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diff --git a/academic/cufflinks/References b/academic/cufflinks/References new file mode 100644 index 0000000000..3434915871 --- /dev/null +++ b/academic/cufflinks/References @@ -0,0 +1,37 @@ +Publications + +Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, +Salzberg SL, Wold B, Pachter L. Transcript assembly and quantification +by RNA-Seq reveals unannotated transcripts and isoform switching +during cell differentiation +Nature Biotechnology doi:10.1038/nbt.1621 + +Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA- +Seq expression estimates by correcting for fragment bias +Genome Biology doi:10.1186/gb-2011-12-3-r22 + +Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel +transcripts in annotated genomes using RNA-Seq +Bioinformatics doi:10.1093/bioinformatics/btr355 + +Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L +Differential analysis of gene regulation at transcript resolution with +RNA-seq +Nature Biotechnology doi:10.1038/nbt.2450 + +REFERENCES +--------------------------- +Cufflinks builds on many ideas, including some +proposed in the following papers: + +Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and Barbara +Wold, "Mapping and quantifying mammalian transcriptomes by RNA-Seq",Nature +Methods, volume 5, 621 - 628 (2008) + +Hui Jiang and Wing Hung Wong, "Statistical Inferences for isoform expression", +Bioinformatics, 2009 25(8):1026-1032 + +Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, +Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel, "Viral +population estimation using pyrosequencing", PLoS Computational Biology, +4(5):e1000074 |