SOOJIN YI

Publications

2014

  • Mendizabal, I., Keller, T. E., Zeng, J. and Yi, S. V. 2014. Epigenetics and Evolution. Integrative and Comparative Biology, in press. doi: 10.1093/icb/icu040. [Abstract]

  • Jameson Kiesling, N. M., Yi, S. V., Xu, K., Sperone, G., and Wildman, D. E. 2014. The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis. Molecular Phylogenetics and Evolution, in press. doi: 10.1016/ympev.2014.03.027. [Abstract]

  • Glastad, K. M., Hunt, B. G., Yi, S. V., and Goodisman, M. A. 2014. Epigenetic inheritance and genome regulation: is DNA methylation linked to ploidy in haplodiploid insects?. Proc. Biol. Sci., in press. doi:10.1098/rspb.2014.0411. [Article]

  • Keller, T. E., and Yi, S. V. 2014. DNA methylation and evolution of duplicate genes. Proc. Natl. Acad. Sci. USA. 111: 5932-5937. doi: 10.1073/pnas.1321420111. [Article]

  • Zeng. J, Nagrajan, H. K., and Yi, S. V. 2014. Fundamental diversity of human CpG islands at multiple biological levels. Epigenetics, 9: 483-491. doi: 10.4161/epi.27654. [Abstract]

    2013

  • Xiao, J. H., Yue, Z., Jia, L. Y., Yang, X. H., Niu, L. H. et al. (Yi, S. V., 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. V., 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. V., 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. V. 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. V. 2013. DNA methylation and transcriptional noise. Epigenetics & Chromatin, 6: 9. [Open Access]

  • Hunt, B. G., Glastad, K. M., Yi, S. V., 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. V., 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. V. 2013. Morris Goodman's hominoid rate slowdown: The importance of being neutral. Molecular Phylogenetics and Evolution, 66: 569-574. [Abstract]

    2012

  • Yi, S. V. 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. V. 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. V., 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. V., 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. V. 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. V. 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. V. 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]

    2011

  • Grbic, M, T Van Leeuwen, RM Clark, et al. (Yi, S. V., 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. V., 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. V. 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. V., 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. V. 2011. Path lengths in protein-protein interaction networks and biological complexity. Proteomics, 11: 1857-1867. [Abstract, PDF]

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

  • Wurm et al. (Yi, S. V. - 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. V., and Streelman, J. T. 2011. Evolution of microRNAs and the diversification of species. Genome Biology and Evolution, 3: 55-65. [Open Access Full Text]

    2010

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

    2009

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

    2008

  • Loh, Y.-H. E., Katz, L. S., Mims, M. C., Kocher, T. D., Yi, S. V., 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. V. (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. V. (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. V. (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. V. (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]

    2007

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

  • Kim, S-H. and Yi, S. V. (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.

    2006

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

  • Yi, S. V. (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. V. (2006). Variable molecular clocks in hominoids. Proc. Natl. Acad. Sci. USA. 103: 1370-1375. [Abstract] [PDF, Supplementary Material]

  • Kim, S.-H., and Yi, S. V. (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]

    2005

  • 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]

    2000-2004

  • 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]