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- Perez, D.M., M.S. Rosenberg, and M.R. Pie (In press) The evolution of waving displays in fiddler crabs
(Uca spp., Crustacea, Ocypodidae).
Biological Journal
of the Linnean Society.
- Rosenberg, M.S., and C.D. Anderson (2011) PASSaGE: Pattern Analysis, Spatial Statistics, and Geographic
Exegesis. Version 2. Methods
in Ecology and Evolution 2(3):229–232.
PDF
- Chen, S.-C., M.S. Rosenberg, and B.G. Lindsay (2011) MixtureTree: A program for
construting phylogeny. BMC
Bioinformatics 12:111.
PubMed
PDF
- Anderson, C.D., and M.S. Rosenberg (2011) Variation in association with manmade habitat
edges exhibited by the Timber Rattlesnake (Crotalus horridus)
in St. Louis County, Missouri. Journal of Herpetology 45(1):50–55.
PDF
- Manel, S., S. Joost, B.K. Epperson, R. Holderegger, A. Storfer, M.S. Rosenberg, K.T. Scribner, and
M.-J. Fortin (2010) Perspectives on the use of landscape genetics to detect genetic
adaptive variation in the field. Molecular Ecology
19(17):3760–3772.
PubMed
PDF
- Anderson, C.D., B.K. Epperson, M.-J. Fortin, R. Holderegger, P.M.A. James, M.S. Rosenberg, K.T.
Scribner, and S. Spear (2010) Considering spatial and temporal scale in landscape-genetic
studies of gene flow. Molecular Ecology
19(17)3565–3575.
PubMed
PDF
- Epperson, B.K., B. McRae, K. Scribner, S.A. Cushman, M.S. Rosenberg, M.-J. Fortin, P.M.A. James,
M. Murphy, S. Manel, P. Legendre, and M.R.T. Dale (2010) Utility of computer simulations
in landscape genetics. Molecular Ecology
19(17):3549–3564.
PubMed
PDF
- Rosenberg, M.S. (2010) A generalized formula for converting chi-square tests to effect sizes for
meta-analysis. PLoS ONE 5(4):e10059.
PubMed
PDF
- Pearson, D.L., C.D. Anderson, B.R. Mitchell, M.S. Rosenberg, R. Navarette, and P. Coopmans
(2010) Testing hypotheses of bird extinctions at Rio Palenque, Ecuador, with informal
species lists. Conservation Biology 24(2):500–510.
Supplemental Material
PubMed
PDF
- Niehuis, O., J.D. Gibson, M.S. Rosenberg, B. Pannebakker, T. Koevoets, A.K. Judson,
C. Desjardins, K. Kennedy, D. Duggan, L.W. Beukeboom, L. van de Zande, D.M. Shuker,
J.H. Werren, and J. Gadau (2010) Recombination and its impact on the
genome of the haplodiploid parasitoid wasp Nasonia.
PLoS ONE 5(1):e8597.
PubMed
PDF
- 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 Western 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., and C.D. Anderson (2011) PASSAGE. Pattern analysis, spatial statistics and geographic
exegesis. Version 2.
- Rosenberg, M.S. (2010) IndelCoder. Version 1. School of Life Sciences,
Arizona State University, Tempe, AZ.
- Rosenberg, M.S. (2005) MySSP: Non-stationary evolutionary sequence
simulation, including indels. Version 1. School of Life Sciences,
Arizona State University, Tempe, AZ.
- Rosenberg, M.S. (2005) Fail-Safe Number Calculator.
Version 1. School of Life Sciences, Arizona State University, Tempe, AZ.
- Rosenberg, M.S. (2001) PASSAGE. Pattern analysis, spatial statistics and geographic
exegesis.
Version 1.0. Department of Biology, Arizona State University, Tempe, AZ.
- Rosenberg, M.S., D.C. Adams, and J. Gurevitch. (2000) MetaWin. Statistical software for
meta-analysis. Version 2.0. Sinauer Associates, Sunderland, Massachusetts.
- 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.
- Chen, S.-C., M. Li, M.S. Rosenberg, and B. Lindsay (2011) Mixture tree construction and its
applications. Pp. 135–147 in Handbook of Statistical
Bioinformatics, H.H.-S. Lu, B. Schölkopf, and H. Zhao, ed. Springer-Verlag.
- Rosenberg, M.S., and T.H. Ogden (2009) Simulation approaches to evaluating alignment
error and methods for comparing alternate alignments. Pp. 179–207 in
Sequence Alignment: Methods, Models, Concepts, and Strategies, M.S. Rosenberg, ed.
University of California Press: Berkeley, CA.
- Rosenberg, M.S. (2009) Sequence alignment: Concepts and history. Pp. 1–22 in
Sequence Alignment: Methods, Models, Concepts, and Strategies, M.S. Rosenberg, ed.
University of California Press: Berkeley, CA.
- Dowling, T.E., P.C. Marsh, C.D. Anderson, M.S. Rosenberg, and A.T. Kelsen. (2008)
Population structure in the roundtail chub (Gila robusta complex) of the Gila
River basin as determined by microsatellites
(Phoenix, AZ: Arizona Game and Fish Department).
- 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.