Michael S. Rosenberg
Computational Evolutionary Biology, Bioinformatics and Genomics
In general, I am interested in understanding the processes that control diversity and similarity among organisms. My interests span a large range of subjects within ecology and evolution, from macroevolution to molecular evolution and from single organisms to populations and ecosystems. My research tends to focus on using novel statistical and computer methodology to better describe and analyze empirical phenomena.
My primary research is a multi-faceted approach to understanding the evolution of genomes, concentrating on mutational patterns and parameters and the spatial structure of genomic elements, using both real and simulated data. Currently, we are profiling alignment error among sequences, examining how this affects down-stream analyses, and looking for solutions that include the uncertainty inherent from the alignment error into these analyses.
I also study numerous aspects of phylogenetic inference, examining the accuracy of phylogenetic methods when a variety of assumptions are violated, such as incomplete taxon sampling or nonstationarity of the evolutionary process.
I am also very interested in the development and use of statistical methods for analyzing spatial patterns in biology and produce a software package, PASSaGE, for general spatial statistical analysis.
In addition, I have strong interests in fiddler crab biology and evolution, meta-analysis, and geometric morphometrics.
Selected Publications
Rosenberg , M. S. (2005) Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics 6:278.
Rosenberg , M. S. (2005) Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinformatics 6:102.
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:64-74.
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: 1-16.
Rosenberg, M. S., S. Subramanian, and S. Kumar (2003) Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology and Evolution 20: 988-993.
Rosenberg, M. S., and S. Kumar (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Molecular Biology and Evolution 20:610-621.
Rosenberg, M. S., and S. Kumar (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52:119-124.
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 25:626-640.
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 25:558-577.
Rosenberg, M. S. (2002) Fiddler crab claw shape variation: A geometric morphometric analysis across the genus Uca. Biological Journal of the Linnean Society 75:147-162.
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 98:10751-10756.
Rosenberg, M. S., and S. Kumar (2001) Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Molecular Biology and Evolution 18:1823-1827.
Rosenberg, M. S. (2001) The systematics and taxonomy of fiddler crabs: A phylogeny of the genus Uca. Journal of Crustacean Biology 21:839-869.
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 97:6067-6072.
Rosenberg, M. S., R. R. Sokal, N. L. Oden, and D. DiGiovanni (1999) Spatial autocorrelation of cancer in Europe. European Journal of Epidemiology 15:15-22.
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 94:12728-12731.
Rosenberg, M. S. (1997) Evolution of shape differences between the major and minor chelipeds of Uca pugnax (Decapoda: Ocypodidae). Journal of Crustacean Biology 17:5259.