Research Topics
Genomes and Genes | Stanley B PoundsSummaryAffiliation: St. Jude Children's Research Hospital Country: USA Publications
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Publications
ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq dataSong 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...- PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variablesStan 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... - Reference alignment of SNP microarray signals for copy number analysis of tumorsStan Pounds
Department of Biostatistics, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
Bioinformatics 25:315-21. 2009..AVAILABILITY: Documented R code is freely available from www.stjuderesearch.org/depts/biostats/refnorm... - Statistical analysis of data from retroviral clonal experiments in the developing retinaStan 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... - Integrated analysis of pharmacologic, clinical and SNP microarray data using Projection Onto the Most Interesting Statistical Evidence with Adaptive Permutation TestingStan 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... 
Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-valuesStan 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...- Estimation and control of multiple testing error rates for microarray studiesStanley 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... - Sample size determination for the false discovery rateStan 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)... - Statistical development and evaluation of microarray gene expression data filtersStan 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... - A procedure to statistically evaluate agreement of differential expression for cross-species genomicsStan 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... - Improving false discovery rate estimationStan 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... - Cross-species genomics matches driver mutations and cell compartments to model ependymomaRobert 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... - Robust estimation of the false discovery rateStan Pounds
Department of Biostatistics, St. Jude Children's Research Hospital 332 N. Lauderdale Street, Memphis, TN 38135, USA
Bioinformatics 22:1979-87. 2006..AVAILABILITY: Libraries of S-plus and R routines to implement the method are freely available from www.stjuderesearch.org/depts/biostats... - Comparative analysis of different approaches to measure treatment response in acute myeloid leukemiaHiroto 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... - Genomic analysis reveals few genetic alterations in pediatric acute myeloid leukemiaIna 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... - Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemiaJun 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... - Severe cardiopulmonary complications consistent with systemic inflammatory response syndrome caused by leukemia cell lysis in childhood acute myelomonocytic or monocytic leukemiaNobuko 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)... - Phase I pharmacokinetic and pharmacodynamic study of the multikinase inhibitor sorafenib in combination with clofarabine and cytarabine in pediatric relapsed/refractory leukemiaHiroto 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... - The genetic basis of early T-cell precursor acute lymphoblastic leukaemiaJinghui 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... - Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemiaCharles 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...