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@INCOLLECTION{chen2014edgerchapter,
  title = {Differential expression analysis of complex {RNA}-seq experiments using {edgeR}},
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  booktitle = {Statistical Analysis of Next Generation Sequence Data},
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@article{ching2014power,
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  publisher={Cold Spring Harbor Lab}
}

@ARTICLE{fu2015egfmcl1,
  author = {N. Y. Fu and A. Rios and B. Pal and R. Soetanto and A. T. L. Lun and K. Liu and T. Beck and S. Best and F. Vaillant and P. Bouillet and A. Strasser and T. Preiss and G. K. Smyth and G. Lindeman and and J. Visvader},
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  title = {{EGF}-mediated induction of {Mcl}-1 at the switch to lactation is essential for alveolar cell survival},
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@ARTICLE{law2014voom,
  author = {C. W. Law and Y. Chen and W. Shi and G. K. Smyth},
  title = {Voom: precision weights unlock linear model analysis tools for {RNA}-seq read counts},
  journal = {Genome Biology},
  year = {2014},
  volume = {15},
  pages = {R29}
}

@ARTICLE{liao2013subread,
  author = {Y. Liao and G. K. Smyth and W. Shi},
  title = {The {S}ubread aligner: fast, accurate and scalable read mapping by seed-and-vote},
  journal = {Nucleic Acids Research},
  year = {2013},
  volume = {41},
  number = {10},
  pages = {e108}
}

@ARTICLE{liao2014featureCounts,
  author = {Y. Liao and G. K. Smyth and W. Shi},
  title = {{featureCounts}: an efficient general-purpose read summarization program},
  journal = {Bioinformatics},
  year = {2014},
  volume = {30},
  number = {7},
  pages = {923-930},
}

@ARTICLE{lim2010transcriptome,
  author = {Lim, E. and Wu, D. and Pal, B. and Bouras, T. and Asselin-Labat, M.L. and Vaillant, F. and Yagita, H. and Lindeman, G.J. and Smyth, G.K. and Visvader, J.E.},
  title = {Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways},
  journal = {Breast Cancer Research},
  year = {2010},
  volume = {12},
  pages = {R21},
  publisher = {BioMed Central}
}

@ARTICLE{love2014deseq2,
  title = {Moderated estimation of fold change and dispersion for {RNA-seq} data with {DESeq2}},
  author = {M. I. Love and W. Huber and S. Anders},
  journal = {Genome Biol.},
  year = {2014},
  volume = {15},
  number = {12},
  pages = {550}
}

@ARTICLE{lun2014denovo,
  title = {De novo detection of differentially bound regions for {ChIP-seq} data using peaks and windows: controlling error rates correctly},
  author = {A. T. L. Lun and G. K. Smyth},
  journal = {Nucleic Acids Research},
  year = {2014},
  volume = {42},
  pages = {e95},
  publisher = {Oxford University Press}
}

@ARTICLE{lun2015diffhic,
  author = {A. T. L. Lun and G. K. Smyth},
  title = {{diffHic}: a Bioconductor package to detect differential genomic interactions in {Hi-C} data},
  journal = {BMC Bioinformatics},
  year = {2015},
  volume = {16},
  pages = {258}
}

@ARTICLE{lun2016delicious,
  title = {It's {DE}-licious: a recipe for differential expression analyses of {RNA}-seq experiments using quasi-likelihood methods in {edgeR}},
  author = {A. T. L. Lun and Y. Chen and G. K. Smyth},
  journal = {Methods in Molecular Biology},
  year = {2016},
  volume = {1418},
  pages = {391-416},
}

@article{lun2016pooling,
  title={Pooling across cells to normalize single-cell {RNA} sequencing data with many zero counts},
  author={Lun, A. T. L. and Bach, K. and Marioni, J. C.},
  journal={Genome Biology},
  volume={17},
  pages={75},
  year={2016},
}

@ARTICLE{lund2012quasiseq,
  author = {Lund, S. P. and Nettleton, D. and McCarthy, D. J. and Smyth, G. K.},
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  journal = {Statistical Applications in Genetics and Molecular Biology},
  year = {2012},
  volume = {11},
  pages = {Article 8},
  number = {5},
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@ARTICLE{mccarthy2009treat,
  author = {D. J. McCarthy and G. K. Smyth},
  title = {Testing significance relative to a fold-change threshold is a {TREAT}},
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  volume = {25},
  pages = {765--771},
  number = {6},
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@ARTICLE{mccarthy2012edgerglm,
  author = {D. J. McCarthy and Y. Chen and G. K. Smyth},
  title = {Differential expression analysis of multifactor {RNA-Seq} experiments with respect to biological variation},
  journal = {Nucleic Acids Research},
  year = {2012},
  volume = {40},
  pages = {4288--4297},
  number = {10},
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@ARTICLE{phipson2016robust,
  author = {B. Phipson and S. Lee and I. J. Majewski and W. S. Alexander and G. K. Smyth},
  year = {2016},
  title = {Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression},
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@article{rajkumar2015experimental,
  title={Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq},
  author={Rajkumar, A. P. and Qvist, P. and Lazarus, R. and Lescai, F. and Ju, J. and Nyegaard, M. and Mors, O. and B{\o}rglum, A. D. and Li, Q. and Christensen, J. H.},
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@ARTICLE{ritchie2015limma,
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  title = {{limma} powers differential expression analyses for {RNA}-sequencing and microarray studies},
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@ARTICLE{robinson2008smallsample,
  author = {M. D. Robinson and G. K. Smyth},
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  pages = {321--332},
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  volume = {11},
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@ARTICLE{robinson2010edger,
  author = {Robinson, M. D. and McCarthy, D. J. and Smyth, G. K.},
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  journal = {Bioinformatics},
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  pages = {139--140},
  number = {1},
  publisher = {Oxford Univ Press}
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  publisher = {bepress}
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@ARTICLE{wu2010roast,
  author = {Wu, D. and Lim, E. and Vaillant, F. and Asselin-Labat, M. L. and Visvader, J. E. and Smyth, G. K.},
  title = {{ROAST}: rotation gene set tests for complex microarray experiments},
  journal = {Bioinformatics},
  year = {2010},
  volume = {26},
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  number = {17},
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@article{wu2013mirna,
  title={The use of {miRNA} microarrays for the analysis of cancer samples with global {miRNA} decrease},
  author={Wu, Di and Hu, Yifang and Tong, Stephen and Williams, Bryan RG and Smyth, Gordon K and Gantier, Michael P},
  journal={RNA},
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  pages={876--888},
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  publisher={Cold Spring Harbor Lab}
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