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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. Huh R, Yang Y, Jiang Y, Shen Y, Li Y# (2019) SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble. Nucleic Acids Res [abstract] [PDF] [software]
  2. Gorkin DU, Qiu Y, Hu M, Fletez-Brant K, Liu T, Schmitt AD, Noor A, Chiou J, Gaulton KJ, Sebat J, Li Y, Hansen KD, Ren B (2019) Common DNA sequence variation influences 3-dimensional conformation of the human genome. Genome Biol 20(1):255 [abstract] [PDF]
  3. Zhao B, Zhang J, Ibrahim JG, Luo T, Santelli RC, Li Y, Li T, Shan Y, Zhu Z, Zhou F, Liao H, Nichols TE, Zhu H (2019) Large-scale GWAS reveals genetic architecture of brain white matter microstructure and genetic overlap with cognitive and mental health traits (n = 17,706). Mol Psychiatry [abstract] [PDF]
  4. Zhao B, Luo T, Li T, Li Y, Zhang J, Shan Y, Wang X, Yang L, Zhou F, Zhu Z; Alzheimer’s Disease Neuroimaging Initiative; Pediatric Imaging, Neurocognition and Genetics, Zhu H (2019) Genome-wide association analysis of 19,629 individuals identifies variants influencing regional brain volumes and refines their genetic co-architecture with cognitive and mental health traits. Nat Genet 51(11):1637-1644 [abstract] [PDF]
  5. Johnson ND, Huang L, Li R, Li Y, Yang Y, Kim HR, Grant C, Wu H, Whitsel EA, Kiel DP, Baccarelli AA, Jin P, Murabito JM, Conneely KN (2019) Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood. Epigenetics [abstract] [PDF]
  6. Agha G, Mendelson MM, ..., Li Y, Zhang G, ..., Whitsel EA, Levy D, Baccarelli AA (2019) Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease. Circulation 140(8):645-657. [abstract] [PDF]
  7. Song M, Yang X, Ren X, Maliskova L, Li B, Jones IR, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon JR, Judge LM, Conklin BR, Song H, Gan L, Shen Y (2019) Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Nat Genet 51(8):1252-1262. [abstract] [PDF]
  8. Zhou X, Chen Y, Mok KY, Kwok TCY, Mok VCT, Guo Q, Ip FC, Chen Y, Mullapudi N; Alzheimer’s Disease Neuroimaging Initiative, Giusti-Rodríguez P, Sullivan PF, Hardy J, Fu AKY, Li Y, Ip NY (2019) Non-coding variability at the APOE locus contributes to the Alzheimer's risk. Nat Commun 10(1):3310. [abstract] [PDF]
  9. Kim ES, Fong K, Lee L, Spiro A, Schwartz J, Whitsel E, Horvath S, Wang C, Hou L, Baccarelli AA, Li Y, Stewart J, Manson JE, Grodstein F, DeMeo DL, Kubzansky LD (2019) Optimism is not associated with two indicators of DNA methylation aging. Aging 11(14):4970-4989. [abstract] [PDF]
  10. Gondalia R, ..., Li Y, Hou L, Baccarelli AA, Whitsel EA (2019) Methylome-wide association study provides evidence of particulate matter air pollution-associated DNA methylation. Environ Int [Epub ahead of print] [abstract] [PDF]
  11. Zhong W, Spracklen CN, Mohlke KL, Zheng X#, Fine J#, Li Y# (2019) Multi-SNP mediation intersection-union test. Bioinformatics [abstract] [PDF] [software]
  12. Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, Ren B, Hu M (2019) MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLoS Comput Biol 15(4):e1006982. [abstract] [PDF] [software]
  13. Fang Z, Weng C, Li H, Tao R, Mai W, Liu X, Lu L, Lai S, Duan Q, Alvarez C, Arvan P, Wynshaw-Boris A, Li Y, Pei Y, Jin F, Li Y (2019) Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes. Cell Rep 26(11):3132-3144. [abstract] [PDF]
  14. Lu AT, Quach A, Wilson JG, Reiner AP, Aviv A, Raj K, Hou L, Baccarelli AA, Li Y, Stewart JD, Whitsel EA, Assimes TL, Ferrucci L, Horvath S (2019) DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging 11(2):303-327 [abstract] [PDF]


  15. Li M, ..., Li Y, ..., Sestan N (2018) Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 362(6420). [abstract] [PDF]
  16. Yang Y, Huh R, Culpepper HW, Lin Y, Love MI, Li Y # (2018) SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data. Bioinformatics [abstract] [PDF] [web] [github]
  17. Horvath S, Oshima J, Martin GM, Lu AT, Quach A, Cohen H, Felton S, Matsuyama M, Lowe D, Kabacik S, Wilson JG, Reiner AP, Maierhofer A, Flunkert J Aviv A, Hou L, Baccarelli AA, Li Y, Stewart JD, Whitsel EA, Ferrucci L, Matsuyama S, Raj K (2018) Epigenetic clock for skin and blood cells applied to Hutchinson Gilford Progeria Syndrome and ex vivo studies. Aging 10(7):1758-1775. [abstract] [PDF]
  18. Zhao B, Ibrahim JG, Li Y, Li T, Wang Y, Shan Y, Zhu Z, Zhou F, Zhang J, Huang C, Liao H, Yang L, Thompson PM, Zhu H (2018) Heritability of Regional Brain Volumes in Large-Scale Neuroimaging and Genetic Studies. Cereb Cortex. [abstract] [PDF]
  19. Bi W, Li Y, Smeltzer MP, Gao G, Zhao S, Kang G (2018) STEPS: an efficient prospective likelihood approach to genetic association analyses of secondary traits in extreme phenotype sequencing. Biostatistics Epub ahead of print [abstract] [PDF]
  20. Story Jovanova O, Nedeljkovic I, Spieler D, ..., Li Y, ..., Amin N (2018) DNA Methylation Signatures of Depressive Symptoms in Middle-aged and Elderly Persons: Meta-analysis of Multiethnic Epigenome-wide Studies. JAMA Psychiatry 75(9):949-959. [abstract] [PDF]
  21. Franceschini N, Kopp JB, Barac A, Martin LW, Li Y, Qian H, Reiner AP, Pollak M, Wallace RB, Rosamond WD, Winkler CA (2018) Association of APOL1 With Heart Failure With Preserved Ejection Fraction in Postmenopausal African American Women. JAMA Cardiol. 3(8):712-720. [abstract] [PDF]
  22. Lin Y, Liu L, Yang S Li Y, Lin D, Zhang X, Yin X (2018) Genotype imputation for Han Chinese population using Haplotype Reference Consortium as reference. Hum Genet. 137(6-7):431-436. [abstract] [PDF]
  23. Li Y, Hu M, Shen Y (2018) Gene Regulation in the 3D Genome. Hum Mol Genet. 27(R2):R228-R233. [abstract] [PDF]
  24. Hu Y, Raffield LM, Polfus LM, ... Li Y, ..., Reiner AP; NHLBI Trans-Omics for Precision Medicine Consortium (2018) A common TCN1 loss-of-function variant is associated with lower vitamin B12 concentration in African Americans. Blood 131(25):2859-2863. [abstract] [PDF]
  25. Wray NR, Ripke S, Mattheisen M, ..., Li Y, ..., Sullivan PF; Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (2018) Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression. Nat Genet. 50(5):668-681. [abstract] [PDF]
  26. Levine ME, Lu AT, Quach A, Chen BH, Assimes TL, Bandinelli S, Hou L, Baccarelli AA, Stewart JD, Li Y, Whitsel EA, Wilson JG, Reiner AP, Aviv A, Lohman K, Liu Y, Ferrucci L, Horvath S (2018) An epigenetic biomarker of aging for lifespan and healthspan. Aging 10(4):573-591. [abstract] [PDF]
  27. Napier MD, Franceschini N, Gondalia R, ..., Li Y, ..., Whitsel EA (2018) Genome-wide association study and meta-analysis identify loci associated with ventricular and supraventricular ectopy. Sci Rep. 8(1):5675. [abstract] [PDF]
  28. Raffield LM, ..., Li Y, ..., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Hematology & Hemostasis, Diabetes, and Structural Variation TOPMed Working Groups, Lettre G, Sankaran VG, Reiner AP (2018) Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease. PLoS Genet. e1007293. [abstract] [PDF]
  29. Zhou X, Chen Y, Mok KY, Zhao Q, Chen K, Chen Y, Hardy J, Li Y, Fu AKY, Guo Q, Ip NY; Alzheimer’s Disease Neuroimaging Initiative (2018) Identification of genetic risk factors in the Chinese population implicates a role of immune system in Alzheimer's disease pathogenesis. Proc Natl Acad Sci U S A. 115(8):1697-1706. [abstract] [PDF]
  30. Raffield LM, Ellis J, Olson NC, Duan Q, Li J, Durda P, Pankratz N, Keating BJ, Wassel CL, Cushman M, Wilson JG, Gross MD, Tracy RP, Rich SS, Reiner AP, Li Y, Willis MS, Lange EM, Lange LA (2018) Genome-wide association study of homocysteine in African Americans from the Jackson Heart Study, the Multi-Ethnic Study of Atherosclerosis, and the Coronary Artery Risk in Young Adults study. J Hum Genet. 63(3):327-337. [abstract] [PDF]
  31. Lu AT, Xue L, Salfati EL, ..., Li Y, ..., Horvath S (2018) GWAS of epigenetic aging rates in blood reveals a critical role for TERT. Nat Commun. 9(1):387. [abstract] [PDF]
  32. Duan Q, Xu Z, Raffield LM, Chang S, Wu D, Lange EM, Reiner AP, Li Y # (2018) A robust and powerful two-step testing procedure for local ancestry adjusted allelic association analysis in admixed populations. Genet Epidemiol. 42(3):288-302. [abstract] [PDF] [website]
  33. Luo Y, Maity A, Wu MC, Smith C, Duan Q, Li Y, Tzeng JY (2018) On the substructure controls in rare variant analysis: Principal components or variance components? Genet Epidemiol. 42(3):276-287. [abstract] [PDF]
  34. Seyerle AA, ..., Duan Q, ..., Li Y, , ..., Avery CL (2018) Pharmacogenomics study of thiazide diuretics and QT interval in multi-ethnic populations: the cohorts for heart and aging research in genomic epidemiology. Pharmacogenomics J. 18(2):215-226. [abstract] [PDF]
  35. Floyd JS, ..., Li Y, Duan Q, ..., Stricker BH (2018) Large-scale pharmacogenomic study of sulfonylureas and the QT, JT and QRS intervals: CHARGE Pharmacogenomics Working Group. Pharmacogenomics J. 18(1):127-135. [abstract] [PDF]


  36. Richard MA, ..., Zhang G, Li Y, ..., Fornage M (2017) DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation. Am J Hum Genet. 101(6):888-902. [abstract] [PDF]
  37. Martin JS, Xu Z, Reiner AP, Mohlke KL, Sullivan P, Ren B, Hu M, Li Y # (2017) HUGIn: Hi-C Unifying Genomic Interrogator. Bioinformatics 33(23):3793-3795. [abstract] [PDF] [slides] [website]
  38. Grant CD, Jafari N, Hou L, Li Y, Stewart JD, Zhang G, Lamichhane A, Manson JE, Baccarelli AA, Whitsel EA, Conneely KN (2017) A longitudinal study of DNA methylation as a potential mediator of age-related diabetes risk. Geroscience 39(5-6):475-489. [abstract] [PDF]
  39. Raffield LM, Zakai NA, Duan Q, Laurie C, Smith JD, Irvin MR, Doyle MF, Naik RP, Song C, Manichaikul AW, Liu Y, Durda P, Rotter JI, Jenny NS, Rich SS, Wilson JG, Johnson AD, Correa A, Li Y, Nickerson DA, Rice K, Lange EM, Cushman M, Lange LA, Reiner AP; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Hematology & Hemostasis TOPMed Working Group (2017) D-Dimer in African Americans: Whole Genome Sequence Analysis and Relationship to Cardiovascular Disease Risk in the Jackson Heart Study. Arterioscler Thromb Vasc Biol. 37(11):2220-2227. [abstract] [PDF]
  40. Kerr KF, Avery CL, Lin HJ, Raffield LM, Zhang QS, Browning BL, Browning SR, Conomos MP, Gogarten SM, Laurie CC, Sofer T, Thornton TA, Hohensee C, Jackson RD, Kooperberg C, Li Y, Méndez-Giráldez R, Perez MV, Peters U, Reiner AP, Zhang ZM, Yao J, Sotoodehnia N, Taylor KD, Guo X, Lange LA, Soliman EZ, Wilson JG, Rotter JI, Heckbert SR, Jain D, Whitsel EA (2017) Genome-wide association study of heart rate and its variability in Hispanic/Latino cohorts. Heart Rhythm. 14(11):1675-1684. [abstract] [PDF]
  41. Graff M, Emery LS, Justice AE, Parra E, Below JE, Palmer ND, Gao C, Duan Q, Valladares-Salgado A, Cruz M, Morrison AC, Boerwinkle E, Whitsel EA, Kooperberg C, Reiner A, Li Y, Rodriguez CJ, Talavera GA, Langefeld CD, Wagenknecht LE, Norris JM, Taylor KD, Papanicolaou G, Kenny E, Loos RJF, Chen YI, Laurie C, Sofer T, North KE (2017) Genetic architecture of lipid traits in the Hispanic community health study/study of Latinos. Lipids Health Dis. 16(1):200. [abstract] [PDF]
  42. Du Y, Martin JS, McGee J, Yang Y, Liu EY, Sun Y, Geihs M, Kong X, Zhou EL, Li Y, Huang J (2017) A SNP panel and online tool for checking genotype concordance through comparing QR codes. PLoS One. 12(9):e0182438. [abstract] [PDF]
  43. Cannon ME, Duan Q, Wu Y, Zeynalzadeh M, Xu Z, Kangas AJ, Soininen P, Ala-Korpela M, Civelek M, Lusis AJ, Kuusisto J, Collins FS, Boehnke M, Tang H, Laakso M, Li Y, Mohlke KL (2017) Trans-ancestry Fine Mapping and Molecular Assays Identify Regulatory Variants at the ANGPTL8 HDL-C GWAS Locus. G3 7(9):3217-3227. [abstract] [PDF]
  44. Hui D, Fang Z, Lin J, Duan Q, Li Y, Hu M, Chen W (2017) LAIT: a local ancestry inference toolkit. BMC Genet. 18(1):83. [abstract] [PDF]
  45. Christophersen IE, Magnani JW, Yin X, Barnard J, Weng LC, Arking DE, Niemeijer MN, Lubitz SA, Avery CL, Duan Q, Felix SB, Bis JC, Kerr KF, Isaacs A, Müller-Nurasyid M, Müller C, North KE, Reiner AP, Tinker LF, Kors JA, Teumer A, Petersmann A, Sinner MF, Buzkova P, Smith JD, Van Wagoner DR, Völker U, Waldenberger M, Peters A, Meitinger T, Limacher MC, Wilhelmsen KC, Psaty BM, Hofman A, Uitterlinden A, Krijthe BP, Zhang ZM, Schnabel RB, Kääb S, van Duijn C, Rotter JI, Sotoodehnia N, Dörr M, Li Y, Chung MK, Soliman EZ, Alonso A, Whitsel EA, Stricker BH, Benjamin EJ, Heckbert SR, Ellinor PT (2017) Fifteen Genetic Loci Associated With the Electrocardiographic P Wave. Circ Cardiovasc Genet. 10(4). [abstract]
  46. Nolte IM, Munoz ML, ..., Li Y, ..., de Geus EJC (2017) Genetic loci associated with heart rate variability and their effects on cardiac disease risk. Nat Commun. 8:15805. [abstract] [PDF]
  47. Gondalia R, Avery CL, Napier MD, Méndez-Giráldez R, Stewart JD, Sitlani CM, Li Y, Wilhelmsen KC, Duan Q, Roach J, North KE, Reiner AP, Zhang ZM, Tinker LF, Yanosky JD, Liao D, Whitsel EA (2017) Genome-wide Association Study of Susceptibility to Particulate Matter-Associated QT Prolongation. Environ Health Perspect. 125(6):067002. [abstract]
  48. Chang J, Tan W, Ling Z, Xi R, Shao M, Chen M, Luo Y, Zhao Y, Liu Y, Huang X, Xia Y, Hu J, Parker JS, Marron D, Cui Q, Peng L, Chu J, Li H, Du Z, Han Y, Tan W, Liu Z, Zhan Q, Li Y, Mao W, Wu C, Lin D (2017) Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations. Nat Commun. 8:15290. [abstract] [PDF]
  49. Noordam R, ..., Duan Q, ..., Li Y, ..., Whitsel EA (2017) A genome-wide interaction analysis of tricyclic/tetracyclic antidepressants and RR and QT intervals: a pharmacogenomics study from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. J Med Genet. 54(5):313-323. [abstract]
  50. Hodonsky CJ, Jain D, Schick UM, Morrison JV, Brown L, McHugh CP, Schurmann C, Chen DD, Liu YM, Auer PL, Laurie CA, Taylor KD, Browning BL, Li Y, Papanicolaou G, Rotter JI, Kurita R, Nakamura Y, Browning SR, Loos RJF, North KE, Laurie CC, Thornton TA, Pankratz N, Bauer DE, Sofer T, Reiner AP (2017) Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos. PLoS Genet. 13(4):e1006760. [abstract] [PDF]
  51. Ng MCY, ..., Duan Q, ..., Li Y, ..., North KE (2017) Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium. PLoS Genet. 13(4):e1006719. [abstract] [PDF]
  52. Yang L, Chang S, Lu Q, Zhang Y, Wu Z, Sun X, Cao Q, Qian Y, Jia T, Xu B, Duan Q, Li Y, Zhang K, Schumann G, Liu D, Wang J, Wang Y, Lu L (2017) A new locus regulating MICALL2 expression was identified for association with executive inhibition in children with attention deficit hyperactivity disorder. Mol Psychiatry. 23(4):1014-1020. [abstract] [PDF]
  53. Quach A, Levine ME, Tanaka T, Lu AT, Chen BH, Ferrucci L, Ritz B, Bandinelli S, Neuhouser ML, Beasley JM, Snetselaar L, Wallace RB, Tsao PS, Absher D, Assimes TL, Stewart JD, Li Y, Hou L, Baccarelli AA, Whitsel EA, Horvath S (2017) Epigenetic clock analysis of diet, exercise, education, and lifestyle factors. Aging 9(2):419-446. [abstract] [PDF]
  54. Sun H, Wang Y, Chen Y, Li Y, Wang S (2017) pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data. Bioinformatics 33(12):1765-1772. [abstract] [PDF]


  55. Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL, Ren B (2016) A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Rep. 17(8):2042-2059. [abstract] [PDF] [Nature Review Genetics Highlight]
  56. Liu C, ..., Duan Q, ..., Li Y, ..., North KE, Liu Y, Waldenberger M, London SJ, Ingelsson E, Levy D (2016) A DNA methylation biomarker of alcohol consumption. Mol Psychiatry. 23(2):422-433. [abstract] [PDF] [slides] [website]
  57. Xu Z, Zhang G, Wu C, Li Y#, Hu M (2016) FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. Bioinformatics 32(17): 2692-5. [abstract] [PDF] [supplementary]
  58. Zhang G, Huang KC, Xu Z, Tzeng JY, Conneely KN, Guan W, Kang J, Li Y# (2016) Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression. Genet Epidemiol.40(4):333-40. [abstract] [PDF] [supplementary] [web]
  59. Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Yue F, Li Y#, Hu M (2016) HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. BMC Res Notes 9(1): 159. [abstract] [PDF]
  60. Naik RP, Wilson JG, Ekunwe L, Mwasongwe S, Duan Q, Li Y, Correa A, Reiner AP (2016) Elevated D-dimer levels in African Americans with sickle cell trait. blood 127(18): 2261-3. [abstract] [PDF]
  61. Below JE, ..., Duan Q, Li Y, ..., Valladares-Salgado A (2016) Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs. Scientific Reports 6:19429. [abstract] [PDF]


  62. Urrutia E, Lee S, Maity A, Zhao N, Shen J, Li Y, Wu MC (2015) Rare variant testing across methods and thresholds using the multi-kernel sequence kernel association test (MK-SKAT). Stat Interface 8(4):495-505. [abstract] [PDF]
  63. Fan R, Wang Y, Chui CY, Chen W, Ren H, Li Y, Boehnke M, Amos CI, Moore JH, Xiong M (2015) Meta-analysis of Complex Diseases at Gene Level with Generalized Functional Linear Models. Genetics 202(2): 457-70. [abstract] [PDF]
  64. Lange EM, Ribado J, Zuhlke KA, Johnson A, Keele G, Li J, Wang Y, Duan Q, Li G, Gao Z, Li Y, Xu J, Zheng SL, Cooney KA (2015) Assessing the Cumulative Contribution of New and Established Common Genetic Risk Factors to Early-Onset Prostate Cancer. Cancer Epidemiol Biomarkers Prev. 25(5): 766-72. [abstract] [PDF]
  65. Xu Z, Zhang G, Jin F, Chen M, Furey TS, Sullivan PF, Qin Z, Hu M#, Li Y# (2015) A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. Bioinformatics 32(5):650-6. [abstract] [PDF]
  66. The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation. Nature 526(7571):68-74. [abstract] [PDF] [supplementary]
  67. Li J, Lange LA, Sabourin J, Duan Q, Valdar W, Willis MS, Li Y, Wilson JG, Lange EM (2015) Genome- and exome-wide association study of serum lipoprotein (α) in the Jackson Heart Study. J Hum Genet. 60(12):755-61. [abstract] [PDF]
  68. Yuan S, Johnston HR, Zhang G, Li Y, Hu YJ, Qin ZS (2015) One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies. PLoS Computational Biology 11(8):e1004448. [abstract] [PDF]
  69. Buchkovich ML, Eklund K, Duan Q, Li Y, Mohlke KL, Furey TS (2015) Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci. BMC Med Genomics 8:43. [abstract] [PDF]
  70. Lanktree MB, Elbers CC, Li Y, Zhang G, Duan Q, Karczewski KJ, Guo Y, Tragante V, North KE, Cushman M, Asselbergs FW, Wilson JG, Lange LA, Drenos F, Reiner AP, Barnes MR, Keating BJ (2015) Genetic meta-analysis of 15,901 African Americans identifies variation in EXOC3L1 is associated with HDL concentration. J Lipid Res. 56(9):1781-6. [abstract] [PDF]
  71. Fan R, Wang Y, Boehnke M, Chen W, Li Y, Ren H, Lobach I, Xiong M (2015) Gene Level Meta-Analysis of Quantitative Traits by Functional Linear Models. Genetics 200(4):1089-104. [abstract] [PDF]
  72. Yan S, Yuan S, Xu Z, Zhang B, Zhang B, Kang G, Byrnes A, Li Y# (2015) Likelihood-based complex trait association testing for arbitrary depth sequencing data. Bioinformatics 31(18):2955-62. [abstract] [PDF]
  73. Yu D, Zhang G, Huang X, Wu C, Tan W, Qiao Y, Chang J, Zhao H, Bi X, Cai J, Li Y#, Lin D (2015) Relatively Small Contribution of Methylation and Genomic Copy Number Aberration to the Aberrant Expression of Inflammation-Related Genes in HBV-Related Hepatocellular Carcinoma. PLoS One 10(5):e0126836. [abstract] [PDF]
  74. Bi W, Kang G, Zhao Y, Cui Y, Yan S, Li Y, ... Zhang JF (2015) SVSI: Fast and Powerful Set-Valued System Identification Approach to Identifying Rare Variants in Sequencing Studies for Ordered Categorical Traits. Ann Hum Genet. 79(4):294-309. [abstract] [PDF]
  75. Demerath EW, Guan W, ..., Li Y, Absher DM, Levy D, Arnett DK, Fornage M, Pankow JS, Boerwinkle E (2015) Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated loci. Human Molecular Genetics 24(15):4464-79. [abstract] [PDF]
  76. Coram MA, Candille SI, Duan Q, Chan KH, Li Y, Kooperberg C, Reiner AP, Tang H (2015) Leveraging Multi-ethnic Evidence for Mapping Complex Traits in Minority Populations: An Empirical Bayes Approach. The American Journal of Human Genetics 96(5):740-52. [abstract] [PDF]
  77. Xu Z, Duan Q, Yan S, Chen W, Li M, Lange E, Li Y# (2015) DISSCO: direct imputation of summary statistics allowing covariates. Bioinformatics 31(15):2434-42. [abstract] [PDF] [Supplementary]
  78. Wang X, Zhang S, Li Y, Li M, Sha Q (2015) A powerful approach to test an optimally weighted combination of rare variants in admixed populations. Genetic Epidemiology 39(4):294-305. [abstract] [PDF]
  79. Abdo N, Xia M, ..., Li Y, Chiu WA, Motsinger-Reif AA, Austin CP, Tice RR, Rusyn I, Wright FA (2015) Population-based in vitro hazard and concentration-response assessment of chemicals: the 1000 genomes high-throughput screening study. Environ Health Perspect 123(5):458-66. [abstract] [PDF]
  80. Hu YJ, Li Y, Auer PL, Lin DY (2015) Integrative analysis of sequencing and array genotype data for discovering disease associations with rare mutations. Proc Natl Acad Sci U S A. 112(4):1019-24. [abstract] [PDF]
  81. Franceschini N, Hu Y, ..., Li Y, ..., Boerwinkle E (2015) Prospective associations of coronary heart disease loci in African Americans using the MetaboChip: the PAGE study. PLoS One 9(12):e113203. [abstract] [PDF]
  82. Li J, Lange LA, Duan Q, ..., Li Y, ..., Lange EM (2015) Genome-wide admixture and association study of serum iron, ferritin, transferrin saturation and total iron binding capacity in African Americans. Human Molecular Genetics 24(2):572-581. [abstract] [PDF]


  83. Huang KC, Sun W, Wu Y, Chen M, Mohlke KL, Lange LA, Li Y # (2014) Association studies with imputed variants using expectation-maximization likelihood-ratio tests. PLoS One 9(11):e110679. [abstract] [PDF]
  84. Ma Y, Zhao J, Wong JS, Ma L, Li W, Fu G, Xu W, Zhang K, Kittles RA, Li Y, Song Q (2014) Accurate inference of local phased ancestry of modern admixed populations. Sci Rep. 4:5800. [abstract] [PDF]
  85. 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 (2014) Genome-wide association scan for variants associated with early-onset prostate cancer. PLoS One 9(4):e93436. [abstract]
  86. Han B, Luo H, Raelson J, Huang J, Li Y, Tremblay J, Hu B, Qi S, Wu J (2014) TGFBI (βIG-H3) is a diabetes-risk gene based on mouse and human genetic studies. Hum Mol Genet. 23(17):4597-611. [abstract] [PDF]
  87. DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium (2014) 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]
  88. Lange LA, Hu Y, ..., Duan Q, Li Y, ..., Willer CJ; NHLBI Grand Opportunity Exome Sequencing Project (2014) 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]
  89. Bizon C, Spiegel M, Chasse SA, Gizer IR, Li Y, Malc EP, Mieczkowski PA, Sailsbery JK, Wang X, Ehlers CL, Wilhelmsen KC (2014) Variant calling in low-coverage whole genome sequencing of a Native American population sample. BMC Genomics 15(1):85. [abstract] [PDF]
  90. Yan S, Li Y# (2014) BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing. Bioinformatics 30(4):480-7. [abstract] [PDF] [supplementary] [web]


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