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. (See online.)

Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K and Liu X (2015). “Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies.” Human Molecular Genetics 24(8):2125-2137. (Pertains to dbNSFP; see online.)

Fitzgerald DM, Bonocora RP, Wade JT (2014). “Comprehensive Mapping of the Escherichia coli Flagellar Regulatory Network.” PLoS Genet 10(10): e1004649. doi:10.1371/journal.pgen.1004649.

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. (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. doi.org/10.1101/gr.078212.108. Epub 2008 Aug 19.

Liu X, Jian X, and Boerwinkle E (2011). “dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions.” Human Mutation. 32:894-899. (Pertains to dbNSFP; see online.)

Liu X, Wu C, Li C and Boerwinkle E (2016). “dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs.” Human Mutation. 37:235-241. (Pertains to dbNSFP; see online.)

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. 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.)

Mukherjee, Supratim & Huntemann, Marcel & Ivanova, Natalia & Kyrpides, Nikos & Pati, Amrita. (2015). Large-scale contamination of microbial isolate genomes by Illumina PhiX control. Standards in genomic sciences. 10. 18. 10.1186/1944-3277-10-18. (See online.)

Nookaew I et al. (2012). “A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.” Nucleic Acids Res. 2012 Nov 1;40(20):10084-97. doi: 10.1093/nar/gks804 (View on PubMed.)

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.

Subramanian A et al. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. doi: 10.1073/pnas.0506580102.

Zhang Y, Liu T, Meyer CA et al. (2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9, R137. (See online.)

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