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