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Personal profile

Personal profile

We are a small research group at the Penn State College of Medicine that works on statistical genetics, complex trait genetics and functional genomics. We actively develop novel methods and apply them to interesting datasets. We also generate datasets using high throughput genotyping and sequencing. More details can be found on our Research page from our lab website or on google scholar.

Lab URL: https://dajiangliu.blog 

Statistical Genetics: Our statistical genetics research focused on method development for analyzing large scale sequence-based association studies. We developed the widely-used software package RAREMETAL and RVTESTS for association analysis and meta-analysis. We are actively conducting research in this area to develop more efficient and powerful methods for studying the genetic basis for complex traits. 

Functional Genomics: We develop computational methods to interpret the GWAS findings using integrative approaches. We are also developing methods to study the functional genomics for X chromosome inactivation. 

Complex Traits: We study a few complex traits in great detail, including lipids and cardiovascular disease, smoking drinking addiction as well as lupus. Many of the applied projects offered interesting problems and motivated our methodology research. 

More details can be found in our publications. 

Selected Publications:

  1. 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: GenomeWebNIH/NIDA)
  2. Brazel DM*, Jiang Y*^, Hughey JM*^,…,Weissenkampen JD^,…, Liu DJ†, Vrieze SExome chip meta-analysis elucidates the genetic architecture of rare coding variants in smoking and drinking behaviorBiological Psychiatry (link)
  3. 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)
  4. 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 BLiu 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
  5. 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 individualsNature Genetics 2017;49(12):1758-1766.
  6. Zhan X, Hu Y, Li B, Abecasis GR & Liu DJ† RVTESTS: An Efficient and Comprehensive Tool for Rare Variant Association Analysis Using Sequence DataBioinformatics, 2016, DOI 10.1093/bioinformatics/btw079
  7. 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 associationNature Genetics,  46, 200–204 (2014)
  8. Zhan X*Liu DJ*  SEQMINER: An R-package to Facilitate the Functional Interpretation of Sequence-based AssociationsGenet Epidemiol. 2015 Sep 23. doi: 10.1002/gepi.21918
  9. Liu DJ†, Leal SM† A unified method for detecting secondary trait associations with rare variants: application to sequence dataPLOS Genetics 8(11): e1003075 (link)
  10. 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)
  11. Liu DJ†, Leal SM†  SEQCHIP: A powerful method to integrate sequence and genotype data for the detection of rare variant associationsBioinformatics 28(13):1745-1751 (link)
  12. Liu DJ, Leal SM† Replication Strategies for Rare Variant Complex Trait Association Studies via Next-Generation SequencingAm J Hum Genet 87:790-801 (link) (media coveage)
  13. 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)  


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Projects 2015 2022

Research Output 2010 2018

  • 1157 Citations
  • 17 h-Index
  • 32 Article
  • 1 Chapter
  • 1 Letter
1 Citations (Scopus)

Adaptive-weight burden test for associations between quantitative traits and genotype data with complex correlations

Wu, X., Guan, T., Liu, D., Novelo, L. G. L. & Bandyopadhyay, D., Sep 1 2018, In : Annals of Applied Statistics. 12, 3, p. 1558-1582 25 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program

The Geisinger-Regeneron DiscovEHR Collaboration, The VA Million Veteran Program, Global Lipids Genetics Consortium & Myocardial Infarction Genetics (MIGen) Consortium, Nov 1 2018, In : Nature Genetics. 50, 11, p. 1514-1523 10 p.

Research output: Contribution to journalArticle

Electronic Health Records
Abdominal Aortic Aneurysm
Hispanic Americans
2 Citations (Scopus)

Proper conditional analysis in the presence of missing data: Application to large scale meta-analysis of tobacco use phenotypes

Jiang, Y., Chen, S., McGuire, D., Chen, F., Liu, M., Iacono, W. G., Hewitt, J. K., Hokanson, J. E., Krauter, K., Laakso, M., Li, K. W., Lutz, S. M., McGue, M., Pandit, A., Zajac, G. J. M., Boehnke, M., Abecasis, G. R., Vrieze, S. I., Zhan, X., Jiang, B. & 1 othersLiu, D., Jul 1 2018, In : PLoS genetics. 14, 7, e1007452.

Research output: Contribution to journalArticle

tobacco use
Tobacco Use
32 Citations (Scopus)

Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

Turcot, V., Lu, Y., Highland, H. M., Schurmann, C., Justice, A. E., Fine, R. S., Bradfield, J. P., Esko, T., Giri, A., Graff, M., Guo, X., Hendricks, A. E., Karaderi, T., Lempradl, A., Locke, A. E., Mahajan, A., Marouli, E., Sivapalaratnam, S., Young, K. L., Alfred, T. & 379 othersFeitosa, M. F., Masca, N. G. D., Manning, A. K., Medina-Gomez, C., Mudgal, P., Ng, M. C. Y., Reiner, A. P., Vedantam, S., Willems, S. M., Winkler, T. W., Abecasis, G., Aben, K. K., Alam, D. S., Alharthi, S. E., Allison, M., Amouyel, P., Asselbergs, F. W., Auer, P. L., Balkau, B., Bang, L. E., Barroso, I., Bastarache, L., Benn, M., Bergmann, S., Bielak, L. F., Blüher, M., Boehnke, M., Boeing, H., Boerwinkle, E., Böger, C. A., Bork-Jensen, J., Bots, M. L., Bottinger, E. P., Bowden, D. W., Brandslund, I., Breen, G., Brilliant, M. H., Broer, L., Brumat, M., Burt, A. A., Butterworth, A. S., Campbell, P. T., Cappellani, S., Carey, D. J., Catamo, E., Caulfield, M. J., Chambers, J. C., Chasman, D. I., Chen, Y. D. I., Chowdhury, R., Christensen, C., Chu, A. Y., Cocca, M., Cook, J. P., Corley, J., Corominas Galbany, J., Cox, A. J., Crosslin, D. S., Cuellar-Partida, G., D'Eustacchio, A., Danesh, J., Davies, G., Bakker, P. I. W., Groot, M. C. H., Mutsert, R., Deary, I. J., Dedoussis, G., Demerath, E. W., Heijer, M., Hollander, A. I., Ruijter, H. M., Dennis, J. G., Denny, J. C., Angelantonio, E., Drenos, F., Du, M., Dubé, M. P., Dunning, A. M., Easton, D. F., Edwards, T. L., Ellinghaus, D., Ellinor, P. T., Elliott, P., Evangelou, E., Farmaki, A. E., Farooqi, I. S., Faul, J. D., Fauser, S., Feng, S., Ferrannini, E., Ferrieres, J., Florez, J. C., Ford, I., Fornage, M., Franco, O. H., Franke, A., Franks, P. W., Friedrich, N., Frikke-Schmidt, R., Galesloot, T. E., Gan, W., Gandin, I., Gasparini, P., Gibson, J., Giedraitis, V., Gjesing, A. P., Gordon-Larsen, P., Gorski, M., Grabe, H. J., Grant, S. F. A., Grarup, N., Griffiths, H. L., Grove, M. L., Gudnason, V., Gustafsson, S., Haessler, J., Hakonarson, H., Hammerschlag, A. R., Hansen, T., Harris, K. M., Harris, T. B., Hattersley, A. T., Have, C. T., Hayward, C., He, L., Heard-Costa, N. L., Heath, A. C., Heid, I. M., Helgeland, Ø., Hernesniemi, J., Hewitt, A. W., Holmen, O. L., Hovingh, G. K., Howson, J. M. M., Hu, Y., Huang, P. L., Huffman, J. E., Ikram, M. A., Ingelsson, E., Jackson, A. U., Jansson, J. H., Jarvik, G. P., Jensen, G. B., Jia, Y., Johansson, S., Jørgensen, M. E., Jørgensen, T., Jukema, J. W., Kahali, B., Kahn, R. S., Kähönen, M., Kamstrup, P. R., Kanoni, S., Kaprio, J., Karaleftheri, M., Kardia, S. L. R., Karpe, F., Kathiresan, S., Kee, F., Kiemeney, L. A., Kim, E., Kitajima, H., Komulainen, P., Kooner, J. S., Kooperberg, C., Korhonen, T., Kovacs, P., Kuivaniemi, H., Kutalik, Z., Kuulasmaa, K., Kuusisto, J., Laakso, M., Lakka, T. A., Lamparter, D., Lange, E. M., Lange, L. A., Langenberg, C., Larson, E. B., Lee, N. R., Lehtimäki, T., Lewis, C. E., Li, H., Li, J., Li-Gao, R., Lin, H., Lin, K. H., Lin, L. A., Lin, X., Lind, L., Lindström, J., Linneberg, A., Liu, C. T., Liu, D., Liu, Y., Lo, K. S., Lophatananon, A., Lotery, A. J., Loukola, A., Luan, JA., Lubitz, S. A., Lyytikäinen, L. P., Männistö, S., Marenne, G., Mazul, A. L., McCarthy, M. I., McKean-Cowdin, R., Medland, S. E., Meidtner, K., Milani, L., Mistry, V., Mitchell, P., Mohlke, K. L., Moilanen, L., Moitry, M., Montgomery, G. W., Mook-Kanamori, D. O., Moore, C., Mori, T. A., Morris, A. D., Morris, A. P., Müller-Nurasyid, M., Munroe, P. B., Nalls, M. A., Narisu, N., Nelson, C. P., Neville, M., Nielsen, S. F., Nikus, K., Njølstad, P. R., Nordestgaard, B. G., Nyholt, D. R., O'Connel, J. R., O'Donoghue, M. L., Olde Loohuis, L. M., Ophoff, R. A., Owen, K. R., Packard, C. J., Padmanabhan, S., Palmer, C. N. A., Palmer, N. D., Pasterkamp, G., Patel, A. P., Pattie, A., Pedersen, O., Peissig, P. L., Peloso, G. M., Pennell, C. E., Perola, M., Perry, J. A., Perry, J. R. B., Pers, T. H., Person, T. N., Peters, A., Petersen, E. R. B., Peyser, P. A., Pirie, A., Polasek, O., Polderman, T. J., Puolijoki, H., Raitakari, O. T., Rasheed, A., Rauramaa, R., Reilly, D. F., Renström, F., Rheinberger, M., Ridker, P. M., Rioux, J. D., Rivas, M. A., Roberts, D. J., Robertson, N. R., Robino, A., Rolandsson, O., Rudan, I., Ruth, K. S., Saleheen, D., Salomaa, V., Samani, N. J., Sapkota, Y., Sattar, N., Schoen, R. E., Schreiner, P. J., Schulze, M. B., Scott, R. A., Segura-Lepe, M. P., Shah, S. H., Sheu, W. H. H., Sim, X., Slater, A. J., Small, K. S., Smith, A. V., Southam, L., Spector, T. D., Speliotes, E. K., Starr, J. M., Stefansson, K., Steinthorsdottir, V., Stirrups, K. E., Strauch, K., Stringham, H. M., Stumvoll, M., Sun, L., Surendran, P., Swift, A. J., Tada, H., Tansey, K. E., Tardif, J. C., Taylor, K. D., Teumer, A., Thompson, D. J., Thorleifsson, G., Thorsteinsdottir, U., Thuesen, B. H., Tönjes, A., Tromp, G., Trompet, S., Tsafantakis, E., Tuomilehto, J., Tybjaerg-Hansen, A., Tyrer, J. P., Uher, R., Uitterlinden, A. G., Uusitupa, M., Laan, S. W., Duijn, C. M., Leeuwen, N., Van Setten, J., Vanhala, M., Varbo, A., Varga, T. V., Varma, R., Velez Edwards, D. R., Vermeulen, S. H., Veronesi, G., Vestergaard, H., Vitart, V., Vogt, T. F., Völker, U., Vuckovic, D., Wagenknecht, L. E., Walker, M., Wallentin, L., Wang, F., Wang, C. A., Wang, S., Wang, Y., Ware, E. B., Wareham, N. J., Warren, H. R., Waterworth, D. M., Wessel, J., White, H. D., Willer, C. J., Wilson, J. G., Witte, D. R., Wood, A. R., Wu, Y., Yaghootkar, H., Yao, J., Yao, P., Yerges-Armstrong, L. M., Young, R., Zeggini, E., Zhan, X., Zhang, W., Zhao, J. H., Zhao, W., Zhou, W., Zondervan, K. T., Rotter, J. I., Pospisilik, J. A., Rivadeneira, F., Borecki, I. B., Deloukas, P., Frayling, T. M., Lettre, G., North, K. E., Lindgren, C. M., Hirschhorn, J. N. & Loos, R. J. F., Jan 1 2018, In : Nature Genetics. 50, 1, p. 26-35 10 p.

Research output: Contribution to journalArticle

Energy Intake
Energy Metabolism
Body Mass Index

Rare loss of function variants in candidate genes and risk of colorectal cancer

NHLBI GO Exome Sequencing Project, Pulmonary Arterial Hypertension (PAH), Severe Asthma Research Program (SARP), Women’s Health Initiative (WHI), Anthropometry Project Team, Blood Count/Hematology Project Team, Blood Pressure Project Team, Data Flow Working Group, Early MI Project Team, ELSI Working Group, Executive Committee, Family Study Project Team, Lipids Project Team, Lung Project Team, Personal Genomics Project Team, Phenotype and Harmonization Working Group, Population Genetics and Statistical Analysis Working Group, Publications and Presentations Working Group, Quantitative Analysis Ad Hoc Task Group, Sequencing and Genotyping Working Group & 15 othersSteering Committee, Stroke Project Team, Structural Variation Working Group, Subclinical/Quantitative Project Team, Acute Lung Injury (ALI), Atherosclerosis Risk in Communities (ARIC), Cardiovascular Health Study (CHS), Chronic Obstructive Pulmonary Disease (COPDGene), Coronary Artery Risk Development in Young Adults (CARDIA), Cystic Fibrosis (CF), Early Pseudomonas Infection Control (EPIC), Framingham Heart Study (FHS), Jackson Heart Study (JHS), Lung Health Study (LHS) & Multi-Ethnic Study of Atherosclerosis (MESA), Oct 1 2018, In : Human genetics. 137, 10, p. 795-806 12 p.

Research output: Contribution to journalArticle

Colorectal Neoplasms
Genetic Testing