Research References

Benjamini Y and Hochberg Y (1995). “Controlling the false discovery rate: a practical and powerful approach to multiple testing.” Journal of the Royal Statistical Society. Series B (Methodological), Vol. 57, No. 1 (1995), pp. 289-300. [Read online]

 

Johnson et al. (2007). "Genome-Wide Mapping of in Vivo Protein-DNA Interactions." Science June 8, 2007; 316(5830):1497-502.

 

Krumm N, Sudmant PH, Ko A, et al. (2012). "Copy number variation detection and genotyping from exome sequence data." Genome Res. published online May 14, 2012. (This reference pertains to the zRPKM and RPKM-CN normalization methods.)

 

Li H, Ruan J, and Durbin R (2008). “Mapping short DNA sequencing reads and calling variants using mapping quality scores.” Genome Res. 2008 Nov;18(11):1851-8. https://doi.org/10.1101/gr.078212.108. Epub 2008 Aug 19.

 

Love MI, Huber W and Anders S (2014) “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology 15:550. https://doi.org/10.1186/s13059-014-0550-8.

 

Mortazavi A, Williams BA, McCue K, Schaeffer L and Wold B (2008). “Mapping and quantifying mammalian transcriptomes by RNA-Seq.” Nature Methods, 5, 621-628. (Pertains to the ChIP-Seq Peak Finder algorithm.)

 

Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26(1), 139-140.

 

Robinson, MD, and Oshlack, A (2010). “A scaling normalization method for differential expression analysis of RNA-seq data.” Genome Biology 11, R25

 

Robinson, MD, and Smyth, GK (2008). “Small sample estimation of negative binomial dispersion, with applications to SAGE data.” Biostatistics 9, 321–332.