Michael D Purugganan

Summary

Affiliation: New York University
Country: USA

Publications

  1. ncbi request reprint Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum
    Si I Li
    Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
    BMC Genomics 15:616. 2014
  2. pmc Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum
    Jonathan M Flowers
    Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
    PLoS Genet 6:e1001013. 2010
  3. pmc Genome-wide patterns of Arabidopsis gene expression in nature
    Christina L Richards
    Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, USA
    PLoS Genet 8:e1002662. 2012
  4. pmc The plant proteome folding project: structure and positive selection in plant protein families
    M M Pentony
    Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
    Genome Biol Evol 4:360-71. 2012
  5. doi request reprint The nature of selection during plant domestication
    Michael D Purugganan
    Department of Biology and Centre for Genomics and Systems Biology, 100 Washington Square East, New York University, New York 10003, USA
    Nature 457:843-8. 2009
  6. doi request reprint Archaeological data reveal slow rates of evolution during plant domestication
    Michael D Purugganan
    Department of Biology and Center for Genomics and Systems Biology, 100 Washington Square East, New York University, New York, New York 10003, USA
    Evolution 65:171-83. 2011
  7. pmc Plasticity regulators modulate specific root traits in discrete nitrogen environments
    Miriam L Gifford
    Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America School of Life Sciences, University of Warwick, Coventry, United Kingdom Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
    PLoS Genet 9:e1003760. 2013
  8. doi request reprint Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana
    Joshua A Banta
    Department of Biology, University of Texas at Tyler, Tyler, TX 75799, USA
    Ecol Lett 15:769-77. 2012
  9. doi request reprint Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice
    Jonathan M Flowers
    Department of Biology and Center for Genomics and Systems Biology, New York University, NY, USA
    Mol Biol Evol 29:675-87. 2012
  10. pmc Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection
    Xianfa Xie
    Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
    PLoS ONE 6:e20670. 2011

Collaborators

Detail Information

Publications24

  1. ncbi request reprint Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum
    Si I Li
    Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
    BMC Genomics 15:616. 2014
    ..different chimeras were compared at five different developmental stages using a customized microarray. Effects of chimerism on global transcriptional patterns associated with social interactions were observed...
  2. pmc Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum
    Jonathan M Flowers
    Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
    PLoS Genet 6:e1001013. 2010
    ..The SNP data indicate that recombination is widespread within D. discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle...
  3. pmc Genome-wide patterns of Arabidopsis gene expression in nature
    Christina L Richards
    Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, USA
    PLoS Genet 8:e1002662. 2012
    ....
  4. pmc The plant proteome folding project: structure and positive selection in plant protein families
    M M Pentony
    Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
    Genome Biol Evol 4:360-71. 2012
    ..Structural information provides new functional insights into specific plant proteins and allows us to map positively selected amino acid sites onto protein structures and view these sites in a structural and functional context...
  5. doi request reprint The nature of selection during plant domestication
    Michael D Purugganan
    Department of Biology and Centre for Genomics and Systems Biology, 100 Washington Square East, New York University, New York 10003, USA
    Nature 457:843-8. 2009
    ....
  6. doi request reprint Archaeological data reveal slow rates of evolution during plant domestication
    Michael D Purugganan
    Department of Biology and Center for Genomics and Systems Biology, 100 Washington Square East, New York University, New York, New York 10003, USA
    Evolution 65:171-83. 2011
    ....
  7. pmc Plasticity regulators modulate specific root traits in discrete nitrogen environments
    Miriam L Gifford
    Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America School of Life Sciences, University of Warwick, Coventry, United Kingdom Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
    PLoS Genet 9:e1003760. 2013
    ..The overall results suggest that there is a pool of genetic variability in plants that controls traits in specific environments, with opportunity to tune crop plants to a given environment. ..
  8. doi request reprint Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana
    Joshua A Banta
    Department of Biology, University of Texas at Tyler, Tyler, TX 75799, USA
    Ecol Lett 15:769-77. 2012
    ....
  9. doi request reprint Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice
    Jonathan M Flowers
    Department of Biology and Center for Genomics and Systems Biology, New York University, NY, USA
    Mol Biol Evol 29:675-87. 2012
    ..Our results suggest that the physical distribution of selected mutations is a primary factor that determines the genomic pattern of polymorphism in wild and domesticated rice species...
  10. pmc Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection
    Xianfa Xie
    Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
    PLoS ONE 6:e20670. 2011
    ..These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups...
  11. ncbi request reprint Population genomics of the Arabidopsis thaliana flowering time gene network
    Jonathan M Flowers
    Department of Biology and Center for Genomics and Systems Biology, New York University, NY, USA
    Mol Biol Evol 26:2475-86. 2009
    ..Although there is some evidence for adaptive evolution in these life-history genes, it appears that slightly deleterious polymorphisms are a major component of natural molecular variation in the flowering time network of A. thaliana...
  12. pmc Candidate gene association mapping of Arabidopsis flowering time
    Ian M Ehrenreich
    Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
    Genetics 183:325-35. 2009
    ..We conservatively estimate that approximately 4-14% of known flowering time genes may harbor common alleles that contribute to natural variation in this life history trait...
  13. doi request reprint Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view
    Pu Huang
    Department of Biology, Washington University, St Louis, MO 63130, USA
    Mol Ecol 21:4593-604. 2012
    ..Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration-drift balance in creating this clinal variation pattern is also discussed...
  14. pmc Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS
    Ulises Rosas
    Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
    Nat Commun 5:3651. 2014
    ..Mutation in this regulatory motif evolved recently and has spread to high frequency in Arabidopsis natural accessions, suggesting a role for these cis-regulatory changes in adaptive variation of flowering time. ..
  15. pmc Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture
    Ulises Rosas
    Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
    Proc Natl Acad Sci U S A 110:15133-8. 2013
    ..This finding supports a role for plasticity responses in phenotypic evolution in natural environments. ..
  16. pmc Sequence variation of MicroRNAs and their binding sites in Arabidopsis
    Ian M Ehrenreich
    Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
    Plant Physiol 146:1974-82. 2008
    ..Overall, our results show that despite differences in the architecture of miRNA-based regulation, miRNAs and their targets are similarly constrained in both plants and animals...
  17. doi request reprint The evolution of plant genomes: scaling up from a population perspective
    Jonathan M Flowers
    Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003 6688, USA
    Curr Opin Genet Dev 18:565-70. 2008
    ....
  18. doi request reprint Migration, isolation and hybridization in island crop populations: the case of Madagascar rice
    Kristie A Mather
    Department of Biology and Center for Genomics and Systems Biology, 1009 Silver, 100 Washington Square East, New York University, New York, NY 10003, USA
    Mol Ecol 19:4892-905. 2010
    ..Finally, despite partial reproductive isolation between japonica and indica, there was evidence of indica/japonica recombination resulting from their hybridization on the island...
  19. pmc Molecular evidence for a single evolutionary origin of domesticated rice
    Jeanmaire Molina
    Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
    Proc Natl Acad Sci U S A 108:8351-6. 2011
    ....
  20. pmc Different evolutionary histories of two cation/proton exchanger gene families in plants
    Inês S Pires
    Department of Biology and Center for Genomics and Systems Biology, New York University, New York, USA
    BMC Plant Biol 13:97. 2013
    ..However, our knowledge about the evolution of NHX and SOS1 stress responsive gene families is still limited...
  21. pmc Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina
    Shivani U Thanawala
    Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
    Dev Cell 25:93-105. 2013
    ..Our findings show how stochastic and regional inputs are integrated to control photoreceptor subtype specification in the Drosophila retina...
  22. doi request reprint The cooperative amoeba: Dictyostelium as a model for social evolution
    Si I Li
    Department of Biology and Center for Genomics and Systems Biology, 1009 Silver, 100 Washington Square East, New York University, New York, NY 10003, USA
    Trends Genet 27:48-54. 2011
    ....
  23. pmc Molecular phylogeography of domesticated barley traces expansion of agriculture in the Old World
    Daisuke Saisho
    Center for Genomics and Systems Biology and Department of Biology, New York University, New York, New York 10003, USA
    Genetics 177:1765-76. 2007
    ..This suggests that cultural diffusion or independent innovation is responsible for the expansion of agriculture to areas of South and East Asia during the Neolithic revolution...
  24. doi request reprint Evolution of crop species: genetics of domestication and diversification
    Rachel S Meyer
    Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place, New York University, New York 10003, USA
    Nat Rev Genet 14:840-52. 2013
    ....