Affiliation: Purdue University
- Mapping and analysis of quantitative trait loci in experimental populationsRebecca W Doerge
Department of Statistics, and Department of Agronomy, and Computational Genomics, Purdue University, West Lafayette, Indiana 47907 1399, USA
Nat Rev Genet 3:43-52. 2002....
- A two-step multiple comparison procedure for a large number of tests and multiple treatmentsHongmei Jiang
Northwestern University, USA
Stat Appl Genet Mol Biol 5:Article28. 2006..When compared via simulation the two-step approach has increased power over a one-step procedure, and controls the FDR at a desire significance level...
- Differential expression--the next generation and beyondPaul L Auer
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Brief Funct Genomics 11:57-62. 2012..With this in mind, we provide a brief review of some of the key challenges that are general to all RNA-seq experiments, namely experimental design, statistical analysis and dimensionality reduction...
- Combining Affymetrix microarray resultsJohn R Stevens
Department of Statistics, Purdue University, 150 N, University Street, West Lafayette, Indiana 47907 2067, USA
BMC Bioinformatics 6:57. 2005..Although the experimental specifics are similar, typically a different list of statistically significant genes result from each data analysis...
- Identification of QTLs controlling gene expression networks defined a prioriDaniel J Kliebenstein
University of California Davis, Department of Plant Sciences, Mail Stop 3, One Shields Ave, Davis, CA 95616 8780, USA
BMC Bioinformatics 7:308. 2006..Since genes are also known to respond as groups due to their membership in networks, effective approaches are needed to investigate transcriptome variation as related to gene network responses...
- A semi-nonparametric mixture model for selecting functionally consistent proteinsLianbo Yu
Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
BMC Bioinformatics 11:486. 2010..One of the largest of these challenges is the selection of functionally consistent proteins...
- An empirical Bayesian method for estimating biological networks from temporal microarray dataAndrea Rau
Purdue University, INRA AgroParisTech, USA
Stat Appl Genet Mol Biol 9:Article 9. 2010..The R and C code used to implement the proposed method are publicly available in the R package ebdbNet...
- Correct estimation of preferential chromosome pairing in autotetraploidsDachuang Cao
Department of Statistics and Purdue University, West Lafayette, Indiana 47907, USA
Genome Res 14:459-62. 2004..Our results directly contradict the current findings of significant preferential pairing and affirm the traditional view of random chromosome segregation in alfalfa...
- Role of transposable elements in heterochromatin and epigenetic controlZachary Lippman
Watson School of Biological Sciences and Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Nature 430:471-6. 2004..This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs...
- Genomic changes in synthetic Arabidopsis polyploidsAndreas Madlung
Department of Biology, University of Washington, Seattle, WA 98195, USA
Plant J 41:221-30. 2005..Activity of selected DNA transposons and the possibly related chromosomal breaks could cause changes by inducing translocations and rearrangements...
- Interacting quantitative trait loci control loss of peripheral tolerance and susceptibility to autoimmune ovarian dysgenesis after day 3 thymectomy in miceRandall J Roper
Department of Veterinary Pathobiology, University of Illinois, Urbana, IL 61802, USA
J Immunol 169:1640-6. 2002....
- Natural variation among Arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acidHans van Leeuwen
Department of Plant Sciences, University of California, Davis, California 95616, USA
Plant Cell 19:2099-110. 2007..Expression level polymorphisms for SA response were abundant at both individual gene and gene-network levels in the seven accessions, suggesting that natural variation for SA response is prevalent in Arabidopsis...