Rosenberg Lab | Publications

publications

journal articles

2013

Stoltzfus, A., H. Lapp, N. Matasci, H. Deus, B. Sidlauskas, C.M. Zmasek, G. Vaidya, E. Pontelli, K. Cranston, R. Vos, C.O. Webb, L.J. Harmon, M. Pirrung, B. O'Meara, M.W. Pennell, S. Mirarab, M.S. Rosenberg, J.P. Balhoff, H.M. Bik, T. Heath, P. Midford, J.W. Brown, E.J. McTavish, J. Sukumaran, M. Westneat, M.E. Alfaro, A. Steele, and G. Jordan (2013) Phylotastic! Making Tree-of-Life knowledge accessible, reusable and convenient. BMC Bioinformatics 14:158.

2012

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.

2011

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. (Full text)

Chen, S.-C., M.S. Rosenberg, and B.G. Lindsay (2011) MixtureTree: A program for constructing phylogeny. BMC Bioinformatics 12:111. (Abstract) (Full text)

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. (Full text) (Google Scholar Citation)

2010

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. (Abstract) (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

Manel, S., S. Joost, B.K. Epperson, R. Holderegger, A. Storfer, M.S. Rosenberg, K. 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. (Abstract) (Full text) (Google Scholar Citation)

Niehuis, O., J.D. Gibson, M.S. Rosenberg, B. Pannebakker, T. Koevoets, A.K. Judson, C.A. 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. (Abstract) (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

Rosenberg, M.S. (2010) A generalized formula for converting chi-square tests to effect sizes for meta-analysis. PLoS ONE 5(4):e10059. (Abstract) (Full text)

2009

Ogden, T.H., J. Osborne, L. Jacobus, and M.F. Whiting (2009) Combined morphological and molecular phylogeny of Ephemerellidae (Ephemeroptera). Zootaxa 1991:28-42. (Google Scholar Citation)

Ogden, T.H., M. Sartori, J.L. Gattolliat, A. Staniczek, T. Soldan, and M.F. Whiting (2009) Towards a new paradigm in mayfly phylogeny (Ephemeroptera): Combined analysis of morphological and molecular data. Systematic Entomology 34(4):616-634. (Google Scholar Citation)

2008

Ogden, T.H., M. Sartori, and M.F. Whiting (2008) Pisciforma, Setisura, and Furcatergalia (Order: Ephemeroptera) are not monophyletic based on 18S rDNA sequences: A reply to Sun et al. (2006). Annals of the Entomological Society of America 101(1):1-6. (Google Scholar Citation)

2007

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. (Abstract) (Full text) (Google Scholar Citation)

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). (Abstract) (Full text) (Google Scholar Citation)

2006

Ogden, T.H., and M.S. Rosenberg (2006) Multiple sequence alignment accuracy and phylogenetic inference. Systematic Biology 55(2):314–328. (Abstract) (Full text) (Google Scholar Citation)

2005

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. (Abstract) (Full text) (Google Scholar Citation)

Ogden, T.H., and M.F. Whiting (2005) Phylogeny of Ephemeroptera (mayflies) based on molecular evidence. Molecular Phylogenetics and Evolution 37(3):625-643. (Google Scholar Citation)

Rosenberg, M.S. (2005) Multiple sequence alignment accuracy and evolutionary distance estimation. 27. Rosenberg, M.S. 2005. Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics 6:278. 6:278. (Abstract) (Full text) (Google Scholar Citation)

Rosenberg, M.S. (2005) MySSP: Non-stationary evolutionary sequence simulation, including indels. Evolutionary Bioinformatics Online 1:81-83. Abstract Full text Google Scholar Citation

Rosenberg, M.S. (2005) Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinformatics 6:102. Abstract Full text Google Scholar Citation

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. (Abstract) (Full text) (Google Scholar Citation)

2004

Rosenberg, M.S. (2004) Wavelet analysis for detecting anisotropy in point patterns. Journal of Vegetation Science 15(2):277–284. (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

2003

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. (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

Rosenberg, M.S., and S. Kumar (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52(1):119–124. (Abstract) (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

2002

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. (Full text) (Google Scholar Citation)

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. (Full text) (Google Scholar Citation)

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. (Full text) (Google Scholar Citation)

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. (Full text) (Google Scholar Citation)

2001

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. (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

2000

Rosenberg, M.S. (2000) The bearing correlogram: A new method of analyzing directional spatial autocorrelation. Geographical Analysis 32(3):267–278. (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

1999

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. (Abstract) (Full text) (Google Scholar Citation)

1998

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. (Abstract) (Full text) (Google Scholar Citation)

1997

Adams, D.C., J. Gurevitch, and M.S. Rosenberg (1997) Resampling tests for meta-analysis of ecological data. Ecology 78(4):1277–1283. (Full text) (Google Scholar Citation)

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. (Full text) (Google Scholar Citation)

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. (Abstract) (Full text) (Google Scholar Citation)

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 . (Full text) (Google Scholar Citation)

 

Edited Books

Rosenberg, M.S. (2009) Sequence Alignment: Methods, Models, Concepts, and Strategies. University of California Press: Berkeley, CA.
Publisher Website

The sequencing of the human genome involved thousands of scientists but used relatively few tools. Today, obtaining sequences is simpler, but aligning the sequences—making sure that sequences from one source are properly compared to those from other sources—remains a complicated but underappreciated aspect of comparative molecular biology. This volume, the first to focus on this crucial step in analyzing sequence data, is about the practice of alignment, the procedures by which alignments are established, and more importantly, how the outcomes of any alignment algorithm should be interpreted. Edited by Michael S. Rosenberg with essays by many of the field's leading experts, Sequence Alignment covers molecular causes, computational advances, approaches for assessing alignment quality, and philosophical underpinnings of the algorithms themselves.

 

 

 

Book Chapters

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. Mengersen, eds. Princeton University Press: Princeton, NJ.
 
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. Mengersen, eds. Princeton University Press: Princeton, NJ.
 
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. Mengersen, eds. Princeton University Press: Princeton, NJ.
 
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. Mengersen, eds. Princeton University Press: Princeton, NJ.

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. (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.

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.

 

Reports

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. Report to Arizona Game and Fish Department.

 

Abstracts

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.

 

Reviews

Rosenberg, M.S. (1998) (Book Review) Modeling Dynamic Biological Systems. Quarterly Review of Biology 73(3):340.

Rosenberg, M.S. (1997) (Software Review) Minitab for Windows. Quarterly Review of Biology 72(2):240–241.

 

Theses

Aziz, M. (2007) Estimating ClustalW pairwise alignment parameters for non-coding DNA sequences. M.S. Thesis. Computational Biosciences, Arizona State University, Tempe, AZ.

Earl-Mirowski, V. (2007) Compare and contrast the effects of using less stringent criteria in BLASTCLUST to a novel iterative method for identifying gene families. M.S. Thesis. Computational Biosciences, Arizona State University, Tempe, AZ.

Goldberg, L. (2006) Extending gene families via predicted ancestral sequences. M.S. Thesis. Computational Biosciences, Arizona State University, Tempe, AZ.

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.

 

Miscellaneous

Ainsworth, E.A., M .S. Rosenberg, and X. Wang (2007) Meta-analysis: The past, present and future. New Phytologist 176(4):742–745.

Rosenberg, M.S. (2005) Why lectures seem to last forever. Journal of Irreproducible Results 49(3):16.