Michael S. Rosenberg’s Laboratory

Computational Evolutionary Biology & Bioinformatics

E-mail: msr@asu.edu

Peer-reviewed Articles

  1. Luque, J., J.H. Christy, A.J.W. Hendy, M.S. Rosenberg, R.W. Portell, K.A. Kerr, and A.R. Palmer (In press) Quaternary intertidal and supratidal crabs (Decapoda, Brachyura) from tropical America and the systematic affinities of fossil fiddler crabs. Journal of Systematic Paleontology.
    0 citations Google Scholar DOI
  2. Stoltzfus, A., M.S. Rosenberg, H. Lapp, A. Budd, K. Cranston, E. Pontelli, S. Oliver, and R.A. Vos (2017) Community and code: Nine lessons from nine NESCent hackathons. F1000Research 6:786. [15 pages]
    0 citations PDF Google Scholar DOI
  3. Dowling, T.E., C.D. Anderson, P.C. Marsh, and M.S. Rosenberg (2015) Population structure in the roundtail chub (Gila robusta complex) of the Gila River basin as determined by microsatellites: evolutionary and conservation implications. PLoS ONE 10(10):e0139832. [21 pages]
    4 citations PDF Pubmed Google Scholar DOI
  4. Rosenberg, M.S. (2014) Contextual cross-referencing of species names for fiddler crabs (genus Uca): An experiment in cyber-taxonomy. PLoS ONE 9(7):e101704. [10 pages]
    3 citations PDF Pubmed Google Scholar DOI
  5. Rosenberg, M.S. (2013) The nomenclatural status of the two “spiny-wristed” fiddler crabs: Uca spinicarpa Rathbun, 1900, and U. hesperiae Crane, 1975 (Crustacea: Brachyura: Ocypodidae). Zootaxa 3716(3):494–500.
    2 citations PDF Pubmed Google Scholar DOI
  6. Perez, D.M., M.S. Rosenberg, and M.R. Pie (2012) The evolution of waving displays in fiddler crabs (Uca spp., Crustacea: Ocypodidae). Biological Journal of the Linnean Society 106(2):307–315.
    9 citations PDF Google Scholar DOI
  7. 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.
    331 citations PDF Google Scholar DOI
  8. Chen, S.-C., M.S. Rosenberg, and B.G. Lindsay (2011) MixtureTree: A program for constructing phylogeny. BMC Bioinformatics 12:111. [3 pages]
    2 citations PDF Pubmed Google Scholar DOI
  9. 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.
    0 citations PDF Google Scholar DOI
  10. Manel, S., S. Joost, B.K. Epperson, R. Holderegger, A. Storfer, M.S. Rosenberg, K.T. Scribner, A. Bonin, 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.
    117 citations PDF Pubmed Google Scholar DOI
  11. 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.
    159 citations PDF Pubmed Google Scholar DOI
  12. 102 citations PDF Pubmed Google Scholar DOI
  13. Rosenberg, M.S. (2010) A generalized formula for converting chi-square tests to effect sizes for meta-analysis. PLoS ONE 5(4):e10059. [3 pages]
    5 citations PDF Pubmed Google Scholar DOI
  14. 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.
    9 citations PDF Pubmed Google Scholar DOI
  15. 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.
    54 citations PDF Pubmed Google Scholar DOI
  16. 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. [Erratum: 2008, 46(2):807-808.]
    60 citations PDF Pubmed Google Scholar DOI
  17. Ogden, T.H., and M.S. Rosenberg (2006) Multiple sequence alignment accuracy and phylogenetic inference. Systematic Biology 55(2):314–328.
    119 citations PDF Pubmed Google Scholar DOI
  18. Rosenberg, M.S. (2005) Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics 6:278. [10 pages]
    41 citations PDF Pubmed Google Scholar DOI
  19. Rosenberg, M.S. (2005) MySSP: Non-stationary evolutionary sequence simulation, including indels. Evolutionary Bioinformatics Online 1:81–83.
    35 citations PDF Pubmed Google Scholar Journal
  20. Rosenberg, M.S. (2005) Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinformatics 6:102. [9 pages]
    39 citations PDF Pubmed Google Scholar DOI
  21. 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.
    285 citations PDF Pubmed Google Scholar DOI
  22. 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 304(1):64–74.
    171 citations PDF Pubmed Google Scholar DOI
  23. 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.
    43 citations PDF Pubmed Google Scholar DOI
  24. Rosenberg, M.S. (2004) Wavelet analysis for detecting anisotropy in point patterns. Journal of Vegetation Science 15(2):277–284.
    40 citations PDF Google Scholar DOI
  25. 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.
    4 citations PDF Pubmed Google Scholar DOI
  26. Hyatt, L.A., M.S. Rosenberg, T.G. Howard, G. Bole, W. Fang, J. Anastasia, K. Brown, R. Grella, K. Hinman, J.P. Kurdziel, and J. Gurevitch (2003) The distance dependence prediction of the Janzen-Connell hypothesis: A meta-analysis. Oikos 103(3):590–602.
    136 citations PDF Google Scholar DOI
  27. 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.
    53 citations PDF Pubmed Google Scholar DOI
  28. 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.
    58 citations PDF Pubmed Google Scholar DOI
  29. Rosenberg, M.S., and S. Kumar (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52(1):119–124.
    83 citations PDF Pubmed Google Scholar DOI
  30. 334 citations PDF Google Scholar DOI
  31. Perry, J.N., A.M. Liebhold, M.S. Rosenberg, J.L. Dungan, M.N. 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.
    278 citations PDF Google Scholar DOI
  32. Dale, M.R.T., P.M. 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.
    180 citations PDF Google Scholar DOI
  33. 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.
    73 citations PDF Google Scholar DOI
  34. 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.
    216 citations PDF Pubmed Google Scholar DOI
  35. 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.
    28 citations PDF Pubmed Google Scholar DOI
  36. 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.
    97 citations PDF Google Scholar DOI
  37. Rosenberg, M.S. (2000) The bearing correlogram: A new method of analyzing directional spatial autocorrelation. Geographical Analysis 32(3):267–278.
    38 citations PDF Google Scholar DOI
  38. Sokal, R.R., N.L. Oden, M.S. Rosenberg, and B.A. Thomson (2000) Cancer incidences in Europe related to mortalities, and ethnohistoric, genetic, and geographic distances. Proceedings of the National Academy of Sciences USA 97(11):6067–6072.
    18 citations PDF Pubmed Google Scholar DOI
  39. 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.
    36 citations PDF Pubmed Google Scholar DOI
  40. 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.
    50 citations PDF Pubmed Google Scholar DOI
  41. 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.
    15 citations PDF Pubmed Google Scholar DOI
  42. 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.
    4 citations PDF Google Scholar DOI
  43. Adams, D.C., J. Gurevitch, and M.S. Rosenberg (1997) Resampling tests for meta-analysis of ecological data. Ecology 78(4):1277–1283.
    256 citations PDF Google Scholar DOI
  44. 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.
    36 citations PDF Google Scholar DOI

Edited Books

  1. Rosenberg, M.S. (2009) Sequence Alignment: Methods, Models, Concepts, and Strategies. University of California Press: Berkeley, CA.
    39 citations Google Scholar DOI

Book Chapters (Peer-reviewed)

  1. Rosenberg, M.S., and C.D. Anderson (2016) Spatial Pattern Analysis. In Oxford Bibliographies in Ecology, D. Gibson, ed. Oxford University Press: New York. [18 pages]
    0 citations Google Scholar DOI
  2. Lajeunesse, M.J., M.S. Rosenberg, and M.D. Jennions (2013) Phylogenetically independent meta-analysis. Pp. 284–299 in Handbook of Meta-analysis in Ecology and Evolution, J. Koricheva, J. Gurevitch and K.L. Mengersen, eds. Princeton University Press: Princeton, NJ.
    13 citations Google Scholar
  3. Jennions, M.D., C.J. Lortie, M.S. Rosenberg, and H.R. Rothstein (2013) Publication and related biases. Pp. 207–236 in Handbook of Meta-analysis in Ecology and Evolution, J. Koricheva, J. Gurevitch and K.L. Mengersen, eds. Princeton University Press: Princeton, NJ.
    48 citations Google Scholar
  4. Rosenberg, M.S. (2013) Moment and least-squares based approaches to meta-analytic inference. Pp. 108–124 in Handbook of Meta-analysis in Ecology and Evolution, J. Koricheva, J. Gurevitch and K.L. Mengersen, eds. Princeton University Press: Princeton, NJ.
    7 citations Google Scholar
  5. Rosenberg, M.S., H.R. Rothstein, and J. Gurevitch (2013) Effect sizes: Conventional choices and calculations. Pp. 61–71 in Handbook of Meta-analysis in Ecology and Evolution, J. Koricheva, J. Gurevitch and K.L. Mengersen, eds. Princeton University Press: Princeton, NJ.
    26 citations Google Scholar
  6. Chen, S.-C., M. Li, M.S. Rosenberg, and B.G. 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, eds. Springer-Verlag: Berlin.
    1 citation PDF Google Scholar DOI
  7. 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.
    2 citations Google Scholar DOI
  8. 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.
    8 citations Google Scholar DOI

Software

  1. Rosenberg, M.S. (2013) Impact Factor Calculator. Version 1.
  2. Rosenberg, M.S., and C.D. Anderson (2011) PASSaGE. Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2.
  3. Rosenberg, M.S. (2010) IndelCoder. Version 1.
  4. Rosenberg, M.S. (2005) Fail-Safe Number Calculator. Version 1.
    1,187 downloads Software websiet Github
    See Rosenberg (2005) Evolution 59:464 for citation info.
  5. Rosenberg, M.S. (2005) MySSP: Non-stationary evolutionary sequence simulation, including indels. Version 1.
    405 downloads Software websiet Github
    See Rosenberg (2005) Evolutionary Bioinformatics Online 1:81 for citation info.
  6. Rosenberg, M.S. (2001) PASSAGE. Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 1.
    263 citations 6,809 downloads Software websiet Google Scholar
  7. Rosenberg, M.S., D.C. Adams, and J. Gurevitch (2000) MetaWin: Statistical Software for Meta-Analysis. Version 2. Sinauer Associates: Sunderland, MA.
    1,437 citations Software websiet Google Scholar
  8. Rosenberg, M.S., D.C. Adams, and J. Gurevitch (1997) MetaWin: Statistical Software for Meta-Analysis with Resampling Tests. Version 1. Sinauer Associates: Sunderland, MA.
    96 citations Software websiet Google Scholar

Reports

  1. 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. Arizona Game and Fish Department: Phoenix, AZ.
    1 citation Google Scholar

Other Publications

  1. Rosenberg, M.S. (2014) A biologist's guide to impact factors. PeerJ Preprints 2:e477v1.
    6 citations PDF Google Scholar DOI
  2. Ainsworth, E.A., M.S. Rosenberg, and X. Wang (2007) Meta-analysis: The past, present and future. New Phytologist 176(4):742–745.
    8 citations PDF Pubmed Google Scholar DOI
  3. Rosenberg, M.S. (2005) Why lectures seem to last forever. Journal of Irreproducible Results 49(3):16.
    PDF Google Scholar

Book/Software Reviews

  1. Rosenberg, M.S. (2015) (Book Review) Handbook of Spatial Point-Pattern Analysis in Ecology. International Journal of Geographical Information Science 29(9):1718–1719.
    PDF Google Scholar DOI
  2. Rosenberg, M.S. (1998) (Book Review) Modeling Dynamic Biological Systems. Quarterly Review of Biology 73(3):340.
    PDF Google Scholar DOI
  3. Rosenberg, M.S. (1997) (Software Review) Minitab for Windows. Quarterly Review of Biology 72(2):240–241.
    PDF Google Scholar DOI

Dissertation

  1. Rosenberg, M.S. (2000) The Comparative Claw Morphology, Phylogeny, and Behavior of Fiddler Crabs (Genus Uca) (doctoral dissertation). Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY.
    8 citations PDF Google Scholar PQ

Abstracts

  1. Honap, T.P., Å. Vågene, A. Herbig, M.S. Rosenberg, J.E. Buikstra, K.I. Bos, J. Krause, and A.C. Stone (2016) Genetic analyses of pre- and post-contact North American Mycobacterium tuberculosis complex strains. American Journal of Physical Anthropology 159(S62):177.
    PDF Google Scholar DOI
  2. Luque, J., A.J.W. Hendy, M.S. Rosenberg, R.W. Portell, and A.R. Palmer (2015) Cenozoic inter-tidal, supra-tidal, and freshwater crabs from tropical America. GSA Abstracts with Programs 47(7):423.
  3. Pfister, L.-A., L.T. Nash, M.S. Rosenberg, and A.C. Stone (2009) Influence of androgen receptor variation in primate and carnivore female social dominance. American Journal of Physical Anthropology 138(S48):210.
    PDF Google Scholar DOI
  4. Pfister, L.-A., M.S. Rosenberg, and A.C. Stone (2008) Full genome comparisons of Mycobacterium: Insight into the origin of tuberculosis and leprosy. American Journal of Physical Anthropology 135(S46):171.
    PDF Google Scholar DOI
  5. Sokal, R.R., N.L. Oden, M.S. Rosenberg, and B.A. Thomson (2000) Cancer incidences in Europe related to ethnohistoric and genetic distances. American Journal of Physical Anthropology 111(S30):286–287.
    PDF Google Scholar DOI

† = lab postdoc; ‡ = lab grad student

Data last updated 2017-11