Slide 47
Slide 47 text
GENETIC
ANALYSIS
of Complex Human Diseases
Further Reading
n RNA-Seq:
u Garber, M., Grabherr, M. G., Guttman, M., & Trapnell, C. (2011). Computational methods for transcriptome annotation and
quantification using RNA-seq. Nature methods, 8(6), 469-77.
u Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008). RNA-seq: an assessment of technical
reproducibility and comparison with gene expression arrays. Genome research, 18(9), 1509-17.
u Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008). Mapping and quantifying mammalian
transcriptomes by RNA-Seq. Nature methods, 5(7), 621-8.
u Ozsolak, F., & Milos, P. M. (2011). RNA sequencing: advances, challenges and opportunities. Nature reviews. Genetics,
12(2), 87-98.
u Toung, J. M., Morley, M., Li, M., & Cheung, V. G. (2011). RNA-sequence analysis of human B-cells. Genome research,
991-998.
u Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews. Genetics,
10(1), 57-63.
n Bowtie/Tophat:
u Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA
sequences to the human genome. Genome biology, 10(3), R25.
u Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (Oxford,
England), 25(9), 1105-11.
n Cufflinks:
u Roberts, A., Pimentel, H., Trapnell, C., & Pachter, L. (2011). Identification of novel transcripts in annotated genomes using
RNA-Seq. Bioinformatics (Oxford, England), 27(17), 2325-9.
u Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., Pimentel, H., et al. (2012). Differential gene and transcript
expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7(3), 562-578.
u Trapnell, C., Williams, B. a, Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., et al. (2010). Transcript
assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell
differentiation. Nature biotechnology, 28(5), 511-5.
n DEXSeq:
u Vignette: http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html.
u Pre-pub manuscript: Anders, S., Reyes, A., Huber, W. (2012). Detecting differential usage of exons from RNA-Seq data.
Nautre Precedings, DOI: 10.1038/npre.2012.6837.2.