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Soojin's full publications list.
Publications
Comparative genomics & epigenomics lab publications.
Preprints
Morgan, R., Loh, E., Singh, D., Mendizabal, I., & Yi, S. V. (2024). DNA methylation differences between the female and male X chromosomes in the human brain. bioRxiv. [2024.04.16.589778] [Full Text]
Yoo, D., Rhie, A., ..., Loh, Y-H. E., ..., Son, D. R., ..., Yi, S. V., ..., Phillippy, A. M., Eichler, E. E. (2024). Complete sequencing of ape genomes. bioRxiv, [2024.07.31.605654] [Full Text]
Jeong, H., Mendizabal, I., Yi, S. V. (2024). Human Brain Aging is Associated with Dysregulation of Cell-Type Epigenetic Identity. Preprint. bioRxiv. 2024;2024.06.01.596981. [Full Text]
2024
Joshy, D., Santpere, G., & Yi, S. V. (2024). Accelerated cell-type-specific regulatory evolution of the human brain. PNAS, 121(52), e2411918121. [Full Text].
Son, D.R., Kong, Y., Tan, Y., Hu, T., Shi, L., Yi, S. V. (2024) Whole-genome DNA methylomes of tree shrew brains reveal conserved and divergent roles of DNA methylation on sex chromosome regulation. BMC Biology. 2024;22(1):277. [Full Text]
Yi, S. V., Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms, Molecular Biology and Evolution, Volume 41, Issue 9, September 2024, msae170, [Full Text]
Makova, K. D., Pickett, B. D., Harris, R. S., Hartley, G. A., Cechova, M., Pal, K., Nurk, S., Yoo, D., Li, Q., Hebbar, P., McGrath, B. C., Antonacci, F., Aubel, M., Biddanda, A., Borchers, M., Bornberg-Bauer, E., Bouffard, G. G., Brooks, S. Y., Carbone, L., Carrel, L., ... Hillis, D. A., ... Loh, Y-H. E., ... Yi, S. V., ... Phillippy, A. M. (2024). The complete sequence and comparative analysis of ape sex chromosomes. Nature. [Full Text]
Bogan, S. N., & Yi, S. V. (2024). Potential role of DNA methylation as a driver of plastic responses to the environment across cells, organisms, and populations. Genome Biology and Evolution, 16(2), Article evae022. [Full Text]
de la Fuente, M., Mendizabal, I., Han, M., Yi, S. V., & Alvarez-Ponce, D. (2024). Asymmetrical evolution of promoter methylation of mammalian genes after duplication. Molecular Biology and Evolution, msae259. [Full Text]
2023
Caglayan, E., Ayhan, F., Liu, Y., Vollmer, R. M., Oh, E., Sherwood, C. C., Preuss, T. M., Yi, S. V., & Konopka, G. (2023). Molecular features driving cellular complexity of human brain evolution. Nature, 620, 1-9. [Full Text]
2022
Lin, S., Yi. S. V. and Qiu, P. 2022. Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing. BMC Genomics. [Full Text]
Zhao, Q., Shao, F., Li, Y., Yi. S. V. and Peng, Z. 2022. Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes. Molecular Ecology. 31: 5831-5845. [Full Text]
Jeong, H.*, Baran, N.*, Sun, D., Chatterjee, P., Layman, T., Balakrishnan, C. N., Maney, D., and Yi. S. V. 2022. Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows. ELife 79387. [Full Text] *co-first authors
Wu, X., Bhatia, N., Grozinger, C. M., and Yi. S. V. 2022. Comparative studies of genomic and epigenetic factors influencing transcriptional variation in two insect species. G3. [Full Text]
Arsala, D., Wu, X., Yi. S. V. and Lynch, J. A. 2022. Dnmt1a is essential for gene body methylation and the regulation of the zygotic genome in a wasp. PLOS Genetics. [Full Text]
2021
Singh, D., and Yi. S. V. 2021. Enhancer pleiotropy, gene expression, and the architecture of human enhancer-gene interactions. Molecular Biology and Evolution. [Full Text]
Singh, D., and Yi. S. V. 2021. On the origin and evolution of SARS-CoV-2. Experimental & Molecular Medicine. 53: 537-547. [Full Text]
Jeong, H.*, Mendizabal, I.*, Berto, S., Chatterjee, P., Layman, T., Usui, N., Toriumi, K., Douglas, C., Singh, D., Huh, I., Preuss, T. M., Konopka, G., and Yi. S. V. 2021. Evolution of DNA methylation in the human brain. Nature Communications 12: 2021. [Full Text] *co-first authors
Singh, D., Sun, D., King, A., Alquezar-Planas, D., Johnson, R., Alvarez-Ponce, D. and Yi. S. V. 2021. Koala methylomes reveal divergent and conserved DNA methylation signatures on X chromosome regulation. Proceedings of the Royal Society B. [Full Text]
Sun, D., Layman, T., Jeong, H., Chatterjee, P., Grogan, K., Merritt, J. Maney, D. L. and Yi. S. V. 2021. Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows. Molecular Ecology. [Full Text]
Yi. S. V. and Goodisman, M. A. D. 2021. The impact of epigenetic information on genome evolution. Philosophical Transactions of the Royal Society B. [Full Text]
2020
Wu, X., Galbraith, D., Chatterjee, P., Jeong, H., Grozinger, C. M., and Yi. S. V. 2020. Lineage and parent-of-origin effects in DNA methylation of honey bees (Apis mellifera) revealed by reciprocal crosses and whole-genome bisulfite sequencing. Genome Biology and Evolution. 12: 1482-1492. [Full Text]
Kyger, R., Luzuriaga-Neira, A., Layman T., Orli Milkewitz Sandberg T., Singh, D., Huchon, D., Peri S., Atkinson S. D., Bartholomew, J. L., Yi. S. V*. and Alvarez-Ponce D.* 2020. Myxosporea (Myxozoa, Cnidaria) lack DNA methylation. * co-corresponding authors. Molecular Biology and Evolution. 38: 393-404. [Full Text]
Merritt, J. R., Grogan, K. E., Zinzow-Kramer, W. M., Sun, D., Ortlund, E. A., Yi. S. V., Maney, D. L. 2020. A supergene-linked estrogen receptor drives alternative phenotype in a polymorphic songbird. Proc. Natl. Acad. Sci. USA. 117: 21673-21680. [Full Text]
Yi, S. V. 2020. Molecular Evolution: A Brief Introduction. In, Ho, S. Eds. The Molecular Evolutionary Clock. Springer.
Wu, X.*, Lindsey, A.*, Chatterjee, P., Werren, J. H., Stouthammer, R., and Yi. S. V. 2020. Distinct epigenomic and transcriptomic reprogramming associated with Wolbachia-mediated asexuality. *co-first authors, PLoS Pathogens. 16 (3): e1008397. [Full Text]
2019
S. Berto*, I. Mendizabal*,N. Usui*, K. Toriumi*, P. Chatterjee, C. Douglas, C. Tamminga, T. M. Preuss, Yi. S. V.# G. Konopka#, 2019. Accelerated evolution of oligodendrocytes in human brain. *co-first authors, # co-corresponding authors, https://doi.org/10.1101/601062. Proc. Natl. Acad. Sci. USA, 116: 24334-24342. [Article]
Sun, D., Maney, D. L., Layman, T. S., Chatterjee, P., and Yi, S. V. 2019. Regional epigenetic differentiation of the Z chromosome between sexes in a female heterogametic system. Genome Research, 29: 1673-1684. [Full Text]
Mendizabal, I*., Berto, S.*, Usui, N*., Toriumi, K*., Chatterjee, P., Douglas, C., Huh, I., Jeong, H., Layman, T., Tamminga, C., Preuss, T. M., Konopka, G.#, and Yi, S. V#. 2019. Cell type-specific epigenetic links to schizophrenia risk in the brain. Genome Biology, 20: 135. [Full Text] * co-first authors, # co-corresponding authors
Spainhour, J. C. C., Lim, H. S., Yi, S. V., and Qiu, P. Correlation patterns between DNA methylation and gene expression in the Cancer Genome Atlas. Cancer Informatics, 18, 1176935119828776. [Full Text]
2018
Lindsey, A. R. I., Kelkar, Y. D., Wu, X., Sun, D., Martinson, E. O., Yan, Z., Rugman-Jones, P. F., Hughes, D. S. T., Murali, S. C., Qu, J., Dugan, S., Lee, S. L., Chao, H., Dinh, H., Han, Y., Doddapaneni, H. V., Worley, K. C., Muzny, D. M., Ye, G., Gibbs, R. A., Richards, S., Yi, S. V., Stouthammer, R., and Werren, J. H. 2018. Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum. BMC Biology, 16: 54. [Full Text]
Huh, I., Mendizabal, I., Park, T., and Yi, S. V. 2018. Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals. PLoS Computational Biology, 14: e1006451. [Full Text]
Jeong, H.*, Wu, X.*, Smith, B., and Yi, S. V. 2018. Genomic landscape of methylation islands in Hymenopteran insects. Genome Biology and Evolution, 10: 2766-2776. [Full Text] * co-first authors
Rishishwar, L., Wang, L., Wang, J., Yi, S. V., Lachance, J., and Jordan, I. K. 2018. Evidence for positive selection on recent human transposable element insertions. Gene, 675: 69-79. [Abstract]
Lee, J. S., Chatterjee, P., Choi, E. Y., Sung, M. K., Oh, J., Won, H., Park, S. M., Kim, Y., J., Yi, S. V., and Choi, J. K. 2018. Selection o the regulation of sympathetic nervous activity in humans and chimpanzees. PLoS Genetics, 14 (4): e1007311. [Full Text]
Feng, B., Yi, S. V., Zhang, M., and Zhou, X. 2018. Development of novel EST-SSR markers for ploidy identification based on de novo transcriptome assembly for Misgurnus anguillicaudatus. PLoS One, 13 (4): e0195829. [Full Text]
Sun, D., Huh, I., Zinzow-Kramer, W. M., Money, D. L., and Yi, S. V. 2018. Rapid regulatory evolution of a non recombining autosome linked to divergent behavioral phenotypes. Proceedings of the National Academy of Sciences USA. 115: 2794-2799. [Full Text]
2017
Yi, S. V. 2017. Insights into Epigenome Evolution from Animal and Plant Genomes. Genome Biology and Evolution, 9: 3189-3201. [Full Text]
Huh, I., Wu, X., Park, T., and Yi, S. V. 2017. Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species. Briefings in Bioinformatics, 20: 33-46. [Full Text]
Mendizabal, I., and Yi, S. V. 2017. Diversity of Human CpG islands. Handbook of Nutrition, Diet and Epigenetics, 265-280. [Link]
Feng, B., Yi, S. V., Li, R., and Zhou, X. 2017. Comparison of age and growth performance of diploid and tetraploid loach Misgurnus anguillicaudatus in the Yangtze River basin, China. Environmental Biology of Fishes, 100: 815-828. doi: 10.1007/s10641-017-0608-z. [Abstract]
Mendizabal, I., Zeng, J., Keller, T. E. and Yi, S. V. 2017. Body-hypomethylated human genes harbor extensive intragenic transcriptional activity and are prone to cancer-associated dysregulation. Nucleic Acids Research, 45: 4390-4400. [Full Text]
2016
Mendizabal, I.*, Shi, L.*, Keller, T. E., Konopka, G., Preuss, T. M., Hsieh, T.-F., Hu, E., Zhang, Z., Su, B. and Yi, S. V. 2016. Comparative methylome analyses identify epigenetic regulatory loci of human brain evolution. Molecular Biology and Evolution, 33: 2947-2959. [Full Text] *co-first authors
Yin, H., Wang, G., Ma, L., Yi, S. V., and Zhang, Z. 2016. What signatures dominantly associate with gene age? Genome Biology and Evolution, 8: 3083-3089. [Full Text]
Keller, T. E., Lasky, J. R. and Yi, S. V. 2016. The multivariate association between genome-wide DNA methylation and climate across the range of Arabidopsis thaliana. Molecular Ecology, 25: 1823-1837. [Full Text]
Keller, T. E., Han, P. and Yi, S. V. 2016. Evolutionary transition of promoter and gene body DNA methylation across invertebrate-vertebrate boundary. Molecular Biology and Evolution, 33: 1019-1028. [Full Text]
Glastad, K. M., Goodisman, M. A. D., Yi, S. V. and Hunt, B. G. 2016. Effects of DNA methylation and chromatin state on rates of molecular evolution in insects. G3, 6: 357-363. [Article]
Mendizabal, I., and Yi, S. V. 2016. Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation. Human Molecular Genetics, 25: 69-82. [Full Text]
2015
Zinzow-Kramer, W. M., Horton, B. M., McKee, C. D., Michaud, J. M., Tharp, G. K., Thomas, J. W., Tuttle, E. M., Yi, S. V., Maney, D. 2015. Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows. Genes, Brain and Behavior, 14: 641-654. doi: 10.1111/gbb.12252. [Full Text]
Sun, D., and Yi, S. V. 2015. Impacts of chromatin states and long-range genomic segments on aging and DNA methylation. PLoS One, 10: e0128517. [Full Text]
Galbraith, D. A.*, Yang, X.*, Niño, E. L., Yi, S. V., and Grozinger, C. M. 2015. Dual genomic response pathways to systemic viral infection in honey bees (Apis mellifera). PLoS Pathogens, 11: e1004713. [Full Text] *co-first authors
Jameson Kiesling, N. M., Yi, S. V., Xu, K., Sperone, G., and Wildman, D. E. 2015. The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis. Molecular Phylogenetics and Evolution, 82 (Pt. B): 386-399. doi: 10.1016/ympev.2014.03.027. [Article]
2014
Zeng. J., and Yi, S. V. 2014. Specific modifications of histone tails, but not DNA methylation, mirror the temporal variation of mammalian recombination hotspots. Genome Biology and Evolution, 6: 2918-2929. doi: 10.1093/gbe/evu230. [Full Text]
Akhshabi, S., Sarda, S., Dovrolis, C. and Yi, S. V. 2014. An explanatory evo-devo model for the developmental hourglass. F1000 Research, 3: 156. doi: 10.12688/f1000research.4583.1. [Full Text]
Huh, I., Zeng, J., Park, T. and Yi, S. V. 2014. Bis-class: a new classification tool of methylation status using Bayes classifier and local methylation information. BMC Genomics, 15: 608. [Full Text]
Mendizabal, I., Keller, T. E., Zeng, J. and Yi, S. V. 2014. Epigenetics and Evolution. Integrative and Comparative Biology, 54: 31-42. doi: 10.1093/icb/icu040. [Full Text]
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., 281: 1785. 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. [Full Text]
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. [Full Text]
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. [Full Text]
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. [Full Text]
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. [Article]
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. [Article]
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. [Article]
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. [Article]
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. [Article]
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. [Full Text]
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. [Article]
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. [Article]
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. [Article]
Elango, N., and Yi, S. V. 2011. Functional relevance of CpG island length for regulation of gene expression. Genetics, 187: 1077-1083. [Abstract]
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]
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.
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.
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.
Presgraves, D. C., and Yi, S. V. (2009). Doubts about complex speciation between humans and chimpanzees. Trends in Ecology and Evolution, 24: 533-540.
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. [Article] *co-first authors
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. [Article]
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.
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.
Elango, N. and Yi, S. V. (2008). DNA methylation and structural and functional bimodality of vertebrate promoters. Molecular Biology and Evolution, 25:(8) 1602-1608. [Article]
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] *co-first authors
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]
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. [Article]
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. [Article]
The partial correlation method described in this paper has been further developed and available at 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]
Yi, S. V. (2006). Non-adaptive evolution of genome complexity. BioEssays, 28: 979-982. [Article]
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]
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. [Article]
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.
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]
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]
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.
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.
Yi, S. and B. Charlesworth. (2003). Unusual pattern of single nucleotide polymorphisms at the exuperantia2 locus of Drosophila pseudoobscura. Genetical Research. 82: 101-106.
Yi, S., Bachtrog, D. and B. Charlesworth. (2003). A survey of chromosomal and nucleotide sequence variation in Drosophila miranda. Genetics. 164: 1369-1381.
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.
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.
Li, W-H., Yi, S. and K. D. Makova. (2002). Male-driven evolution. Current Opinions in Genetics and Development. 12: 650-656.
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.
Yi, S. and B. Charlesworth. (2000). A selective sweep associated with a recent gene transposition in Drosophila miranda. Genetics. 156: 1753-1763.
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.
