Scott W Roy

Summary

Publications

  1. pmc Resolution of a deep animal divergence by the pattern of intron conservation
    Scott William Roy
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 102:4403-8. 2005
  2. pmc Intron length distributions and gene prediction
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Nucleic Acids Res 35:4737-42. 2007
  3. pmc Spliceosomal introns as tools for genomic and evolutionary analysis
    Manuel Irimia
    Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
    Nucleic Acids Res 36:1703-12. 2008
  4. pmc Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans
    Qi Zhou
    CAS Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
    BMC Genomics 13:109. 2012
  5. pmc Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
    Manuel Irimia
    Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 7:188. 2007
  6. pmc The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification
    David Hoogewijs
    Department of Biology and Center for Molecular Phylogeny and Evolution, Ghent University, B 9000 Ghent, Belgium
    BMC Evol Biol 8:279. 2008
  7. ncbi request reprint A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1447-57. 2007
  8. ncbi request reprint Evolutionary conservation of UTR intron boundaries in Cryptococcus
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1140-8. 2007
  9. ncbi request reprint On the incidence of intron loss and gain in paralogous gene families
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1579-81. 2007
  10. ncbi request reprint Widespread intron loss suggests retrotransposon activity in ancient apicomplexans
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1926-33. 2007

Collaborators

Detail Information

Publications45

  1. pmc Resolution of a deep animal divergence by the pattern of intron conservation
    Scott William Roy
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 102:4403-8. 2005
    ..We find that only the ecdysozoa grouping satisfies these predictions, with P < 10(-6). Simulations show that our method, unlike some previous methods, is largely insensitive to rate variation between branches...
  2. pmc Intron length distributions and gene prediction
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Nucleic Acids Res 35:4737-42. 2007
    ....
  3. pmc Spliceosomal introns as tools for genomic and evolutionary analysis
    Manuel Irimia
    Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
    Nucleic Acids Res 36:1703-12. 2008
    ..We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions...
  4. pmc Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans
    Qi Zhou
    CAS Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
    BMC Genomics 13:109. 2012
    ..12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility...
  5. pmc Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
    Manuel Irimia
    Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 7:188. 2007
    ....
  6. pmc The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification
    David Hoogewijs
    Department of Biology and Center for Molecular Phylogeny and Evolution, Ghent University, B 9000 Ghent, Belgium
    BMC Evol Biol 8:279. 2008
    ..In silico analysis of the genome of Caenorhabditis elegans revealed an unexpectedly high number of globin genes featuring a remarkable diversity in gene structure, amino acid sequence and expression profiles...
  7. ncbi request reprint A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1447-57. 2007
    ..These results also provide evidence that multiple intron insertion into the same site is rare, further supporting the notion that early eukaryotic ancestors were very intron rich...
  8. ncbi request reprint Evolutionary conservation of UTR intron boundaries in Cryptococcus
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1140-8. 2007
    ..These results focus attention on the functional roles of eukaryotic UTRs and deepen the mystery of UTR intron splicing...
  9. ncbi request reprint On the incidence of intron loss and gain in paralogous gene families
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1579-81. 2007
    ..Statistical reanalysis of the data suggests, instead, that intron losses have outnumbered intron gains in paralogous gene families...
  10. ncbi request reprint Widespread intron loss suggests retrotransposon activity in ancient apicomplexans
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:1926-33. 2007
    ..By contrast, Cryptosporidium introns are less evolutionary conserved with Toxoplasma than are introns from other apicomplexans; thus the few remaining introns are not simply indispensable ancestral introns...
  11. doi request reprint Rare genomic characters do not support Coelomata: intron loss/gain
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 25:620-3. 2008
    ..2005a. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408.). Instead, we show that our conclusions are likely to be robust to such concerns...
  12. pmc Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 25:1192-8. 2008
    ..Finally, we find a lack of synapomorphic gene losses, suggesting a low rate of ancestral gene loss in Plasmodium...
  13. doi request reprint When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioessays 30:601-5. 2008
    ..Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html)...
  14. ncbi request reprint Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 24:171-81. 2007
    ..This pattern implies that rates of intron creation were higher during earlier periods of evolution and further focuses attention on the causes of initial intron proliferation...
  15. pmc Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Genome Res 16:1270-5. 2006
    ..We suggest that intron loss/gain in some eukaryotic lineages may be concentrated in relatively short episodes coincident with occasional TE invasions...
  16. ncbi request reprint Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 23:2259-62. 2006
    ....
  17. pmc Intron mis-splicing: no alternative?
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, USA
    Genome Biol 9:208. 2008
    ..This striking inefficiency deepens the mystery of the proliferation and persistence of introns...
  18. ncbi request reprint The evolution of spliceosomal introns: patterns, puzzles and progress
    Scott William Roy
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Nat Rev Genet 7:211-21. 2006
    ....
  19. pmc Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number
    Scott William Roy
    Department of Organismic and Evolutionary Biology, Harvard, Cambridge, Massachusetts 02138, USA
    Genome Res 16:750-6. 2006
    ..The observed pattern suggests that the availability of stochastic intron loss and gain mutations can be a major determinant of changes in intron number...
  20. ncbi request reprint Intron-rich ancestors
    Scott W Roy
    Allan Wilson Centre, Massey University, Palmerston North, New Zealand
    Trends Genet 22:468-71. 2006
    ..These results refocus our attention on the evolutionary history and importance of introns in early eukaryotic evolution...
  21. doi request reprint Quantitative regulation of alternative splicing in evolution and development
    Manuel Irimia
    Departament de Genetica, and Institut de Biomedicina IBUB, Universitat de Barcelona, Barcelona, Spain
    Bioessays 31:40-50. 2009
    ..We discuss the potential role of changes in developmental regulation of AS as an additional layer in complex gene regulatory networks and in the emergence of genetic novelties...
  22. ncbi request reprint Coevolution of genomic intron number and splice sites
    Manuel Irimia
    Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
    Trends Genet 23:321-5. 2007
    ..It seems that eukaryotic ancestors had relatively large intron numbers and 'weak' 5'ss, a pattern associated with frequent alternative splicing in modern organisms...
  23. pmc The pattern of intron loss
    Scott W Roy
    Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 102:713-8. 2005
    ..Our results support a reverse transcriptase-mediated model of intron loss...
  24. doi request reprint Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    RNA Biol 9:12-21. 2012
    ....
  25. pmc Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures
    Manuel Irimia
    Department of Genetics, School of Biology, University of Barcelona, Barcelona, Spain
    Genome Biol Evol 3:551-64. 2011
    ..These results attest to the importance of locus-specific splicing functions in differences in structural evolution across genes, as well as to commonalities of forces shaping the evolution of individual genes along different lineages...
  26. pmc Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain
    Scott W Roy
    Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 100:7158-62. 2003
    ....
  27. ncbi request reprint Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis
    Manuel Irimia
    Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
    Mol Biol Evol 25:375-82. 2008
    ..Finally, we demonstrate an inverse relationship between AS and gene duplication, suggesting that the latter may be primarily responsible for the emergence of new functional transcripts in nematodes...
  28. doi request reprint Sequence diversity and evolutionary dynamics of the dimorphic antigen merozoite surface protein-6 and other Msp genes of Plasmodium falciparum
    Scott W Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Bethesda, MD 20894, USA
    Gene 443:12-21. 2009
    ..Second, a comparison of PfMsp-9 with the P. reichenowi ortholog indicated retention of a significant inter-unit diversity within an 18-base pair repeat within the coding region of P. falciparum, but homogenization in P. reichenowi...
  29. pmc Complex early genes
    Scott W Roy
    Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 102:1986-91. 2005
    ..Intron losses outnumber gains over a large range of eukaryotic lineages. These results show that early eukaryotic gene structures were very complex, and that simplification, not embellishment, has dominated subsequent evolution...
  30. pmc Intronization, de-intronization and intron sliding are rare in Cryptococcus
    Scott W Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Evol Biol 9:192. 2009
    ..Two recent papers suggest that such changes may be a major force in remodeling of eukaryotic gene structures, however the rate of occurrence of such changes has not been assessed at the genomic level...
  31. pmc Rates of intron loss and gain: implications for early eukaryotic evolution
    Scott William Roy
    Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 102:5773-8. 2005
    ....
  32. pmc The origin of recent introns: transposons?
    Scott W Roy
    Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Genome Biol 5:251. 2004
    ..A recent study makes considerable progress by identifying numerous recently gained introns in nematodes - although it remains difficult to distinguish definitively between models of intron gain...
  33. doi request reprint Mystery of intron gain: new data and new models
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
    Trends Genet 25:67-73. 2009
    ..In addition, we introduce two potential mechanisms for intron creation, based on hybrid RNA-DNA reverse splicing and on template switching errors by reverse transcriptase...
  34. pmc Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    PLoS Genet 4:e1000148. 2008
    ....
  35. pmc Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    PLoS ONE 4:e5800. 2009
    ....
  36. pmc Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brain
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona E08028, Spain
    Proc Natl Acad Sci U S A 108:5319-24. 2011
    ..In addition, we find that tissue-specific Nova expression patterns emerged independently in other lineages, suggesting independent assembly of tissue-specific regulatory networks...
  37. pmc Phylogenomics: gene duplication, unrecognized paralogy and outgroup choice
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 4:e4568. 2009
    ..Overall, these results generalize the utility of closely-related outgroups for phylogenetic analysis...
  38. pmc The signal of ancient introns is obscured by intron density and homolog number
    Scott William Roy
    Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 99:15513-7. 2002
    ..This finding matches the expectation of the mixed model of intron origin, in which a fraction of phase zero introns are left from the assembly of the first genes, while other introns have been added in the course of evolution...
  39. doi request reprint Patterns of polymorphism in genomic regions flanking three highly polymorphic surface antigens in Plasmodium falciparum
    Olukemi K Amodu
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Mol Biochem Parasitol 159:1-6. 2008
    ..A higher ratio of SNPs to indels than previously reported for P. falciparum was observed. An 11 bp repeat upstream of msp2 showed an intriguing pattern of polymorphism possibly suggestive of purifying selection on total allele length...
  40. pmc Probing evolutionary repeatability: neutral and double changes and the predictability of evolutionary adaptation
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 4:e4500. 2009
    ..5x10(-7)%) pathways were characterized by consistently increasing resistance, thus only a tiny fraction of possible paths are accessible by positive selection. I further explore these data in several ways...
  41. doi request reprint Origin of introns by 'intronization' of exonic sequences
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
    Trends Genet 24:378-81. 2008
    ..Intronization is more common than the reverse process, loss of splicing of retained introns. Finally, these findings link alternative splicing with modern intron creation...
  42. ncbi request reprint Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata
    Manuel Irimia
    Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
    Mol Biol Evol 24:1604-7. 2007
    ..Including the additional species paints a very different picture, with 13 remaining characters consistent with Ecdysozoa versus only 1 consistent with Coelomata...
  43. ncbi request reprint Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes
    Scott William Roy
    Mol Biol Evol 23:1824-7. 2006
    ..5 billion years. Nine other predicted introns are due to annotation errors reflecting apparent mistakes in the E. histolytica genome assembly. These results underscore the massive differences in intron gain rates through evolution...
  44. ncbi request reprint Recent evidence for the exon theory of genes
    Scott William Roy
    Genetica 118:251-66. 2003
    ..Thus, this moderated form of the Exon Theory of Genes still offers a coherent picture of the origin and evolutionary history of the intron-exon structure of eukaryotic genes...
  45. doi request reprint Rare genomic characters do not support Coelomata: RGC_CAMs
    Scott William Roy
    J Mol Evol 66:308-15. 2008
    ..These results indicate that the Coelomata signal is a long-branch artifact...