Yun Li, PhD

Yun Li Assistant Professor

Research Interests

Key words:  statistical genetics


My research has focused on the development and implementation of hidden Markov models (HMM) to unravel the genetic basis of common diseases. The proposed HMMs can efficiently reconstruct haplotypes, impute missing genotypes, and analyze shotgun sequence data. My methods are flexible enough to accommodate phased haplotype, genotype, or shotgun sequence data. The implemented software, MACH, can efficiently handle millions of genetic markers on thousands of individuals. I am extending the methods to call SNPs and phase them simultaneously from low-depth resequencing data. My research also involves evaluation of the genotype imputation method when applied to a diverse panel of world populations, assessment of post-imputation analyzing strategies, development of a computational efficient aligner that maps short shotgun reads to the reference genome, and application of the aligner to data from the 1000 Genomes Project.


Selected Publications


Chambers JC, Zhang W, Li Y, Sehmi J, Wass MN, et al. (2009) Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels. Nature Genetics. in press.

Li Y, Willer CJ, Sanna S, Abecasis GR (2009) Genotype imputation. Annual Review Genomics and Human Genetics 10: 387-406.

Huang L, Li Y, Singleton AB, Hardy JA, Abecasis GR, Rosenberg NA, Scheet P (2009) Genotype imputation accuracy across worldwide human populations. American Journal of Human Genetics. 84(2): 235-250.

Kathiresan S, Willer CJ, Peloso G, Demissie S, Musunuru K, Schadt E, Kaplan L, Bennett D, Li Y, et al (2009) Common variants at 30 loci contribute to polygenic dyslipidemia. Nature Genetics 41(1): 56-65.

Gaulton KJ, Willer CJ, Li Y, Scott LJ, Conneely KN, et al (2008) Comprehensive association study of type 2 diabetes and related quantitative traits with 222 candidate genes. Diabetes 57(11):3136-3144.

Chambers JC, Elliott P, Zabaneh D, Zhang W, Li Y, Froguel P, Balding D, Scott J, Kooner JS (2008) Common genetic variation near the melanocortin-4 receptor gene is associated with waist circumference and insulin resistance. Nature Genetics 40(6):716-718.

The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449(7164):851-861.

Scott JL, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, et al (2007) A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316(5829):1341-1345.


Lab Members

  • Eric Yi Liu
Graduate Student ::Email
  • Andrea Byrnes
Graduate Student ::Email
  • Elvis Kuan-Chieh Huang
Graduate Student ::Email