Stan Pounds, PhD
Stan Pounds, PhD

Stan Pounds, PhD

Member, St. Jude Faculty

  • Director, Biostatistics Division for Computational Biology and Bioinformatics

Departments

Education

BS – Harding University, Searcy, Arkansas (1997)
PhD – Texas A&M University, College Station, Texas (2002)

Research Interests

I develop statistical methods for genomics studies conducted at St. Jude. I develop methods to estimate the false discovery rate (FDR), perform power and sample size calculations for microarray studies, pre-process SNP microarray data, detect genomic lesions using SNP microarray data, and explore the association microarray data with multiple clinical variables simultaneously.

Selected Publications

Andersson A, Ma J, Wang J, Chen X, Gedman AL, Dang J, Nakitandwe J, Holmfeld L, Parker M, Easton J, Huether R, Kriwacki R, Rusch M, Wu G, Li Y, Mulder H, Raimondi S, Pounds S, Kang G, Shi L, Becksforth J, Gupta P, Payne-Turner D, Vadodaria B, Boggs K, Yergeau D, Manne J, Song G, Edmonson M, Nagahawatte P, Wei L, Cheng C, Pei D, Sutton R, Venn NC, Chetcuti A, Rush A, Catchpoole D, Heldrup J, Rioretos T, Lu C, Ding L, Pui C-H, Shurtleff S, Mullighan CG, Mardis ER, Wilson RK, Gruber TA, Zhang J, Downing JR. The landscape of somatic mutations in Infant MLL rearranged acute lymphoblastic leukemias. Nature Genetics 2015. Epub ahead of print. PMID 25730765.

Chen X, Gupta P, Wang J, Nakitandwe J, Roberts K, Dalton JD, Parker M, Patel S, Holmfeldt L, Payne D, Easton J, Ma J, Rusch M, Wu G, Patel A, Baker S, Dyer MA, Shurtleff SA, Espy S,Pounds S, Downing JR, Ellison D, Mullighan CG, Zhang J. CONSERTING: an accurate method for detecting somatic DNA copy number alterations in whole genome sequencing data. Nature Methods2015.

Kang G, Bi W, Zhao Y, Zhang J-F, Yang JJ, Xu H, Loh ML, Hunger SP, Relling MV, Pounds S, Cheng C. A New System Identification Approach to Identifying Genetic Variants in Sequencing Studies for A Binary Phenotype. Human Heredity 78:104-16, 2014.

Liu Z, Pounds S. An R Package that Automatically Collects and Archives Details for Reproducible Computing. BMC Bioinformatics 15:138, 2014.

Pawlikowska I, Wu G, Edmonson M, Liu Z, Gruber T, Zhang J, Pounds S. The Most Informative Spacing Test Effectively Discovers Biologically Relevant Outliers or Multiple Modes in Expression. Bioinformatics 30:1400-1408, 2014.

Rubnitz JE, Inaba H, Leung W, Pounds S, Cao X, Coustan-Smith E, Campana D, Ribeiro RC, Pui C-H. Definition of Cure of Childhood Acute Myeloid Leukemia. Cancer 210:2490-6, 2014.

Wu G, Diaz AK, Paugh BS, Rankin SL, Ju B, Li y, Zhu X, Qu C, Chen X, Zhang J, Easton J, Edmonson M, Ma X, Lu C, Nagahawatte P, Hedlund E, Rusch M, Pounds S, Lin T, Onar-Thomas A, Huether, Kriwacki R, Parker M, Gupta P, Becksforth J, Wei L, Mulder HL, Boggs K, Vadodaria B, Yergeau D, Russell JC, Ochoa K, Fulton RS, Fulton LL, Jones C, Boop FA, Broniscer A, Wetmore C, Gajjar A, Ding L, Mardis ER, Wilson RK, Taylor MR, Downing JR, Ellison DW, Zhang J, Baker SJ. The genomic landscape of intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nature Genetics 46:444-50, 2014.

Mortland L, Alonzo TA, Walter RB, Gerbing RB, Mitra AK, Pollard JA, Loken MR, Hirsch B, Raimondi S, Franklin J, Pounds S, Cao X, Rubnitz JE, Ribeiro RC, Gamis A, Meshinchi S, Lamba JK. Clinical Significance of CD33 Non-synonymous Single Nucleotide Polymorphisms in Pediatric Patients with Acute Myeloid Leukemia Treated with Gemtuzumab-Ozogamicin Containing Chemotherapy. Clinical Cancer Research 19:1620-7, 2013.

O’Hear C, Inaba H, Pounds S, Shi L, Dahl G, Bowman WP, Taub JW, Pui C-H, Ribeiro RC, Coustan-Smith E, Campana D, Rubnitz JE. Gemtuzumab ozogamicin can reduce minimal residual disease in childhood acute myeloid leukemia. Cancer 119:4036-43, 2013.

Pounds S, Cheng C, Li S, Liu Z, Zhang J, Mullighan C. A Genomic Random Interval Model for Statistical Analysis of Genomic Lesion Data. Bioinformatics 29: 2088-95, 2013.

Pounds SB, Gao CL, Zhang H. Empirical Bayesian Selection of Hypothesis Testing Procedures for Analysis of Sequence Count Expression Data. Statistical Applications in Genetics and Molecular Biology 11:5, 2012.

Robinson G, Parker M, Kranenburg TA, Lu C, Chen X, Ding L, Phoenix TN, Hedlund E, Wei L, Zhu X, Chalhoub N, Baker SJ, Huether R, Kriwacki R, Curley N, Thiruvenkatam R, Wang J, Wu G, Rusch M, Hong X, Becksfort J, Gupta P, Ma J, Easton J, Vadodaria B, Onar-Thomas A, Lin T, Li S, Pounds S, Paugh S, Zhao D, Kawauchi D, Roussel MF, Finkelstein D, Ellison DW, Lau CC, Bouffet E, Hassall T, Gururangan S, Cohn R, Fulton RS, Fulton LL, Dooling DJ, Ochoa K, Gajjar A, Mardis ER, Wilson RK, Downing JR, Zhang J, Gilbertson RJ. Novel mutations target distinct subgroups of medulloblastoma. Nature 488:43-48, 2012.

Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, Chen X, Ulyanov A, Wu G, Wilson M, Wang J, Brennan R, Rusch M, Manning AL, Ma J, Easton J, Shurtleff S, Mullighan C, Pounds S, Mukatira S, Gupta P, Neale G, Zhao D, Lu C, Fulton RS, Fulton LL, Hong X, Dooling DJ, Ochoa K, Naeve C, Dyson NJ, Mardis ER, Bahrami A, Ellison D, Wilson RK, Downing JR, Dyer MA. A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature 481:329-334, 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 481:157-63, 2012.

Pounds S, Gao C, Johnson R, Wright K, Poppleton H, Finkelstein D, Leary S, and Gilbertson R. A Procedure to Statistically Evaluate Agreement of Differential Expression for Cross-Species Genomics.Bioinformatics 27: 2098-103, 2011. Bioconductor package available; featured in the St. Jude 2011 Scientific Report.

Pounds S, Cheng C, Cao X, Crews KR, Plunkett WA, Gandhi V, Rubnitz JE, Ribeiro RC, Downing JR, and Lamba J. PROMISE: A Tool to Identify Genomic Variables with a Specific Biologically Interesting Pattern of Associations with Multiple Endpoint Variables. Bioinformatics 25: 2013-2019, 2009. Bioconductor package available.

Pounds S, Cheng C, Mullighan C, Raimondi SC, Shurtleff S, Downing JR. Reference Alignment of SNP Microarray Signals for Copy Number Analysis of Tumors, Bioinformatics, 25: 315-321, 2009. Featured in the 2/24/09 issue of BioArray News and the St. Jude 2010 Scientific Report.

Last update: May 2015