Soojin Yi, Associate Professor
Ph.D., Ecology and Evolution, University of Chicago
Office: Parker H. Petit Biotechnology (IBB) 3302
Comparative Genomics, Molecular Evolution, Bioinformatics, Population Genetics
My work focuses on understanding the genetic basis of naturally occurring variation within and between species. What causes differences between individuals in phenotypic traits (such as hair color, smell, disease susceptibility and so on), and how do these variations within a species relate to the evolution of different species? The evolution of human specific traits is an especially exciting example of such topics. We use multidisciplinary approaches, ranging from computational methods to advanced biochemical analyses. I have ideas for several exciting and specific projects, with various amount of projected duration time to fit different needs of investigators.
Comparative Genomics and Bioinformatics
Some current computational projects in my laboratory are to understand rates and patterns of molecular evolution in the whole genome level and to understand the determinants of spatial distributions of genes and other elements in the mammalian genomes. To answer these questions, we analyze many levels of data, such as nucleotide sequence divergence between species, expression variation within and between species, and other functional data.
Another topic in my laboratory is to understand evolution of non-coding regions of primate genomes. Non-coding (not encoding amino acid sequences) parts of genome have been regarded as largely non-functional, until recently. This is true for most of the non-coding genomic regions, in which mutations do not have any effect on its holders' fitness, in other words, 'neutral'. However, recent comparative analyses of complete genomes suggest otherwise. We are interested in contrasting different evolutionary rates and patterns between 'neutral' and 'functional' non-coding regions of primate genomes. This project involves both experimental and computational work.
Functional Evolutionary Genomics
I am also interested in understanding the functional significance of molecular changes occurring on an evolutionary timescale during primate evolution. Computational analyses of evolutionary rates and patterns often suggest that some molecular changes have been targets of natural selection. I am interested in rigorously testing such hypotheses, using experimental methods. For example, I examined co-evolution of growth hormones and its receptors from human, monkey and rat using bia-core interaction assay. I plan to develop functional assays for other proteins and non-coding functional nucleotides and test their roles in primate evolution.
Molecular Population Genetics
The pattern of molecular variation within a population is determined by the interplay between general forces operating on the whole population (such as effective population size, demographic history, mating pattern) and specific forces (such as natural selection) operating on each genomic region. Using molecular data and statistical inference, we can undercover and distinguish the effects of different factors. I have kept my interest in population genetics since my PhD and will be happy to advise students who are interested in population genetics of any species.
Nasonia Genome Working Group (Yi, S. - member) (2010). Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science, 327: 343-348.
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]
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]
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., 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]
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.
Presgraves, D. C., and Yi, S. (2009). Doubts about complex speciation between humans and chimpanzees. Trends in Ecology and Evolution, 24: 533-540.
Yi, S., and Goodisman, M. A. D. (2009). Computational approaches for understanding the evolution of DNA methylation in animals. Epigenetics, 4: 551-556.
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]