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Scott W.

Allan Wilson Centre for Ph: +64 6 350 5515 x7626
Molecular Ecology and Evolution Fax: +64 6 350 5626
Massey University
Palmerston North, NZ

EDUCATION Ph.D. in Molecular Biology, Harvard University 2005

Advisor: Walter Gilbert
Dissertation: Evolutionary inferences from the pattern of
intron conservation
• Coursework in Coalescent Theory, Theoretical
Population Genetics, Computational Biology, Evolution
and Development, and Gene Regulation

B.A. in Biochemical Sciences, Harvard University 1999

• Coursework in Population Genetics, Molecular and
Cellular Biology, Physics, and Applied Mathematics.

RESEARCH NCBI, Postdoctoral Researcher 2007 (anticipated)

Supervisor: Eugene Koonin

Allan Wilson Centre, Postdoctoral Researcher 2006

Supervisor: David Penny
Evolution of spliceosomal introns and alternative splicing.
• Compared genomes of recently diverged species
drawn from various eukaryotic lineages, revealing low
rates of intron gain, ongoing reduction in intron
number, and substantial rate variations.
• Performed analyses of inter- and intragenomic patterns
of intron sequence and alternative splicing, suggesting
an early eukaryotic origin of alternative splicing.
• Developed a hypothesis for the origin of the
spliceosome and spliceosomal introns.

Harvard University, Postdoctoral Researcher 2005

Supervisor: Dan Hartl
Balancing selection and evolution of Plasmodium falciparum.
• Studied blood-stage malaria surface antigens under
balancing selection among two distinct allelic classes.
o Provided evidence for balancing selection
within MSP1 allelic classes, suggesting new
vaccine strategies.

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.

Harvard University, Graduate Student 1999-2004

Advisor: Walter Gilbert
Evolutionary inferences from the pattern of spliceosomal
intron conservation
• Devised methods for reconstructing spliceosomal
intron loss and gain from patterns of intron position
conservation across widely diverged eukaryotes.
• Provided evidence for a role for mRNAs in intron loss
but not intron gain in various eukaryotic lineages.
• Devised a novel phylogenetic method employing
intron positions as characters.
• Demonstrated a dearth of intron loss and gain in a
genome-wide comparison of mouse and human genes.
• Studied the implications of patterns in intron positions
to the introns-early/introns-late debate.

University College of London, Research Assistant 1999

Adviser: Janet Thornton
• Wrote programs in C to incorporate gene structure
information into protein structure databases.

Harvard University, Undergraduate Assistant 1996-1999

Advisor: Walter Gilbert
• Wrote programs in C and Perl to investigate the
relationship between gene and protein structures to
test predictions of the introns-early hypothesis.

ADDITIONAL Teaching fellow at Harvard 1999-2005
EXPERIENCE ‘Genetics/Genomics,’ ‘Lab Electronics,’ ‘The Swing Era’

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

DISTINCTIONS Society of Mol Biol and Evol meeting 2005

Award for best poster by a postdoctoral researcher

Walter Fitch Symposium, SMBE meeting 2004

Selected for symposium for promising young investigators

Harvard College Scholarship 1994-1999

Recognizes academic achievement


Talk for symposium: Introns early, introns late: the sequel

American Genetics Association Meeting 2007

Untangling the mysteries of transcript splicing in eukaryotes

Partner Institute for Comp. Biology, Shanghai 2006

Evolution of spliceosomal introns and alternative splicing

Beijing Normal University, Beijing 2006

Evolution of alternative splicing in eukaryotes

LUCA: ten years after, Les Treilles, France 2006

Introns early/late/earlyish and Gildoodarblagoism: ideas,
data, history, surprises, ironies

SMBE Meeting 2005

How, when, and why of spliceosomal introns: some answers
and some guesses

University of Chicago, 2005

Evidence for complex early eukaryotic gene structures

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-
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,
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,
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-
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.

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

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
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.