Selected Publications

*: Equal contribution
†: Corresponding author
^: Lab trainee

1. Khunsriraksakul C^, …, Tsoi LC*, Jiang B*, Liu DJ*† Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus Nature Communications, 2023 (link)
2. Chen F*^, Wang X*^, Jang S*, …, Jiang B†, Vrieze S†, Liu DJ† Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing, Nature Genetics, 2023 (link) (Media coverage: Penn State News).
3. Saunders G*, Wang X*^, Chen F*^, Jang S*, Liu M*, Wang C*^, …, Liu DJ†, Vrieze S†. Genetic diversity fuels gene discovery for tobacco and alcohol use. Nature. 2022 (link) (selected media coverage: Penn State News, Daily Mail, New Scientist, GenomeWeb, Nature Asia Nature News; Companion research briefing at Nature; WITF interview)
4. Yang S, Wang S, Wang Y, Rong R, Kim J, Li B, Koh AY, Xiao G, Li Q, Liu DJ†, Zhan X†. MB-SupCon: Microbiome-based predictive models via Supervised Contrastive Learning. J Mol Biol. 2022:167693. (link) (media coverage: Penn State News and Penn State Health News ).
5. Khunsriraksakul C^, McGuire D^, Sauteraud R^, Chen F^, Yang L^, Wang L^, Hughey J^, Eckert S^, Weissenkampen JD^, Shenoy G, Marx O, Carrel L, Jiang B†, Liu DJ†. Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association study, Nature Communications (link) (media coverage:  Penn State News and Penn State Health News).
6. Sauteraud R^, Stahl JM, James J, Englebright M, Chen F^, Zhan X, Carrel L†, Liu DJ† Inferring Genes that Escape X Chromosome Inactivation (with XCIR) Reveals Important Contribution of Variable Escape Genes to Sex-biased Diseases, Genome Research (link) (media coverage: Penn State News)
7. McGuire D^, Jiang Y^, Liu M, Weissenkampen JD^, Eckert S^, Yang L^, Chen F^, GSCAN, Berg A, Vrieze S, Jiang B†, Li Q† & Liu DJ† Model-based assessment of replicability for genome-wide association meta-analysis, Nature Communications (link) (media coverage: AcademicTimes, Penn State News)
8. Yang L^, Jiang S, Jiang B, Liu DJ†, Zhan X† Seqminer2: An Efficient Tool to Query and Retrieve Genotypes for Statistical Genetics Analyses from Biobank Scale Sequence Dataset, Bioinformatics (link)
9. Jiang Y*^, Chen S*, Wang X*^, …, Vrieze SI*, Jiang B†*, Zhan X†*, Liu DJ*, Association Analysis and Meta-Analysis of Multi-allelic Variants for Large Scale Sequence Data, Genes (link) (biorxiv)
10. Liu M*, Jiang Y^{*^}, Wedow R*, Li Y*, Chen F^,…, Liu DJ†, Vrieze S†, Association studies of 1.2 million individuals yield new insights in the genetic etiology of tobacco and alcohol use. Nature Genetics (link) (media coverage: GenomeWeb, NIH/NIDA,澎湃新闻, Penn State Health News, Penn State News, Fox43 TV Interview)
11. Brazel DM*, Jiang Y*^{^}, Hughey JM*^{^},…,Weissenkampen JD^,…, Liu DJ†, Vrieze S†. Exome chip meta-analysis elucidates the genetic architecture of rare coding variants in smoking and drinking behavior, Biological Psychiatry (link)(Companion Commentary) (media coverage: NIDA Notes )
12. Erzurumluoglu AM*, Liu M*, Jackson VE*, …,Jiang Y^, Chen F^,…, Tobin MD*, Vrieze S*, Liu DJ†*, Howson JMM†* Meta-analysis of up to 622,409 individuals identifies 41 novel smoking behaviour associated genetic loci Molecular Psychiatry (link)
13. Jiang Y*^, Chen S*, McGuire D^, Chen F^, Liu M, Iacono WG, Hewitt JK, Hokanson JE, Krauter K, Laakso M, Li KW, Lutz SM, McGue M, McGuire D, Pandit A, Zajac G, Boehnke M, Abecasis GR, Vrieze SI, Zhan X, Jiang B†, Liu DJ†. Proper Conditional Analysis in the Presence of Missing Data: Application to Large Scale Meta-analysis of Tobacco Use Phenotypes, PLOS Genetics 14(7):e1007452
14. Liu DJ*, Peloso GM*, Yu H*, Butterworth AS*, Wang X*, Mahajan A*, Saleheen D*, Emdin C*, …..,Howson JMM, Danesh J, McCarthy MI, Cowan CA, Abecasis G, Deloukas P, Musunuru K, Willer CJ, Kathiresan S. Exome-wide association study of plasma lipids in >300,000 individuals. Nature Genetics 2017;49(12):1758-1766.
15. Zhan X, Hu Y, Li B, Abecasis GR & Liu DJ† RVTESTS: An Efficient and Comprehensive Tool for Rare Variant Association Analysis Using Sequence Data, Bioinformatics, 2016, DOI 10.1093/bioinformatics/btw079
16. Liu DJ†*, Peloso GM*, Zhan X, Holmen O, Zawistowski M, Feng S, Nikpay M, Auer PL, Goel A, Zhang H, Peters U, Farrall M, Orho-Melander M, Kooperberg C, McPherson R, Watkins H, Willer CJ, Hveem, K, Melander O, Kathiresan S, Abecasis GR Meta-analysis of gene-level tests of rare variant association, Nature Genetics,  46, 200–204 (2014)
17. Zhan X*^†, Liu DJ*^†  SEQMINER: An R-package to Facilitate the Functional Interpretation of Sequence-based Associations, Genet Epidemiol. 2015 Sep 23. doi: 10.1002/gepi.21918
18. Liu DJ†, Leal SM† A unified method for detecting secondary trait associations with rare variants: application to sequence data, PLOS Genetics 8(11): e1003075 (link)
19. Liu DJ, Leal SM† Estimating genetic effects and quantifying missing heritability explained by identified rare variant associations, Am J Hum Genet 91:585-596 (link) (media coverage) (Highlights in Nature Genetics)
20. Liu DJ†, Leal SM†  SEQCHIP: A powerful method to integrate sequence and genotype data for the detection of rare variant associations, Bioinformatics 28(13):1745-1751 (link)
21. Liu DJ, Leal SM† Replication Strategies for Rare Variant Complex Trait Association Studies via Next-Generation Sequencing, Am J Hum Genet 87:790-801 (link) (media coveage)
22. Liu DJ, Leal SM^† A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions,PLOS Genetics 6:e1001156 (link) (media coverage)