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Michael S. Rosenberg, PhD

Associate Professor

The Biodesign Institute, Evolutionary Medicine and Informatics

Bio

Michael S. Rosenberg is an associate professor in the Center for Evolutionary Medicine and Informatics of the Biodesign Institute and the School of Life Sciences at Arizona State University.

Dr. Rosenberg's research is primarily in computational evolutionary biology and bioinformatics. In general, he is interested in understanding the processes that control diversity and similarity among organisms; this ranges across a broad array of subjects within ecology and evolution, from phylogenetics and macroevolution to molecular evolution and from single organisms to populations and ecosystems. Many issues in bioinformatics and genomics can only be evaluated in an evolutionary context; understanding the history of species, genes and the genome is necessary to both measure parameters and to define patterns of mutation that lead to phenotypic differences among species or genetic disease.

Dr. Rosenberg's research encompasses a multi-faceted approach to computational evolutionary biology, but tends to focus on novel statistical and computer methodology (e.g., simulation, spatial statistics, meta-analysis, and geometric morphometrics) to better describe and analyze empirical phenomena.

Major projects in his lab currently include (1) the evaluation and role of sequence alignment on bioinformatics and phylogenetics, and (2) the development of methods and software for spatial analysis and statistics in biology. Dr. Rosenberg is also one of the world experts on fiddler crab systematics and evolution.

Dr. Rosenberg received his Ph.D. in 2000 from the Department of Ecology & Evolution of the State University of New York at Stony Brook. He received his bachelor's degree in 1994 from Northwestern University with a triple major in biology, anthropology, and geology.

Lab Web Page

www.rosenberglab.net

Research Interests

Computational evolutionary biology and ecology; bioinformatics; sequence alignment; phylogenetics; spatial analysis and statistics; genomics; fiddler crab biology and evolution; meta-analysis; geometric morphometrics

Memberships

  • American Association for the Advancement of Science
  • Scientific Research Society of North America (Sigma Xi)
  • Society for Molecular Biology and Evolution
  • Society of Systematic Biologists
  • Society for the Study of Evolution

 

Working Groups/Workshops

  • 2009-2010, An interdisciplinary approach to advancing landscape genetics (Co-PI), National Center for Ecological Analysis and Synthesis, Santa Barbara, CA
  • 2006-2007, SEED: Proposal to develop a novel journal concept for evolutionary meta-analyses (Invited Working Group Member), National Evolutionary Synthesis Center, Durham, NC
  • 2006-2007, Meta-analysis in ecology: Lessons, challenges and future (Invited Working Group Member), National Center for Ecological Analysis and Synthesis, Santa Barbara, CA
  • 2005, MARC Winter Institute (Participant), National Academies Summer Institutes on Undergraduate Education in Biology, Santa Cruz, CA
  • 2002, Meta-Analysis: Synthesis across studies in plant pathology (Invited Workshop Instructor), American Phytopathological Society annual meeting, Milwaukee, WI
  • 1999-2000, Integrating the statistical modeling of spatial data in ecology (Invited Working Group Member), National Center for Ecological Analysis and Synthesis, Santa Barbara, CA

 

Previous Positions

  • 2009-2010, Sabbatical Fellow, National Evolutionary Synthesis Center, Durham, NC
  • 2003-2008, Assistant Professor, School of Life Sciences, Arizona State University
  • 2003, Assistant Professor, Department of Biology, Arizona State University
  • 2000-2002, Faculty Research Associate, Department of Biology, Arizona State University
  • 1995-1999, Graduate Research Assistant, Department of Ecology & Evolution, State University of New York at Stony Brook
  • 1994-1995 & 1998-2000, Graduate Teaching Assistant, Department of Ecology & Evolution, State University of New York at Stony Brook
  • 1997, Short Term Fellow, Smithsonian Tropical Research Institute
  • 1991, Intern, Vertebrate Fossils Department, Carnegie Museum of Natural History
  • 1991-1994, Computing Consultant, Northwestern University Information Technology

 

Publications

Research Articles

  • Anderson, C.D., and M.S. Rosenberg (In press) Variation in association with manmade habitat edges exhibited by the Timber Rattlesnake (Crotalus horridus) in St. Louis County, Missouri. Journal of Herpetology.
  • 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.
  • 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.
  • 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.
  • Rosenberg, M.S. (2010) A generalized formula for converting chi-square tests to effect sizes for meta-analysis. PLoS ONE 5(4):e10059
  • 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.
  • 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.
  • 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.
  • 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)
  • Ogden, T.H., and M.S. Rosenberg (2006) Multiple sequence alignment accuracy and phylogenetic inference. Systematic Biology 55(2):314-328.
  • Rosenberg, M.S. (2005) Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics 6:278.
  • Rosenberg, M.S. (2005) MySSP: Non-stationary evolutionary sequence simulation, including indels. Evolutionary Bioinformatics Online 1:81-83.
  • Rosenberg, M.S. (2005) Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinformatics 6:102.
  • 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.
  • 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.
  • 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.
  • Rosenberg, M.S. (2004) Wavelet analysis for detecting anisotropy in point patterns. Journal of Vegetation Science 15(2):277-284.
  • 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.
  • 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.
  • 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.
  • 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.
  • Rosenberg, M.S., and S. Kumar (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52(1):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(5):626-640.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Rosenberg, M.S. (2000) The bearing correlogram: A new method of analyzing directional spatial autocorrelation. Geographical Analysis 32(3):267-278./li>
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Adams, D.C., J. Gurevitch, and M.S. Rosenberg (1997) Resampling tests for meta-analysis of ecological data. Ecology 78(4):1277-1283.
  • 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.

Software

  • 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.

Edited Books

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

Book Chapters

  • 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.

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 (Phoenix, AZ: Arizona Game and Fish Department).

Other Publications

  • 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.

Book/Software Reviews

  • Rosenberg, M.S. (1998) Modeling Dynamic Biological Systems. Quarterly Review of Biology 73(3):340.
  • Rosenberg, M.S. (1997) Minitab for Windows. Quarterly Review of Biology 72(2):240-241.

Thesis

  • 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.

Published 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.

Selected Publications

2007

  • Ainsworth, E A, Rosenberg, Michael, Wang, X. Meta-analysis: The past, present and future. (2007).
  • Ogden, T H, Rosenberg, Michael. How should gaps be treated in parsimony? A comparison of approaches using simulation. Molecular Phylogenetics and Evolution (2007).
  • Ogden, T H, Rosenberg, Michael. Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP. Systematic Biology (2007).

2006

  • Ogden, T H, Rosenberg, Michael. Multiple sequence alignment accuracy and phylogenetic inference. Systematic Biology (2006).

2005

  • Gadagkar, S R, Rosenberg, Michael, Kumar, S. Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree. Journal of Experimental Zoology. B. Molecular and Developmental Evolution (2005).
  • Rosenberg, Michael. MySSP: Non-stationary evolutionary sequence simulation, including indels. Evolutionary Bioinformatics Online (2005).
  • Rosenberg, Michael. Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics (2005).
  • Rosenberg, Michael. Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinformatics (2005).
  • Rosenberg, Michael. The file-drawer problem revisited: A general weighted method for calculating fail-safe numbers in meta-analysis. Evolution (2005).
  • Rosenberg, Michael. Why lectures seem to last forever. Journal of Irreproducible Results (2005).
  • Rosenberg, Michael. MySSP. Non-stationary evolutionary sequence simulation, including indels. (2005).

2004

  • Rosenberg, Michael. Wavelet analysis for detecting anisotropy in point patterns. Journal of Vegetation Science (2004).
  • Rosenberg, Michael, Garrett, K A, Su, Z, Bowden, R L. Meta-analysis in plant pathology: Synthesizing research results. Phytopathology (2004).
  • Sokal, R R, Oden, N L, Rosenberg, Michael, Thomson, B A. 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 (2004).

2003

  • Hyatt, L A, Rosenberg, Michael, Howard, T G, Bole, G, Fang, W, Anastasia, J, Brown, K, Grella, R, Hinman, K, Kurdziel, J P, Gurevitch, J. The distance dependence prediction of the Janzen-Connell hypothesis: A meta-analysis. Oikos (2003).
  • Rosenberg, Michael, Kumar, S. Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Molecular Biology and Evolution (2003).
  • Rosenberg, Michael, Kumar, Sudhir. Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology (2003).
  • Rosenberg, Michael, Subramanian, S, Kumar, S. Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology and Evolution (2003).

2002

  • Dale, M R T, Dixon M-J Fortin, P, Legendre, P, Myers, D E, Rosenberg, Michael. Conceptual and mathematical relationships among methods for spatial analysis. Ecography (2002).
  • Jakomulska, A, Perry, J, Dungan, J L, Dale, M, Miriti, M, Fortin, M -J, Legendre, P, Citron-Pousty, S, Rosenberg, Michael. A balanced view of scaling in spatial statistical analysis. Ecography (2002).
  • Perry, J N, Liebhold, A, Rosenberg, Michael, Dungan, J, Miriti, M, Jakomulska, A, Citron- Pousty, S. Illustration and guidelines for selecting statistical methods for quantifying spatial patterns in ecological data. Ecography (2002).
  • Rosenberg, Michael. Fiddler crab claw shape variation: A geometric morphometric analysis across the genus Uca. Biological Journal of the Linnean Society (2002).

2001

  • Rosenberg, Michael. The systematics and taxonomy of fiddler crabs: A phylogeny of the genus Uca. Journal of Crustacean Biology (2001).
  • Rosenberg, Michael. PASSAGE. Pattern analysis, spatial statistics and geographic exegesis. (2001).
  • Rosenberg, Michael, Kumar, S. Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Molecular Biology and Evolution (2001).

2000

  • Rosenberg, Michael. The bearing correlogram: A new method of analyzing directional spatial autocorrelation. Geographical Analysis (2000).
  • Rosenberg, Michael, Adams, Dean C, Gurevitch, Jessica. MetaWin. Statistical software for meta-analysis. (2000).
  • Sokal, R R, Oden, N L, Rosenberg, Michael, Thomson, B A. Cancer incidences in Europe related to mortalities, and ethnohistoric, genetic, and geographic distances. Proceedings of the National Academy of Sciences USA (2000).

1999

  • Rosenberg, Michael, Sokal, Robert R, Oden, Neal L, DiGiovanni, Donna. Spatial autocorrelation of cancer in Europe. European Journal of Epidemiology (1999).

1998

  • Adams, Dean C, Rosenberg, Michael. Partial-warps, phylogeny, and ontogeny: A comment on Fink and Zelditch (1995). Systematic Biology (1998).

1997

  • Adams, Dean C, Gurevitch, Jessica, Rosenberg, Michael. Resampling tests for meta-analysis of ecological data. Ecology (1997).
  • Rosenberg, Michael. Evolution of shape differences between the major and minor chelipeds of Uca pugnax (Decapoda: Ocypodidae). Journal of Crustacean Biology (1997).
  • Sokal, Robert R, Oden, Neal L, Rosenberg, Michael, DiGiovanni, Donna. Ethnohistory, genetics and cancer mortality in Europeans. Proceedings of the National Academy of Sciences USA (1997).
  • Sokal, Robert R, Oden, Neal L, Rosenberg, Michael, DiGiovanni, Donna. The patterns of historical population movements in Europe and some of their genetic consequences. American Journal of Human Biology (1997).