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Publications of the Li Group

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preprint

  1. Mu W*, Luo T*, Barrera A, Bounds LR, Klann TS, ter Weele M, Bryois J, Crawford GE, Sullivan PF, Gersbach CA, Love MI, Li Y(2024+) Machine learning methods for predicting guide RNA effects in CRISPR epigenome editing experiments. [preprint] [GitHub] [Figure Scripts]
  2. Jiang Z, Sullivan PF, Li T, Zhao B, Wang X, Luo T, Huang S, Guan PY, Chen J, Yang Y, Stein JL, Li Y, Liu D, Sun L, Zhu H (2024+) The pivotal role of the X-chromosome in the genetic architecture of the human brain. [preprint]
  3. Wen J, Li G, Chen J, Sun Q, Liu W, Guan W, Lai B, Szatkiewicz JP, He X, Sullivan PF, Li Y(2024+) DeepGWAS: Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network. [preprint] [GitHub]
  4. Khaire A, Wen J, Yang X, Shen Y, Li Y(2024+) A Semi-Supervised Ensemble Approach to Rank Potential Causal Variants and Their Target Genes in Microglia for Alzheimer’s Disease. [preprint]
  5. Zhao B, ..., Luo T, ..., Li Y, Stein JL, Wang Y, Zhu H (2022+) Genetic influences on the shape of brain ventricular and subcortical structures. [preprint] [BIG-KP]
  6. Zhao B, ..., Luo T, ..., Li Y, Stein JL, Zhu H (2022+) Genetic influences on the intrinsic and extrinsic functional organizations of the cerebral cortex. [preprint] [BIG-KP]
  7. Giusti-Rodríguez P*, Lu L*, Yang Y*, Crowley C, ..., Jin F#, Hu M#, Li Y#, Sullivan PF# (2020+) Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits. [preprint]
Top

    2024

  1. IGVF Consortium (2024) Deciphering the impact of genomic variation on function. Nature 633(8028):47-57. [abstract]
  2. Liu W, Zhong W, Giusti-Rodríguez P, Jiang Z, Wang GW, Sun H, Hu M#, Li Y# (2024) SnapHiC-G: identifying long-range enhancer-promoter interactions from single-cell Hi-C data via a global background model. Brief Bioinform. 25(5):bbae426. [abstract] [GitHub]
  3. Wen J, Sun Q, Huang L, Zhou L, Doyle MF, Ekunwe L, Durda P, Olson NC, Reiner AP, Li Y#, Raffield LM# (2024) Gene expression and splicing QTL analysis of blood cells in African American participants from the Jackson Heart Study. Genetics 228(1):iyae098. [abstract] [web]
  4. Zhao B, Li Y, Fan Z, Wu Z, Shu J, Yang X, Yang Y, Wang X, Li B, Wang X, Copana C, Yang Y, Lin J, Li Y, Stein JL, O'Brien JM, Li T, Zhu H (2024) Eye-brain connections revealed by multimodal retinal and brain imaging genetics. Nat Commun. 15(1):6064. [abstract] [BIG-KP]
  5. Yu H, Wu D, Mishra S, Shen G, Sun H, Hu M#, Li Y# (2024) SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. Commun Biol. 7(1):834. [abstract] [GitHub]
  6. Sun Q, Karafin MS, Garrett ME, Li Y, Ashley-Koch A, Telen MJ (2024) A genome-wide association study of alloimmunization in the TOPMed OMG-SCD cohort identifies a locus on chromosome 12. Transfusion 64(9):1772-1783. [abstract]
  7. Chen BD, Lee C, Tapia AL, Reiner AP, Tang H, Kooperberg C, Manson JE, Li Y#, Raffield LM# (2024) Proteome-wide association study using cis and trans variants and applied to blood cell and lipid-related traits in the Women's Health Initiative study. Genet Epidemiol. 48(7):310-323. [abstract]
  8. Sun Q, Yang Y, Rosen JD, Chen J, Li X, Guan W, Jiang MZ, Wen J, Pace RG, Blackman SM, Bamshad MJ, Gibson RL, Cutting GR, O'Neal WK, Knowles MR, Kooperberg C, Reiner AP, Raffield LM, Carson AP, Rich SS, Rotter JI, Loos RJF, Kenny E, Jaeger BC, Min YI, Fuchsberger C, Li Y (2022) MagicalRsq-X: A cross-cohort transferable genotype imputation quality metric. Am J Hum Genet. S0002-9297(24)00116-2. [abstract] [pdf] [GitHub] [Interview]
  9. Pan W, Shan Y, Li C, Huang S, Li T, Li Y, Zhu H (2024) FPLS-DC: functional partial least squares through distance covariance for imaging genetics. Bioinformatics 40(4):btae173. [abstract]
  10. Hou K, Gogarten S, Kim J, Hua X, Dias JA, Sun Q, Wang Y, Tan T; Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working Group; Atkinson EG, Martin A, Shortt J, Hirbo J, Li Y, Pasaniuc B, Zhang H (2024) Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations. Bioinformatics 40(4):btae148. [abstract] [pdf]
  11. Shan Y, Huang C, Li Y, Zhu H (2024) Merging or ensembling: integrative analysis in multiple neuroimaging studies. Biometrics 80(1) https://doi.org/10.1093/biomtc/ujae003 [abstract] [full text]
  12. Jeng XJ, Hu Y, Sun Q, Li Y (2024) Weak signal inclusion under dependence and applications in genome-wide association study. Ann. Appl. Stat. 18(1): 841-857. [full text]
  13. Suzuki K, et al (2024) Genetic drivers of heterogeneity in type 2 diabetes pathophysiology. Nature 627(8003):347-357 [abstract]
  14. Sun Q, Rowland BT, Chen J, Mikhaylova AV, Avery C, Peters U, Lundin J, Matise T, Buyske S, Tao R, Mathias RA, Reiner AP, Auer PL, Cox NJ, Kooperberg C, Thornton TA, Raffield LM, Li Y (2024) Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-differential effects via GAUDI. Nat Commun. 15(1):1016. [abstract] [pdf] [GitHub]
  15. Reynolds LM, ..., Li Y, ..., Vitolins MZ (2024) Diet Quality and Epigenetic Aging in the Women's Health Initiative. J Acad Nutr Diet. S2212-2672(24)00002-9. [abstract] [pdf]
  16. Hughes O, ..., Li Y, ..., Morris AP, Franceschini N (2024) Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas. Cell Genom. 4(1):100468. [abstract] [pdf]
  17. Skinner HG, ..., Li Y, Whitsel EA, Zannas AS (2024) Stressful life events, social support, and epigenetic aging in the Women's Health Initiative. J Am Geriatr Soc. 72(2):349-360. [abstract] [full text]

    2023

  18. Chen J, Mu W, Li Y, Li D (2023) On the Identifiability and Interpretability of Gaussian Process Models. 37th Conference on Neural Information Processing Systems (NeurIPS 2023) [abstract] [pdf]
  19. Rosen J, Lee L, Abnousi A, Chen J, Wen J, Hu M#, Li Y# (2023) HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets. Comput Struct Biotechnol J. https://doi.org/10.1016/j.csbj.2023.01.003 [abstract] [pdf] [GitHub]
  20. Ren X, Yang H, ..., Chen J, ..., Li Y, Ziv E, Shen Y (2023) High-throughput PRIME-editing screens identify functional DNA variants in the human genome. Mol Cell. 83(24):4633-4645.e9. [abstract] [pdf]
  21. Jakubek YA, ..., Li Y, Desai P, Bick AG, Reiner AP, Scheet P, Auer PL (2023) Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing. Nat Genet. 55(11):1912-1919. [abstract] [pdf]
  22. Guintivano J, ..., Li Y, ..., Sullivan P (2023) Meta-Analyses of Genome-Wide Association Studies for Postpartum Depression. Am J Psychiatry. 180(12):884-895. [abstract] [full text]
  23. Yang X, Wen J, Yang H, Jones IR, Zhu X, Liu W, ..., Van Buren E, Jiang MZ, ..., Li Y#, Shen Y# (2023) Functional characterization of Alzheimer's disease genetic variants in microglia. Nat Genet. 55(10):1735-1744. [abstract] [pdf] [Research Briefing]
  24. Lee H, Yu M, Li X, Zhu C, Zhang Y, Yu H, Chen Z, Mishra S, Ren B, Li Y#, Hu M# (2023) SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data. Brief Bioinform. doi: 10.1093/bib/bbad315. [abstract] [pdf] [software]
  25. Lee H, Yu H, ..., Chen J, ..., Li Y#, Hu M# (2023) SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. Nat Commun. 14(1):4873. [abstract] [pdf] [software]
  26. Keshawarz A, ..., Wen J, Li Y, ..., Levy D (2023) Expression quantitative trait methylation analysis elucidates gene regulatory effects of DNA methylation: the Framingham Heart Study. Sci Rep. 13(1):12952. [abstract] [pdf]
  27. Sun Q, Rowland B, Wang W, Miller-Fleming TW, Cox N, Graff M, Faucon A, Shuey MM, Blue EE, Auer P, Li Y, Sankaran VG, Reiner AP, Raffield LM (2023) Genetic examination of hematological parameters in SARS-CoV-2 infection and COVID-19. Blood Cells Mol Dis. 103:102782. doi: 10.1016/j.bcmd.2023.102782. [abstract] [full text]
  28. Cai Y, ..., Li Y, ..., Reiner AP (2023) Differences in the Circulating Proteome in Individuals with versus without Sickle Cell Trait. Clin J Am Soc Nephrol. 18(11):1416-1425. [abstract] [full text]
  29. Sun Q, ..., Thomas NE, Cox NJ, Li Y#, Mohlke KL#, Sayed CJ# (2023) Genetic Variants Associated With Hidradenitis Suppurativa. JAMA Dermatol. e232217. doi: 10.1001/jamadermatol.2023.2217. [abstract] [full text]
  30. Dekker J, ..., Li Y, ..., Zhong S (2023) Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell. 83(15):2624-2640. [abstract] [pdf]
  31. Van Buren E, ..., Li Y, Cho MH, Kesimer M, Kelada SNP (2023) Genetic regulators of sputum mucin concentration and their associations with COPD phenotypes. PLoS Genet 19(6):e1010445. [abstract] [pdf]
  32. Zhao B, ..., Luo T, ..., Li Y, Stein JL, Zhu H (2023) Heart-brain connections: Phenotypic and genetic insights from magnetic resonance images Science 380(6648):abn6598. [abstract] [pdf]
  33. Little P, Liu S, Zhabotynsky V, Li Y, Lin DY, Sun W (2023) A computational method for cell type-specific expression quantitative trait loci mapping using bulk RNA-seq data. Nat Commun 14(1):3030. [abstract] [pdf]
  34. Jiang MZ, Aguet F, Ardlie K, Chen J, ..., Love MI#, Raffield LM#, Li Y# (2023) Canonical correlation analysis for multi-omics: Application to cross-cohort analysis. PLoS Genet 19(5):e1010517. [abstract] [pdf]
  35. Sullivan PF, ..., Sun Q, ..., Wen J, ..., Li Y, ..., Chen J, ..., Zoonomia Consortium (2023) Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science 380(6643):eabn2937. [abstract] [pdf]
  36. Zhou YH, ..., Liu W, ..., Sun Q, Wen J, Li Y, ..., Knowles MR(2023) Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole Genome Analysis of 7,840 Patients. Am J Respir Crit Care Med. doi: 10.1164/rccm.202209-1653OC [abstract] [pdf]
  37. Chen J*, Luo T*, Jiang M, Liu J, Gupta GP, Li Y (2023) Cell composition inference and identification of layer-specific spatial transcriptional profiles with POLARIS. Sci Adv. 9(9):eadd9818. doi: 10.1126/sciadv.add9818. [abstract] [pdf] [GitHub]

    2022

  38. Liyanage JSS, ..., Li Y, ..., Kang G(2022) A Versatile and Efficient Novel Approach for Mendelian Randomization Analysis with Application to Assess the Causal Effect of Fetal Hemoglobin on Anemia in Sickle Cell Anemia. Mathematics 10(20), 3743; https://doi.org/10.3390/math10203743 [full text]
  39. Wheeler MM, ..., Wen J, ..., Jiang M, ..., Li Y, ..., Auer PL#, Reiner AP# (2022) Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun. 13(1):7592. doi: 10.1038/s41467-022-35354-7. [abstract] [pdf]
  40. Wen J, Trost B, Engchuan W, Halvorsen M, Pallotto LM, Mitina A, Ancalade N, Farrell M, Backstrom I, Guo K, Pellecchia G, Thiruvahindrapuram B, Giusti-Rodriguez P, Rosen JD, Li Y, Won H, Magnusson PKE, Gyllensten U, Bassett AS, Hultman CM, Sullivan PF, Yuen RKC, Szatkiewicz JP (2022) Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia. Mol Psychiatry. doi: 10.1038/s41380-022-01857-4. [abstract] [pdf]
  41. Zhong W, Kollipara A, Liu Y, Wang Y, O'Connell CM, Poston TB, Yount K, Wiesenfeld HC, Hillier SL, Li Y, Darville T, Zheng X (2022) Genetic susceptibility loci for Chlamydia trachomatis endometrial infection influence expression of genes involved in T cell function, tryptophan metabolism and epithelial integrity. Front Immunol. 13:1001255. doi: 10.3389/fimmu.2022.1001255. [abstract] [pdf]
  42. Jain P, Binder A, Chen B, Parada H, Gallo LC, Alcaraz J, Horvath S, Bhatti P, Whitsel EA, Jordahl K, Baccarelli AA, Hou L, Stewart JD, Li Y, LaMonte MJ, Manson JE, LaCroix AZ (2022) The association of epigenetic age acceleration and multimorbidity at age 90 in the Women's Health Initiative. J Gerontol A Biol Sci Med Sci. doi: 10.1093/gerona/glac190. [abstract] [full-text] [pdf]
  43. Wang C, DeMeo DL, Kim ES, Cardenas A, Fong KC, Lee LO, Spiro A 3rd, Whitsel EA, Horvath S, Hou L, Baccarelli AA, Li Y, Stewart JD, Manson JE, Grodstein F, Kubzansky LD, Schwartz JD (2022) Epigenome-wide analysis of DNA methylation and optimism in women and men. Psychosom Med. doi: 10.1097/PSY.0000000000001147. [abstract] [full-text] [pdf]
  44. Sun Q, Yang Y, Rosen JD, Jiang MZ, Chen J, Liu W, Wen J, Raffield LM, Pace RG, Zhou YH, Wright FA, Blackman SM, Bamshad MJ, Gibson RL, Cutting GR, Knowles MR, Schrider DR, Fuchsberger C, Li Y (2022) MagicalRsq: Machine-learning-based genotype imputation quality calibration. Am J Hum Genet. 109(11):1986-1997. [abstract] [pdf] [GitHub]
  45. Zhong W*, Liu W*, Chen J, Sun Q, Hu M#, Li Y# (2022) Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variants. Front Cell Dev Biol. doi: 10.3389/fcell.2022.957292. [abstract] [pdf]
  46. Jain P, Binder AM, Chen B, Parada H Jr, Gallo LC, Alcaraz J, Horvath S, Bhatti P, Whitsel EA, Jordahl K, Baccarelli AA, Hou L, Stewart JD, Li Y, Justice JN, LaCroix AZ (2022) Analysis of Epigenetic Age Acceleration and Healthy Longevity Among Older US Women. JAMA Netw Open. 5(7):e2223285. [abstract] [pdf]
  47. Chen J*, Liu W*, Luo T*, Yu Z, Jiang MZ, Wen J, Gupta GP, Giusti P, Zhu H, Yang Y, Li Y (2022) A comprehensive comparison on cell-type composition inference for spatial transcriptomics data. Brief Bioinform. bbac245. doi: 10.1093/bib/bbac245. [abstract] [full-text] [pdf] [GitHub]
  48. Li X*, Lee L*, Abnousi A, Yu M, Liu W, Huang L, Li Y#, Hu M# (2022) SnapHiC2: A computationally efficient loop caller for single cell Hi-C data. Comput Struct Biotechnol J. 20:2778-2783. [abstract] [full-text] [pdf] [GitHub]
  49. Shan Y, Cole SA, Haack K, Melton PE, Best LG, Bizon C, Kobes S, Köroğlu Ç, Baier LJ, Hanson RL, Sanna S, Li Y, Franceschini N (2022) Association of protein function-altering variants with cardiometabolic traits: the strong heart study. Sci Rep. 12(1):9317. [abstract] [full-text] [pdf]
  50. Mahajan A, ..., Raffield LM, ..., Duan Q, ..., Li Y, ..., Morris AP (2022) Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation. Nat Genet. 54(5):560-572. [abstract] [full-text] [pdf]
  51. Huang L*, Rosen JD*, Sun Q*, Chen J, ..., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Raffield LM, Reiner AP, Auer PL#, Li Y# (2022) TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data. Am J Hum Genet. 109(6):1175-1181. [abstract] [PDF] [web]
  52. Holliday KM, ..., Li Y, ..., Whitsel EA (2022) Gaseous air pollutants and DNA methylation in a methylome-wide association study of an ethnically and environmentally diverse population of U.S. adults. Environ Res. 212(Pt C):113360. [abstract] [full-text] [pdf]
  53. Huang L, Yang Y, Li G, Jiang M, Wen J, Abnousi A, Rosen JD, Hu M, Li Y# (2022) A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data. Brief Bioinform. 23(3):bbac145. doi: 10.1093/bib/bbac145. [abstract] [full-text] [pdf]
  54. Liu W*, Zhong W*, Chen J, Huang B, Hu M#, Li Y# (2022) Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization. Genes 13(4):586. [abstract] [PDF]
  55. Yu M, Li Y, Hu M (2022) Mapping chromatin loops in single cells. Trends Genet. 38(7):637-640. [abstract] [full-text] [pdf]
  56. Zhao B, Li T, Smith SM, Xiong D, Wang X, Yang Y, Luo T, Zhu Z, Shan Y, Matoba N, Sun Q, Yang Y, Hauberg ME, Bendl J, Fullard JF, Roussos P, Lin W, Li Y, Stein JL, Zhu H (2022) Common variants contribute to intrinsic human brain functional networks. Nat Genet. 54(4):508-517. [abstract] [PDF] [BIG-KP]
  57. Van Buren E, Hu M, Cheng L, Wrobel J, Wilhelmsen K, Su L, Li Y#, Wu D# (2022) TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation. Brief Bioinform. doi: 10.1093/bib/bbac084. [abstract] [full-text] [pdf] [GitHub]
  58. Liyanage JSS, Estepp JH, Srivastava K, Li Y, Mori M, Kang G (2022) GMEPS: a fast and efficient likelihood approach for genome-wide mediation analysis under extreme phenotype sequencing. Stat Appl Genet Mol Biol. 21(1). doi: 10.1515/sagmb-2021-0071. [abstract] [full-text]
  59. Rowland B, Huh R, Hou Z, Crowley C, Wen J, Shen Y, Hu M, Giusti-Rodríguez P, Sullivan PF, Li Y (2022) THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data. PLoS Genet. 18(3):e1010102. [abstract] [PDF] [GitHub]
  60. Liu W, Sun Q, Huang L, Bhattacharya A, Wang GW, Tan X, Kuban KCK, Joseph RM, O'Shea TM, Fry RC#, Li Y#, Santos HP Jr#(2022) Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm. J Neurodev Disord. 14(1):16. [abstract] [PDF]
  61. Rowland B, Venkatesh S, Tardaguila M, Wen J, Rosen JD, Tapia AL, Sun Q, Graff M, Vuckovic D, Lettre G, Sankaran VG, Voloudakis G, Roussos P, Huffman JE, Reiner AP, Soranzo N, Raffield LM, Li Y (2022) Transcriptome-wide association study in UK biobank Europeans identifies associations with blood cell traits. Hum Mol Genet. doi: 10.1093/hmg/ddac011. [abstract] [full-text] [pdf]
  62. Bhattacharya A, Freedman AN, Avula V, Harris R, Liu W, Pan C, Lusis AJ, Joseph RM, Smeester L, Hartwell HJ, Kuban KCK, Marsit CJ, Li Y, O'Shea TM, Fry RC, Santos HP Jr (2022) Placental genomics mediates genetic associations with complex health traits and disease. Nat Commun. 13(1):706. [abstract] [PDF]
  63. Wen J*, Lagler TM*, Sun Q, Yang Y, Chen J, Harigaya Y, Sankaran VG, Hu M, Reiner AP, Raffield LM, Li Y (2022) Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types. PLoS Genet. 18(1):e1009984. [abstract] [PDF]
  64. Sun Q*, Liu W*, Rosen JD, Huang L, Pace RG, Dang H, Gallins PJ, Blue EE, Ling H, Corvol H, Strug LJ, Bamshad MJ, Gibson RL, Pugh EW, Blackman SM, Cutting GR, O'Neal WK, Zhou Y, Wright FA, Knowles MR, Wen J#, Li Y#, on behalf of the Cystic Fibrosis Genome Project (2022) Leveraging TOPMed imputation server and constructing a cohort-specific imputation reference panel to enhance genotype imputation among cystic fibrosis patients. HGG Adv. doi.org/10.1016/j.xhgg.2022.100090. [abstract] [PDF]
  65. Sun Q*, Crowley CA*, Huang L, Wen J, Chen J, Bao EL, Auer PL, Lettre G, Reiner AP, Sankaran VG, Raffield LM, Li Y (2022) From GWAS variant to function: A study of ∼148,000 variants for blood cell traits. HGG Adv. 3(1):100063. [abstract] [PDF] [web]
  66. Inoue Y, Graff M, Howard AG, Highland HM, Young KL, Harris KM, North KE, Li Y, Duan Q, Gordon-Larsen P (2022) Do adverse childhood experiences and genetic obesity risk interact in relation to body mass index in young adulthood? Findings from the National Longitudinal Study of Adolescent to Adult Health. Pediatr Obes. doi: 10.1111/ijpo.12885. [abstract] [PDF]
  67. Yang Y*, Sun Q*, Huang L, Broome JG, Correa A, Reiner A; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Raffield LM#, Yang Y#, Li Y# (2022) eSCAN: scan regulatory regions for aggregate association testing using whole-genome sequencing data. Brief Bioinform. 23(1):bbab497 [abstract] [PDF] [web]
  68. Tapia AL, Rowland BT, Rosen JD, Preuss M, Young K, Graff M, Choquet H, Couper DJ, Buyske S, Bien SA, Jorgenson E, Kooperberg C, Loos RJF, Morrison AC, North KE, Yu B, Reiner AP, Li Y#, Raffield LM# (2022) A large-scale transcriptome-wide association study (TWAS) of 10 blood cell phenotypes reveals complexities of TWAS fine-mapping. Genet Epidemiol. 46(1):3-16. [abstract] [PDF] [web]

    2021

  69. Olson NC, Raffield LM, Moxley AH, Miller-Fleming TW, Auer PL, Franceschini N, Ngo D, Thornton TA, Lange EM, Li Y, Nickerson DA, Zakai NA, Gerszten RE, Cox NJ, Correa A, Mohlke KL, Reiner AP (2021) Soluble Urokinase Plasminogen Activator Receptor: Genetic Variation and Cardiovascular Disease Risk in Black Adults. Circ Genom Precis Med. 14(6):e003421. [abstract] [PDF]
  70. Mikhaylova AV, McHugh CP, Polfus LM, Raffield LM, ..., Sun Q, ..., Li Y, ..., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Reiner AP, Auer PL (2021) Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program. Am J Hum Genet. Sep 23:S0002-9297(21)00306-2. doi: 10.1016/j.ajhg.2021.08.007. [abstract] [PDF]
  71. Rosen JD, Yang Y, Abnousi A, Chen J, Song M, Jones IR, Shen Y, Hu M, Li Y# (2021) HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets. Current issues in molecular biology 108(5):874-893. [abstract] [PDF] [GitHub]
  72. Little A, Hu Y, Sun Q, ..., Li Y, Auer PL, Thornton T, Reiner AP, Johnson AD, Raffield LM# (2021) Whole genome sequence analysis of platelet traits in the NHLBI trans-omics for precision medicine initiative. Human molecular genetics doi: 10.1093/hmg/ddab252. [abstract] [PDF]
  73. Ren X, Wang M, Li B, Jamieson K, Zheng L, Jones IR, Li B, Takagi MA, Lee J, Maliskova L, Tam TW, Yu M, Hu R, Lee L, Abnousi A, Li G, Li Y, Hu M, Ren B, Wang W, Shen Y (2021) Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Science advances doi: 10.1126/sciadv.abi4360. [abstract] [PDF]
  74. Ma H, Liu Z, Yang Y, Feng D, Dong Y, Garbutt TA, Hu Z, Wang L, Luan C, Cooper CD, Li Y, Welch JD, Qian L, Liu J (2021) Functional coordination of non-myocytes plays a key role in adult zebrafish heart regeneration. EMBO Rep. 22(11):e52901. [abstract] [PDF]
  75. Liu W, Yang Y, Abnousi A, Zhang Q, Kubo N, Beem JSM, Li Y#, Hu M# (2021) MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples. HGG advances. doi: 10.1016/j.xhgg.2021.100036. [abstract] [PDF] [software]
  76. Yu M, Abnousi A, Zhang Y, Li G, Lee L, Chen Z, Fang R, Lagler TM, Yang Y, Wen J, Sun Q, Li Y, Ren B, Hu M (2021) SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. Nature methods doi: 10.1038/s41592-021-01231-2. [abstract] [PDF] [GitHub]
  77. Li G, Luan C, Dong Y, Xie Y, Zentz SC, Zelt R, Roach J, Liu J, Qian L, Li Y#, Yang Y# (2021) ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte Cells. Int J Mol Sci. doi: 10.3390/ijms22168943. [abstract] [PDF] [web]
  78. Zheng X, Zhong W, O'Connell CM, Liu Y, Haggerty CL, Geisler WM, Anyalechi GE, Kirkcaldy RD, Wiesenfeld HC, Hillier SL, Steinkampf MP, Hammond KR, Fine J, Li Y, Darville T (2021) Host Genetic Risk Factors for Chlamydia trachomatis-Related Infertility in Women. J Infect Dis. doi: 10.1093/infdis/jiab149. [abstract] [pdf]
  79. Sun Q, Graff M, Rowland B, Wen J, Huang L, Miller-Fleming TW, Haessler J, Preuss MH, Chai JF, Lee MP, Avery CL, Cheng CY, Franceschini N, Sim X, Cox NJ, Kooperberg C, North KE, Li Y#, Raffield LM# (2021) Analyses of biomarker traits in diverse UK biobank participants identify associations missed by European-centric analysis strategies. Journal of human genetics doi: 10.1038/s10038-021-00968-0. [abstract] [PDF]
  80. Wen J, Xie M, Rowland B, Rosen JD, Sun Q, Chen J, Tapia AL, Qian H, Kowalski MH, Shan Y, Young KL, Graff M, Argos M, Avery CL, Bien SA, Buyske S, Yin J, Choquet H, Fornage M, Hodonsky CJ, Jorgenson E, Kooperberg C, Loos RJF, Liu Y, Moon JY, North KE, Rich SS, Rotter JI, Smith JA, Zhao W, Shang L, Wang T, Zhou X, Reiner AP, Raffield LM, Li Y# (2021) Transcriptome-Wide Association Study of Blood Cell Traits in African Ancestry and Hispanic/Latino Populations. Genes doi: 10.3390/genes12071049. [abstract] [PDF]
  81. Filer DL, Kuo F, Brandt AT, Tilley CR, Mieczkowski PA, Berg JS, Robasky K, Li Y, Bizon C, Tilson JL, Powell BC, Bost DM, Jeffries CD, Wilhelmsen KC (2021) Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing. BMC Bioinformatics 22(1):374. [abstract] [PDF]
  82. Hu B, Won H, Mah W, Park RB, Kassim B, Spiess K, Kozlenkov A, Crowley CA, Pochareddy S, Li Y, Dracheva S, Sestan N, Akbarian S, Geschwind DH(2021) Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders. Nat Commun. 12(1):3968. [abstract] [PDF]
  83. Zhao B, Li T, Yang Y, Wang X, Luo T, Shan Y, Zhu Z, Xiong D, Hauberg ME, Bendl J, Fullard JF, Roussos P, Li Y, Stein JL, Zhu H (2021) Common genetic variation influencing human white matter microstructure. Science doi: 10.1126/science.abf3736. [abstract] [PDF]
  84. Hu Y, Bien SA, Nishimura KK, Haessler J, Hodonsky CJ, Baldassari AR, Highland HM, Wang Z, Preuss M, Sitlani CM, Wojcik GL, Tao R, Graff M, Huckins LM, Sun Q, Chen MH, Mousas A, Auer PL, Lettre G, Tang W, Qi L, Thyagarajan B, Buyske S, Fornage M, Hindorff LA, Li Y, Lin D, Reiner AP, North KE, Loos RJF, Raffield LM, Peters U, Avery CL, Kooperberg C (2021) Multi-ethnic genome-wide association analyses of white blood cell and platelet traits in the Population Architecture using Genomics and Epidemiology (PAGE) study. BMC genomics. 22(1):432. [abstract] [PDF]
  85. You C, Zhou Z, Wen J, Li Y, Pang CH, Du H, Wang Z, Zhou XH, King DA, Liu CT, Huang J (2021) Polygenic Scores and Parental Predictors: An Adult Height Study Based on the United Kingdom Biobank and the Framingham Heart Study. Front Genet. 12:669441. doi: 10.3389/fgene.2021.669441. [abstract] [PDF]
  86. Zhao B, Shan Y, Yang Y, Yu Z, Li T, Wang X, Luo T, Zhu Z, Sullivan P, Zhao H, Li Y#, Zhu H# (2021) Transcriptome-wide association analysis of brain structures yields insights into pleiotropy with complex neuropsychiatric traits. Nat Commun. 12(1):2878. [abstract] [PDF]
  87. Gondalia R, ..., Li Y, ..., Whitsel EA (2021) Epigenetically mediated electrocardiographic manifestations of sub-chronic exposures to ambient particulate matter air pollution in the Women's Health Initiative and Atherosclerosis Risk in Communities Study. Environ Res. doi: 10.1016/j.envres.2021.111211. [abstract] [PDF]
  88. Hu Y, ..., Raffield LM, ..., Sun Q, ..., Li Y, ..., Reiner AP; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium (2021) Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. Am J Hum Genet. 108(5):874-893. [abstract] [PDF]
  89. Zhu A, Matoba N, Wilson EP,Tapia AL, Li Y, Ibrahim JG, Stein JL, Love MI (2021) MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity. PLoS Genet. 17(4):e1009455. [abstract] [PDF] [software]
  90. Yang Y, Li G, Xie Y, Wang L, Yang Y, Liu J, Qian Li#, Li Y# (2021) iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement. [abstract] [PDF] [GitHub] [LiLabSoftware]
  91. Jiang Y, Li W, Lindsey-Boltz LA, Yang Y, Li Y, Sancar A (2021) Super hotspots and super coldspots in the repair of UV-induced DNA damage in the human genome. The Journal of biological chemistry doi: 10.1016/j.jbc.2021.100581. [abstract] [PDF]
  92. Bhattachary A, Li Y, Love MI (2021) MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies. PLoS Genet. 17(3):e1009398. [abstract] [PDF] [software]
  93. Taliun A, ..., Abecasis GR (2021) Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 590(7845):290-299. [abstract] [PDF]
  94. Lagler TM, Yang Y, Abnousi A, Hu M, Li Y# (2021) HiC-ACT: Improved Detection of Chromatin Interactions from Hi-C Data via Aggregated Cauchy Test. American Journal of Human Genetics 108, 257–268. [abstract] [PDF] [software]
  95. Crowley C, Yang Y, Qiu Y, Hu B, Abnousi A, Lipiński J, Plewczyński D, Wu D, Won H, Ren B, Hu M, Li Y# (2021) FIREcaller: Detecting frequently interacting regions from Hi-C data. Comput Struct Biotechnol J. 19:355-362. [abstract] [PDF] [software]
  96. Lin B, ..., Raffield LM, ..., Qian H, ..., Li Y, ..., Franceschini N (2021) Whole genome sequence analyses of eGFR in 23,732 people representing multiple ancestries in the NHLBI trans-omics for precision medicine (TOPMed) consortium. EBioMedicine doi:10.1016/j.ebiom.2020. [abstract] [PDF]
  97. Do WL, Whitsel EA, Costeira R, Masachs OM, Le Roy CI, Bell JT, RStaimez L, Stein AD, Smith AK, Horvath S, Assimes TL, Liu S, Manson JE, Shadyab AH, Li Y, Hou L, Bhatti P, Jordahl K, Narayan KMV, Conneely KN (2021) Epigenome-wide association study of diet quality in the Women's Health Initiative and TwinsUK cohort. Int J Epidemiol. doi: 10.1093/ije/dyaa215. [abstract] [PDF]
  98. Zhong W, Darville T, Zheng X#, Fine J#, Li Y# (2021) Generalized Multi-SNP Mediation Intersection-Union Test. Biometrics doi: 10.1111/biom.13418. [abstract] [PDF]
  99. Bruinsma RL, Fajgenbaum K, Yang Y, Del Mar Melendez-Gonzalez M, Mohlke KL, Li Y, Sayed C (2021) Assessment of Familial Risk in Patients with Hidradenitis Suppurativa. The British journal of dermatology doi:10.1111/bjd.19664. [abstract] [PDF]
    Top

    2020

  100. Song M, ..., Wen J, Rosen JD,..., Liu W, ..., Li Y, ..., Hu M, Shen Y (2020) Cell-type-specific 3D epigenomes in the developing human cortex. Nature [abstract] [PDF]
  101. Li G, Raffield LM, Logue M, Miller MW, Santos HP Jr, O'Shea TM, Fry RC, Li Y# (2020) CUE: CpG impUtation ensemble for DNA methylation levels across the human methylation450 (HM450) and EPIC (HM850) BeadChip platforms. Epigenetics doi: 10.1080/15592294.2020. [abstract] [PDF] [software]
  102. Van Buren E, Hu M, Weng C, Jin F, Li Y, Wu D#, Li Y# (2020) TWO-SIGMA: A novel two-component single cell model-based association method for single-cell RNA-seq data. Genet Epidemiol. doi: 10.1002/gepi.22361. [abstract] [PDF] [software]
  103. Spracklen CN, ..., Li Y, ..., Mohlke KL (2020) Adiponectin GWAS loci harboring extensive allelic heterogeneity exhibit distinct molecular consequences. PLoS Genet. 16(9):e1009019. [abstract] [PDF]
  104. Justice AE, ..., Li Y, ..., North KE (2020) Methylome-wide association study of central adiposity implicates genes involved in immune and endocrine systems. Epigenomics 12(17):1483-1499. [abstract] [PDF]
  105. Vuckovic D, ..., Raffield LM, ..., Qian H, ..., Rosen JD, ..., Li Y, ..., Sankaran VG, Soranzo N (2020) The Polygenic and Monogenic Basis of Blood Traits and Diseases. Cell 182(5):1214-1231. [abstract] [PDF]
  106. Chen MH*, Raffield LM*, Mousas A*, ..., Qian H, ..., Rosen JD, ..., Li Y, ..., Auer PL, Lettre G (2020) Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations. Cell 182(5):1198-1213 [abstract] [PDF]
  107. Matoba N, Liang D, Sun H, Aygün N, McAfee JC, Davis JE, Raffield LM, Qian H, Piven J, Li Y, Kosuri S, Won H, Stein JL (2020) Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism. Translational psychiatry 10, 265. [abstract] [PDF]
  108. Colicino E, ..., Zhang G, ..., Li Y, ..., Baccarelli A (2020) Blood DNA methylation sites predict death risk in a longitudinal study of 12, 300 individuals. Aging 12(14): 14092-14124. [abstract] [PDF]
  109. Qian H, Kowalski MH, Kramer HJ, Tao R, Lash JP, Stilp AM, Can J, Li Y, Franceschini N (2020) Genome-wide Association of Kidney Traits in Hispanics/Latinos Using Dense Imputed Whole Genome Sequencing Data: The Hispanic Community Health Study/Study of Latinos. Circ Genom Precis Med [abstract] [PDF]
  110. Lu L, ..., Rosen JD, Xu Z, ..., Li Y, ..., Jin F (2020) Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases. Mol Cell. [abstract] [PDF]
  111. Yang Y, Li G, Qian H, Wilhelmsen KC, Shen Y, Li Y (2020) SMNN: batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection. Brief Bioinform. [abstract] [PDF] [software]
  112. Yang X, Bergenholtz S, Maliskova L, Pebworth MP, Kriegstein AR, Li Y, Shen Y, Szatkiewicz JP (2020) SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription. PLoS One 15(4):e0228760 [abstract] [PDF]
  113. Yang Y, Li Y, Sancar A, Oztas O (2020) The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation. The Journal of Biological Chemistry [abstract] [PDF]
  114. Halvorsen M*, Huh R*, Oskolkov N*, Wen J*, ..., Li Y, ..., Sullivan PF, Szatkiewicz JP (2020) Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia. Nat Commun. [abstract] [PDF]
  115. Hodonsky CJ, Baldassari AR, Bien SA, Raffield LM, Highland HM, Sitlani CM, Wojcik GL, Tao R, Graff M, Tang W, Thyagarajan B, Buyske S, Fornage M, Hindorff LA, Li Y, Lin D, Reiner AP, North KE, Loos RJF, Kooperberg C, Avery CL (2020) Ancestry-specific associations identified in genome-wide combined-phenotype study of red blood cell traits emphasize benefits of diversity in genomics. BMC Genomics 21(1):228. doi: 10.1186/s12864-020-6626-9. [abstract] [PDF]
  116. Zhong W, Dong L, Poston TB, Darville T, Spracklen CN, Wu D, Mohlke KL, Li Y, Li Q, Zheng X (2020) Inferring Regulatory Networks From Mixed Observational Data Using Directed Acyclic Graphs. Front Genet [abstract] [PDF]
  117. Dong M, Thennavan A, Urrutia E, Li Y, Perou CM, Zou F, Jiang Y (2020) SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references. Brief Bioinform. [abstract] [PDF]
  118. Gondalia R, ..., Li Y, Hou L, Baccarelli AA, Whitsel EA (2020) Leukocyte Traits and Exposure to Ambient Particulate Matter Air Pollution in the Women's Health Initiative and Atherosclerosis Risk in Communities Study. Environ Health Perspect. 128(1):17004. [abstract] [PDF]
  119. Raffield LM, ..., Kowalski MH, ..., Li Y, ..., Auer PL; TOPMed Inflammation Working Group; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium (2020) Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts. Am J Hum Genet. 106(1):112-120. [abstract] [PDF]
  120. Kowalski MH*, Qian H*, Hou Z, Rosen JD, Tapia AL, Shan Y, Jain D, ..., TOPMed Hematology & Hemostasis Working Group, Raffield LM#, Reiner AP#, Li Y# (2020) Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations. PLoS Genet 15(12):e1008500 [abstract] [PDF]
  121. Huh R, Yang Y, Jiang Y, Shen Y, Li Y# (2020) SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble. Nucleic Acids Res [abstract] [PDF] [software]
    Top

    2019

  122. 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]
  123. Li G, Yang Y, Van Buren E, Li Y# (2019) Dropout imputation and batch effect correction for single-cell RNA sequencing data. Journal of Bio-X Research 2, 169-177. [PDF]
  124. 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]
  125. 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. 26(8):3943-3955. [abstract] [PDF]
  126. 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]
  127. 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]
  128. 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]
  129. 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]
  130. 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]
  131. 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]
  132. Zhong W, Spracklen CN, Mohlke KL, Zheng X#, Fine J#, Li Y# (2019) Multi-SNP mediation intersection-union test. Bioinformatics [abstract] [PDF] [github (latest)] [CRAN (old)]
  133. 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]
  134. 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]
  135. 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]
    Top

    2018

  136. Li M, ..., Li Y, ..., Sestan N (2018) Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 362(6420). [abstract] [PDF]
  137. Wang Y, Zhang B, Zhang L, An L, Xu J, Li D, Choudhary M, Li Y, Hu M, Hardison R, Wang T, Yue F (2018) The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biology 19(1):151. [abstract] [PDF] [web]
  138. 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]
  139. 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]
  140. 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]
  141. 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 21(1):33-49. [abstract] [PDF]
  142. 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]
  143. 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]
  144. 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]
  145. Li Y, Hu M, Shen Y (2018) Gene Regulation in the 3D Genome. Hum Mol Genet. 27(R2):R228-R233. [abstract] [PDF]
  146. 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]
  147. 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]
  148. 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]
  149. 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]
  150. 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]
  151. 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]
  152. 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]
  153. 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]
  154. 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]
  155. 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]
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    2017

  156. 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]
  157. 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]
  158. 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]
  159. 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]
  160. 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]
  161. 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]
  162. 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]
  163. 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]
  164. 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]
  165. 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]
  166. 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]
  167. 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]
  168. 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]
  169. 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]
  170. 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]
  171. 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]
  172. 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]
  173. 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]
  174. 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]
  175. 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]
  176. 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]
    Top

    2016

  177. 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]
  178. 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]
  179. 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]
  180. 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]
  181. 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]
  182. 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]
  183. 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]
    Top

    2015

  184. 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]
  185. 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]
  186. 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]
  187. 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]
  188. The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation. Nature 526(7571):68-74. [abstract] [PDF] [supplementary]
  189. 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]
  190. 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]
  191. 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]
  192. 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]
  193. 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]
  194. 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]
  195. 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]
  196. 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]
  197. 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]
  198. 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]
  199. 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]
  200. 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]
  201. 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]
  202. 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]
  203. 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]
    Top

    2014

  204. 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]
  205. 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]
  206. 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]
  207. 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]
  208. 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]
  209. 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]
  210. 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]
  211. 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]
  212. 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]
    Top

    2013

  213. Wu Y, Marvelle AF, Li J, Croteau-Chonka DC, Feranil AB, Kuzawa CW, Li Y, Adair LS, Mohlke KL (2013) Genetic association with lipids in Filipinos: waist circumference modifies an APOA5 effect on triglyceride levels. J Lipid Res 54(11):3198-205. [abstract] [PDF]
  214. Franceschini N, Fox E, ..., Duan Q, Li Y, ..., Keating BJ, Zhu X (2013) 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]
  215. Duan Q*, Liu EY*, Auer PL*, Zhang G*, ..., Lange LA#, Li Y# (2013) Imputation of coding variants in African Americans: better performance using data from the exome sequencing project. Bioinformatics 29(21):2744-9. [abstract] [PDF] [supplementary]
  216. Byrnes AE, Wu MC, Wright FA, Li M, Li Y# (2013) The value of statistical or bioinformatics annotation for rare variant association with quantitative trait. Genetic Epidemiology 37(7):666-74. [abstract] [PDF]
  217. 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 (2013) 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]
  218. 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 (2013) Risk prediction of esophageal squamous-cell carcinoma with common genetic variants and lifestyle factors in Chinese population. Carcinogenesis 34(8):1782-17866. [abstract] [PDF]
  219. 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 (2013) The Case-Only Test for Gene-Environment Interaction is Not Uniformly Powerful: An Empirical Example. Genetic Epidemiology 37(4):402-7. [abstract] [PDF]
  220. 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 (2013) Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies. Nucleic Acids Research 41(7):e88. [abstract] [PDF]
  221. Kang J*, Huang KC*, Xu Z, Wang Y, Abecasis GR, Li Y# (2013) AbCD: arbitrary coverage design for sequencing-based genetic studies. Bioinformatics 29(6):799-801. [abstract] [PDF]
  222. Duan Q, Liu EY, Croteau-Chonka DC, Mohlke KL, Li Y# (2013) A comprehensive SNP and indel imputability database. Bioinformatics 29(4):528-31. [abstract] [PDF] [web]
    Top

    2012

  223. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56-65. [abstract] [PDF]
  224. Butler AM, Yin X, ..., Li Y, ..., Avery CL (2012) 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]
  225. 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*# (2012) 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]
  226. Liu EY, Li M, Wang W, Li Y# (2012) MaCH-Admix: Genotype Imputation for Admixed Populations. Genetic Epidemiology 37(1):25-37. [abstract] [PDF] [web]
  227. Chen W, Li B, Zeng Z, Sanna S, Sidore C, Busonero F, Kang HM, Li Y, Abecasis G (2012) Genotype calling and haplotyping in parent-offspring trios. Genome Research 23(1):142-51. [abstract] [PDF] [wiki]
  228. Mao X, Li Y, Liu Y, Lange L, Li M (2012) Testing Genetic Association With Rare Variants in Admixed Populations. Genetic Epidemiology 37(1):38-47. [abstract] [PDF]
  229. Wu C, Kraft P, Zhai K, Chang J, Wang Z, Li Y, ..., Lin D (2012) 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]
  230. Huang J, Liu EY, Welch R, Willer C, Hindorff LA, Li Y# (2012) WikiGWA: an open platform for collecting and using genome-wide association results. Eur J Hum Genet 21(4):471-3. [abstract] [PDF] [web]
  231. Li Y, Chen W, Liu EY, Zhou YH (2012) Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data. Statistics in Biosciences [online] [PDF]
  232. 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 (2012) An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337(6090):100-104. [abstract] [PDF]
  233. Dastani Z, Hivert MF, ..., Li Y, ..., Richards JB (2012) 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]
  234. Palmer ND, McDonough CW, ..., Li Y, ..., Bowden DW (2012) A genome-wide association search for type 2 diabetes genes in African Americans. PLoS One 7(1):e29202. [abstract] [PDF]
  235. Huang J, Ellinghaus D, Franke A, Howie B, Li Y# (2012) 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]
  236. Liu EY*, Buyske S, ..., North KE, Li Y# (2012) 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]
  237. Cho YS, Chen CH, ..., Li Y, ..., Mohlke KL, Kato N, Han BG, Seielstad M (2012) 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]
  238. Wu Y, McDade TW, Kuzawa CW, Borja J, Li Y, Adair LS, Mohlke KL, Lange LA (2012) 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]
  239. 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 (2012) Population-specific coding variant underlies genome-wide association with adiponectin level. Human Molecular Genetics 21(2):463-71. [abstract] [PDF]
    Top

    2011

  240. Chambers JC, Zhang W, ..., Li Y, ..., Elliott P, Kooner JS (2011) Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nat Genet. 43(11):1131-8. [abstract] [PDF]
  241. Li L, Li Y, Browning SR, Browning BL, Slater AJ, Kong X, Aponte JL, Mooser VE, Chissoe SL, Whittaker JC, Nelson MR, Ehm MG (2011) Performance of genotype imputation for rare variants identified in exons and flanking regions of genes. PLoS One 6(9):e24945. [abstract] [PDF]
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  243. Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X (2011) Rare-variant association testing for sequencing data with the sequence kernel association test. American Journal of Human Genetics 89(1):82-93. [abstract] [PDF]
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  245. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG (2011) Widespread RNA and DNA Sequence Differences in the Human Transcriptome. Science 333(6038):53-58. [abstract] [PDF]
  246. Conrad DF et al (2011) Variation in genome-wide mutation rates within and between human families. Nature Genetics 43(7):712-4. [abstract]
  247. Li Y, Sidore C, Kang HM, Boehnke M, Abecasis GR (2011) Low-coverage sequencing: Implications for design of complex trait association studies. Genome Research 21(6):940-951. [abstract] [PDF] [wiki]
  248. Wassel CL, Lange LA, ..., Li Y, ..., Reiner AP (2011) 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] [full article]
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    Top

    2010

  252. 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 (2010) 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]
  253. Zawistowski M, Gopalakrishnan S, Ding J, Li Y, Grimm S, Zollner S (2010) Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. American Journal of Human Genetics 87: 604-617. [abstract] [PDF]
  254. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genetic Epidemiology 34(8): 816-834. [abstract] [PDF] [wiki]
  255. Li Y, Byrnes AE, Li M (2010) 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]
  256. Sudmant PH et al (2010) Diversity of human copy number variation and multicopy genes. Science 330(6004):641-6. [abstract]
  257. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073. [abstract] [PDF]
  258. Stuart PE, Nair RP, Ellinghaus E, Ding J, Tejasvi T, Gudjonsson JE, Li Y, ..., Elder JT (2010) Genome-wide association analysis identifies three psoriasis susceptibility loci. Nat Genet. 42(11): 1000-4. [abstract] [PDF]
  259. Ellinghaus E, Ellinghaus D, ..., Li Y, ..., Franke A (2010) Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2. Nat Genet. 42(11): 991-995. [abstract] [PDF]
  260. Wu Y, Li Y, ..., Mohlke KL (2010) 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]
  261. Kapur K, Johnson T, ..., Li Y, ..., Bergmann S (2010) Genome-wide meta-analysis for serum calcium identifies significantly associated SNPs near the calcium-sensing receptor (CASR) gene. PLoS Genetics 6: e1001035. [abstract] [PDF]
  262. Willer CJ, Li Y, Abecasis GR (2010) METAL: Fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26: 2190-2191. [abstract] [PDF]
  263. Sanna S, Pitzalis M, ..., Li Y, ..., Schlessinger D, Cucca F (2010) Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis. Nat Genet. 42(6): 495-497. [abstract] [PDF]
  264. Chambers JC, Zhang W, ..., Li Y, ..., Kooner JS (2010) Genetic loci influencing kidney function and chronic kidney disease. Nat Genet. 42(5): 373-375. [abstract] [PDF]
  265. Lange LA, Croteau-Chonka DC, ..., Li Y, ..., Mohlke KL (2010) 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]
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    Top

    2009

  267. Chambers JC, Zhang W, Li Y, ..., Kooner JS (2009) Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels. Nat Genet. 41(11): 1170-1172. [abstract] [PDF]
  268. Li Y, Willer CJ, Sanna S, Abecasis GR (2009) Genotype imputation. Annual Review Genomics and Human Genetics 10: 387-406. [abstract] [PDF]
  269. 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): 235-50. [abstract] [PDF]
  270. Nair RP, Duffin KC, ..., Li Y, ..., Abecasis GR (2009) Genome-wide scan reveals association of psoriasis with IL-23 and NF-kB pathways. Nat Genet. 41(2): 199-204. [abstract] [PDF]
  271. Kathiresan S, Willer CJ, ..., Li Y, ..., Cupples LA (2009) Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet. 41(1): 56-65. [abstract] [PDF]
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    2008

  272. Yuan X, Waterworth D, ..., Li Y, ..., Kooner JS, Mooser V (2008) 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]
  273. Gaulton KJ, Willer CJ, Li Y, ..., Mohlke KL (2008) Comprehensive association study of type 2 diabetes and related quantitative traits with 222 candidate genes. Diabetes 57: 3136-44. [abstract] [PDF]
  274. 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. Nat Genet. 40(6):716-8. [abstract] [PDF]
  275. Zeggini E, Scott LJ, ..., Li Y, ..., Altshuler D (2008) 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]
  276. Willer CJ, Sanna S, ..., Li Y, ..., Abecasis GR (2008) Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet. 40(2):161-9. [abstract] [PDF]
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    2007

  277. Sabeti PC et al (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449(7164): 913-8. [abstract]
  278. The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-61. [abstract] [PDF]
  279. Scott JL, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, ..., Boehnke M (2007) A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316:1341-5. [abstract] [PDF]
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    2006

  280. Li M, Atmaca-Sonmez P, ..., Li Y, ..., Abecasis GR (2006) CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration. Nat Genet. 38:1049-54. [abstract] [PDF]
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