Estimating the Occurrence of False Positives and False Negatives in Microarray Studies by Approximating and Partitioning the Empirical Distribution of P-values. - Stan Pounds; Stephan W. Morris (Bioinform., 2003)

Improving false discovery rate estimation. - Stan Pounds; Cheng Cheng (Bioinform., 2004)

Sample size determination for the false discovery rate. - Stan Pounds; Cheng Cheng (Bioinform., 2005)

Statistical Development and Evaluation of Microarray Gene Expression Data Filters. - Stan Pounds; Cheng Cheng (J. Comput. Biol., 2005)

Estimation and control of multiple testing error rates for microarray studies. - Stan Pounds (Briefings Bioinform., 2006)

Robust estimation of the false discovery rate. - Stan Pounds; Cheng Cheng (Bioinform., 2006)

A permutation-based method to identify loss-of-heterozygosity using paired genotype microarray data. - Stan Pounds; Cheng Cheng; Wenjian Yang; Arzu Onar; Christine Hartford; Susana C. Raimondi; Mary Relling (BMC Bioinform., 2008)

Robust detection method for differential expression studies. - Shesh N. Rai; Stanley Pounds (BMC Bioinform., 2008)

Integrated Analysis of Pharmacokinetic, Clinical, and SNP Microarray Data Using Projection onto the Most Interesting Statistical Evidence with Adaptive Permutation Testing. - Stan Pounds; Xueyuan Cao; Cheng Cheng; Jun J. Yang; Dario Campana; William E. Evans; Ching-Hon Pui; Mary Relling (BIBM, 2009)

Erratum: sample size determination for the false discovery rate. - Stan Pounds; Cheng Cheng (Bioinform., 2009)

PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables. - Stan Pounds; Cheng Cheng; Xueyuan Cao; Kristine R. Crews; William Plunkett; Varsha Gandhi; Jeffrey Rubnitz; Raul C. Ribeiro; James R. Downing; Jatinder Lamba (Bioinform., 2009)

Reference alignment of SNP microarray signals for copy number analysis of tumors. - Stan Pounds; Cheng Cheng; Charles Mullighan; Susana C. Raimondi; Sheila Shurtleff; James R. Downing (Bioinform., 2009)

The beta-binomial distribution for estimating the number of false rejections in microarray gene expression studies. - Daniel Hunt; Cheng Cheng; Stanley Pounds (Comput. Stat. Data Anal., 2009)

Assumption adequacy averaging as a concept for developing more robust methods for differential gene expression analysis. - Stanley Pounds; Shesh N. Rai (Comput. Stat. Data Anal., 2009)

A Bayesian change-point algorithm for detecting copy number alteration. - Fridtjof Thomas; Stanley Pounds (BMC Bioinform., 2010)

A procedure to statistically evaluate agreement of differential expression for cross-species genomics. - Stan Pounds; Cuilan Lani Gao; Robert A. Johnson; Karen D. Wright; Helen Poppleton; David Finkelstein; Sarah E. S. Leary; Richard J. Gilbertson (Bioinform., 2011)

Integrated analysis of pharmacologic, clinical and SNP microarray data using Projection Onto the Most Interesting Statistical Evidence with Adaptive Permutation Testing. - Stan Pounds; Xueyuan Cao; Cheng Cheng; Jun J. Yang; Dario Campana; Ching-Hon Pui; William E. Evans; Mary Relling (Int. J. Data Min. Bioinform., 2011)

An empirical Bayes approach for analysis of diverse periodic trends in time-course gene expression data. - Mehmet Kocak; E. Olusegun George; Saumyadipta Pyne; Stanley Pounds (Bioinform., 2013)

A genomic random interval model for statistical analysis of genomic lesion data. - Stan Pounds; Cheng Cheng; Shaoyu Li; Zhifa Liu; Jinghui Zhang; Charles Mullighan (Bioinform., 2013)

PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays. - Shengping Yang; Stanley Pounds; Kun Zhang 012; Zhide Fang (Bioinform., 2013)

Our strategy to achieve and document reproducible computing. - Nisrine Enyinda; Zhifa Liu; Areg Negatu; Stan Pounds (BMC Bioinform., 2013)

Empirical Bayesian selection of hypothesis testing procedures for analysis of digital gene expression data. - Stan Pounds; Cuilan Lani Gao (BMC Bioinform., 2013)

Subgroup and outlier detection analysis. - Gang Wu 016; Iwona Pawlikowska; Tanja Gruber; James R. Downing; Jinghui Zhang; Stan Pounds (BMC Bioinform., 2013)

The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression. - Iwona Pawlikowska; Gang Wu 016; Michael N. Edmonson; Zhifa Liu; Tanja Gruber; Jinghui Zhang; Stan Pounds (Bioinform., 2014)

An R Package that Automatically Collects and Archives Details for Reproducible Computing. - Zhifa Liu; Stan Pounds (BMC Bioinform., 2014)

CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoints. - Xueyuan Cao; Kristine R. Crews; James R. Downing; Jatinder Lamba; Stanley Pounds (BMC Bioinform., 2016)

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016. - Eric C. Rouchka; Julia H. Chariker; Benjamin J. Harrison; Juw Won Park; Xueyuan Cao; Stanley Pounds; Susana C. Raimondi; James R. Downing; Raul C. Ribeiro; Jeffrey Rubnitz; Jatinder Lamba; Bernie J. Daigle Jr.; et al. (BMC Bioinform., 2016)

Statistical selection of biological models for genome-wide association analyses. - Wenjian Bi; Guolian Kang; Stanley Pounds (BIBM, 2017)

POST: A framework for set-based association analysis in high-dimensional data. - Xueyuan Cao; E. Olusegun George; Mingjuan Wang; Dale B. Armstrong; Cheng Cheng; Susana C. Raimondi; Jeffrey E. Rubnitz; James R. Downing; Mondira Kundu; Stanley Pounds (BIBM, 2017)

Pan-cancer genome and transcriptome analyses of 1, 699 paediatric leukaemias and solid tumours. - Xiaotu Ma; Yu Liu; Yanling Liu; Ludmil B. Alexandrov; Michael N. Edmonson; Charles Gawad; Xin Zhou; Yongjin Li; Michael Rusch; John Easton; Robert Huether; Veronica Gonzalez-Pena; et al. (Nat., 2018)

Gene-set distance analysis (GSDA): a powerful tool for gene-set association analysis. - Xueyuan Cao; Stan Pounds (BMC Bioinform., 2021)