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Roy
Allan Wilson Centre for Ph: +64 6 350 5515 x7626
Molecular Ecology and Evolution Fax: +64 6 350 5626
Massey University scottwroy@gmail.com
Palmerston North, NZ
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o Provided evidence for a chimeric origin of P.
falciparum MSP6 alleles by recombination
between additional now-extinct allelic classes.
o Formally defined allelic dimorphism, showing
MSP3 is not dimorphic, as previously reported.
o Developed and tested hypotheses for the origin
of allelic dimorphism.
• Studied patterns of linkage equilibrium in genome-
wide P. falciparum polymorphism microarray data.
• Showed that genotypes from multiply-infected malaria
infections suggest single mosquito transmission of
multiple strains between infected hosts.
• Formulated theoretical arguments showing that self-
incompatibility alleles in plants are likely to arise
through dual-specificity intermediates.
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ADDITIONAL Teaching fellow at Harvard 1999-2005
EXPERIENCE ‘Genetics/Genomics,’ ‘Lab Electronics,’ ‘The Swing Era’
Referee
Science, Trends in Genetics, Genome Research, Genome
Biology, Nucleic Acids Research, Molecular Biology and
Evolution, FEBs Letters, PLoS Computational Biology,
Journal of Molecular Evolution, Human Genetics, Genetica,
Gene, Bioinformatics
Grant Review
National Institutes of Health
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PUBLICATIONS
1. Roy, S. W. & Penny, D. (2007) Patterns of intron loss and gain in plants: intron
loss-dominated evolution and a genome-wide comparison of O. sativa and A.
thaliana. Mol Biol Evol 24, 171-81.
2. Roy, S. W., Ferreira, M. U. & Hartl, D. L. (2007) Evolution of allelic
dimorphism in malarial surface antigens. Heredity [epub online].
3. Roy, S. W. & Penny, D. (2006) Smoke without fire: most reported cases of
intron gain in nematodes instead reflect intron losses. Mol Biol Evol 23, 2592-
62.
4. Roy, S. W. & Penny, D. (2006) Large-scale intron conservation and order-of-
magnitude variation in intron loss/gain rates in apicomplexan evolution.
Genome Res 16, 1270-1275.
5. Roy, S. W., Irimia, M. & Penny, D. (2006) Very little intron gain in Entamoeba
histolytica genes laterally transferred from prokaryotes. Mol Biol Evol 23,
1824-7.
6. Roy, S. W. (2006) Intron rich ancestors. Trends Genet 22, 468-71.
7. Roy, S. W. & Hartl, D. L. (2006) Very little intron loss/gain in Plasmodium:
intron loss/gain mutation rates and intron number. Genome Res 16, 750-6.
8. Roy, S. W. & Gilbert, W. (2006) The evolution of spliceosomal introns:
patterns, puzzles and progress. Nat Rev Genet 7, 211-21.
9. Roy, S. W. & Gilbert, W. (2005) Rates of intron loss and gain: Implications for
early eukaryotic evolution. PNAS 102, 5773-8.
10. Roy, S. W. & Gilbert, W. (2005) Resolution of a deep animal divergence by
the pattern of intron conservation. PNAS 102, 4403-8.
11. Roy, S. W. & Gilbert, W. (2005) Complex early genes. PNAS 102, 1986-91.
12. Roy, S. W. & Gilbert, W. (2005) The pattern of intron loss. PNAS 102, 713-8.
13. Roy, S. W. (2004) The origin of recent introns: transposons? Genome Biol 5,
251.
14. Roy, S. W. (2003) Recent evidence for the exon theory of genes. Genetica
188, 251-66.
15. Roy, S. W., Fedorov, A. & Gilbert, W. (2003) Large-scale comparison of intron
positions in mammalian genes shows intron loss but no gain. PNAS 100, 7158-
62.
16. Fedorov, A., Roy, S., Fedorova, A. & Gilbert, W. (2003) Mystery of intron gain.
Genome Res 13, 2236-41.
17. Fedorov, A., Roy, S., Cao, X. & Gilbert, W. (2003) Phylogenetically older
introns strongly correlate with module boundaries in ancient proteins.
Genome Res 13, 1155-7.
18. Roy, S. W., Fedorov, A. & Gilbert, W. (2002) The signal of ancient introns is
obscured by intron density and homolog number. PNAS 99, 15513-7.
19. Fedorov, A., Cao, X., Saxonov, S., de Souza, S.J., Roy, S. W. & Gilbert, W.
(2001) Intron distribution difference for 276 ancient and 131 modern genes
suggests the existence of ancient introns. PNAS 98, 13177-82.
20. Roy, S. W., Lewis, B. P., Fedorov, A. & Gilbert, W. (2001) Footprints of
primordial introns on the eukaryotic genome. Trends Genet 17, 496-501.
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21. Roy, S. W., Nosaka, M., de Souza, S. J. & Gilbert, W. (1999) Centripetal
modules and ancient introns. Gene 238, 85-91.
22. De Souza, S. J., Long, M., Klein, R. J., Roy, S., Lin, S. & Gilbert, W. (1998)
Toward a resolution of the introns early/late debate: only phase zero introns
are correlated with the structure of ancient proteins. PNAS 95, 5094-9.
23. De Souza, S. J., Long, M., Schoenbach, L., Roy, S. W. & Gilbert, W. (1997) The
correlation between introns and the three-dimensional structure of proteins.
Gene 205, 141-4.
24. De Souza, S. J., Long, M., Schoenbach, L., Roy, S. W. & Gilbert, W. (1996)
Intron positions correlate with module boundaries in ancient proteins. PNAS
93, 14632-6.
In review
25. Amodu, O. K., Hartl, D. L., & Roy, S. W. (2006) Patterns of polymorphism in
genomic regions flanking three highly polymorphic surface antigens in
Plasmodium falciparum. In revision for J Mol Evol.
26. Roy, S. W. & Penny, D. (2006) A very high fraction of unique intron positions
in the intron-rich diatom Thalassiosira pseudonana indicates significant intron
gain. In revision for Mol Biol Evol.
27. Roy, S. W. & Hartl, D. L. (2006) Large differences in rates of intron loss and
gain in the evolutionary history of Drosophila. In revision for Genome Res.
28. Roy, S. W. (2006) Sex and the single origin of the spliceosome. Invited by
Trends Genet.
29. Irimia, M., Penny, D., & Roy, S. W. (2006) Co-evolution of genomic intron
number and 5’ splice sites: implications for the evolution of alternative
splicing. Submitted to Trends Genet.
30. Stajich, J. E., Dietrich, F. S., & Roy, S. W. (2006) Comparative genomic
analysis of fungal genes reveals intron rich ancestors. Submitted to Genome
Biol.
In preparation (selected)
31. Irimia, M., Rukov, J. L., Penny, D., & Roy, S. W. (2006) Functional and
evolutionary analysis of alternatively spliced genes suggests an early
eukaryotic origin of alternative splicing.
32. Roy, S. W., Hartl, D. L., & Ferreira, M. U. Evidence for balancing selection
within allelic families of P. falciparum MSP1: implications for vaccine
development.
33. Roy, S. W., Hartl, D. L., & Ferreira, M. U. A new hypothesis for the origin of
allelic dimorphism in Plasmodium. In preparation for Trends Parasitol.
34. Roy, S. W., Hartl, D. L., & Ferreira, M. U. Patterns of polymorphism in
Plasmodium falciparum MSP6: implications for origins of allelic polymorphism.
In preparation for Mol Biol Evol.
35. Roy, S. W. Pollen limitation, dual-specificity intermediates, and the origin of
new self-incompatibility alleles. In preparation for Plant Cell.
36. Roy, S. W., Hartl, D. L. & Ferreira, M. U. The origin of multiple P. falciparum
infections in areas of low endemicity. In preparation for Trends Parasitol.