Cheng Cheng, PhD
Cheng Cheng, PhD

Cheng Cheng, PhD

Member, St. Jude Faculty



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.

  • Statistical inference methods in systems biology and genome-wide integrated analysis, with emphasis on applications to cancer genomics
  • Validation inference in genome-wide studies
  • Estimation and control of false discovery rates; assessment of statistical significance in massive multiple comparisons applied to biomedical research, such as genome-wide studies
  • Analysis of high-dimensional and large data sets, data mining, dimension reduction and visualization, variable (feature) selection for cluster analysis, modeling, and classification
  • Methodologies of multivariate analysis: nonparametric methods combining linear or nonlinear projections and function estimation
  • Applications of percentiles (quantiles) in data analysis and modeling
  • Methods of analyzing general distance (similarity) and non-dimensional data, visualization, cluster analysis, and multidimensional scaling.

Selected Publications

Pounds S, Cheng C, Li S, Zhang J, Mullighan C. Genomic random interval models for statistical analysis of genomic lesion data. Bioinformatics 29(17):2088-2095, 2013. doi: 10.1093/bioinformatics/btt372.

Xu H, Yang W, Perez-Andreu V, Devidas M, Fan Y, Cheng C, Pei D, Scheet P, Burchard EG, Eng C, Huntsman S, Torgerson DG, Dean M, Winick MJ, Martin PL, Camitta BM, Bowman PW, Willman CL, Carroll WL, Mullighan CG, Bhojwani D, Hunger SP, Pui C-H, Evans WE, Relling MV, Loh ML, Yang JJ. Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations. J Natl Cancer Inst 105(10):733-742, 2013.

Xu L, Cheng C, George EO, Homayouni R. Literature aided determination of data quality and statistical significance threshold for gene expression studies. BMC Genomics 13(suppl 8):S23, 2012.

Cheng C. Integration of diverse statistical evidence of gene-trait association in systems biology studies. Chemistry and Biodiversity 9(5):935-944, 2012; invited paper for Special Issue on Systems Biology: Molecular Networks and Disease NIHMS414396.

Yang JJ, Cheng C, Devidas M, Cao X, Campana D, Yang W, Fan Y, Neale G, Cox N, Scheet P, Borowitz MJ, Winick NJ, Martin PL, Bowman WP, Camitta B, Reaman GH, Carroll WL, Willman CL, Hunger SP, Evans WE, Pui CH, Loh M, Relling MV. Genome-wide association study identifies germline polymorphisms associated with relapse of childhood acute lymphoblastic leukemia. Blood 120:4197-4204, 2012.

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.

Gao C, Cheng C. A Phenotype-driven dimension reduction (PhDDR) approach to integrated genomic association analyses. Proceedings of 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society pp.6837-6840, 2011. PMCID: PMC3652376 *Invited paper for the special session on Informatics for Integrated Genomics.

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. Chem Biodivers 9(5):935-44, 2012. *Invited paper for a special issue of Chemistry and Biodiversity.

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. Theor Biol Med Model 7:18, 2010.

Coustan-smith E, Mullighan CG, Onciu M, Behm FG, Raimondi SC, Pei D, Cheng C, Su X, Rubnitz JE, Basso G, Biondi A, Pui C-H, Downing JR, Campana D. Early T-cell precursor leukemia: a subtype of very high-risk acute lymphoblastic leukemia identified in two independent cohorts. Lancet Oncol 10:147-56, 2009. PMID: 19147408

Trevino L, Shimasaki N, Yang W, Panetta C, Cheng C, Pei, D, Chan D, Sparreboom A, Giacomini KM, Pui C-H, Evans WE, Relling MV. Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects. J Clin Oncol 27:5972-5978, 2009.

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. N Engl J Med 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. N Engl J Med 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. Comput Stat Data Anal 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. Comput Stat Data Anal 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. Am J Hum Genet 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.

Last update: September 2014