Rivera GK, Leung W, Sandlund JT, Riberio RC, Relling RV, Kun LE, Evans, WE, and Hudson MM. Extended follow up of long-term survivors of childhood acute lymphoblastic leukemia. New England Journal of Medicine 349:640-649, 2003.

Cheok MH, Yang W, Pui CH, Downing JR, Cheng C, Naeve CW, Relling MV, Evans WE. Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells. Nature Genet ics 34:85-90, 2003.

Kuo, M-L, Duncavich E, Cheng C, Pei D, Sherr C, and Roussel MF. Arf induces p53-dependent and in-dependent anti-proliferative genes. Cancer Research 1;63(5):1046-53, 2003.

Yeoh E-J, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R., Behm FG, Raimondi SC, Relling MV, Patel A, Cheng C, Campana D, Wilkins D, Zhou X, Li J, Liu H, Pui C-H, Evans, WE, Naeve C, Wong L, and Downing JR. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 1:133-143, 2002.

Cheng C. Almost-sure uniform error bounds of general smooth estimators of quantile density functions. Statistics and Probability Letters 59:183-194, 2002.

Cheng C, Tong YL. Concentration order on a metric space, with some statistical applications. Statistics and Probability Letters 44:327-335, 1999.

Cheng C. Uniform consistency of generalized kernel estimators of quantile density. Annals of Statistics 23:2285-2291, 1995.

Kaigh WD, Cheng C. Subsampling quantile estimators and uniformity criteria. Communications in Statistics – A. 20:539-560, 1991.

Last update: January 2012