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1. Feldman, M. W. and S. P. Otto (1989) More on recombination and selection in the modifier theory of sex-ratio distortion. Theoretical Population Biology 35: 207-225.
2. Otto, S. P. and V. Walbot (1990) DNA methylation in eukaryotes: Kinetics of demethylation and de novo methylation during the life cycle. Genetics 124: 429-437.
3. Liberman, U., M. W. Feldman, I. Eshel, and S. P. Otto (1990) Two-locus autosomal sex determination: On the evolutionary genetic stability of the even sex ratio. Proceedings of the National Academy of Sciences (USA) 87: 2013-2017.
4. Feldman, M. W. and S. P. Otto (1991) A comparative approach to the population-genetics theory of segregation distortion. American Naturalist 137: 443-456.
5. Feldman, M. W., F. B. Christiansen, and S. P. Otto (1991) Lewontin and Kojima meet Fisher: Linkage in a symmetric model of sex determination. Genetics 129: 297-312.
6. Otto, S. P. (1991) On evolution under sexual and viability selection: A two-locus diploid model. Evolution, 45: 1443-1457.
7. Wiener, P., M. W. Feldman, and S. P. Otto (1992) On genetic segregation and the evolution of sex. Evolution, 46: 775-782.
8. Otto, S. P. and D. B. Goldstein (1992) Recombination and the evolution of diploidy. Genetics, 131: 745-751.
9. Otto, S. P., C. Sassaman, and M. W. Feldman (1993) Sex-ratio evolution in Eulimnadia texana. American Naturalist, 141: 329-337.
10. Otto, S. P., M. W. Feldman, and F B Christiansen (1994) Some advantages and disadvantages of recombination. In Lecture Notes in Biomathematics, ed S A Levin, pp 198-211. Springer-Verlag, New York.
11. Otto, S. P. (1994) The role of deleterious and beneficial mutations in the evolution of ploidy levels. Lectures on Mathematics in the Life Sciences, ed. M. Kirkpatrick, 25: 69-96.
12. Orr, H. A. and S. P. Otto (1994) Does diploidy increase the rate of adaptation? Genetics, 136: 1475-1480.
13. Cummings, M., S. P. Otto, and J. Wakeley (1995) The sampling properties of DNA sequence data in phylogenetic analysis. Molecular Biology and Evolution, 12: 814-822.
14. Bergman, A., S. P. Otto, and M. W. Feldman (1995) On the evolution of recombination in haploids and diploids. I. Deterministic models. Complexity, 1: 49-56.
15. Bergman, A., S. P. Otto, and M. W. Feldman (1995) On the evolution of recombination in haploids and diploids. II. Stochastic models. Complexity, 1: 57-67.
16. Otto, S. P. and M. E. Orive (1995) Evolutionary consequences of mutation and selection within an individual. Genetics, 141: 1173-1187.
17. Feldman, M. W., S. P. Otto, and F. B. Christiansen (1995) Statistics of discrete-valued traits under vertical transmission. Morrison Institute for Population and Resource Studies, Working Paper Series #0064.
18. Otto, S. P., F. B. Christiansen, and M. W. Feldman (1995) Genetic and cultural inheritance of continuous traits. Morrison Institute for Population and Resource Studies, Working Paper Series #0065.
19. Otto, S. P., Cummings, M., and J. Wakeley (1996) Inferring phylogenies from DNA sequence data: The effects of sampling. In New Uses for New Phylogenies, ed. P Harvey, pp. 103-115. Oxford University Press, Oxford.
20. Otto, S. P. and J. Marks (1996) Mating systems and the evolutionary transition between haploidy and diploidy. Biological Journal of the Linnean Society, 57: 197-218.
21. Otto, S. P. and N. Barton (1997) The evolution of recombination: Removing the limits to natural selection. Genetics, 147: 879-906.
22. Feldman, M. W. and S. P. Otto (1997) Heritability from twins and other relatives. Science, 278: 1383-1384 (Correspondence).
23. Otto, S. P. and M. C. Whitlock (1997) The probability of fixation in populations of changing size. Genetics, 146: 723-733.
24. Otto, S. P. and M. W. Feldman (1997) Deleterious mutations, variable epistatic interactions, and the evolution of recombination. Theoretical Population Biology, 51: 134-147.
25. Otto, S. P. (1997) News and Views: Unraveling gene interactions. Nature 390: 343.
26. Feldman, M. W., S. P. Otto, and F. B. Christiansen (1997) Population genetic perspectives on the evolution of recombination. Annual Review of Genetics, 30: 261-295.
27. Otto, S. P. and I. Hastings (1998) Mutation and selection within the individual. In Mutation and Evolution, eds. R C Woodruff and J N Thompson, pp. 507-524. Kluwer Academic Publishers, Netherlands. (Reprint of Otto and Hastings, 1998, Genetica, 102/103: 507-524.)
28. Otto, S. P. and I. Hastings (1998) Mutation and selection within the individual. Genetica, 102/103: 507-524.
29. Mable, B. and S. P. Otto (1998) The evolution of life cycles with haploid and diploid phases. BioEssays, 20: 453-462.
30. Christiansen, F. B., S. P. Otto, M. W. Feldman, and A. Bergman (1998) Waiting with and without recombination: The time to production of a double mutant. Theoretical Population Biology, 53: 199-215.
31. Otto, S. P. and Y. Michalakis (1998) The evolution of recombination in changing environments. Trends in Ecology and Evolution, 13: 145-151.
32. Hughes, J. S. and S. P. Otto (1999) Ecology and the evolution of biphasic life cycles. American Naturalist, 154: 306-320.
33. Otto, S. P. and D. Bourguet (1999) Balanced polymorphisms and the evolution of dominance. American Naturalist, 153: 561-574.
34. Whitlock, M. and S. P. Otto (1999) The panda and the phage: compensatory mutations and the persistence of small populations. Trends in Ecology and Evolution, 14: 293-294.
35. Cummings, M., S. P. Otto, and J. Wakeley (1999) Genes and other samples of DNA sequence data for phylogenetic inference. Biological Bulletin, 196: 345-350.
36. Otto, S. P. and J. Whitton (2000) Polyploid incidence and evolution. Annual Review of Genetics, 34: 401-437.(Web Table)
37. Otto, S. P. (2000) Detecting the form of selection from DNA sequence data. Trends in Genetics, 16: 526-529.
38. Otto, S. P. and C. D. Jones (2000) Detecting the undetected: Estimating the total number of loci underlying a trait in QTL analyses. Genetics, 156: 2093-2107.
39. Poon, A. and S. P. Otto (2000) Compensating for our load of mutations: Freezing the mutational meltdown. Evolution, 54: 1467-1479.
40. Lenormand, T. and S. P. Otto (2000) The evolution of recombination in a heterogeneous environment. Genetics. 156: 423-438.
41. Feldman, M. W., S. P. Otto, and F. B. Christiansen (2000) Genes, culture, and inequality. In Meritocracy and Inequality, eds. K Arrow, S Bowles, and S Durlauf, pp. 61-85. Princeton University Press, New Jersey.
42. Phillips, P. C., S. P. Otto, and M. C. Whitlock (2000) Beyond the average: The evolutionary importance of epistasis and the variability of epistatic effects. In Epistasis and the Evolutionary Process, eds. J Wolf, E D Brodie III, and M J Wade, pp. 20-38. Oxford University Press, Oxford.
43. Otto, S. P. and N. Barton (2001) Selection for recombination in small populations. Evolution, 55: 1921-1931.
44. Otto, S. P. (2001) Eliminating the cost of sex with sexual selection. TREE (Journal Club entry), 16: 602.
45. Otto, S. P. and P. Jarne (2001) Haploids: Happening or hapless. Science (Perspective), 292: 2441-2443.
46. Heilbuth, J. C., K. L. Ilves, and S. P. Otto (2001) The consequences of dioecy for seed dispersal: Modeling the "seed-shadow" handicap. Evolution, 55: 880-888.
47. Day, T. and S. P. Otto (2001) Fitness. Encyclopaedia of Life Science. Nature Publishing Group, http://www.els.net.
48. Otto, S. P. (2001) Genetics of Intelligence. In International Encyclopedia of the Social and Behavioral Sciences, eds. N. J. Smelser and P. B. Baltes, pp. 7651-7658. Elsevier Science Ltd. Pergamon, Oxford.
49. Mable, B. and S. P. Otto (2001) Masking and purging mutations following EMS treatment in haploid, diploid, and tetraploid yeast (Saccharomyces cerevisiae). Genetical Research, 77: 9-26.
50. Vamosi, J. C. and S. P. Otto (2002) When looks can kill: The evolution of sexually-dimorphic floral display and the extinction of dioecious plants. Proc. Roy. Soc., London B. 269: 1187-1194.
51. Brinkman, F. S. L., J. L. Blanchard, A. Cherkasov, H. Greberg, Y. Av-Gay, R. C. Brunham, R. C. Fernandez, B. B. Finlay, S. P. Otto, B. F. F. Ouellette, P. J. Keeling, A. M. Rose, R. E. W. Hancock and S. J. M. Jones (2002). Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria and the chloroplast. Genome Research. 12:1159-1167.
52. Otto, S. P. and T. Lenormand (2002) Resolving the paradox of sex and recombination. Nature Reviews Genetics, 3: 252-261.
53. Otto, S. P. and P. Yong (2002) The evolution of gene duplicates. Advances in Genetics 46: 451-483 (Homology Effects, eds. J. Dunlap and C.-ting Wu, Academic Press, San Diego CA).
54. Clark, A. G. and S. P. Otto (2002) Population genetics and molecular evolution of whole genomes (Editorial overview). Current Opinion in Genetics and Development, 12: 631-633.
55. Otto, S. P. and M. Whitlock, M. (in press) Fixation probabilities and times. Encyclopedia of the Human Genome. Nature Publishing Group.
56. Otto, S. P. (2003) The advantages of segregation and the evolution of sex. Genetics, 164: 1099-1118.
57. Dolgin, E. and Otto, S. P. (2003) Segregation and the evolution of sex under overdominant selection. Genetics, 164: 1119-1128.
58. Peters, A. D. and S. P. Otto (2003) Liberating genetic variance through sex. BioEssays, 25: 533-537.
59. Otto, S. P. (2003) In polyploids, one plus one does not equal two. TREE, 18: 431-433.
60. Haywood-Farmer, E. and Otto, S. P. (2003) The evolution of genomic base composition in bacteria. Evolution, 57: 1783-1792.
61. Vamosi, J. C., S. P. Otto, and S. C. H. Barrett (2003) Phylogenetic analysis of the ecological correlates of dioecy. Journal of Evolutionary Biology, 16: 1006-1018.
62. Otto, S. P. (2004) Two steps forward, one step back: The pleiotropic effects of favoured alleles. Proc. Roy. Soc., London B., 271: 705-714.