Affiliation: Arizona State University
- The file-drawer problem revisited: a general weighted method for calculating fail-safe numbers in meta-analysisMichael S Rosenberg
Center for Evolutionary Functional Genomics, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, Arizona 85287 4501, USA
Evolution 59:464-8. 2005..A general, weighted fail-safe calculation, grounded in the meta-analysis framework, applicable to both fixed- and random-effects models, is proposed. Recent meta-analyses published in Evolution are used for illustration...
- Multiple sequence alignment accuracy and phylogenetic inferenceT Heath Ogdenw
Center for Evolutionary Functional Genomics, The Biodesign Institute, and the School of Life Sciences, Arizona State University, Tempe, Arizona 85287 4501, USA
Syst Biol 55:314-28. 2006..Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction...
- How should gaps be treated in parsimony? A comparison of approaches using simulationT Heath Ogden
Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA
Mol Phylogenet Evol 42:817-26. 2007..Data sets with higher sequence divergence and more pectinate tree shapes with variable branch lengths are more affected by gap coding than datasets associated with shallower non-pectinate tree shapes...
- Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*T Heath Ogden
Department of Biological Sciences, Idaho State University, Idaho 83209, USA
Syst Biol 56:182-93. 2007..38% of the time they were equally accurate). Comparisons between POY hypothesized alignments and the true alignments indicated that, on average, as alignment error increased, topological accuracy decreased...
- Phylotastic! Making tree-of-life knowledge accessible, reusable and convenientArlin Stoltzfus
Institute for Bioscience and Biotechnology Research, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
BMC Bioinformatics 14:158. 2013..Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces...
- MixtureTree: a program for constructing phylogenyShu Chuan Chen
School of Mathematical and Statistical Sciences, Arizona State University, Tempe, 85287, USA
BMC Bioinformatics 12:111. 2011..In addition to the mixture algorithm with three different optimization options, the program also implements a bootstrap procedure with majority-rule consensus...
- A generalized formula for converting chi-square tests to effect sizes for meta-analysisMichael S Rosenberg
Center for Evolutionary Medicine and Informatics, The Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
PLoS ONE 5:e10059. 2010..A corrected formula is provided...
- Taxon sampling, bioinformatics, and phylogenomicsMichael S Rosenberg
Department of Biology, Arizona State University, Tempe, Arizona 85287 1501, USA
Syst Biol 52:119-24. 2003
- Multiple sequence alignment accuracy and evolutionary distance estimationMichael S Rosenberg
Center for Evolutionary Functional Genomics, The Biodesign Institute, and the School of Life Sciences, Arizona State University, Tempe, AZ 85287 4501, USA
BMC Bioinformatics 6:278. 2005....
- Evolutionary distance estimation and fidelity of pair wise sequence alignmentMichael S Rosenberg
Center for Evolutionary Functional Genomics, The Biodesign Institute, and the School of Life Sciences, Arizona State University, Tempe, AZ 84287 4501, USA
BMC Bioinformatics 6:102. 2005..Evolutionary distances are a critical measure in comparative genomics and molecular evolutionary biology. A simulation study was used to examine the effect of alignment accuracy of DNA sequences on evolutionary distance estimation...
- Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inferenceMichael S Rosenberg
Department of Biology and Center for Evolutionary Functional Genomics, Arizona State University, USA
Mol Biol Evol 20:610-21. 2003..In these specific simulation conditions, we did not find a significant interaction between phylogenetic accuracy and substitution pattern heterogeneity among lineages, even when the taxon sampling is increased...
- Considering spatial and temporal scale in landscape-genetic studies of gene flowCorey Devin Anderson
Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ 85287 4501, USA
Mol Ecol 19:3565-75. 2010....
- Testing hypotheses of bird extinctions at Rio Palenque, Ecuador, with informal species listsDavid L Pearson
School of Life Sciences, Arizona State University, Tempe, AZ 85287 4501, USA
Conserv Biol 24:500-10. 2010....
- Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene treeSudhindra R Gadagkar
Department of Biology, University of Dayton, Dayton, Ohio 46469 2320, USA
J Exp Zool B Mol Dev Evol 304:64-74. 2005..Therefore, it will be prudent to report the number of individual genes supporting an inferred clade in the concatenated sequence tree, in addition to the bootstrap support...
- Recombination and its impact on the genome of the haplodiploid parasitoid wasp NasoniaOliver Niehuis
School of Life Sciences, Arizona State University, Tempe, Arizona, USA
PLoS ONE 5:e8597. 2010..Our results imply that the genomes of haplodiploid and of diploid higher eukaryotes do not differ systematically in their recombination rates and associated parameters...
- Patterns of transitional mutation biases within and among mammalian genomesMichael S Rosenberg
Center for Evolutionary Functional Genomics and Department of Biology, Arizona State University, USA
Mol Biol Evol 20:988-93. 2003..The estimates show no relationship to potential intrachromosomal or interchromosomal effects. This uniformity points to similarity in point mutation processes in genomic regions with substantially different GC-content biases...
- A new protocol for evaluating putative causes for multiple variables in a spatial setting, illustrated by its application to European cancer ratesRobert R Sokal
Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794 5245, USA
Am J Hum Biol 16:1-16. 2004..Etiological and other extrinsic information on the cancers map significantly into the five clusters, demonstrating their epidemiological relevance...
- Sequence alignment fidelity in genomics and bioinformaticsMichael Rosenberg; Fiscal Year: 2009....
- Sequence alignment fidelity in genomics and bioinformaticsMichael S Rosenberg; Fiscal Year: 2010....