Stanley B Pounds

Summary

Affiliation: St. Jude Children's Research Hospital
Country: USA

Publications

  1. pmc An R package that automatically collects and archives details for reproducible computing
    Zhifa Liu
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis TN 38105, USA
    BMC Bioinformatics 15:138. 2014
  2. pmc A genomic random interval model for statistical analysis of genomic lesion data
    Stan Pounds
    Department of Biostatistics, Department of Computational Biology and Department of Pathology, St Jude Children s Research Hospital, Memphis, TN 38135, USA
    Bioinformatics 29:2088-95. 2013
  3. pmc ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data
    Song Wu
    Department of Biostatistics, St, Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Theor Biol Med Model 7:18. 2010
  4. pmc A procedure to statistically evaluate agreement of differential expression for cross-species genomics
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN, USA
    Bioinformatics 27:2098-103. 2011
  5. pmc Integrated analysis of pharmacologic, clinical and SNP microarray data using Projection Onto the Most Interesting Statistical Evidence with Adaptive Permutation Testing
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Int J Data Min Bioinform 5:143-57. 2011
  6. pmc PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Bioinformatics 25:2013-9. 2009
  7. pmc Reference alignment of SNP microarray signals for copy number analysis of tumors
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Bioinformatics 25:315-21. 2009
  8. pmc Statistical analysis of data from retroviral clonal experiments in the developing retina
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Brain Res 1192:178-85. 2008
  9. ncbi request reprint Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, 332 N Lauderdale St, Memphis, TN 38105 2794, USA
    Bioinformatics 19:1236-42. 2003
  10. ncbi request reprint Improving false discovery rate estimation
    Stan Pounds
    Department of Biostatistics, MS 262 St Jude Children s Research Hospital, 332 N Lauderdale Street, Memphis, TN 38105 2794, USA
    Bioinformatics 20:1737-45. 2004

Collaborators

Detail Information

Publications23

  1. pmc An R package that automatically collects and archives details for reproducible computing
    Zhifa Liu
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis TN 38105, USA
    BMC Bioinformatics 15:138. 2014
    ..In many applications, it is infeasible to manually maintain an accurate and complete record of all these details about a particular analysis...
  2. pmc A genomic random interval model for statistical analysis of genomic lesion data
    Stan Pounds
    Department of Biostatistics, Department of Computational Biology and Department of Pathology, St Jude Children s Research Hospital, Memphis, TN 38135, USA
    Bioinformatics 29:2088-95. 2013
    ....
  3. pmc ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data
    Song Wu
    Department of Biostatistics, St, Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Theor Biol Med Model 7:18. 2010
    ..However, high cost and high rate of false discovery of transcription factor binding sites identified from ChIP-Seq data significantly limit its application...
  4. pmc A procedure to statistically evaluate agreement of differential expression for cross-species genomics
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN, USA
    Bioinformatics 27:2098-103. 2011
    ..In principle, microarrays collect the necessary data to evaluate the transcriptomic fidelity of an animal model in terms of the similarity of expression with the human disease. However, statistical methods for this purpose are lacking...
  5. pmc Integrated analysis of pharmacologic, clinical and SNP microarray data using Projection Onto the Most Interesting Statistical Evidence with Adaptive Permutation Testing
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Int J Data Min Bioinform 5:143-57. 2011
    ..In the analysis of a paediatric leukaemia data set, PROMISE effectively identifies genomic features that exhibit a biologically meaningful pattern of association with multiple endpoint variables...
  6. pmc PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Bioinformatics 25:2013-9. 2009
    ..However, to our knowledge, there is no statistical procedure designed to detect specific patterns of association with multiple endpoint variables...
  7. pmc Reference alignment of SNP microarray signals for copy number analysis of tumors
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Bioinformatics 25:315-21. 2009
    ..In our study of acute lymphoblastic leukemia, RSA-RAP gives copy number analysis results that show substantially better concordance with cytogenetics than do two other alignment procedures...
  8. pmc Statistical analysis of data from retroviral clonal experiments in the developing retina
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Brain Res 1192:178-85. 2008
    ..We anticipate that this will serve as a guide for future statistical analyses of retroviral lineage studies and will help to provide a uniform standard in the field...
  9. ncbi request reprint Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, 332 N Lauderdale St, Memphis, TN 38105 2794, USA
    Bioinformatics 19:1236-42. 2003
    ..Essentially any distribution of p-values can be expressed as such a mixture by extracting a uniform density from it...
  10. ncbi request reprint Improving false discovery rate estimation
    Stan Pounds
    Department of Biostatistics, MS 262 St Jude Children s Research Hospital, 332 N Lauderdale Street, Memphis, TN 38105 2794, USA
    Bioinformatics 20:1737-45. 2004
    ..Unfortunately, the BUM approach is reliable only in settings where the assumed model accurately represents the actual distribution of p-values...
  11. ncbi request reprint Statistical development and evaluation of microarray gene expression data filters
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    J Comput Biol 12:482-95. 2005
    ..S-plus and R routines to implement the pooled p-value and error-minimizing pooled p-value filters have been developed and are available from www.stjuderesearch.org/depts/biostats/index.html...
  12. ncbi request reprint Sample size determination for the false discovery rate
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital 332 N Lauderdale Street, Memphis, TN 38135, USA
    Bioinformatics 21:4263-71. 2005
    ..There is not a widely applicable method to determine the sample size for experiments basing statistical significance on the false discovery rate (FDR)...
  13. ncbi request reprint Estimation and control of multiple testing error rates for microarray studies
    Stanley B Pounds
    Department of Biostatistics, MS 768, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Brief Bioinform 7:25-36. 2006
    ..Finally, these methods are classified in a manner that suggests the appropriate method for specific applications and diagnostic procedures that can identify problems in the analysis are described...
  14. pmc Cross-species genomics matches driver mutations and cell compartments to model ependymoma
    Robert A Johnson
    Department of Developmental Neurobiology, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
    Nature 466:632-6. 2010
    ..Our data demonstrate the power of cross-species genomics to meticulously match subgroup-specific driver mutations with cellular compartments to model and interrogate cancer subgroups...
  15. ncbi request reprint Robust estimation of the false discovery rate
    Stan Pounds
    Department of Biostatistics, St Jude Children s Research Hospital 332 N Lauderdale Street, Memphis, TN 38135, USA
    Bioinformatics 22:1979-87. 2006
    ..Therefore, it is difficult to reliably estimate the FDR when p-values are discrete or based on one-sided tests...
  16. pmc Comparative analysis of different approaches to measure treatment response in acute myeloid leukemia
    Hiroto Inaba
    Department of Oncology, MS 260, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 3678, USA
    J Clin Oncol 30:3625-32. 2012
    ..Response can now be assessed by minimal residual disease (MRD) monitoring with flow cytometry or polymerase chain reaction (PCR). We determined the relation among the results of these approaches and their prognostic value...
  17. pmc Genomic analysis reveals few genetic alterations in pediatric acute myeloid leukemia
    Ina Radtke
    Department of Pathology, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    Proc Natl Acad Sci U S A 106:12944-9. 2009
    ..These data reflect a remarkably low burden of genomic alterations within pediatric de novo AML, which is in stark contrast to most other human malignancies...
  18. pmc Feasibility, efficacy, and adverse effects of outpatient antibacterial prophylaxis in children with acute myeloid leukemia
    Hiroto Inaba
    Department of Oncology, St Jude Children s Research Hospital, Memphis, Tennessee Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee
    Cancer 120:1985-92. 2014
    ..Intensive chemotherapy for pediatric acute myeloid leukemia incurs the risk of infectious complications, but the benefits of antibiotic prophylaxis remain unclear...
  19. pmc Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia
    Jun J Yang
    St Jude Children s Research Hospital, Memphis, TN 38105, USA
    JAMA 301:393-403. 2009
    ..Pediatric acute lymphoblastic leukemia (ALL) is the prototype for a drug-responsive malignancy. Although cure rates exceed 80%, considerable unexplained interindividual variability exists in treatment response...
  20. ncbi request reprint Severe cardiopulmonary complications consistent with systemic inflammatory response syndrome caused by leukemia cell lysis in childhood acute myelomonocytic or monocytic leukemia
    Nobuko Hijiya
    Department of Hematology Oncology, St Jude Children s Research Hospital, Memphis, Tennessee 38105 2794, USA
    Pediatr Blood Cancer 44:63-9. 2005
    ..Life-threatening pulmonary complications that coincide with cell lysis during early chemotherapy and that mimic systemic inflammatory response syndrome (SIRS) have been reported in patients with acute myeloid leukemia (AML)...
  21. pmc The genetic basis of early T-cell precursor acute lymphoblastic leukaemia
    Jinghui Zhang
    Department of Computational Biology and Bioinformatics, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Nature 481:157-63. 2012
    ..These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL...
  22. pmc Phase I pharmacokinetic and pharmacodynamic study of the multikinase inhibitor sorafenib in combination with clofarabine and cytarabine in pediatric relapsed/refractory leukemia
    Hiroto Inaba
    Department of Oncology, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    J Clin Oncol 29:3293-300. 2011
    ..To assess the toxicity, pharmacokinetics, and pharmacodynamics of multikinase inhibitor sorafenib in combination with clofarabine and cytarabine in children with relapsed/refractory leukemia...
  23. ncbi request reprint Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia
    Charles G Mullighan
    Department of Pathology, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Nature 446:758-64. 2007
    ..Moreover, these data demonstrate the power of high-resolution, genome-wide approaches to identify new molecular lesions in cancer...