• Zeng. J, Nagrajan, H. K., and Yi, S., 2014. Fundamental diversity of human CpG islands at multiple biological levels. Epigenetics, 9. doi: 10.4161/epi.27654. [Early edition]


  • Xiao, J. H., Yue, Z., Jia, L. Y., Yang, X. H., Niu, L. H. et al. (Yi, S., Yang, X.- members). 2013. Obligate mutualism within a host drives the extreme specialization of a fig wasp genome. Genome Biology, 14:R141. [Open Access]

  • Kocher, S. D., Li, C., Yang, W., Tan, H., Yi, S., Yang, X., Hoekstra, H. E., Zhang, G., Pierce, N. E., and Yu, D. W. 2013. The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biology, 14:R142. [Open Access]

  • Hall, D. W., Yi, S., and Goodisman, M. A. D., 2013. Kin selection, genomics and caste-antagonistic pleiotropy. Biology Letters, 9. doi: 10.1098/rsbl.2013.0309. [Open Access]

  • Xu, K., Wang, J., Elango, N, and Yi, S., 2013. The evolution of lineage-specific clusters of single nucleotide substitutions in the human genome. Molecular Phylogenetics & Evolution, 69: 276-285. [Open Access]

  • Huh, I., Zeng, J., Park, T., and Yi, S., 2013. DNA methylation and transcriptional noise. Epigenetics & Chromatin, 6: 9. [Open Access]

  • Hunt, B. G., Glastad, K. M., Yi, S., and Goodisman, M. A. D., 2013. The function of intragenic DNA methylation: Insights from insect epigenomics. Integrative and Comparative Biology, 53: 319-328.

  • Hunt, B. G., Glastad, K. M., Yi, S., and Goodisman, M. A. D., 2013. Patterning and regulatory associations of DNA methylation are mirrored by histone modifications in insects. Genome Biology and Evolution, 5: 591-598. [Open Access]

  • Yi, S. 2013. Morris Goodman's hominoid rate slowdown: The importance of being neutral. Molecular Phylogenetics and Evolution, 66: 569-574. [Open Access]


  • Yi, S. 2012. Birds do it, bees do it, worms and ciliates do it too: DNA methylation from unexpected corners of the tree of life. Genome Biology, 13: 174. [Open Access]

  • Zeng, J., Konopka, G., Hunt, B. G., Preuss, T., Geschwind, D., and Yi, S. 2012. Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. American Journal of Human Genetics, 91: 455-465. [Abstract, PDF],[README for processed data, CpG file, nonCpG file]

  • Jjingo, D., Conley, A. B., Yi, S., Lunyak, V. V., and I. K. Jordan. 2012. On the presence and role of human gene-body DNA methylation. Oncotarget, 3: 462-474. [Open Access Full Text]

  • Jameson, N., Xu, Ke., Yi, S., D. E. Wildman. 2012. Development and annotation of molecular markers from New World monkeys. Molecular Ecology Resources, 12: 950-955. [Abstract, PDF]

  • Sarda, S., Zeng, J., Hunt, B. G., and Yi, S. 2012. The evolution of invertebrate gene body methylation. Molecular Biology and Evolution, 29: 1907-1916. [Abstract, PDF]

  • Xu, K., Oh, S., Park, T., Presgraves, D. C., and Yi, S. 2012. Lineage-specific variation in slow- and fast-X evolution in primates. Evolution, 66: 1751-1761. [Abstract, PDF]

  • Park, J., Xu, K., Park, T., and Yi, S. 2012. What are the determinants of gene expression levels and breadths in the human genome? Human Molecular Genetics, 21: 46-56. [Open Access Full Text]


  • Grbic, M, T Van Leeuwen, RM Clark, et al. (Yi, S., Zeng, J.- members) 2011. The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479: 487-492. [Open Access Full Text]

  • Hunt, B. G., Ometto, L., Wurm, Y., Shoemaker, D., Yi, S., Keller, L., and Goodisman, M. A. D. 2011. Relaxed selection is a precursor to the evolution of phenotypic plasticity. Proc. Natl. Acad. Sci. USA., 108: 15936-15941. [Abstract,PDF]

  • Park, J., Peng, Z., Zeng, J. Elango, N., Park, T., Wheeler, D., Werren, J. H., and Yi, S. 2011. Comparative analyses of DNA methylation and sequence evolution using Nasonia genomes. Molecular Biology and Evolution, 28: 3345-3354. [Abstract, PDF]

  • Glastad, K., Hunt, B. G., Yi, S., and Goodisman, M. A. D., 2011. DNA methylation in insects: on the brink of the epigenomic era. Insect Molecular Biology, 20: 553-565. [Abstract, PDF]

  • Xu, K., Bezakova, I., Bunimocivh, L., and Yi, S. 2011. Path lengths in protein-protein interaction networks and biological complexity. Proteomics, 11: 1857-1867. [Abstract, PDF]

  • Elango, N., and Yi, S. 2011. Functional relevance of CpG island length for regulation of gene expression. Genetics, 187: 1077-1083. [Abstract, PDF]

  • Wurm et al. (Yi, S. - member) 2011. The genome of the fire ant Solenopsis invicta. Proc. Natl. Acad. Sci. USA., 108: 5679-5684. doi: 10.1073/pnas.1009690108. [Abstract, PDF]

  • Loh, Y.-H., Yi, S., and Streelman, J. T. 2011. Evolution of microRNAs and the diversification of species. Genome Biology and Evolution, 3: 55-65. [Open Access Full Text]


  • Zeng, J., and Yi, S. 2010. DNA methylation and genome evolution in honeybee: gene length, expression, functional enrichment co-vary with the evolutionary signature of DNA methylation. Genome Biology and Evolution, doi: 10.1093/gbe/evq060. [Open Access Full Text]

  • Hunt, B. G, Brisson, J. A., Yi, S., and Goodisman, M. A. D. 2010. Functional conservation of DNA methylation in the pea aphid and the honeybee. Genome Biology and Evolution, doi: 10.1093/gbe/evq057. [Open Access Full Text]

  • Hunt, B. G, Wyder, S., Elango, N., Werren, J. H., Zdobnov, E. M., Yi, S., and Goodisman, M. A. D. 2010. Sociality is linked to rates of protein evolution in a highly social insect. Molecular Biology and Evolution, 27: 497-500. [ PDF]

  • Nasonia Genome Working Group (Yi, S. - member) (2010). Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science, 327: 343-348. [Abstract, PDF]


  • Yi, S., and Goodisman, M. A. D. (2009). Computational approaches for understanding the evolution of DNA methylation in animals. Epigenetics, 4: 551-556. [ PDF]

  • Presgraves, D. C., and Yi, S. (2009). Doubts about complex speciation between humans and chimpanzees. Trends in Ecology and Evolution, 24: 533-540. [ PDF]

  • Wildman, D. E., Jameson, N. M., Opazo, J. C. and Yi, S. (2009). A fully resolved genus level phylogeny of neotropical primates (Platyrrhini). Molecular Phylogenetics and Evolution, 53: 694-702.

  • Elango, N., Hunt, B. G., Goodisman, M. A. D., and Yi, S. (2009). DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera . Proc. Natl. Acad. Sci. USA., 106: 11206-11211. [Abstract]

  • Peng, Z., Elango, N., Wildman, D. E., Yi, S. (2009). Primate phylogenomics: developing numerous non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation. BMC Genomics, 10: 247. [Open Access Full Text]

  • Elango, N., Lee, J., Peng, Z., Loh, Y.-H. E., Yi, S. (2009). Evolutionary rate variation in Old World monkeys. Biology Letters, 5: 405-408. [Abstract, PDF]

  • Hazen, T. H., Kennedy, D. K., Chen, S., Yi, S., and P. A. Sobecky (2009). Inactivation of mismatch repair increases diversity of Vibrio parahaemolyticus. Environmental Microbiology, 11:(5) 1254-1266. [Abstract, PDF]


  • Loh, Y.-H. E., Katz, L. S., Mims, M. C., Kocher, T. D., Yi, S., and J. T. Streelman (2008). Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids. Genome Biology, 9: R113. [Open Access Full Text, PDF]

  • Elango, N. and Yi, S. (2008). DNA methylation and structural and functional bimodality of vertebratet promoters. Molecular Biology and Evolution, 25:(8) 1602-1608. [Abstract, PDF]

  • Elango, N., Kim, S-H., NISC Comparative Sequencing Group, Vigoda, E. and Yi, S. (2008). Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLoS Computational Biology 4:(2) e1000015. [Open Access Full Text, PDF]

  • Warden, C. D., Kim, S-H. and Yi, S. (2008). Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins. PLoS One 3:(2) e1559. [Open Access Full Text, PDF]

  • Kim, S-H. and Yi, S. (2008). Mammalian nonsynonymous sites are not overdispersed: Comparative genomic analysis of index of dispersion of mammalian proteins. Molecular Biology and Evolution, 25:(2) 634-642. [Abstract, PDF]


  • Yi, S. (2007). Understanding neutral genomic molecular clocks. Evolutionary Biology, 34: 144-151. [Abstract] [PDF]

  • Kim, S-H. and Yi, S. (2007). Understanding relationship between sequence and functional evolution in yeast proteins. Genetica, 131: 151-156. [Abstract] [PDF, Supplementary Material]

    To use the partial correlation method used in this paper, click this [link]

  • Yi, S. and W-H. Li. (2007). Episodic molecular evolution of some protein hormones in primates and its implications for primate adaptation. In, Ravosa, M. J. and, M. Dagosto. Eds. Developments in Primatology: Progress and Prospects. Kluwer Academic/Plenum Publishers. New York, NY, USA. pp. 739-773.


  • Kim, S.-H.*, Elango, N.*, Warden, C., Vigoda, E., and Yi, S. (2006). Heterogenous genomic molecular clocks in primates. PLoS Genetics, 2: e163. * equal contribution [Full Text, PDF]

  • Yi, S. (2006). Non-adaptive evolution of genome complexity. BioEssays, 28: 979-982. [Abstract] [PDF]

  • Elango, N., J. W. Thomas, NISC Comparative Sequencing Group, and Yi, S. (2006). Variable molecular clocks in hominoids. Proc. Natl. Acad. Sci. USA. 103: 1370-1375. [Abstract] [PDF, Supplementary Material]

  • Kim, S.-H., and Yi, S. (2006). Correlated asymmetry between sequence and functional divergence of duplicate proteins in Saccharomyces cerevisiae. Molecular Biology and Evolution, 23: 1068-1075. [Abstract] [PDF, Supplementary Material]


  • Yi, S. and J. T. Streelman. (2005). Genome size is negatively correlated with effective population size in ray-finned fishes. Trends in Genetics, 21: 643-646. [Abstract] [PDF, Supplementary Material]

  • Yi, S. and W-H. Li. (2005). Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in hominoids. Molecular Biology and Evolution, 22: 1223-1230. [Abstract] [PDF]

  • Bartolome, C., Maside, X. Yi, S., Grant, A. L., and B. Charlesworth. (2005). Patterns of selection on synonymous and non-synonymous variants in Drosophila miranda. Genetics, 169: 1495-1507. [Abstract] [PDF]


  • Yi, S., Summers, T. J., Pearson, N. M., and W-H. Li.  (2004). Recombination has little effect on the rate of sequence divergence in pseudoautosomal boundary 1 among humans and great apes. Genome Research, 14: 37-43. [Abstract] [PDF]

  • Yi, S. (2003). Synonymous and nonsynonymous rates. pp. In, Cooper, D. N. et al. Eds. Encyclopedia of the Human Genome. Nature Publishing Group Reference. New York, NY, USA. [Abstract]

  • Yi, S. and B. Charlesworth.  (2003). Unusual pattern of single nucleotide polymorphisms at the exuperantia2 locus of Drosophila pseudoobscura. Genetical Research. 82: 101-106. [Abstract] [PDF]

  • Yi, S., Bachtrog, D. and B. Charlesworth.  (2003). A survey of chromosomal and nucleotide sequence variation in Drosophila miranda. Genetics. 164: 1369-1381. [Abstract] [PDF]

  • Li, W-H. and Yi, S. (2002). Molecular evolution. pp. 750-756 In, Pagel, M. at al. Eds. Encyclopedia of Evolution. Vol II. Oxford University Press. New York, NY. USA. [Abstract]

  • Yi, S., Ellsworth, D. and W-H. Li.  (2002). Slow molecular clocks in Old World monkeys, apes, and humans. Molecular Biology and Evolution. 19: 2192-2198. [Abstract] [PDF]

  • Li, W-H., Yi, S. and K. D. Makova. (2002). Male-driven evolution. Current Opinions in Genetics and Development. 12: 650-656. [Abstract] [PDF]

  • Yi, S., Bernat, B., Pal, G., Kossiakoff, A. and W-H. Li.  (2002). Functional promiscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormones. Molecular Biology and Evolution. 19: 1083-1092. [Abstract] [PDF]

  • Yi, S. and B. Charlesworth.  (2000). A selective sweep associated with a recent gene transposition in Drosophila miranda. Genetics. 156: 1753-1763. [Abstract] [PDF]

  • Yi, S. and B. Charlesworth.  (2000). Contrasting patterns of molecular evolution of genes on the new and old sex chromosomes of Drosophila miranda. Molecular Biology and Evolution. 17: 703-717. [Abstract] [PDF]