| [1] | Roy NC, Altermann E, Park ZA, McNabb WC (2011) A comparison of analog and next-generation transcriptomic tools for mammalian studies. Brief Funct Genomics 10: 135–50.
|
| [2] | Crawford JE, Guelbeogo WM, Sanou A, Traoré A, Vernick KD, et al. (2010) De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-Seq technology. PLoS One 5: e14202.
|
| [3] | Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644–52.
|
| [4] | Trapnell C, Pachter L, Salzberg SL (2009) Tophat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105–11.
|
| [5] | Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, et al. (2010) Mapsplice: accurate mapping of RNA-Seq reads for splice junction discovery. Nucleic Acids Res 38: e178.
|
| [6] | Kim D, Salzberg SL (2011) Tophat-fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 12: R72.
|
| [7] | Smith AM, Heisler LE, St Onge RP, Farias-Hesson E, Wallace IM, et al. (2010) Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res 38: e142.
|
| [8] | van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most "dark matter" transcripts are associated with known genes. PLoS Biol 8: e1000371.
|
| [9] | McIntyre LM, Lopiano KK, Morse AM, Amin V, Oberg AL, et al. (2011) Rna-Seq: technical variability and sampling. BMC Genomics 12: 293.
|
| [10] | Wu Z (2009) A review of statistical methods for preprocessing oligonucleotide microarrays. Stat Methods Med Res 18: 533–41.
|
| [11] | Pachter L (2011) Models for transcript quantification from RNA-Seq. ArXiv 1104.3889.
|
| [12] | Nakagawa S, Cuthill IC (2007) Effect size, confidence interval and statistical significance: a practical guide for biologists. Biol Rev Camb Philos Soc 82: 591–605.
|
| [13] | Parks DH, Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715–21.
|
| [14] | Pearson K (1896) Mathematical contributions to the theory of evolution. { on a form of spurious correlation which may arise when indices are used in the measurement of organs. Proceedings ofthe Royal Society of London 60: 489–498.
|
| [15] | Aitchison J, J Egozcue J (2005) Compositional data analysis: Where are we and where should we be heading? Mathematical Geology 37: 829–850.
|
| [16] | Pawlowsky-Glahn V, Egozcue JJ (2006) Compositional data and their analysis: an introduction. Geological Society, London, Special Publications 264: : 1–10.
|
| [17] | Egozcue J, Pawlowsky-Glahn V (2005) Groups of parts and their balances in compositional data analysis. Mathematical Geology 37: 795–828.
|
| [18] | Egozcue JJ, Pawlowsky-Glahn V, Mateu-Figueras G, Barcel O-Vidal C (2003) Isometric logratio transformations for compositional data analysis. mathematical geology. Math Geol 35: 279–300.
|
| [19] | Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) Rna-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509–17.
|
| [20] | Polymenakou PN, Lampadariou N, Mandalakis M, Tselepides A (2009) Feb Phylogenetic diversity of sediment bacteria from the southern cretan margin, eastern mediterranean sea. Syst Appl Microbiol 32: 17–26.
|
| [21] | Rosenthal AZ, Matson EG, Eldar A, Leadbetter JR (2011) Rna-Seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture. ISME J 5: 1133–42.
|
| [22] | Robinson MD, Smyth GK (2008) Small-sample estimation of negative binomial dispersion, with applications to sage data. Biostatistics 9: 321–332.
|
| [23] | Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
|
| [24] | Newey WK, McFadden D (1994) Large sample estimation and hypothesis testing. In:Engle R, McFadden D, editors, Handbook of Econometrics, Elsevier Science, volume 4, chapter 35. pp. 2111–2245.
|
| [25] | Jaynes ET, Bretthorst GL (2003) Probability theory: the logic of science. Cambridge, UK:Cambridge University Press. URL http://www.loc.gov/catdir/samples/cam033？/2002071486.html.
|
| [26] | Bela A Frigyik AK, Gupta MR (2010) Introduction to the Dirichlet distribution and related processes. Technical Report UWEETR-2010-0006, Department of Electrical Engineering, University of Washington. URL http://www.ee.washington.edu/research/gu？ptalab/publications/UWEETR-2010-0006.pdf.
|
| [27] | Berger J, Bernardo J (1992) Ordered group reference priors with application to the multinomial problem. Biometrika 79: 25.
|
| [28] | Bernardo J (2005) Reference analysis. Bayesian Thinking, Modeling and Computation 25: 17–90.
|
| [29] | Berger JO, Bernardo JM, Sun D (2009) The formal definition of reference priors. Annals of Statistics 37: 905–938.
|
| [30] | Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGSeq: an R package for identifying differentially expressed genes from RNA-Seq data. Bioinformatics 26: 136–8.
|
| [31] | Macklaim MJ, Fernandes DA, Di Bella MJ, Hammond JA, Reid G, et al.. (2013) Comparative meta-RNA-Seq of the vaginal microbiota and differential expression by lactobacillus iners in health and dysbiosis. Microbiome doi: 10.1186/2049-2618-1-12.
|
| [32] | Langmead B (2010) Aligning short sequencing reads with bowtie. Curr Protoc Bioinformatics Chapter 11: Unit 11.7.
|
| [33] | Friedman J, Alm EJ (2012) Inferring correlation networks from genomic survey data. PLoS Comput Biol 8: e1002687.
|
| [34] | La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, et al. (2012) Hypothesis testing and power calculations for taxonomic-based human microbiome data. PLoS One 7: e52078.
|
| [35] | Holmes I, Harris K, Quince C (2012) Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One 7: e30126.
|
| [36] | Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Research 20: 180–189.
|
| [37] | Altman DG, Bland JM (1983) Measurement in medicine: The analysis of method comparison studies. Journal of the Royal Statistical Society Series D (The Statistician)32 :pp. 307–317.
|
| [38] | Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–40.
|
| [39] | Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511–5.
|
| [40] | Mols M, van Kranenburg R, Tempelaars MH, van Schaik W, Moezelaar R, et al. (2010) Comparative analysis of transcriptional and physiological responses of bacillus cereus to organic and inorganic acid shocks. Int J Food Microbiol 137: 13–21.
|
| [41] | Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB (2011) The real cost of sequencing: higher than you think! . Genome Biol 12: 125.
|
| [42] | Kvam VM, Liu P, Si Y (2012) A comparison of statistical methods for detecting differentially expressed genes from RNA-Seq data. Am J Bot 99: 248–56.
|
| [43] | Hamady M, Knight R (2009) Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res 19: 1141–52.
|
| [44] | Rodriguez-Brito B, Rohwer F, Edwards RA (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics 7: 162.
|
| [45] | Efron B, Tibshirani R (1993) An introduction to the bootstrap, volume 57. New York:Chapman & Hall. URL http://www.loc.gov/catdir/enhancements/f？y0730/93004489-d.html.
|
| [46] | Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3: e3042.
|
| [47] | Gilbert JA, Meyer F, Schriml L, Joint IR, Muhling M, et al. (2010) Metagenomes and metatranscriptomes from the l4 long-term coastal monitoring station in the western English Channel. Stand Genomic Sci 3: 183–93.
|
| [48] | McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, et al. (2010) Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci U S A 107: 16420–7.
|
| [49] | White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352.
|
| [50] | Faith JJ, McNulty NP, Rey FE, Gordon JI (2011) Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 333: 101–4.
|
| [51] | Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, et al. (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A 107: 7503–8.
|
| [52] | Kristiansson E, Hugenholtz P, Dalevi D (2009) ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics 25: 2737–8.
|
| [53] | Hardcastle TJ, Kelly KA (2013) Empirical bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution. BMC Bioinformatics 14: 135.
|
| [54] | Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, 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 40: 10084–97.
|
| [55] | Nugent RP, Krohn MA, Hillier SL (1991) Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation. J Clin Microbiol 29: 297–301.
|
| [56] | Li W, Godzik A (2006) CD-Hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658–9.
|
| [57] | Oliveros JC (2007). Venny. an interactive tool for comparing lists with Venn diagrams. URLhttp://bioinfogp.cnb.csic.es/tools/venny？/index.html.
|
