A general modular framework for gene set enrichment analysis, BMC Bioinformatics, vol.10, issue.1, p.47, 2009. ,
Differential expression analysis for sequence count data, Genome Biology, vol.11, issue.10, p.106, 2010. ,
Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis arenosa, Plant Physiology, vol.171, issue.1, pp.437-451, 2016. ,
A pathogenesis-based transcript signature in donor-specific antibody-positive kidney transplant patients with normal biopsies, Genomics Data, vol.2, pp.357-360, 2014. ,
Adapting for heteroscedasticity in linear models, The Annals of Statistics, vol.10, issue.4, pp.1224-1233, 1982. ,
Robust Locally Weighted Regression and Smoothing Scatterplots, Journal of the American Statistical Association, vol.74, issue.368, pp.829-836, 1979. ,
Score Test of Homogeneity for Survival Data, Lifetime data analysis, vol.1, pp.145-156, 1995. ,
What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment, Statistical Applications in Genetics and Molecular Biology, vol.15, issue.2, pp.87-105, 2016. ,
Algorithm AS 155: The Distribution of a Linear Combination of chi-2 Random Variables, Journal of the Royal Statistical Society. Series C (Applied Statistics), vol.29, issue.3, pp.323-333, 1980. ,
The enigmatic role of mast cells in dominant tolerance, Current Opinion in Organ Transplantation, vol.14, issue.4, pp.332-337, 2009. ,
Differentially expressed gene transcripts using RNA sequencing from the blood of immunosuppressed kidney allograft recipients, PLoS ONE, vol.10, issue.5, pp.1-14, 2015. ,
Computing the distribution of quadratic forms: Further comparisons between the LiuTang-Zhang approximation and exact methods, Computational Statistics and Data Analysis, vol.54, issue.4, pp.858-862, 2010. ,
Applied longitudinal analysis, vol.998, 2012. ,
Analyzing gene expression data in terms of gene sets: Methodological issues, Bioinformatics, vol.23, issue.8, pp.980-987, 2007. ,
Testing against a high dimensional alternative, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol.68, pp.477-493, 2006. ,
The molecular phenotype of kidney transplants: Personal viewpoint, American Journal of Transplantation, vol.10, issue.10, pp.2215-2222, 2010. ,
Removing technical variability in RNA-seq data using conditional quantile normalization, Biostatistics, vol.13, issue.2, pp.204-216, 2012. ,
, , 2015.
, Time-Course Gene Set Analysis for Longitudinal Gene Expression Data, PLOS Computational Biology, vol.11, issue.6, p.1004310
Detection of deregulated modules using deregulatory linked path, PloS one, vol.8, issue.7, p.70412, 2013. ,
Gene set analysis using variance component tests, BMC Bioinformatics, vol.14, issue.1, p.210, 2013. ,
Late kidney allograft loss: What we know about it, and what we can do about it, Clinical Journal of the American Society of Nephrology, vol.3, issue.2, pp.56-67, 2008. ,
Random-effects models for longitudinal data, Biometrics, vol.38, issue.4, pp.963-974, 1982. ,
voom: Precision weights unlock linear model analysis tools for RNA-seq read counts, Genome biology, vol.15, issue.2, p.29, 2014. ,
EBSeq-HMM: A Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments, Bioinformatics, vol.31, issue.16, pp.2614-2622, 2015. ,
Variance component testing in generalised linear models with random effects, Biometrika, vol.84, issue.2, pp.309-326, 1997. ,
Kernel machine SNP-set analysis for censored survival outcomes in genome-wide association studies, Genetic Epidemiology, vol.35, issue.7, pp.620-631, 2011. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome biology, vol.15, issue.12, p.550, 2014. ,
Microarrays, deep sequencing and the true measure of the transcriptome, BMC Biology, vol.9, issue.1, p.34, 2011. ,
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays, Genome Research, vol.18, issue.9, pp.1509-1517, 2008. ,
, , 2012.
, Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation, Nucleic Acids Research, vol.40, issue.10, pp.4288-4297
On multipletesting correction in genome-wide association studies, Genetic Epidemiology, vol.32, issue.6, pp.567-573, 2008. ,
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series, Bioinformatics, vol.30, issue.18, pp.2598-602, 2014. ,
Mast cell quantitation in renal transplant biopsy specimens as a potential marker for the cumulative burden of tissue injury, Transplantation Proceedings, vol.45, issue.4, pp.1469-1471, 2013. ,
Algorithm to find gene expression profiles of deregulation and identify families of disease-altered genes, Bioinformatics, vol.5, issue.9, pp.1103-1113, 2006. ,
Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline, Briefings in Bioinformatics, vol.17, issue.3, pp.393-407, 2016. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, issue.1, pp.139-140, 2010. ,
Molecular diagnosis of antibodymediated rejection in human kidney transplants, American Journal of Transplantation, vol.13, issue.4, pp.971-983, 2013. ,
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proceedings of the National Academy of Sciences of the United States of America, vol.102, issue.43, pp.15545-15550, 2005. ,
A unified mixed effects model for gene set analysis of time course microarray experiments, Statistical Applications in Genetics and Molecular Biology, vol.8, issue.1, pp.1-18, 2009. ,
ROAST: Rotation gene set tests for complex microarray experiments, Bioinformatics, vol.26, issue.17, pp.2176-2182, 2010. ,
Rare-variant association testing for sequencing data with the sequence kernel association test, American Journal of Human Genetics, vol.89, issue.1, pp.82-93, 2011. ,