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: 289-300. [Pertains to the FDR (Benjamini Hochberg) method].
Bolstad BM (2004). “Low-level analysis of high-density oligonucleotide array data: background, normalization, and summarization.” Dissertation. University of California, Berkeley. http://bmbolstad.com/Dissertation/Bolstad_2004_Dissertation.pdf.
Campbell CD, Sampas N, Tsalenko A, Sudmant PH, Kidd JM, Malig M, Vu TH, et al. (2011). "Population-Genetic Properties of Differentiated Human Copy- Number Polymorphisms." The American Journal of Human Genetics, 88(3), 317–332. doi:10.1016/j.ajhg.2011.02.004.
Chun S and Fay JC (2009). “Identification of deleterious mutations within three human genomes.” Genome Res., 19, 1553-1561.
Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, et al. (2010). "Origins and functional impact of copy number variation in the human genome." Nature, 464(7289), 704–712. doi:10.1038/nature08516.
Cooper GM et al. (2005). “Distribution and intensity of constraint in mammalian genomic sequence.” Genome Res., 15, 901–913.
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. [dbNSFP reference; see online]
Drăghici S. (2003). “Data analysis tools for DNA microarrays.” Boca Raton, FL:Chapman & Hall/CRC. (Pertains to the Student's t-test.)
Garber M et al. (2009). “Identifying novel constrained elements by exploiting biased substitution patterns.” Bioinformatics 25, i54-62.
Georgi B, Voight BF, Bucan M (2013). “From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes.” PLOS Genetics, May 9, 2013. DOI: 10.1371/journal.pgen.1003484.
Holm S. (1979). “A simple sequentially rejective multiple test procedure.” Scandinavian Journal of Statistics, 6, 65–70. (Pertains to the Holm-Bonferroni method.)
Huang N, Lee I, Marcotte EM, Hurles ME (2010). “Characterizing and Predicting Haploinsufficiency in the Human Genome.” PLOS Genetics, October 14, 2010. DOI: 10.1371/journal.pgen.1001154.
Ionita-Laza I, Makarov V, Yoon S, Raby B, Buxbaum, J, Nicolae DL, Lin X. (2011). "Finding Disease Variants in Mendelian Disorders by Using Sequence Data: Methods and Applications." The American Journal of Human Genetics, Volume 89, Issue 6, December 2011, Pages 701-712.
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003). “Exploration, normalization, and summaries of high-density oligonucleotide array probe level data.” Biostatistics, Vol. 4, No. 2: 249-64.
Johnson DS, Mortazavi A, Myers RM, and Wold B (2007). “Genome-Wide Mapping of in Vivo Protein-DNA Interactions.” Science 316, 1497-1502. (Pertains to the Simple Peak Finder.)
Jpopgen: The dbNSFP database at the Jpopgen website [dbNSFP reference].
Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, et al. (2008). "Mapping and sequencing of structural variation from eight human genomes." Nature, 453(7191), 56–64. doi:10.1038/nature06862.
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.)
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. [dbNSFP reference; view on PubMed].
Liu X, Jian X, and Boerwinkle E (2013). “dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations.” Human Mutation, 34:E2393-E2402. [View on PubMed].
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. [dbNSFP reference; 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. 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.)
MacArthur DG et al. (2012). “A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes.” Science Vol. 335 no. 6070 pp. 823-828. DOI: 10.1126/science.1215040.
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.)
Pollard KS et al. (2010). “Detection of nonneutral substitution rates on mammalian phylogenies.” Genome Res., 20, 110-121.
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. (edgeR reference).
Robinson, MD, and Smyth, GK (2008). “Small sample estimation of negative binomial dispersion, with applications to SAGE data.” Biostatistics 9, 321–332. (edgeR reference).
Sathirapongsasuti JF, Lee H, Horst BAJ, Brunner G, Cochran AJ, Binder S, Quackenbush J, et al. (2011). "Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV." Bioinformatics, 27(19), 2648–2654. doi:10.1093/bioinformatics/btr462.
Schwarz JM, et al. (2014). “MutationTaster2: mutation prediction for the deep-sequencing age.” Nat. Methods, 11, 361-362.
The Sequence Ontology website [variant nomenclature reference].
Siepel A et al. (2005). “Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.” Genome Res., 15, 1034–1050.
Smyth GK (2004) "Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments," Statistical Applications in Genetics and Molecular Biology: Vol. 3: Iss. 1, Article 3. (Pertains to the Moderated t-test.)
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, et al. (2010). "Diversity of human copy number variation and multicopy genes." Science, 330(6004), 641–646. doi:10.1126/science.1197005.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM., Brown M, Li W, and Liu XS (2008). “Model-based Analysis of ChIP-Seq (MACS).” Genome Biology. 9, R137. (Pertains to the MACS Peak Finder.)
Zook JM et al. (2014). “Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.” Nature Biotechnology, published online 2/16/2014, ahead of print.