In general, our research is centered on elucidating the genetic basis and mechanism of complex diseases and traits of animals and humans, which can potentially leads to higher production of economically important traits for domestic animals, and can also results in better prediction and cure of diseases. In particular, we focus on developing statistical approaches and computing tools to boost the power of current and next-generation sequencing-based genetic studies, including approaches to facilitating accurate and powerful tests of association, to detecting gene-gene interactions, and to integrating a variety of biological knowledge from genetic, genomic, and epigenetic studies. We are also applying these approaches and tools to empirical animal and human datasets to solve real-world problems. Additionally, we are interested in detecting selection signatures and elucidating evolutionary history of animals and humans by applying population genetics approaches to large-scale sequencing data in different populations.
Abinash Padhi, Mona G. Ghaly, Li Ma, "Testis-enriched heat shock protein A2 (HSPA2): Adaptive advantages of the birds with internal testes over the mammals with testicular descent", Scientific Reports, 6: 18770, 2016
Li Ma, Gabriel Hoffman, Alon Keinan, "X-inactivation informs variance-based testing for X-linked association of a quantitative trait", BMC Genomics, 16 (1), 241, 2015
Abinash Padhi, Li Ma, "Time-dependent selection pressure on two arthropod-borne RNA viruses in the same serogroup", Infection, Genetics and Evolution, 32: 255-264, 2015
Li Ma, Jeffrey R O'Connell, Paul M VanRaden, Botong Shen, Abinash Padhi, Chuanyu Sun, Derek M Bickhart, John B Cole, Daniel J Null, George E Liu, Yang Da, George R Wiggans, "Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis", PLoS Genetics, 11(11): e1005387, 2015
Abinash Padhi, Li Ma, "A testis‐specific gene within a widely expressed gene: Contrasting evolutionary patterns of two differentially expressed mammalian proteins encoded by a single gene, CAMK4", Animal Genetics, 46: 683–692, 2015
L Ma, C Ballantyne, A Brautbar, A Keinan, "Analysis of multiple association studies provides evidence of an expression QTL hub in gene-gene interaction network affecting HDL cholesterol levels", PLoS ONE, 9 (3), e92469, 2014
E Gazave, L Ma, D Chang, A Coventry, F Gao, D Muzny, E Boerwinkle, R Gibbs, CF Sing, AG Clark, A Keinan, "Neutral genomic regions refine models of recent rapid human population growth", PNAS, 111 (2) 757-762, 2014
Abinash Padhi, Li Ma, "Molecular Evolutionary and Epidemiological Dynamics of Genotypes 1G and 2B of Rubella Virus", PLoS ONE, 9(10): e110082, 2014
Abinash Padhi, Li Ma, "Genetic and epidemiological insights into the emergence of peste des petits ruminants virus (PPRV) across Asia and Africa", Scientific Reports, 4: 7040, 2014
L Ma, AG Clark, A Keinan. Gene-based Testing of Interactions in Association Studies of Quantitative Traits. PLoS Genetics 9 (2), e1003321, 2013.
L Ma, G Wiggans, SW Wang, TS Sonstegard, J Yang, BA Crooker, JB Cole, CP Van Tassell, TJ Lawlor, Y Da, Effect of sample stratification on dairy GWAS results. BMC Genomics 13:536, 2012.
L Ma, CM Ballantyne, JW Belmont, A Keinan, A Brautbar, Interaction between SNPs in the RXRA and near ANGPTL3 gene region inhibit apolipoprotein B reduction following statin-fenofibric acid therapy in individuals with mixed dyslipidemia, Journal of Lipid Research, 2012.
L Ma, A Brautbar, E Boerwinkle, CF Sing, AG Clark, A Keinan, Knowledge-Driven Analysis Identifies a Gene–Gene Interaction Affecting High-Density Lipoprotein Cholesterol Levels in Multi-Ethnic Populations. PLoS Genet 8(5): e1002714, 2012.
H Zhang, X Hu, Z Wang, Y Zhang, S Wang, N Wang, L Ma, et al., Selection Signature Analysis Implicates the PC1/PCSK1 region for Chicken Abdominal Fat Content, PLoS ONE 7(7): e40736, 2012.
L Xie, C Luo, C Zhang, R Zhang, J Tang, Q Nie, L Ma, et al. Genome-Wide Association Study Identified a Narrow Chromosome 1 Region Associated with Chicken Growth Traits. PLoS ONE 7(2): e30910, 2012.
J Cole, G Wiggans, L Ma, et al. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. BMC Genomics 12(1): 408, 2011.
X Gu, C Feng, L Ma, et al. Genome-Wide Association Study of Body Weight in Chicken F2 Resource Population. PLoS ONE 6(7): e21872, 2011.
L Ma, SZ Han, J Yang, and Y Da, Multi-locus Test Conditional on Confirmed Effects Leads to Increased Power in Genome-wide Association Studies. PLoS ONE 5(11), 2010.
L Ma, J Yang, HB Runesha, T Tanaka, L Ferrucci, S Bandinelli, and Y Da, Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham Heart Study data. BMC Medical Genetics, 11:55, 2010.
L Ma, HB Runesha, D Dvorkin, JR Garbe, and Y Da, Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies. BMC Bioinformatics, 9: 315, 2008.
L Ma, D Dvorkin, JR Garbe, Y Da: Genome-wide analysis of single-locus and epistasis SNP effects on anti-cyclic citrullinated peptide as a measure of rheumatoid arthritis. BMC Proceedings, 1(Suppl 1):S127, 2007.
YC Mao, NR London, L Ma, D Dvorkin, and Y Da, Detection of SNP epistasis effects of quantitative traits using an extended Kempthorne model. Physiological Genomics, 28: 46-52, 2006.