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- Ogden, T. H., and M. S. Rosenberg (2007) Alignment and topological accuracy of the
direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*.
Systematic Biology 56(2):182-193.
PubMed
PDF
- Ogden, T. H., and M. S. Rosenberg (2007) How should gaps be treated in parsimony? A comparison
of approaches using simulation. Molecular
Phylogenetics and Evolution 42(3):817-826.
PubMed
PDF (Erratum: 2008, 46(2):807-808 PDF)
- Ogden, T. H., and M. S. Rosenberg (2006) Multiple sequence alignment accuracy and phylogenetic inference.
Systematic Biology 55(2):314-328.
PubMed PDF
- Rosenberg, M. S. (2005) Multiple sequence alignment accuracy and evolutionary distance estimation.
BMC Bioinformatics 6:278.
PubMed PDF
- Rosenberg, M. S. (2005) MySSP: Non-stationary evolutionary sequence
simulation, including indels.
Evolutionary Bioinformatics Online 1:81-83.
PDF
- Rosenberg, M. S. (2005) Evolutionary distance estimation and fidelity of pair wise sequence alignment.
BMC Bioinformatics 6:102.
PubMed PDF
- Rosenberg, M. S. (2005) The file-drawer problem revisited: A general weighted method for
calculating fail-safe numbers in meta-analysis.
Evolution
59(2):464-468.
PubMed PDF
- Gadagkar, S. R., M. S. Rosenberg, and S. Kumar (2005) Inferring species
phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree.
Journal of Experimental
Zoology. B. Molecular and Developmental Evolution 304B(1):64-74.
PubMed PDF
- Rosenberg, M. S., K. A. Garrett, Z. Su, and R. L. Bowden (2004)
Meta-analysis in plant pathology: Synthesizing research results.
Phytopathology 94(9):1013-1017.
PDF
- Rosenberg, M. S. (2004) Wavelet analysis for detecting anisotropy in point patterns.
Journal of Vegetation Science 15(2):277-284.
PDF
- Sokal, R. R., N. L. Oden, M. S. Rosenberg, and B. A. Thomson (2004) A new protocol for evaluating
putative causes for multiple variables in a spatial setting, illustrated by its
application to European cancer rates.
American
Journal of Human Biology 16(1):1-16.
PubMed PDF
- Hyatt, L. A., M. S. Rosenberg, T. G. Howard, G. Bole, W. Fang, J. Anastasia, K. Brown, R.
Grella, K. Hinman, J. Kurdziel, and J. Gurevitch (2003) The
distance dependence prediction of the Janzen-Connell hypothesis: A meta-analysis.
Oikos 103(3):590-602.
PDF
- Rosenberg, M. S., S. Subramanian, and S. Kumar (2003) Patterns of transitional
mutation biases within and among mammalian genomes.
Molecular Biology and Evolution
20(6):988-993.
PubMed PDF
- Rosenberg, M. S., and S. Kumar (2003) Heterogeneity of nucleotide frequencies
among evolutionary lineages and phylogenetic inference.
Molecular Biology and Evolution 20(4):610-621.
PubMed PDF
- Rosenberg, M. S., and S. Kumar (2003) Taxon sampling, bioinformatics, and
phylogenomics. Systematic Biology 52(1):119-124.
PubMed PDF
- Dungan, J. L., J. Perry, M. Dale, S. Citron-Pousty, M.-J. Fortin, A. Jakomulska, P. Legendre, M. Miriti,
and M. S. Rosenberg (2002) A balanced view of scaling in spatial
statistical analysis. Ecography 25(5):626-640.
PDF
- Perry, J. N., A. Liebhold, M. S. Rosenberg, J. Dungan, M. Miriti, A. Jakomulska, and S.
Citron-Pousty (2002) Illustration and guidelines for selecting
statistical methods for quantifying spatial patterns in ecological data.
Ecography 25(5):578-600.
PDF
- Dale, M. R. T., P. Dixon. M.-J. Fortin, P. Legendre, D. E. Myers, and M. S. Rosenberg
(2002) Conceptual and mathematical relationships among methods for spatial analysis.
Ecography 25(5):558-577.
PDF
- Rosenberg, M. S. (2002) Fiddler crab claw shape variation: A geometric morphometric analysis across
the genus Uca.
Biological
Journal of the Linnean Society 75(2):147-162.
PDF
- Rosenberg, M. S., and S. Kumar (2001) Incomplete taxon sampling is not a
problem for phylogenetic inference. Proceedings
of the National Academy of Sciences USA 98(19):10751-10756.
PubMed PDF
- Rosenberg, M. S., and S. Kumar (2001) Traditional phylogenetic reconstruction methods reconstruct
shallow and deep evolutionary relationships equally well.
Molecular Biology and Evolution 18(9):1823-1827.
PubMed PDF
- Rosenberg, M. S. (2001) The systematics and taxonomy of fiddler crabs: A phylogeny of the genus
Uca. Journal of Crustacean Biology 21(3):839-869.
PDF
- Rosenberg, M. S. (2000) The bearing correlogram: A new method of
analyzing directional spatial autocorrelation.
Geographical Analysis 32(3):267-278.
PDF
- Sokal, R. R., N. L. Oden, M. S. Rosenberg, and B. A. Thomson (2000)
Cancer incidences in Europe related to ethnohistoric and genetic
distances. Proceedings of the National Academy
of Sciences USA 97(11):6067-6072.
PubMed PDF
- Rosenberg, M. S., R. R. Sokal, N. L. Oden, and D. DiGiovanni (1999)
Spatial autocorrelation of cancer in Europe.
European Journal of Epidemiology
15(1):15-22.
PubMed PDF
- Adams, D. C., and M. S. Rosenberg (1998) Partial-warps, phylogeny,
and ontogeny: A comment on Fink and Zelditch (1995).
Systematic Biology
47(1):168-173.
PubMed PDF
- Sokal, R. R., N. L. Oden, M. S. Rosenberg, and D. DiGiovanni (1997)
Ethnohistory, genetics and cancer mortality in Europeans.
Proceedings
of the National Academy of Sciences USA 94(23):12728-12731.
PubMed PDF
- Sokal, R. R., N. L. Oden, M. S. Rosenberg, and D. DiGiovanni (1997)
The patterns of historical population movements in Europe and some of their genetic consequences.
American Journal of Human Biology 9(3):391-404.
PDF
- Adams, D. C., J. Gurevitch, and M. S. Rosenberg (1997) Resampling
tests for meta-analysis of ecological data.
Ecology 78(4):1277-1283.
PDF
- Rosenberg, M. S. (1997) Evolution of shape differences between the
major and minor chelipeds of Uca pugnax (Decapoda: Ocypodidae).
Journal of Crustacean Biology 17(1):52-59.
PDF
- Rosenberg, M. S. (2005) MySSP: Non-stationary evolutionary sequence
simulation, including indels. Version 1. School of Life Sciences,
Arizona State University, Tempe, AZ.
Website
- Rosenberg, M. S. (2005) Fail-Safe Number Calculator.
Version 1. School of Life Sciences, Arizona State University, Tempe, AZ.
Website
- Rosenberg, M. S. (2001) PASSAGE. Pattern analysis, spatial statistics and geographic
exegesis.
Version 1.0. Department of Biology, Arizona State University, Tempe, AZ.
Website
- Rosenberg, M. S., D. C. Adams, and J. Gurevitch. (2000) MetaWin. Statistical software for
meta-analysis. Version 2.0. Sinauer Associates, Sunderland, Massachusetts.
Website
- Rosenberg, M. S., D. C. Adams, and J. Gurevitch. (1997) MetaWin. Statistical software for
meta-analysis with resampling tests. Version 1.0. Sinauer Associates, Sunderland, Massachusetts.
- Rosenberg, M. S. (2009 In press) Sequence Alignment: Methods, Models, Concepts, and Strategies.
University of California Press: Berkeley, CA.
- Rosenberg, M. S. (2009 In press) Sequence alignment: Concepts and history. Pp. ??? in
Sequence Alignment: Methods, Models, Concepts, and Strategies, M. S. Rosenberg, ed.
University of California Press: Berkeley, CA.
- Rosenberg, M. S., and T. H. Ogden (2009 In press) Simulation approaches to evaluating alignment
error and methods for comparing alternate alignments. Pp. ??? in
Sequence Alignment: Methods, Models, Concepts, and Strategies, M. S. Rosenberg, ed.
University of California Press: Berkeley, CA.
- Rosenberg, M. S. (2000) The Comparative Claw Morphology, Phylogeny, and Behavior of Fiddler Crabs
(Genus Uca). Ph.D. Thesis. Department of Ecology and Evolution, State University of New York at
Stony Brook, Stony Brook, NY.
