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
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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