Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies
暂无分享,去创建一个
Xiang Zhou | Shiquan Sun | Mengjie Chen | Jiaqiang Zhu | Sahar Mozaffari | Carole Ober | Xiaoping Zhou | C. Ober | Mengjie Chen | S. Mozaffari | Shiquan Sun | Jiaqiang Zhu
[1] Wei Li,et al. MOABS: model based analysis of bisulfite sequencing data , 2014, Genome Biology.
[2] John D. Blischak,et al. Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels , 2014, bioRxiv.
[3] L. Almasy,et al. Multipoint quantitative-trait linkage analysis in general pedigrees. , 1998, American journal of human genetics.
[4] D. Koller,et al. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals , 2013, Genome research.
[5] Alkes L. Price,et al. Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals , 2011, PLoS genetics.
[6] M. Stephens,et al. Genome-wide Efficient Mixed Model Analysis for Association Studies , 2012, Nature Genetics.
[7] Harvey Goldstein,et al. Improved Approximations for Multilevel Models with Binary Responses , 1996 .
[8] Xiang Zhou,et al. Polygenic Modeling with Bayesian Sparse Linear Mixed Models , 2012, PLoS genetics.
[9] P. Sullivan,et al. Heritability and Genomics of Gene Expression in Peripheral Blood , 2014, Nature Genetics.
[10] D Y Lin,et al. Improving the power of association tests for quantitative traits in family studies , 2006, Genetic epidemiology.
[11] P. Visscher,et al. Pitfalls of predicting complex traits from SNPs , 2013, Nature Reviews Genetics.
[12] Pedro G. Ferreira,et al. Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.
[13] Roberto M. Lang,et al. Integrated analyses of gene expression and genetic association studies in a founder population , 2016, Human molecular genetics.
[14] Daniel J. Gaffney,et al. A survey of best practices for RNA-seq data analysis , 2016, Genome Biology.
[15] Gunnar Rätsch,et al. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation , 2015, eLife.
[16] Nicholas G Martin,et al. Contribution of genetic variation to transgenerational inheritance of DNA methylation , 2014, Genome Biology.
[17] Aviv Regev,et al. Genetic determinants of co-accessible chromatin regions in T cell activation across humans , 2016, bioRxiv.
[18] J. Byrd,et al. DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia , 2016, Nature Genetics.
[19] S. Redline,et al. Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models. , 2016, American journal of human genetics.
[20] G. Abecasis,et al. A general test of association for quantitative traits in nuclear families. , 2000, American journal of human genetics.
[21] P. Visscher,et al. GCTA: a tool for genome-wide complex trait analysis. , 2011, American journal of human genetics.
[22] H. Kang,et al. Variance component model to account for sample structure in genome-wide association studies , 2010, Nature Genetics.
[23] G. Barton,et al. How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? , 2015, RNA.
[24] Ying Liu,et al. FaST linear mixed models for genome-wide association studies , 2011, Nature Methods.
[25] Hae Kyung Im,et al. Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues , 2016, bioRxiv.
[26] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[27] Colin D. Meiklejohn,et al. Genome-Wide Gene Expression Effects of Sex Chromosome Imprinting in Drosophila , 2013, G3: Genes, Genomes, Genetics.
[28] Robin M. Murray,et al. Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population , 2012, PLoS genetics.
[29] Joseph K. Pickrell,et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing , 2010, Nature.
[30] W. G. Hill,et al. Heritability in the genomics era — concepts and misconceptions , 2008, Nature Reviews Genetics.
[31] Xihong Lin. Estimation using penalized quasilikelihood and quasi-pseudo-likelihood in Poisson mixed models , 2007, Lifetime data analysis.
[32] N. Breslow,et al. Approximate inference in generalized linear mixed models , 1993 .
[33] Sara Martino,et al. Animal Models and Integrated Nested Laplace Approximations , 2013, G3: Genes, Genomes, Genetics.
[34] E. Schadt,et al. Genetic inheritance of gene expression in human cell lines. , 2004, American journal of human genetics.
[35] C. Amos. Robust variance-components approach for assessing genetic linkage in pedigrees. , 1994, American journal of human genetics.
[36] P. Visscher,et al. Common SNPs explain a large proportion of heritability for human height , 2011 .
[37] Fred A. Wright,et al. A powerful and flexible approach to the analysis of RNA sequence count data , 2011, Bioinform..
[38] Xiaoping Zhou. A Unified Framework for Variance Component Estimation with Summary Statistics in Genome-wide Association Studies , 2016, bioRxiv.
[39] Woncheol Jang,et al. A Numerical Study of PQL Estimation Biases in Generalized Linear Mixed Models Under Heterogeneity of Random Effects , 2009, Commun. Stat. Simul. Comput..
[40] Xiang Zhou,et al. Non-parametric genetic prediction of complex traits with latent Dirichlet process regression models , 2017, Nature Communications.
[41] G. Barton,et al. Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? , 2016, RNA.
[42] Robin Thompson,et al. Average information REML: An efficient algorithm for variance parameter estimation in linear mixed models , 1995 .
[43] N. Breslow,et al. Bias correction in generalised linear mixed models with a single component of dispersion , 1995 .
[44] Lei Zhang,et al. Negative binomial mixed models for analyzing microbiome count data , 2017, BMC Bioinformatics.
[45] Jun S. Liu,et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.
[46] J. Wakefield,et al. Bayesian inference for generalized linear mixed models. , 2010, Biostatistics.
[47] R. Myers,et al. Gender-Specific Gene Expression in Post-Mortem Human Brain: Localization to Sex Chromosomes , 2004, Neuropsychopharmacology.
[48] Eran Halperin,et al. Association testing of bisulfite-sequencing methylation data via a Laplace approximation , 2017, Bioinform..
[49] H. Stefánsson,et al. Genetics of gene expression and its effect on disease , 2008, Nature.
[50] N. Breslow,et al. Bias Correction in Generalized Linear Mixed Models with Multiple Components of Dispersion , 1996 .
[51] William J. Browne,et al. Bayesian and likelihood-based methods in multilevel modeling 1 A comparison of Bayesian and likelihood-based methods for fitting multilevel models , 2006 .
[52] Laura J. Scott,et al. The genetic regulatory signature of type 2 diabetes in human skeletal muscle , 2016, Nature Communications.
[53] D. Gianola,et al. Genomic Heritability: What Is It? , 2014, PLoS genetics.
[54] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[55] N. Goldman,et al. Improved estimation procedures for multilevel models with binary response: a case‐study , 2001 .
[56] D. Absher,et al. A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data , 2015, bioRxiv.
[57] A. Feinberg,et al. Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.
[58] Matthew Stephens,et al. The genetic architecture of gene expression levels in wild baboons , 2014, bioRxiv.
[59] Xiang Zhou,et al. Differential expression analysis for RNAseq using Poisson mixed models , 2016, bioRxiv.