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...
- Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomicsFeng Lin
Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
BMC Genomics 15:18. 2014..We thus sequenced, analyzed, and compared the transcriptomes of 10 near isogenic lines (NILs), each with a unique Rps gene/allele, and the susceptible parent Williams, pre- and post-inoculation with the pathogen...
- 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...
- 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...
- 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...
- 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...
- 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....