Casey W Dunn

Summary

Affiliation: Brown University
Country: USA

Publications

  1. doi request reprint The hidden biology of sponges and ctenophores
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St, Providence, RI 02906, USA Electronic address
    Trends Ecol Evol 30:282-91. 2015
  2. doi request reprint The evolution of animal genomes
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St, Providence, RI 02906, USA Electronic address
    Curr Opin Genet Dev 35:25-32. 2015
  3. pmc Agalma: an automated phylogenomics workflow
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
    BMC Bioinformatics 14:330. 2013
  4. pmc Characterization of differential transcript abundance through time during Nematostella vectensis development
    Rebecca Rae Helm
    Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, RI 02912, USA
    BMC Genomics 14:266. 2013
  5. doi request reprint Broad phylogenomic sampling improves resolution of the animal tree of life
    Casey W Dunn
    Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, Hawaii 96813, USA
    Nature 452:745-9. 2008
  6. doi request reprint Evolution: out of the ocean
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Curr Biol 23:R241-3. 2013
  7. pmc Assessing the root of bilaterian animals with scalable phylogenomic methods
    Andreas Hejnol
    Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA
    Proc Biol Sci 276:4261-70. 2009
  8. pmc Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda
    Felipe Zapata
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02906, USA
    Proc Biol Sci 281:20141739. 2014
  9. pmc Molecular evidence for deep evolutionary roots of bilaterality in animal development
    David Q Matus
    Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA
    Proc Natl Acad Sci U S A 103:11195-200. 2006
  10. doi request reprint Resolving the evolutionary relationships of molluscs with phylogenomic tools
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
    Nature 480:364-7. 2011

Detail Information

Publications24

  1. doi request reprint The hidden biology of sponges and ctenophores
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St, Providence, RI 02906, USA Electronic address
    Trends Ecol Evol 30:282-91. 2015
    ..As we discuss here, key details of this new model hinge on a better understanding of the Porifera and Ctenophora, which have each been hypothesized to be sister to all other animals, but are poorly studied and often misrepresented. ..
  2. doi request reprint The evolution of animal genomes
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St, Providence, RI 02906, USA Electronic address
    Curr Opin Genet Dev 35:25-32. 2015
    ..This will require far greater genome sampling both across and within species, extensive phenotype data, a well resolved animal phylogeny, and advances in comparative methods. ..
  3. pmc Agalma: an automated phylogenomics workflow
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
    BMC Bioinformatics 14:330. 2013
    ..In addition, methodological improvements made in the context of one study often cannot be easily applied and evaluated in the context of other studies...
  4. pmc Characterization of differential transcript abundance through time during Nematostella vectensis development
    Rebecca Rae Helm
    Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, RI 02912, USA
    BMC Genomics 14:266. 2013
    ..We provide an overview of changes in the transcriptome through development, and examine the maternal to zygotic transition, which has been difficult to investigate with other tools...
  5. doi request reprint Broad phylogenomic sampling improves resolution of the animal tree of life
    Casey W Dunn
    Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, Hawaii 96813, USA
    Nature 452:745-9. 2008
    ..Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree...
  6. doi request reprint Evolution: out of the ocean
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Curr Biol 23:R241-3. 2013
    ..This has important implications for our understanding of the historical interactions of terrestrial organisms with each other and their physical environments...
  7. pmc Assessing the root of bilaterian animals with scalable phylogenomic methods
    Andreas Hejnol
    Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA
    Proc Biol Sci 276:4261-70. 2009
    ..The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past...
  8. pmc Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda
    Felipe Zapata
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02906, USA
    Proc Biol Sci 281:20141739. 2014
    ..These results reject the prevalent hypothesis of gastropod phylogeny, Orthogastropoda. Our dated tree is congruent with a possible end-Permian recovery of some gastropod clades, namely Caenogastropoda and some Heterobranchia subclades. ..
  9. pmc Molecular evidence for deep evolutionary roots of bilaterality in animal development
    David Q Matus
    Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA
    Proc Natl Acad Sci U S A 103:11195-200. 2006
    ..vectensis could possess antecedents of the organization of the bilaterian central nervous system...
  10. doi request reprint Resolving the evolutionary relationships of molluscs with phylogenomic tools
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
    Nature 480:364-7. 2011
    ..This well-resolved tree will constitute a framework for further studies of mollusc evolution, development and anatomy...
  11. ncbi request reprint Molecular phylogenetics of the siphonophora (Cnidaria), with implications for the evolution of functional specialization
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
    Syst Biol 54:916-35. 2005
    ..Cnidaria; colonial animals; deep sea; division of labor; functional specialization; Hydrozoa; phylogenetics; Siphonophores.]...
  12. doi request reprint Phylogenomic Analyses Support Traditional Relationships within Cnidaria
    Felipe Zapata
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
    PLoS ONE 10:e0139068. 2015
    ....
  13. pmc Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows
    Stefan Siebert
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
    PLoS ONE 6:e22953. 2011
    ..Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing...
  14. ncbi request reprint The evolution of colony-level development in the Siphonophora (Cnidaria:Hydrozoa)
    Casey W Dunn
    Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA
    Dev Genes Evol 216:743-54. 2006
    ..This descriptive work will enable future mechanistic and molecular studies of colony-level development in the siphonophores...
  15. pmc Phylogenetic analysis of gene expression
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA Department of Biostatistics and Center for Statistical Sciences, Brown University, Providence, RI 02903, USA
    Integr Comp Biol 53:847-56. 2013
    ..These topics are relevant to high-throughput phenotypic data well beyond gene expression. ..
  16. doi request reprint Toward a statistically explicit understanding of de novo sequence assembly
    Mark Howison
    Center for Computation and Visualization and Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Bioinformatics 29:2959-63. 2013
    ..Those assemblers that do report uncertainty take different approaches to describing multiple assembly hypotheses and the support for each...
  17. doi request reprint Phyutility: a phyloinformatics tool for trees, alignments and molecular data
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Bioinformatics 24:715-6. 2008
    ..Its simple command-line interface allows for easy integration into scripted analyses, and is able to handle large datasets with an integrated database...
  18. doi request reprint Automation and Evaluation of the SOWH Test with SOWHAT
    Samuel H Church
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
    Syst Biol 64:1048-58. 2015
    ..These results will help others implement and evaluate the SOWH test and allow us to provide recommendations for future applications of the SOWH test. SOWHAT is available for download from https://github.com/josephryan/SOWHAT. ..
  19. doi request reprint An Integrated Perspective on Phylogenetic Workflows
    August Guang
    Department of Applied Math, Brown University, 182 George St, Providence, RI 02906, USA Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St, Providence, RI 02912, USA
    Trends Ecol Evol 31:116-26. 2016
    ..This perspective unifies currently disparate advances, and will help investigators evaluate which steps would benefit the most from additional computation and future methods development. ..
  20. ncbi request reprint Re-evaluation of characters in Apolemiidae (Siphonophora), with description of two new species from Monterey Bay, California
    Stefan Siebert
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Zootaxa 3702:201-32. 2013
    ....
  21. pmc Bayesian genome assembly and assessment by markov chain monte carlo sampling
    Mark Howison
    Center for Computation and Visualization, Brown University, Providence, Rhode Island, United States of America
    PLoS ONE 9:e99497. 2014
    ..GABI is freely available under a GPL license from https://bitbucket.org/mhowison/gabi. ..
  22. doi request reprint The histology of Nanomia bijuga (Hydrozoa: Siphonophora)
    Samuel H Church
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island
    J Exp Zool B Mol Dev Evol 324:435-49. 2015
    ..This work provides a greater understanding of epithelial diversity within the cnidarians, and will be a foundation for future studies on N. bijuga, including functional assays and gene expression analyses...
  23. ncbi request reprint Complex colony-level organization of the deep-sea siphonophore Bargmannia elongata (Cnidaria, Hydrozoa) is directionally asymmetric and arises by the subdivision of pro-buds
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Dev Dyn 234:835-45. 2005
    ..This initial description of development in a deep-sea siphonophore provides an example of how precise colony-level organization can arise, and illustrates that the morphological complexity of cnidarians is greater than is often assumed...
  24. pmc Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals
    Vincent J Lynch
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06551, USA
    Proc Biol Sci 271:2201-7. 2004
    ..These results support the idea that adaptive evolution of transcription factors can be an integral part in the evolution of novel structures...