Analysis and design of RNA sequencing experiments for identifying isoform regulation
10.1038/nmeth.1528
Crossref journal-article
Springer Science and Business Media LLC
Nature Methods (297)
Bibliography

Katz, Y., Wang, E. T., Airoldi, E. M., & Burge, C. B. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods, 7(12), 1009–1015.

Authors 4
  1. Yarden Katz (first)
  2. Eric T Wang (additional)
  3. Edoardo M Airoldi (additional)
  4. Christopher B Burge (additional)
References 38 Referenced 1,206
  1. Matlin, A.J., Clark, F. & Smith, C.W.J. Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol. 6, 386–398 (2005). (10.1038/nrm1645) / Nat. Rev. Mol. Cell Biol. by AJ Matlin (2005)
  2. Christofk, H.R. et al. The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth. Nature 452, 230–233 (2008). (10.1038/nature06734) / Nature by HR Christofk (2008)
  3. Rowen, L. et al. Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics 79, 587–597 (2002). (10.1006/geno.2002.6734) / Genomics by L Rowen (2002)
  4. Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008). (10.1038/nature07509) / Nature by ET Wang (2008)
  5. Mortazavi, A., Williams, B.A.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621–628 (2008). (10.1038/nmeth.1226) / Nat. Methods by A Mortazavi (2008)
  6. Pan, Q., Shai, O., Lee, L.J., Frey, B.J. & Blencowe, B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413–1415 (2008). (10.1038/ng.259) / Nat. Genet. by Q Pan (2008)
  7. Yassour, M. et al. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc. Natl. Acad. Sci. USA 106, 3264–3269 (2009). (10.1073/pnas.0812841106) / Proc. Natl. Acad. Sci. USA by M Yassour (2009)
  8. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010). (10.1038/nbt.1621) / Nat. Biotechnol. by C Trapnell (2010)
  9. Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503–510 (2010). (10.1038/nbt.1633) / Nat. Biotechnol. by M Guttman (2010)
  10. Griffith, M., Griffith, O.L., Mwenifumbo, J., Goya, R. & Morrissy, A.S. Alternative expression analysis by RNA sequencing. Nat. Methods 7, 843–847 (2010). (10.1038/nmeth.1503) / Nat. Methods by M Griffith (2010)
  11. Venables, J.P. et al. Identification of alternative splicing markers for breast cancer. Cancer Res. 68, 9525–9531 (2008). (10.1158/0008-5472.CAN-08-1769) / Cancer Res. by JP Venables (2008)
  12. Jiang, H. & Wong, W.H. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25, 1026–1032 (2009). (10.1093/bioinformatics/btp113) / Bioinformatics by H Jiang (2009)
  13. Venables, J.P. et al. Cancer-associated regulation of alternative splicing. Nat. Struct. Mol. Biol. 16, 670–676 (2009). (10.1038/nsmb.1608) / Nat. Struct. Mol. Biol. by JP Venables (2009)
  14. Xiao, X. et al. Splice site strength-dependent activity and genetic buffering by poly-G runs. Nat. Struct. Mol. Biol. 16, 1094–1100 (2009). (10.1038/nsmb.1661) / Nat. Struct. Mol. Biol. by X Xiao (2009)
  15. Millevoi, S. & Vagner, S. Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation. Nucleic Acids Res. 38, 2757–2774 (2010). (10.1093/nar/gkp1176) / Nucleic Acids Res. by S Millevoi (2010)
  16. Alkan, S.A., Martincic, K. & Milcarek, C. The hnRNPs F and H2 bind to similar sequences to influence gene expression. Biochem. J. 393, 361–371 (2006). (10.1042/BJ20050538) / Biochem. J. by SA Alkan (2006)
  17. Millevoi, S. et al. A physical and functional link between splicing factors promotes pre-mRNA 3′ end processing. Nucleic Acids Res. 37, 4672–4683 (2009). (10.1093/nar/gkp470) / Nucleic Acids Res. by S Millevoi (2009)
  18. Honoré, B., Baandrup, U. & Vorum, H. Heterogeneous nuclear ribonucleoproteins F and H/H' show differential expression in normal and selected cancer tissues. Exp. Cell Res. 294, 199–209 (2004). (10.1016/j.yexcr.2003.11.011) / Exp. Cell Res. by B Honoré (2004)
  19. Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A. & Burge, C.B. Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320, 1643–1647 (2008). (10.1126/science.1155390) / Science by R Sandberg (2008)
  20. Mayr, C. & Bartel, D.P. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673–684 (2009). (10.1016/j.cell.2009.06.016) / Cell by C Mayr (2009)
  21. Li, J., Jiang, H. & Wong, W.H. Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol. 11, R50 (2010). (10.1186/gb-2010-11-5-r50) / Genome Biol. by J Li (2010)
  22. Cooper, T.A., Wan, L. & Dreyfuss, G. RNA and disease. Cell 136, 777–793 (2009). (10.1016/j.cell.2009.02.011) / Cell by TA Cooper (2009)
  23. Zhang, L., Lee, J.E., Wilusz, J. & Wilusz, C.J. The RNA-binding protein CUGBP1 regulates stability of tumor necrosis factor mRNA in muscle cells: implications for myotonic dystrophy. J. Biol. Chem. 283, 22457–22463 (2008). (10.1074/jbc.M802803200) / J. Biol. Chem. by L Zhang (2008)
  24. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009). (10.1186/gb-2009-10-3-r25) / Genome Biol. by B Langmead (2009)
  25. Li, B., Ruotti, V., Stewart, R.M., Thomson, J.A. & Dewey, C.N. Rna-seq gene expression estimation with read mapping uncertainty. Bioinformatics 26, 493–500 (2010). (10.1093/bioinformatics/btp692) / Bioinformatics by B Li (2010)
  26. Zhang, H., Hu, J., Recce, M. & Tian, B. PolyADB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res. 33, D116–D120 (2005). (10.1093/nar/gki055) / Nucleic Acids Res. by H Zhang (2005)
  27. Wang, L. et al. A statistical method for the detection of alternative splicing using rna-seq. PLoS ONE 5, e8529 (2010). (10.1371/journal.pone.0008529) / PLoS ONE by L Wang (2010)
  28. Denoeud, F. et al. Annotating genomes with massive-scale RNA sequencing. Genome Biol. 9, R175 (2008). (10.1186/gb-2008-9-12-r175) / Genome Biol. by F Denoeud (2008)
  29. Trapnell, C., Pachter, L. & Salzberg, S.L. Tophat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009). (10.1093/bioinformatics/btp120) / Bioinformatics by C Trapnell (2009)
  30. Ameur, A., Wetterbom, A., Feuk, L. & Gyllensten, U. Global and unbiased detection of splice junctions from rna-seq data. Genome Biol. 11, R34 (2010). (10.1186/gb-2010-11-3-r34) / Genome Biol. by A Ameur (2010)
  31. Au, K.F., Jiang, H., Lin, L., Xing, Y. & Wong, W.H. Detection of splice junctions from paired-end rna-seq data by splicemap. Nucleic Acids Res. 38, 4570–4578 (2010). (10.1093/nar/gkq211) / Nucleic Acids Res. by KF Au (2010)
  32. Wu, T.D. & Nacu, S. Fast and snp-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873–881 (2010). (10.1093/bioinformatics/btq057) / Bioinformatics by TD Wu (2010)
  33. O'Hagan, A. & Forster, J. Kendall's advanced theory of statistics, vol. 2b: Bayesian inference. (2nd edn.) J. Am. Stat. Assoc. 100, 1465–1466 (2005). / J. Am. Stat. Assoc. by A O'Hagan (2005)
  34. Liu, J.S. Monte Carlo Strategies in Scientific Computing (Springer Series in Statistics) (Springer, 2008).
  35. Airoldi, E.M. Getting started in probabilistic graphical models. PLOS Comput. Biol. 3, e252 (2007). (10.1371/journal.pcbi.0030252) / PLOS Comput. Biol. by EM Airoldi (2007)
  36. Aitchison, J. & Shen, S.M. Logistic-normal distributions: some properties and uses. Biometrika 67, 261–272 (1980). (10.2307/2335470) / Biometrika by J Aitchison (1980)
  37. Chen, M. & Man Shao, Q. Monte Carlo estimation of Bayesian credible and HPD intervals. J. Comput. Graph. Statist. 8, 69–92 (1998). (10.1080/10618600.1999.10474802) / J. Comput. Graph. Statist. by M Chen (1998)
  38. Kass, R.E. & Raftery, A.E. Bayes factors. J. Am. Stat. Assoc. 90, 773–795 (1995). (10.1080/01621459.1995.10476572) / J. Am. Stat. Assoc. by RE Kass (1995)
Dates
Type When
Created 14 years, 10 months ago (Nov. 7, 2010, 1:16 p.m.)
Deposited 6 months, 1 week ago (Feb. 27, 2025, 12:16 p.m.)
Indexed 22 minutes ago (Sept. 7, 2025, 3:08 p.m.)
Issued 14 years, 10 months ago (Nov. 7, 2010)
Published 14 years, 10 months ago (Nov. 7, 2010)
Published Online 14 years, 10 months ago (Nov. 7, 2010)
Published Print 14 years, 9 months ago (Dec. 1, 2010)
Funders 0

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@article{Katz_2010, title={Analysis and design of RNA sequencing experiments for identifying isoform regulation}, volume={7}, ISSN={1548-7105}, url={http://dx.doi.org/10.1038/nmeth.1528}, DOI={10.1038/nmeth.1528}, number={12}, journal={Nature Methods}, publisher={Springer Science and Business Media LLC}, author={Katz, Yarden and Wang, Eric T and Airoldi, Edoardo M and Burge, Christopher B}, year={2010}, month=nov, pages={1009–1015} }