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  1. Zhao B, ..., Luo T, ..., Li Y, Stein JL, Zhu H (2022+) Heart-brain connections: phenotypic and genetic insights from 40,000 cardiac and brain magnetic resonance images. [preprint] [BIG-KP]
  2. 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]
  3. 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]


  1. 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] [GitHub]
  2. 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] [GitHub]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. Yu M, Li Y, Hu M (2022) Mapping chromatin loops in single cells. Trends Genet. 38(7):637-640. [abstract] [full-text]
  10. 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]
  11. 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] [GitHub]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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. [abstract] [PDF]
  19. 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]
  20. 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]
  21. 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]
  22. 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]


  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. 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]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
  44. 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]
  45. Bhattachary A, Li Y, Love MI (2021) MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies. PLoS Genet. 17(3):e1009398. [abstract] [PDF] [software]
  46. Taliun A, ..., Abecasis GR (2021) Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 590(7845):290-299. [abstract] [PDF]
  47. 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]
  48. 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]
  49. 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]
  50. 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]
  51. 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]
  52. 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]


  53. 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]
  54. 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]
  55. 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]
  56. 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]
  57. 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]
  58. 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]
  59. 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]
  60. 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]
  61. 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]
  62. 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]
  63. 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]
  64. 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]
  65. 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]
  66. 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]
  67. 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]
  68. 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]
  69. 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]
  70. 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]
  71. 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]
  72. 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]
  73. 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]
  74. 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]


  75. 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]
  76. 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]
  77. 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]
  78. 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]
  79. 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]
  80. 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]
  81. 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]
  82. 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]
  83. 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]
  84. 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]
  85. 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)]
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