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Publications of the Li Group

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Lab Member;    *: First or co-first Author;    #: Corresponding or co-corresponding author


  1. Huang KC, Sun W, Wu Y, Chen M, Mohlke KL, Lange LA, Li Y. Association studies with imputed variants using expectation-maximization likelihood-ratio tests. PLoS One9(11):e110679. [abstract] [PDF]
  2. Li J, Lange LA, Duan Q, Lu Y, Singleton AB, Zonderman AB, Evans MK, Li Y, Taylor HA, Willis MS, Nalls M, Wilson JG, Lange EM. Genome-wide admixture and association study of serum iron, ferritin, transferrin saturation and total iron binding capacity in African Americans. Human Molecular Genetics [Epub ahead of print] [abstract] [PDF]
  3. Ma Y, Zhao J, Wong JS, Ma L, Li W, Fu G, Xu W, Zhang K, Kittles RA, Li Y, Song Q. Accurate inference of local phased ancestry of modern admixed populations. Sci Rep. 4:5800. [abstract] [PDF]
  4. Lange EM, Johnson AM, Wang Y, Zuhlke KA, Lu Y, Ribado JV, Keele GR, Li J, Duan Q, Li G, Gao Z, Li Y, Xu J, Isaacs WB, Zheng S, Cooney KA. Genome-wide association scan for variants associated with early-onset prostate cancer. PLoS One 9(4):e93436. [abstract]
  5. DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat Genet. 46(3):234-44. [abstract] [PDF] [supplementary]
  6. Lange LA, Hu Y, ..., Duan Q, Li Y, ..., Willer CJ; NHLBI Grand Opportunity Exome Sequencing Project. Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol. American Journal of Human Genetics 94(2):233-45. [abstract] [PDF] [supplementary]
  7. Bizon C, Spiegel M, Chasse SA, Gizer IR, Li Y, Malc EP, Mieczkowski PA, Sailsbery JK, Wang X, Ehlers CL, Wilhelmsen KC. Variant calling in low-coverage whole genome sequencing of a Native American population sample. BMC Genomics 15(1):85. [abstract] [PDF]
  8. Yan S, Li Y#. BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing. Bioinformatics [Epub ahead of print] [abstract] [PDF] [supplementary] [web]


  1. Wu Y, Marvelle AF, Li J, Croteau-Chonka DC, Feranil AB, Kuzawa CW, Li Y, Adair LS, Mohlke KL. Genetic association with lipids in Filipinos: waist circumference modifies an APOA5 effect on triglyceride levels. J Lipid Res 54(11):3198-205. [abstract] [PDF]
  2. Franceschini N, Fox E, ..., Duan Q, Li Y, ..., Keating BJ, Zhu X. Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations. Am J Hum Genet. 93(3):545-54. [abstract] [PDF]
  3. Duan Q*, Liu EY*, Auer PL*, Zhang G*, ..., Lange LA#, Li Y#. Imputation of coding variants in African Americans: better performance using data from the exome sequencing project. Bioinformatics 29(21):2744-9. [abstract] [PDF] [supplementary]
  4. Byrnes AE, Wu MC, Wright FA, Li M, Li Y#. The value of statistical or bioinformatics annotation for rare variant association with quantitative trait. Genetic Epidemiology 37(7):666-74. [abstract] [PDF]
  5. Coram MA, Duan Q, Hoffmann TJ, Thornton T, Knowles JW, Johnson NA, Ochs-Balcom HM, Donlon TA, Martin LW, Eaton CB, Robinson JG, Risch NJ, Zhu X, Kooperberg C, Li Y, Reiner AP, Tang H. Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations. Am J Hum Genet 92(6):904-16. [abstract] [PDF]
  6. Chang J, Huang Y, Wei L, Ma B, Miao X, Li Y, Hu Z, Yu D, Jia W, Liu Y, Tan W, He Z, Ke Y, Wu T, Shen H, Zeng Y, Wu C, Lin D. Risk prediction of esophageal squamous-cell carcinoma with common genetic variants and lifestyle factors in Chinese population. Carcinogenesis 34(8):1782-17866. [abstract] [PDF]
  7. Wu C, Chang J, Ma B, Miao X, Zhou Y, Liu Y, Li Y, Wu T, Hu Z, Shen H, Jia W, Zeng Y, Lin D, Kraft P. The Case-Only Test for Gene-Environment Interaction is Not Uniformly Powerful: An Empirical Example. Genetic Epidemiology 37(4):402-7. [abstract] [PDF]
  8. Ramasamy A, Trabzuni D, Gibbs JR, Dillman A, Hernandez DG, Arepalli S, Walker R, Smith C, Ilori GP, Shabalin AA, Li Y, Singleton AB, Cookson MR; for NABEC, Hardy J; for UKBEC, Ryten M, Weale ME. Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies. Nucleic Acids Research 41(7):e88. [abstract] [PDF]
  9. Kang J*, Huang KC*, Xu Z, Wang Y, Abecasis GR, Li Y#. AbCD: arbitrary coverage design for sequencing-based genetic studies. Bioinformatics 29(6):799-801. [abstract] [PDF]
  10. Duan Q, Liu EY, Croteau-Chonka DC, Mohlke KL, Li Y#. A comprehensive SNP and indel imputability database. Bioinformatics 29(4):528-31. [abstract] [PDF] [web]


  1. The 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56-65. [abstract] [PDF]
  2. Butler AM, Yin X, ..., Li Y, ..., Avery CL. Novel Loci Associated With PR Interval in a Genome-Wide Association Study of 10 African American Cohorts. Circ Cardiovasc Genet. 5(6):639-46. [abstract] [PDF]
  3. Auer PL*, Johnsen JM*, Johnson AD*, Logsdon BA*, Lange LA*, Nalls MA, Zhang G, Franceschini N, Fox K, Lange EM, Rich SS, O'Donnell CJ, Jackson RD, Wallace RB, Chen Z, Graubert TA, Wilson JG, Tang H*, Lettre G*, Reiner AP*#, Ganesh SK*, Li Y*#. Imputation of Exome Sequence Variants into Population- Based Samples and Blood-Cell-Trait-Associated Loci in African Americans: NHLBI GO Exome Sequencing Project. American Journal of Human Genetics 91(5):794-808. [abstract] [Highlight in Nature Reviews Genetics] [PDF]
  4. Liu EY, Li M, Wang W, Li Y#. MaCH-Admix: Genotype Imputation for Admixed Populations. Genetic Epidemiology 37(1):25-37. [abstract] [PDF] [web]
  5. Chen W, Li B, Zeng Z, Sanna S, Sidore C, Busonero F, Kang HM, Li Y, Abecasis G. Genotype calling and haplotyping in parent-offspring trios. Genome Research [Epub ahead of print] [abstract] [PDF] [wiki]
  6. Mao X, Li Y, Liu Y, Lange L, Li M. Testing Genetic Association With Rare Variants in Admixed Populations. Genetic Epidemiology 37(1):38-47. [abstract] [PDF]
  7. Wu C, Kraft P, Zhai K, Chang J, Wang Z, Li Y, ..., Lin D. Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions. Nat Genet. 44(10):1090-7. [abstract] [PDF]
  8. Huang J, Liu EY, Welch R, Willer C, Hindorff LA, Li Y#. WikiGWA: an open platform for collecting and using genome-wide association results. Eur J Hum Genet Epub ahead of print] [abstract] [PDF] [web]
  9. Li Y, Chen W, Liu EY, Zhou YH. Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data. Statistics in Biosciences [online] [PDF]
  10. Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Zollner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337(6090):100-104. [abstract] [PDF]
  11. Dastani Z, Hivert MF, ..., Li Y, ..., Richards JB. Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. PLoS Genetics 8(3):e1002607. [abstract] [PDF]
  12. Palmer ND, McDonough CW, ..., Li Y, ..., Bowden DW. A genome-wide association search for type 2 diabetes genes in African Americans. PLoS One 7(1):e29202. [abstract] [PDF]
  13. Huang J, Ellinghaus D, Franke A, Howie B, Li Y#. 1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data. Eur J Hum Genet 20(7):801-5. [abstract] [PDF]
  14. Liu EY*, Buyske S, ..., North KE, Li Y#. Genotype Imputation of Metabochip SNPs Using a Study-Specific Reference Panel of ~4,000 Haplotypes in African Americans From the Women's Health Initiative. Genetic Epidemiology 36:107-117. [abstract] [PDF]
  15. Cho YS, Chen CH, ..., Li Y, ..., Mohlke KL, Kato N, Han BG, Seielstad M. Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. Nat Genet. 44(1):67-72. [abstract] [PDF]
  16. Wu Y, McDade TW, Kuzawa CW, Borja J, Li Y, Adair LS, Mohlke KL, Lange LA. Genome-wide Association with C-Reactive Protein Levels in CLHNS: Evidence for the CRP and HNF1A Loci and their Interaction with Exposure to a Pathogenic Environment. Inflammation 35(2):574-83. [abstract] [PDF]
  17. Croteau-Chonka DC, Wu Y, Li Y, Fogarty MP, Lange LA, Kuzawa CW, McDade TW, Borja JB, Luo J, AbdelBaky O, Combs TP, Adair LS, Lange EM, Mohlke KL. Population-specific coding variant underlies genome-wide association with adiponectin level. Human Molecular Genetics 21(2):463-71. [abstract] [PDF]


  1. Chambers JC, Zhang W, ..., Li Y, ..., Elliott P, Kooner JS. Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nat Genet. 43(11):1131-8. [abstract] [PDF]
  2. Li L, Li Y, Browning SR, Browning BL, Slater AJ, Kong X, Aponte JL, Mooser VE, Chissoe SL, Whittaker JC, Nelson MR, Ehm MG. Performance of genotype imputation for rare variants identified in exons and flanking regions of genes. PLoS One 6(9):e24945. [abstract] [PDF]
  3. Marth GT et al. The functional spectrum of low-frequency coding variation. Genome Biology 12(9):R84. [abstract] [PDF]
  4. Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X. Rare-variant association testing for sequencing data with the sequence kernel association test. American Journal of Human Genetics 89(1):82-93. [abstract] [PDF]
  5. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. Widespread RNA and DNA Sequence Differences in the Human Transcriptome. Science 333(6038):53-58. [abstract] [PDF]
  6. Li Y, Sidore C, Kang HM, Boehnke M, Abecasis GR. Low-coverage sequencing: Implications for design of complex trait association studies. Genome Research 21(6):940-951. [abstract] [PDF] [wiki]
  7. Wassel CL, Lange LA, ..., Li Y, ..., Reiner AP. Association of genomic loci from a cardiovascular gene SNP array with fibrinogen levels in European Americans and African-Americans from six cohort studies: the Candidate gene Association Resource (CARe). Blood 117(1):268-275. [abstract] [PDF]
  8. Zheng J, Li Y, Abecasis GR, Scheet P. A comparison of approaches to account for uncertainty in analysis of imputed genotypes. Genetic Epidemiology 35(2): 102-110. [abstract] [PDF]


  1. Ding J, Gudjonsson JE, Liang L, Stuart PE, Li Y, Chen W, Weichenthal M, Ellinghaus E, Franke A, Cookson W, Nair RP, Elder JT, Abecasis GR. Gene expression in skin and lymphoblastoid cells: refined statistical method reveals extensive overlap in cis-eQTL signals. American Journal of Human Genetics 87: 779-789. [abstract] [PDF]
  2. Zawistowski M, Gopalakrishnan S, Ding J, Li Y, Grimm S, Zollner S. Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. American Journal of Human Genetics 87: 604-617. [abstract] [PDF]
  3. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genetic Epidemiology 34(8): 816-834. [abstract] [PDF] [wiki]
  4. Li Y, Byrnes AE, Li M. To identify associations with rare variants, just WHaIT: Weighted Haplotype and Imputation-based Tests. American Journal of Human Genetics 87: 728-735. [abstract] [PDF] [errata]
  5. The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073. [abstract] [PDF]
  6. Stuart PE, Nair RP, Ellinghaus E, Ding J, Tejasvi T, Gudjonsson JE, Li Y, ..., Elder JT. Genome-wide association analysis identifies three psoriasis susceptibility loci. Nat Genet. 42(11): 1000-4. [abstract] [PDF]
  7. Ellinghaus E, Ellinghaus D, ..., Li Y, ..., Franke A. Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2. Nat Genet. 42(11): 991-995. [abstract] [PDF]
  8. Wu Y, Li Y, ..., Mohlke KL. Genome-wide association study for adiponectin levels in Filipino women identifies CDH13 and a novel uncommon haplotype at KNG1-ADIPOQ. Human Molecular Genetics 19(24): 4955-4964. [abstract] [PDF]
  9. Kapur K, Johnson T, ..., Li Y, ..., Bergmann S. Genome-wide meta-analysis for serum calcium identifies significantly associated SNPs near the calcium-sensing receptor (CASR) gene. PLoS Genetics 6: e1001035. [abstract] [PDF]
  10. Willer CJ, Li Y, Abecasis GR. METAL: Fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26: 2190-2191. [abstract] [PDF]
  11. Sanna S, Pitzalis M, ..., Li Y, ..., Schlessinger D, Cucca F. Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis. Nat Genet. 42(6): 495-497. [abstract] [PDF]
  12. Chambers JC, Zhang W, ..., Li Y, ..., Kooner JS. Genetic loci influencing kidney function and chronic kidney disease. Nat Genet. 42(5): 373-375. [abstract] [PDF]
  13. Lange LA, Croteau-Chonka DC, ..., Li Y, ..., Mohlke KL. Genome-wide association study of homocysteine levels in Filipinos provides evidence for CPS1 in women and a stronger MTHFR effect in young adults. Human Molecular Genetics 19: 2050-2058. [abstract] [PDF]
  14. Dupuis J, Langenberg C, ..., Li Y, ..., Barroso I. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet. 42(2): 105-116. [abstract] [PDF]


  1. Chambers JC, Zhang W, Li Y, ..., Kooner JS. Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels. Nat Genet. 41(11): 1170-1172. [abstract] [PDF]
  2. Li Y, Willer CJ, Sanna S, Abecasis GR. Genotype imputation. Annual Review Genomics and Human Genetics 10: 387-406. [abstract] [PDF]
  3. Huang L, Li Y, Singleton AB, Hardy JA, Abecasis GR, Rosenberg NA, Scheet P. Genotype imputation accuracy across worldwide human populations. American Journal of Human Genetics 84(2): 235-50. [abstract] [PDF]
  4. Nair RP, Duffin KC, ..., Li Y, ..., Abecasis GR. Genome-wide scan reveals association of psoriasis with IL-23 and NF-kB pathways. Nat Genet. 41(2): 199-204. [abstract] [PDF]
  5. Kathiresan S, Willer CJ, ..., Li Y, ..., Cupples LA. Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet. 41(1): 56-65. [abstract] [PDF]


  1. Yuan X, Waterworth D, ..., Li Y, ..., Kooner JS, Mooser V. Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes. American Journal of Human Genetics 83:520-8. [abstract] [PDF]
  2. Gaulton KJ, Willer CJ, Li Y, ..., Mohlke KL. Comprehensive association study of type 2 diabetes and related quantitative traits with 222 candidate genes. Diabetes 57: 3136-44. [abstract] [PDF]
  3. Chambers JC, Elliott P, Zabaneh D, Zhang W, Li Y, Froguel P, Balding D, Scott J, Kooner JS. Common genetic variation near the melanocortin-4 receptor gene is associated with waist circumference and insulin resistance. Nat Genet. 40(6):716-8. [abstract] [PDF]
  4. Zeggini E, Scott LJ, ..., Li Y, ..., Altshuler D. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet. 40(5):638-45. [abstract] [PDF]
  5. Willer CJ, Sanna S, ..., Li Y, ..., Abecasis GR. Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet. 40(2):161-9. [abstract] [PDF]


  1. The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-61. [abstract] [PDF]
  2. Scott JL, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, ..., Boehnke M. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316:1341-5. [abstract] [PDF]


  1. Li M, Atmaca-Sonmez P, ..., Li Y, ..., Abecasis GR. CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration. Nat Genet. 38:1049-54. [abstract] [PDF]