Stephen A Smith

Summary

Affiliation: Yale University
Country: USA

Publications

  1. doi request reprint Rates of molecular evolution are linked to life history in flowering plants
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, 21 Sachem Street, Post Office Box 208105, Yale University, New Haven, CT 06520 8105, USA
    Science 322:86-9. 2008
  2. pmc Bioactive endophytes warrant intensified exploration and conservation
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 3:e3052. 2008
  3. 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
  4. doi request reprint The origins of C4 grasslands: integrating evolutionary and ecosystem science
    Erika J Edwards
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Science 328:587-91. 2010
  5. ncbi request reprint Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales)
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Syst Biol 59:322-41. 2010
  6. doi request reprint Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia)
    Margaret E K Evans
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Am Nat 173:225-40. 2009
  7. doi request reprint Understanding angiosperm diversification using small and large phylogenetic trees
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
    Am J Bot 98:404-14. 2011
  8. 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
  9. pmc Patterns in the assembly of temperate forests around the Northern Hemisphere
    Michael J Donoghue
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Philos Trans R Soc Lond B Biol Sci 359:1633-44. 2004
  10. doi request reprint treePL: divergence time estimation using penalized likelihood for large phylogenies
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 28:2689-90. 2012

Detail Information

Publications20

  1. doi request reprint Rates of molecular evolution are linked to life history in flowering plants
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, 21 Sachem Street, Post Office Box 208105, Yale University, New Haven, CT 06520 8105, USA
    Science 322:86-9. 2008
    ....
  2. pmc Bioactive endophytes warrant intensified exploration and conservation
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 3:e3052. 2008
    ..Here we provide direct evidence from bioassays of endophytes isolated from tropical plants and bioinformatic analyses that novel biology will indeed yield novel chemistry of potential value...
  3. 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...
  4. doi request reprint The origins of C4 grasslands: integrating evolutionary and ecosystem science
    Erika J Edwards
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Science 328:587-91. 2010
    ....
  5. ncbi request reprint Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales)
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Syst Biol 59:322-41. 2010
    ..These results suggest a possible model for the origin of the Madrean-Tethyan disjunction pattern...
  6. doi request reprint Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia)
    Margaret E K Evans
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Am Nat 173:225-40. 2009
    ..Our data are also consistent with Axelrod's hypothesis that the spread of arid conditions in western North America stimulated diversification of arid-adapted lineages...
  7. doi request reprint Understanding angiosperm diversification using small and large phylogenetic trees
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
    Am J Bot 98:404-14. 2011
    ..Mega-phylogenetic studies of diversification hold great promise for revealing new patterns, but we will need to focus more attention on properly specifying null expectation...
  8. 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...
  9. pmc Patterns in the assembly of temperate forests around the Northern Hemisphere
    Michael J Donoghue
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Philos Trans R Soc Lond B Biol Sci 359:1633-44. 2004
    ..Fortunately, many more plant groups show relevant disjunction patterns and could soon be added to such analyses...
  10. doi request reprint treePL: divergence time estimation using penalized likelihood for large phylogenies
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 28:2689-90. 2012
    ..We compare this approach with existing software including r8s, PATHd8 and BEAST...
  11. pmc Phylogenetic analyses reveal the shady history of C4 grasses
    Erika J Edwards
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Proc Natl Acad Sci U S A 107:2532-7. 2010
    ..Furthermore, we argue that the evolution of cold tolerance in certain C(3) lineages is an overlooked innovation that has profoundly influenced the patterning of grassland communities across the globe...
  12. ncbi request reprint Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping
    Brian R Moore
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Syst Biol 55:662-76. 2006
    ..These methods have been implemented in the freely available program, tREeBOOT...
  13. pmc Analyzing and synthesizing phylogenies using tree alignment graphs
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Comput Biol 9:e1003223. 2013
    ..Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. ..
  14. pmc Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
    Ya Yang
    Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Ave, Ann Arbor, MI 48109 1048, USA
    BMC Genomics 14:328. 2013
    ..By doing so we evaluate strategies for optimizing total gene coverage and minimizing assembly chimeras and redundancy...
  15. 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...
  16. 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...
  17. doi request reprint Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis
    Richard H Ree
    Department of Botany, Field Museum of Natural History, Chicago, Illinois 60605, USA
    Syst Biol 57:4-14. 2008
    ..The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference...
  18. ncbi request reprint Amphibian resources on the internet
    Michael W Nolan
    Department of Biomedical Sciences and Pathobiology, VMRCVM, Virginia Polytechnic Institute and State University, Duck Pond Drive, Blacksburg, VA 24061 0442, USA
    ILAR J 48:290-6. 2007
    ..For each web site, descriptive titles, web addresses, and a brief review are provided. Note that the authors of this review cannot assure the accuracy of content in these web resources...
  19. pmc Expression and functional activity of PPARgamma in pancreatic beta cells
    Hannah J Welters
    Institute of Biomedical and Clinical Science, Peninsula Medical School, Plymouth, Devon, UK
    Br J Pharmacol 142:1162-70. 2004
    ..Taken together, the present data suggest that, at least under in vitro conditions, thiazolidinediones do not exert direct protective effects against fatty acid-mediated cytotoxicity in pancreatic beta cells...
  20. ncbi request reprint A recombinant vaccine expressing a mammalian Mycobacterium sp. antigen is immunostimulatory but not protective in striped bass
    David J Pasnik
    Department of Biomedical Sciences and Pathobiology, Virginia Maryland Regional College of Veterinary Medicine VMRCVM, Virginia Polytechnic Institute and State University VPI and SU, Duck Pond Drive, Blacksburg, VA 24061, USA
    Vet Immunol Immunopathol 95:43-52. 2003
    ..However, survival studies determined that inoculated fish failed to demonstrate cross-protective responses after live Mycobacterium marinum challenge 70 days post-inoculation...