Research Output 1992 2017

2017

A comparison study of multivariate fixed models and Gene Association with Multiple Traits (GAMuT) for next-generation sequencing

Chiu, C. Y., Jung, J., Wang, Y., Weeks, D. E., Wilson, A. F., Bailey-Wilson, J. E., Amos, C. I., Mills, J. L., Boehnke, M., Xiong, M. & Fan, R. Jan 1 2017 In : Genetic Epidemiology. 41, 1, p. 18-34 17 p.

Research output: Contribution to journalArticle

Linear Models
Analysis of Variance
Genes
Multivariate Analysis
Phenotype

A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data

Lin, N., Zhu, Y., Fan, R. & Xiong, M. Oct 1 2017 In : PLoS Computational Biology. 13, 10, e1005788

Research output: Contribution to journalArticle

pleiotropy
Canonical Correlation Analysis
statistics
Phenotype
Statistics

Bagging Nearest-Neighbor Prediction independence Test: An efficient method for nonlinear dependence of two continuous variables

Wang, Y., Li, Y., Liu, X., Pu, W., Wang, X., Wang, J., Xiong, M., Yao Shugart, Y. & Jin, L. Dec 1 2017 In : Scientific Reports. 7, 1, 12736

Research output: Contribution to journalArticle

RNA
DNA
Statistics
Testing

Functional regression method for whole genome eQTL epistasis analysis with sequencing data

Xu, K., Jin, L. & Xiong, M. May 18 2017 In : BMC Genomics. 18, 1, 385

Research output: Contribution to journalArticle

Genome
RNA
Genes
Gene Expression
Single Nucleotide Polymorphism

Meta-analysis of quantitative pleiotropic traits for next-generation sequencing with multivariate functional linear models

Chiu, C. Y., Jung, J., Chen, W., Weeks, D. E., Ren, H., Boehnke, M., Amos, C. I., Liu, A., Mills, J. L., Ting Lee, M. L., Xiong, M. & Fan, R. Feb 1 2017 In : European Journal of Human Genetics. 25, 3, p. 350-359 10 p.

Research output: Contribution to journalArticle

Meta-Analysis
Linear Models
Multivariate Analysis
Genotype
Lipids
2016
3 Citations

A Comparison Study of Fixed and Mixed Effect Models for Gene Level Association Studies of Complex Traits

Fan, R., Chiu, C. Y., Jung, J., Weeks, D. E., Wilson, A. F., Bailey-Wilson, J. E., Amos, C. I., Chen, Z., Mills, J. L. & Xiong, M. Dec 1 2016 In : Genetic Epidemiology. 40, 8, p. 702-721 20 p.

Research output: Contribution to journalArticle

Genes
Genotype
1 Citations

A new statistical framework for genetic pleiotropic analysis of high dimensional phenotype data

Wang, P., Rahman, M., Jin, L. & Xiong, M. Nov 7 2016 In : BMC Genomics. 17, 1, 881

Research output: Contribution to journalArticle

Phenotype
Structural Models
Genetic Structures
Genetic Pleiotropy
Exome
1 Citations

Copy number variation of HLA-DQA1 and APOBEC3A/3B contribute to the susceptibility of systemic sclerosis in the Chinese han population

Guo, S., Li, Y., Wang, Y., Chu, H., Chen, Y., Liu, Q., Guo, G., Tu, W., Wu, W., Zou, H., Yang, L., Xiao, R., Ma, Y., Zhang, F., Xiong, M., Jin, L., Zhou, X. & Wang, J. May 1 2016 In : Journal of Rheumatology. 43, 5, p. 880-886 7 p.

Research output: Contribution to journalArticle

Systemic Scleroderma
Population
Genome
HLA-DQA1 antigen
HLA-DRB5 Chains
2 Citations

Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits

Zhang, F., Xie, D., Liang, M. & Xiong, M. Apr 1 2016 In : PLoS Genetics. 12, 4, e1005965

Research output: Contribution to journalArticle

epistasis
quantitative traits
phenotype
Phenotype
Genetic Structures
4 Citations

Gene-Based Association Analysis for Censored Traits Via Fixed Effect Functional Regressions

Fan, R., Wang, Y., Yan, Q., Ding, Y., Weeks, D. E., Lu, Z., Ren, H., Cook, R. J., Xiong, M., Swaroop, A., Chew, E. Y. & Chen, W. Feb 1 2016 In : Genetic Epidemiology. 40, 2, p. 133-143 11 p.

Research output: Contribution to journalArticle

Proportional Hazards Models
Genes
Exome
Genome-Wide Association Study
Genetic Models
4 Citations

Genome-wide gene-gene interaction analysis for next-generation sequencing

Zhao, J., Zhu, Y. & Xiong, M. Mar 1 2016 In : European Journal of Human Genetics. 24, 3, p. 421-428 8 p.

Research output: Contribution to journalArticle

Exome
Genome
Single Nucleotide Polymorphism
Case-Control Studies
Myocardial Infarction
4 Citations

Meta-analysis of complex diseases at gene level with generalized functional linear models

Fan, R., Wang, Y., Chiu, C. Y., Chen, W., Ren, H., Li, Y., Boehnke, M., Amos, C. I., Moore, J. H. & Xiong, M. Feb 1 2016 In : Genetics. 202, 2, p. 457-470 14 p.

Research output: Contribution to journalArticle

Meta-Analysis
Linear Models
Genes
Genetic Models
Exome
1 Citations

Random bits forest: A strong classifier/regressor for big data

Wang, Y., Li, Y., Pu, W., Wen, K., Shugart, Y. Y., Xiong, M. & Jin, L. Jul 22 2016 In : Scientific Reports. 6, 30086

Research output: Contribution to journalArticle

Classifiers
Neural networks
Testing
Learning systems
Genes

Wearable computing for fully automated myocardial infarction classification

Zewdie, G. & Xiong, M. 2016 Proceedings of the 8th International Conference on Bioinformatics and Computational Biology, BICOB 2016. The International Society for Computers and Their Applications (ISCA), p. 17-22 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Electrocardiography
Myocardial Infarction
Ordinary differential equations
Cardiovascular Diseases
Point-of-Care Systems
2015
1424 Citations

A global reference for human genetic variation

Auton, A. , Abecasis, G. R. , Altshuler, D. M. , Durbin, R. M. , Bentley, D. R. , Chakravarti, A. , Clark, A. G. , Donnelly, P. , Eichler, E. E. , Flicek, P. , Gabriel, S. B. , Gibbs, R. A. , Green, E. D. , Hurles, M. E. , Knoppers, B. M. , Korbel, J. O. , Lander, E. S. , Lee, C. , Lehrach, H. , Mardis, E. R. & 30 others Marth, G. T., McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Boerwinkle, E., Doddapaneni, H., Han, Y., Korchina, V., Kovar, C., Lee, S., Muzny, D., Reid, J. G., Zhu, Y., Chang, Y., Feng, Q., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Lan, T., Li, G., Jun, G., Fu, Y., Liu, X., Xiong, M. & Harmanci, A. O. Sep 30 2015 In : Nature. 526, 7571, p. 68-74 7 p.

Research output: Contribution to journalReview article

Medical Genetics
Genome
Single Nucleotide Polymorphism
Exome
High-Throughput Nucleotide Sequencing
2 Citations
Markov Chains
Markov Chain Model
Bayes Theorem
Continuous-time Markov Chain
Nutrition

An estimating equation approach to dimension reduction for longitudinal data

Xu, K., Guo, W., Xiong, M., Zhu, L. & Jin, L. Jan 1 2015 In : Biometrika. 103, 1, p. 189-203 15 p.

Research output: Contribution to journalArticle

Estimating Equation
Covariance Structure
Dimension Reduction
Longitudinal Data
Sufficient Dimension Reduction

Dynamic Model for RNA-seq Data Analysis

Li, L. & Xiong, M. 2015 In : BioMed Research International. 2015, 916352

Research output: Contribution to journalArticle

Dynamic models
RNA
Transcription
Genes
Gene Expression Profiling
4 Citations

Efficient test for nonlinear dependence of two continuous variables

Wang, Y., Li, Y., Cao, H., Xiong, M., Shugart, Y. Y. & Jin, L. Aug 19 2015 In : BMC Bioinformatics. 16, 1, 260

Research output: Contribution to journalArticle

Continuous Variables
Testing
Statistical Power
Evaluate
Kidney Neoplasms
1 Citations

Functional principal component analysis and randomized sparse clustering algorithm for medical image analysis

Lin, N., Jiang, J., Guo, S. & Xiong, M. Jul 21 2015 In : PLoS One. 10, 7, e0132945

Research output: Contribution to journalArticle

Cluster analysis
Principal Component Analysis
Clustering algorithms
Principal component analysis
Image analysis
13 Citations

Gene level meta-analysis of quantitative traits by functional linear models

Fan, R., Wang, Y., Boehnke, M., Chen, W., Li, Y., Ren, H., Lobach, I. & Xiong, M. Aug 1 2015 In : Genetics. 200, 4, p. 1089-1104 16 p.

Research output: Contribution to journalArticle

Meta-Analysis
Linear Models
Genes
Exome
Genome-Wide Association Study
20 Citations

Identification and validation of the methylation biomarkers of non-small cell lung cancer (nsclc)

Guo, S., Yan, F., Xu, J., Bao, Y., Zhu, J., Wang, X., Wu, J., Li, Y., Pu, W., Liu, Y., Jiang, Z., Ma, Y., Chen, X., Xiong, M., Jin, L. & Wang, J. Jan 22 2015 In : Clinical Epigenetics. 7, 1, p. 2-9 8 p.

Research output: Contribution to journalArticle

DNA Methylation
Non-Small Cell Lung Carcinoma
Methylation
Biomarkers
Oligonucleotide Array Sequence Analysis
1 Citations

Multiple functional linear model for association analysis of RNA-seq with imaging

Jiang, J., Lin, N., Guo, S., Chen, J. & Xiong, M. Jun 1 2015 In : Quantitative Biology. 3, 2, p. 90-102 13 p.

Research output: Contribution to journalArticle

Functional Linear Model
Functional Principal Component Analysis
Thermionic emission
RNA
Linear Models
4 Citations

Pathway analysis with next-generation sequencing data

Zhao, J., Zhu, Y., Boerwinkle, E. & Xiong, M. Apr 14 2015 In : European Journal of Human Genetics. 23, 4, p. 507-515 9 p.

Research output: Contribution to journalArticle

Principal Component Analysis
Myocardial Infarction
Exome
Research Personnel
26 Citations

Pleiotropy analysis of quantitative traits at gene level by multivariate functional linear models

Wang, Y., Liu, A., Mills, J. L., Boehnke, M., Wilson, A. F., Bailey-Wilson, J. E., Xiong, M., Wu, C. O. & Fan, R. May 1 2015 In : Genetic Epidemiology. 39, 4, p. 259-275 17 p.

Research output: Contribution to journalArticle

Linear Models
Sequence Analysis
Genetic Pleiotropy
Genes
Lipids

Statistical Analysis of High-Dimensional Genetic Data in Complex Traits

Park, T., Van Steen, K., Lou, X. Y. & Xiong, M. 2015 In : BioMed Research International. 2015, 564273

Research output: Contribution to journalEditorial

Heritable Quantitative Trait
Genetic Models
2014
12 Citations

Epistasis analysis for quantitative traits by functional regression model

Zhang, F., Boerwinkle, E. & Xiong, M. 2014 In : Genome Research. 24, 6, p. 989-998 10 p.

Research output: Contribution to journalArticle

Exome
Single Nucleotide Polymorphism
Genome
National Heart, Lung, and Blood Institute (U.S.)
Genes
13 Citations

Generalized functional linear models for gene-based case-control association studies

Fan, R., Wang, Y., Mills, J. L., Carter, T. C., Lobach, I., Wilson, A. F., Bailey-Wilson, J. E., Weeks, D. E. & Xiong, M. Nov 1 2014 In : Genetic Epidemiology. 38, 7, p. 622-637 16 p.

Research output: Contribution to journalArticle

Case-Control Studies
Linear Models
Genes
Exome
Hirschsprung Disease
4 Citations

Genome-wide association tests of inversions with application to psoriasis

Ma, J., Xiong, M., You, M., Lozano, G. & Amos, C. I. 2014 In : Human Genetics. 133, 8, p. 967-974 8 p.

Research output: Contribution to journalArticle

Psoriasis
Genome
Principal Component Analysis
Single Nucleotide Polymorphism
Genotype
74 Citations

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Delaneau, O. , Marchini, J. , McVeanh, G. A. , Donnelly, P. , Lunter, G. , Marchini, J. L. , Myers, S. , Gupta-Hinch, A. , Iqbal, Z. , Mathieson, I. , Rimmer, A. , Xifara, D. K. , Kerasidou, A. , Churchhouse, C. , Altshuler, D. M. , Gabriel, S. B. , Lander, E. S. , Gupta, N. , Daly, M. J. , DePristo, M. A. & 30 others Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Genovese, G., Handsaker, R. E., Hartl, C., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Li, H., Reich, D., Durbin, R. M., Hurles, M. E., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., Jun, G., Fu, Y., Liu, X., Xiong, M. & Harmanci, A. O. Jun 13 2014 In : Nature Communications. 5, 3934

Research output: Contribution to journalArticle

genome
Haplotypes
polymorphism
nucleotides
Genes
7 Citations

Significant SNPs have limited prediction ability for thyroid cancer

Guo, S., Wang, Y. L., Li, Y., Jin, L., Xiong, M., Ji, Q. H. & Wang, J. Jun 1 2014 In : Cancer Medicine. 3, 3, p. 731-735 5 p.

Research output: Contribution to journalArticle

Thyroid Neoplasms
Single Nucleotide Polymorphism
Population
Genome-Wide Association Study
Area Under Curve
2013
4 Citations

Bayesian Detection of Causal Rare Variants under Posterior Consistency

Liang, F. & Xiong, M. Jul 26 2013 In : PLoS One. 8, 7, e69633

Research output: Contribution to journalArticle

Detectors
detectors
testing
Exome
Bayes Theorem
30 Citations

Canonical correlation analysis for RNA-seq co-expression networks

Hong, S., Chen, X., Jin, L. & Xiong, M. Apr 2013 In : Nucleic Acids Research. 41, 8

Research output: Contribution to journalArticle

RNA
Biological Phenomena
Gene Expression
Squamous Cell Neoplasms
Gene Expression Profiling
26 Citations

Functional linear models for association analysis of quantitative traits

Fan, R., Wang, Y., Mills, J. L., Wilson, A. F., Bailey-Wilson, J. E. & Xiong, M. Nov 2013 In : Genetic Epidemiology. 37, 7, p. 726-742 17 p.

Research output: Contribution to journalArticle

Linkage Disequilibrium
Linear Models
Genome
Stochastic Processes
Genetic Linkage
11 Citations
Principal Component Analysis
Genome-Wide Association Study
Schizophrenia
Technology
Phenotype
2012
1 Citations

Ancestry informative marker set for han chinese population

Qu, H. Q., Li, Q., Xu, S., McCormick, J. B., Fisher-Hoch, S. P., Xiong, M., Qian, J. & Jin, L. Mar 2012 In : G3: Genes, Genomes, Genetics. 2, 3, p. 339-341 3 p.

Research output: Contribution to journalArticle

Population
Precision Medicine
Genetic Heterogeneity
Genome
Health
1691 Citations

An integrated map of genetic variation from 1,092 human genomes

Altshuler, D. M. , Durbin, R. M. , Abecasis, G. R. , Bentley, D. R. , Chakravarti, A. , Clark, A. G. , Donnelly, P. , Eichler, E. E. , Flicek, P. , Gabriel, S. B. , Gibbs, R. A. , Green, E. D. , Hurles, M. E. , Knoppers, B. M. , Korbel, J. O. , Lander, E. S. , Lee, C. , Lehrach, H. , Mardis, E. R. , Marth, G. T. & 30 others McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Li, Z., Liu, X., Lu, Y., Ma, X., Jun, G., Fu, Y., Liu, X., Xiong, M. & Harmanci, A. O. Nov 1 2012 In : Nature. 491, 7422, p. 56-65 10 p.

Research output: Contribution to journalArticle

Human Genome
Genome
Population
Single Nucleotide Polymorphism
Exome
2 Citations
Genome-Wide Association Study
Information Content
Sequencing
Statistic
Genome
35 Citations

Family-based association studies for next-generation sequencing

Zhu, Y. & Xiong, M. Jun 8 2012 In : American Journal of Human Genetics. 90, 6, p. 1028-1045 18 p.

Research output: Contribution to journalArticle

Principal Component Analysis
Population
Pedigree
Technology
30 Citations

Genome-wide gene-environment interaction analysis for asbestos exposure in lung cancer susceptibility

Wei, S., Wang, L. E., Mchugh, M. K., Han, Y., Xiong, M., Amos, C. I., Spitz, M. R. & Wei, Q. W. Aug 2012 In : Carcinogenesis. 33, 8, p. 1531-1537 7 p.

Research output: Contribution to journalArticle

Gene-Environment Interaction
Asbestos
Lung Neoplasms
Genome
Genes
16 Citations

Longitudinal Association Analysis of Quantitative Traits

Fan, R., Zhang, Y., Albert, P. S., Liu, A., Wang, Y. & Xiong, M. Dec 2012 In : Genetic Epidemiology. 36, 8, p. 856-869 14 p.

Research output: Contribution to journalArticle

Stochastic Processes
Blood Pressure
Education
Linkage Disequilibrium
Medical Genetics
6 Citations

Manifold learning for human population structure studies

Siu, H., Jin, L. & Xiong, M. Jan 17 2012 In : PLoS One. 7, 1, e29901

Research output: Contribution to journalArticle

human population
population structure
learning
Learning
Principal component analysis
6 Citations

Natural and orthogonal interaction framework for modeling gene-environment interactions with application to lung cancer

Ma, J., Xiao, F., Xiong, M., Andrew, A. S., Brenner, H., Duell, E. J., Haugen, A., Hoggart, C., Hung, R. J., Lazarus, P., Liu, C., Matsuo, K., Mayordomo, J. I., Schwartz, A. G., Staratschek-Jox, A., Wichmann, E., Yang, P. & Amos, C. I. Sep 2012 In : Human Heredity. 73, 4, p. 185-194 10 p.

Research output: Contribution to journalArticle

Gene-Environment Interaction
Statistical Models
Lung Neoplasms
Genetic Models
Single Nucleotide Polymorphism
15 Citations

Present Y chromosomes reveal the ancestry of Emperor CAO Cao of 1800 years ago

Wang, C., Yan, S., Hou, Z., Fu, W., Xiong, M., Han, S., Jin, L. & Li, H. Mar 2012 In : Journal of Human Genetics. 57, 3, p. 216-218 3 p.

Research output: Contribution to journalArticle

Y Chromosome
Haplotypes
Famous Persons
Ancient History
History
82 Citations
LDL Receptors
Apolipoproteins B
LDL Lipoproteins
Hepatocytes
Proprotein Convertase 9
23 Citations

Quantitative trait locus analysis for next-generation sequencing with the functional linear models

Luo, L., Zhu, Y. & Xiong, M. Aug 2012 In : Journal of Medical Genetics. 49, 8, p. 513-524 12 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
Linear Models
Multivariate Analysis
Genome
RNA
6 Citations

Weighted pedigree-based statistics for testing the association of rare variants

Shugart, Y. Y., Zhu, Y., Guo, W. & Xiong, M. Nov 24 2012 In : BMC Genomics. 13, 1, 667

Research output: Contribution to journalArticle

Pedigree
Genome-Wide Association Study
Population Characteristics
Population
Software
2011
6 Citations

Accelerating Haplotype-Based Genome-Wide association study using perfect phylogeny and Phase-Known reference data

He, Y., Li, C., Amos, C. I., Xiong, M., Ling, H. & Jin, L. 2011 In : PLoS One. 6, 7, e22097

Research output: Contribution to journalArticle

Genome-Wide Association Study
Phylogeny
Haplotypes
haplotypes
Genes
59 Citations

Association studies for next-generation sequencing

Luo, L., Boerwinkle, E. & Xiong, M. Jul 2011 In : Genome Research. 21, 7, p. 1099-1108 10 p.

Research output: Contribution to journalArticle

Principal Component Analysis
Genome-Wide Association Study
Technology
Genome
Phenotype
35 Citations

Entropy-based information gain approaches to detect and to characterize gene-gene and gene-environment interactions/correlations of complex diseases

Fan, R., Zhong, M., Wang, S., Zhang, Y., Andrew, A., Karagas, M., Chen, H., Amos, C. I., Xiong, M. & Moore, J. H. Nov 2011 In : Genetic Epidemiology. 35, 7, p. 706-721 16 p.

Research output: Contribution to journalArticle

Gene-Environment Interaction
Entropy
Urinary Bladder Neoplasms
Genes
Information Theory