Michael Rosenberg

Summary

Affiliation: Arizona State University
Country: USA

Publications

  1. ncbi The file-drawer problem revisited: a general weighted method for calculating fail-safe numbers in meta-analysis
    Michael 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
  2. ncbi Multiple sequence alignment accuracy and phylogenetic inference
    T 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
  3. ncbi How should gaps be treated in parsimony? A comparison of approaches using simulation
    T Heath Ogden
    Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA
    Mol Phylogenet Evol 42:817-26. 2007
  4. ncbi 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
  5. ncbi MixtureTree: a program for constructing phylogeny
    Shu Chuan Chen
    School of Mathematical and Statistical Sciences, Arizona State University, Tempe, 85287, USA
    BMC Bioinformatics 12:111. 2011
  6. ncbi A generalized formula for converting chi-square tests to effect sizes for meta-analysis
    Michael 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
  7. ncbi Taxon sampling, bioinformatics, and phylogenomics
    Michael S Rosenberg
    Department of Biology, Arizona State University, Tempe, Arizona 85287-1501, USA
    Syst Biol 52:119-24. 2003
  8. ncbi Multiple sequence alignment accuracy and evolutionary distance estimation
    Michael 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
  9. ncbi Evolutionary distance estimation and fidelity of pair wise sequence alignment
    Michael 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
  10. ncbi Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference
    Michael S Rosenberg
    Department of Biology and Center for Evolutionary Functional Genomics, Arizona State University, USA
    Mol Biol Evol 20:610-21. 2003

Research Grants

  1. Sequence alignment fidelity in genomics and bioinformatics
    Michael Rosenberg; Fiscal Year: 2009
  2. Sequence alignment fidelity in genomics and bioinformatics
    Michael S Rosenberg; Fiscal Year: 2010

Detail Information

Publications16

  1. ncbi The file-drawer problem revisited: a general weighted method for calculating fail-safe numbers in meta-analysis
    Michael 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...
  2. ncbi Multiple sequence alignment accuracy and phylogenetic inference
    T 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...
  3. ncbi How should gaps be treated in parsimony? A comparison of approaches using simulation
    T 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...
  4. ncbi 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...
  5. ncbi MixtureTree: a program for constructing phylogeny
    Shu 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...
  6. ncbi A generalized formula for converting chi-square tests to effect sizes for meta-analysis
    Michael 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...
  7. ncbi Taxon sampling, bioinformatics, and phylogenomics
    Michael S Rosenberg
    Department of Biology, Arizona State University, Tempe, Arizona 85287-1501, USA
    Syst Biol 52:119-24. 2003
  8. ncbi Multiple sequence alignment accuracy and evolutionary distance estimation
    Michael 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
    ....
  9. ncbi Evolutionary distance estimation and fidelity of pair wise sequence alignment
    Michael 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...
  10. ncbi Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference
    Michael 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...
  11. ncbi Considering spatial and temporal scale in landscape-genetic studies of gene flow
    Corey 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
    ....
  12. ncbi Testing hypotheses of bird extinctions at Rio Palenque, Ecuador, with informal species lists
    David L Pearson
    School of Life Sciences, Arizona State University, Tempe, AZ 85287 4501, USA
    Conserv Biol 24:500-10. 2010
    ....
  13. ncbi Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree
    Sudhindra 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...
  14. ncbi Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia
    Oliver 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...
  15. ncbi Patterns of transitional mutation biases within and among mammalian genomes
    Michael 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...
  16. ncbi A new protocol for evaluating putative causes for multiple variables in a spatial setting, illustrated by its application to European cancer rates
    Robert 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...

Research Grants2

  1. Sequence alignment fidelity in genomics and bioinformatics
    Michael Rosenberg; Fiscal Year: 2009
    ....
  2. Sequence alignment fidelity in genomics and bioinformatics
    Michael S Rosenberg; Fiscal Year: 2010
    ....