Past Faculty - Nianjun Liu, Ph.D.

Nianjun Liu, Ph.D. Department of Biostatistics
Ryals Public Health Bldg
University of Alabama at Birmingham
Birmingham, AL 35294
Full CV
Current Location

Dr. Liu received his BS (Computational Mathematics) and MS (Applied Mathematics) from Peking University, and his M.Phil. and Ph.D. (Biostatistics) from Yale University. After getting his PhD, he joined the faculty of the University of Alabama at Birmingham where he is currently an associate professor in the Department of Biostatistics, the Section on Statistical Genetics. His research focuses on statistical genetics/genomics, bioinformatics, and clinical trial including genetic linkage and association analysis, disequilibrium mapping, haplotype analysis, population genetics, genome-wide-association studies and next-generation sequencing data analysis, pharmacogenomics, risk prediction, personalized medicine, and integrative analysis of multiple types of omics data. Dr. Liu not only dedicates in methodology development, he also has great interest and extensive experience in collaboration with researchers for a wide range of studies such as in obesity, cardiovascular diseases, lung injury, rheumatoid arthritis, mental disorders, cancer, Parkinson disease, organ transplant, pharmacogenetics and personalized medicine, and dental disorders.


  • F-SKAT (SNP Set/Sequence Association Test for familial data with various types of traits)

    F-SKAT is an R program for conducting SNP-set association tests for familial data with various types of traits based on kernel machine methods for data from candidate gene, GWAS, and genome-wide sequencing association studies.



  • 2015
  • 2014
  • 2013
  • 2012
  • 2011
  • 2010
  • 2009
  • 2008
  • 2007
  • 2006
  • 2005
  • pre 2005
  1. N. Liu (2015) QTL mapping – Current status and challenges: Comment on “Mapping complex traits as a dynamic system” by L. Sun and R. Wu. Physics of Life Reviews, [doi: 10.1016/j.plrev.2015.04.002]
  2. Q. Yan, D. E. Weeks, J. C. Celedón, H. K. Tiwari, B. Li, X. Wang, W. Lin, X. Lou, G. Gao, W. Chen, and N. Liu (2015) Associating Multivariate Quantitative Phenotypes with Genetic Variants in Family Samples with a Novel Kernel Machine Regression Method. Genetics (In press).
  3. Q. Yan, H. K. Tiwari, N. Yi, G. Gao, K. Zhang, W. Lin, XY. Lou, N. Liu* (2015) A Sequence Kernel Association Test for Dichotomous Traits in Family Samples under a Generalized Linear Mixed Model. Human Heredity 79(2):60-68. PMCID: Publisher provided directly to PMC.
  4. D. Zhi, N. Liu, K. Zhang (2015) On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative reads. Methods 79-80:41-6. [PMCID: PMC4437872]
  5. N. A. Limdi, T. M. Brown, Q. Yan, J. L. Thigpen, A. Shendre, N. Liu, C. E. Hill, D. K. Arnett, and T. M. Beasley (2015) Race influences warfarin dose changes associated with genetic factors. Blood (In press)
  6. W. Chen, C. Ren, H. Qin, K. J. Archer, W. Ouyang, N. Liu, X. Chen, X. Luo, X. Zhu, S. Sun, and G. Gao (2015) A Generalized Sequential Bonferroni Procedure for GWAS in Admixed Populations Incorporating Admixture Mapping Information into Association Tests. Human Heredity (In press)
  7. H. Akhter, C. Ballinger, T. van Groen, N. Liu, E. M. Postlethwait, and R. Liu (2015) Cyclic ozone exposure accelerates memory decline and induces gender-dependent neuropathology in an animal model of Alzheimer’s disease. Toxicological Sciences (In press)
  1. G. Chen, N. Liu, Y.C. Klimentidis, X. Zhu, D. Zhi, X. Wang, X. Lou (2014) A unified GMDR method for detecting gene-gene interactions in family and unrelated samples with application to nicotine dependence. Human Genetics 133(2):139-150. [PMCID: PMC3947150]
  2. W. Lin*, XY. Lou, G. Gao, N. Liu* (2014) Rare Variant Association Testing by Adaptive Combination of P-values. PLoS ONE, 9: e85728. [PMCID: PMC3893264]
  3. Q. Yan, H. K. Tiwari, N. Yi, W. Lin, G. Gao, X. Lou, X. Cui, and N. Liu* (2014) Kernel-Machine Testing Coupled with a Rank-Truncation Method for Genetic Pathway Analysis. Genetic Epidemiology 38(5): 447-456.[ PMCID: PMC4073214]
  4. J. Wu, G-B Chen, D. Zhi, N. Liu, K. Zhang (2014) A hidden Markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns. Front. Genet. 5:267. [PMCID: PMC4129397]
  5. H-M Xu, X-W Sun, T. Qi, W. Lin, N. Liu, XY. Lou (2014) Multivariate dimensionality reduction approaches to identify gene-gene and gene-environment interactions underlying multiple complex traits. PLoS ONE 9(9): e108103. [PMCID: PMC4178067]
  6. N. Liu, E. Archer, V. Srinivasasainagendra, DB Allison (2014) A Statistical Framework for Testing the Causal Effects of Fetal Drive. Front. Genet. 5:464. [doi: 10.3389/fgene.2014.00464] [PMCID: PMC4292723]
  1. W. Li n , O. Dubuisson, R . Rubicz, N. Liu , D . B. Allison, J . E. Cu rran, A.G. Comuzzie, J. Blangero, C . T. Leach, H . Göring, and N . V. Dhurandhar (201 3 ) . Long term changes in adiposity and glycemic control are associated with past adenovirus infection. Diabetes Care 3 6:701 - 707 . [PMCID: PMC3579356]
  2. M.A. Perera, L.H. Cavallari, N.A. Limdi, E.R. Gamazon, A. Konkashbaev, R. Daneshjou, A. Pluzhnikov, D.C. Crawford, J. Wang, N. Liu et al. (2013) Genetic variants associated with warfarin dose in African - American individuals: a genome - wide association study . Lancet 382(9894):790 - 6. [PMCID: PMC3759580]
  3. W. Chen, X. Chen, K.J. Archer, N. Liu , Q. Li, Z. Zhao, S. Sun, G. Gao (2013) A rapid association test procedure robust under different genetic models accounting for population str atification. Human Heredity 75:23 - 33. [PMCID: PMC3786013]
  4. W. Lin , N. Yi, X. Lou, D. Zhi, K. Zhang, G. Gao, H.K. Tiwari, N. Liu * (2013) Haplotype Kernel Association Test as a Powerful Method to Identify Chromosomal Regions Harboring Uncommon Causal Variant s. Genetic Epidemiology 37(6):560 - 70
  5. P. Li , H. Tiwari, W. Lin, D.B. Allison, W . Chung, R . Leibel, N. Yi, and N. Liu * (2013) Genetic Association Analysis of 30 Genes Related to Obesity in European American Population. International Journal of Obesity (Ac cepted). [PMCID: PMC3909018]
  1. D. Zhi, J. Wu, N. Liu, K. Zhang (2012) Genotype Calling from Next Generation Sequencing Data using Haplotype Information of Reads. Bioinformatics. 28(7): 938 - 946. [PMCID: PMC3493122]
  2. G. Gao, G. Kang, J. Wang, W. Chen, H. Qin, B. Jiang, Q. Li, C. Sun, N. Liu, K.J. Archer, D.B. Allison (2012) A Generalized Sequential Bonferroni Procedure Using Smoothed Weights for Genome-Wide Association Studies Incorporating Information on Hardy-Weinberg Disequilibrium among Cases. Hum Hered. 73:1-13. [PMID: 22212195]
  3. W. Lin, H.K. Tiwari, G. Gao, K. Zhang, J.J. Arcaroli, E. Abraham, N. Liu (2012) Similarity-based multi-marker association tests for continuous traits. Annals of Human Genetics. 76(3):246 - 260. [PMCID: PMC3329946]
  4. W. Lin , N. Yi, D. Zhi, K. Zhang, G. Gao, H.K. Tiwari, N. Liu * (2012) Haplotype - based methods for detecting uncommon causal variants with common SNPs . Genetic Epidemiology 36:572 - 58 2 . [PMCID: PMC3513398]
  5. W. Lin , N. Liu* (2012) Reducing Bias of Allele Frequency Estimates by Modeling SNP Genotype Data with Informative Missingness. Front. Gene. 3:107. [doi: 10.3389/fgene.2012.00107] [PMCID: PMC3376470]
  6. S. Wang , W. Chen , X. Chen, F. Hu, K . Archer, N. Liu , S. Sun and G. Gao (2012). Double genomic control is not effective to correct for population stratification in Meta - analysis for genome - wide association studies. Front. Gene. 3: 300. [doi:: 10.3389/fgene.2012.00300] [PMCID: PMC3529452]
  1. B. Zhang, D. Zhi, K. Zhang, G. Gao, N.A. Limdi, N. Liu (2011) Practical Consideration of Genotype Imputation: Sample Size, Window Size, Reference Choice, and Untyped Rate. Statistics and Its Interface Vol. 4, No. 3: 339-352. [PMCID: PMC3269888]
  2. W. Lin, B. Zhang, N. Yi, G. Gao, N. Liu (2011) Evaluation of pooled association tests for rare variant identification. BMC Proceedings 2011, 5(Suppl 9):S118. [PMID: 22373333] [PMCID: PMC3287842] [NIHMSID: NIHMS353951]
  3. W. Chen, X. Gao, J. Wang, C. Sun, W. Wan, D. Zhi, N. Liu, X. Chen, G. Gao (2011) Evaluation of association tests for rare variants using simulated data sets in the Genetic Analysis Workshop 17 data. BMC Proceedings 2011, 5(Suppl 9):S86. [PMID: 22373475] [PMCID: PMC3287927] [NIHMSID: NIHMS297654]
  4. N. Liu, H. Zhao, A. Patki, N.A. Limdi, D.B. Allison (2011) Controlling Population Structure in Human Genetic Association Studies with Samples of Unrelated Individuals. Statistics and Its Interface Vol. 4, No. 3: 317-326. [PMCID: PMC3269890]
  5. J. Arcaroli, N. Liu, N. Yi, E. Abraham (2011) Association between IL-32 genotypes and outcome in infection-associated acute lung injury. Critical Care, 15: R138. [PMCID: PMC3219007]
  6. N. Yi, N. Liu, D. Zhi, J. Li (2011) Hierarchical generalized linear models for multiple groups of rare and common variants: jointly estimating group and individual-variant effects. PLoS Genet 7(12): e1002382. [PMCID: PMC3228815]
  1. N.A. Limdi, M. Wadelius, L. Cavallari, N. Eriksson, D.C. Crawford, M.M. Lee, C. Chen, A. Motsinger-Reif, H. Sagreiya, N. Liu, A.H.B. Wu, B.F. Gage, A. Jorgensen, M. Pirmohamed, J. Shin, G. Suarez-Kurtz, S.E. Kimmel, J.A. Johnson, T.E. Klein and M.J. Wagner (2010) Warfarin Pharmacogenetics: A single VKORC1 polymorphism is predictive of dose across three racial groups. Blood Vol. 115, No. 18: 3827-3834. [PMCID: PMC2865873]
  1. W.K. Chung, A. Patki, N. Matsuoka, B.B. Boyer, N. Liu, S.K. Musani, A. Goropashnaya, P.L. Tan, N. Katsanis, S.B. Johnson, P.K. Gregersen, D.B. Allison, R.L. Leibel, H.K. Tiwari (2009) Analysis of 30 Genes (355 SNPS) Related to Energy Homeostasis for Association with Adiposity in European-American and Yup'ik Eskimo Populations. Human Heredity 67:193-205. [PMID: 19077438] [PMCID: PMC2715950]
  2. N. Liu, D. Zhang, H. Zhao (2009) Genotyping Error Detection in Samples of Unrelated Individuals without Replicate Genotyping. Human Heredity 67:154-162. [PMCID: PMC2782542]
  3. G. Kang, K. Ye, N. Liu, D. Allison, G. Gao (2009) Weighted Multiple Hypothesis Testing Procedures. Statistical Applications in Genetics and Molecular Biology Vol. 8: Iss. 1, Article 23 (DOI: 10.2202/1544-6115.1437). [PMCID: PMC2703613]
  4. N. Liu, R. Bucala, H. Zhao (2009) Modeling Informatively Missing Genotypes in Haplotype Analysis. Communications in Statistics – Theory and Methods 38(18): 3445 – 3460. [PMCID: PMC2801447]
  5. G. Kang, D. Childers, N. Liu, K. Zhang, G. Gao (2009) Genome-wide association studies of rheumatoid arthritis data via multiple hypothesis testing methods for correlated tests. BMC Proceedings 2009, 3(Suppl 7):S38. [PMCID: PMC2795936]
  6. D. Childers, G. Kang, N. Liu, G. Gao, K. Zhang (2009) Application of imputation methods to the analysis of rheumatoid arthritis data in genome-wide association studies. BMC Proceedings 2009, 3(Suppl 7):S24. [PMCID: PMC2795921]
  1. Liu N, Zhang D, Zhao H. (2008) Genotyping Error Detection in Samples of Unrelated Individuals without Replicate Genotyping. Hum Hered. 15;67(3):154-162. [PMID: 19077433]
  2. Limdi NA, Beasley TM, Crowley MR, Goldstein JA, Rieder MJ, Flockhart DA, Arnett DK, Acton RT, Liu N. (2008) VKORC1 polymorphisms, haplotypes and haplotype groups on warfarin dose among African-Americans and European-Americans. Pharmacogenomics. 9(10):1445-58. [PMID: 18855533] [PMCID: PMC2586955]
  3. Liu N, Zhang K, Zhao H. (2008) Haplotype-association analysis. Adv Genet. 60:335-405. [PMID: 18358327]
  4. J.M. Kelley, L.B. Hughes, R. Feng, N. Liu, M.A. Padilla, L.K. Vaughan, S.L. Bridges (2008) Evaluating Linkage Disequilibrium and Recombination Provides a Haplotype-tagging SNP Panel of the Major Histocompatibility Complex in African Americans. Genes and Immunity 9:271–273. [PMID: 18305489]
  5. Arcaroli J, Sankoff J, Liu N, Allison DB, Maloney J, Abraham E. (2008) Association between urokinase haplotypes and outcome from infection-associated acute lung injury. Intensive Care Med. 34(2):300-7. [PMID: 17994220]
  1. S. Musani, D. Shriner, N. Liu, R. Feng, C. Coffey, N. Yi, H. Tiwari, D. Allison (2007) Detection of GenexGene Interactions in Genome-Wide Association Studies of Human Population Data. Human Heredity 63:67-84. [PMID: 17283436]
  2. Z. Feng, N. Liu, and H. Zhao (2007). Haplotype inference and association analysis in unrelated samples. In “Current Topics in Human Genetics: Studies in Complex Diseases” (H. W. Deng, H. Shen, Y. J. Liu, and H. Hu, eds.), pp. 135–176. World Scientific Publishing Company, Singapore
  1. N. Liu, I. Beerman, R. Lifton, H. Zhao (2006) Haplotype Analysis in the Presence of Informatively Missing Genotype Data. Genetic Epidemiology 30: 290–300. [PMID: 16528706]
  2. B. Wu, N. Liu, H. Zhao (2006) PSMIX: an R Package for Population Structure Inference via Maximum Likelihood Method. BMC Bioinformatics 2006, 7:317. [PMID: 16792813]
  3. N. Liu, H. Zhao (2006) A Non-parametric Approach to Population Structure Inference Using Multilocus Genotypes. Human Genomics 2(6): 353-364. [PMID: 16848973]
  4. D. Redden, J. Divers, L. Vaughan, H. Tiwari, M. Beasley, J. Fernandez, R. Kimberly, R. Feng, M. Padilla, N. Liu, M. Miller, D. Allison (2006) Regional admixture mapping and structured association testing: conceptual unification and an extensible general linear model. PLoS Genet 2(8): e137. [PMID: 16934005]
  5. S. Wu, L. Leng, Z. Feng, N. Liu, H. Zhao, C. McDonald, A. Lee, F. Arnett, P. Gregersen, M. Mayes, R. Bucala (2006) Macrophage migration inhibitory factor promoter polymorphisms and the clinical expression of scleroderma. Arthritis and Rheumatism 54: 3661-3669. [PMID: 17075815]
  1. J.H. Krystal, W. Abi-Saab, E. Perry, C. D’Souza, N. Liu, R. Gueorguieva, L. McDougall, T. Hunsberger, A. Belger, L. Levine, A. Breier (2005) Preliminary Evidence of Attenuation of the Disruptive Effects of the NMDA Glutamate Receptor Antagonist, Ketamine, on Working Memory by Pretreatment with the Group II Metabotropic Glutamate Receptor (mGluR) Agonist, LY354740, in Healthy Human Subjects. Psychopharmacology 179: 303-309. [PMID: 15309376]
  2. N. Liu, L. Chen, S. Wang, C. Oh, H. Zhao (2005) Comparison of Single Nucleotide Polymorphisms and Microsatellites in Inference of Population Structure. BMC Genetics 2005, 6(Suppl 1):S26. [PMID: 16451635]
  3. L. Chen, N. Liu, S. Wang, C. Oh, H. Zhao (2005) Whole Genome Association Studies in Alcoholism Comparing Different Phenotypes Using Single-Nucleotide Polymorphisms and Microsatellites. BMC Genetics 2005, 6(Suppl 1):S130. [PMID: 16451589]
  4. S. Wang, S. Huang, N. Liu, L. Chen, C. Oh, H. Zhao (2005) Whole-Genome Linkage Analysis in Mapping alcoholism genes Using Single Nucleotide Polymorphisms and Microsatellites. BMC Genetics 2005, 6(Suppl 1):S28. [PMID: 16451637]
  5. C. Oh, S. Wang, N. Liu, L. Chen, H. Zhao (2005) A Bayesian Genome Screening of Maximum Number of Drinks as an Alcoholism Phenotype with the New Haseman-Elston Method. BMC Genetics 2005, 6(Suppl 1):S116. [PMID: 16451573]
  6. S. Huang, S. Wang, N. Liu, L. Chen, C. Oh, H. Zhao (2005) Whole-Genome Scan in Mapping Recombination Modifier Genes Using Single Nucleotide Polymorphisms and Microsatellites. BMC Genetics 2005, 6(Suppl 1):S51. [PMID: 16451663]
  7. Y. Liu, N. Liu, H. Zhao (2005) Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics 21: 3279-3285. [PMID: 15905281]
  1. N. Liu, S.L. Sawyer, N. Mukherjee, A.J. Pakstis, J.R. Kidd, K.K. Kidd, A.J. Brookes, H. Zhao (2004) Haplotype Block Structures Show Significant Variation among Populations. Genetic Epidemiology 27: 385-400. [PMID: 15389924]
  2. G. Sanacora, R.M. Berman, A. Cappiello, D. Oren, A. Kugaya, N. Liu, R. Gueorguieva, D. Fasula, D. Charney (2004) Addition of the α2-Antagonist Yohimbine to Fluoxetine: Effects on Rate of Antidepressant Response. Neuropsychopharmacology 29: 1166-1171. [PMID: 15010697]