References
- Bracco, L. and Kearsey, J. (2003).The relevanceof alternative RNA splicing to pharmacogenomics. TRENDS in Biotech. 21, 346-352 https://doi.org/10.1016/S0167-7799(03)00146-X
- Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., Roth, R., George, D., Eletr, S., Albrecht, G., Vermaas, E., Williams, S.R., Moon, K., Burcham, T., Pallas, M., DuBridge, R.B., Kirchner, J., Fearon, K., Mao, J., and Corcoran, K. (2000). Geneexpression analysisby massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnol. 18, 630-634 https://doi.org/10.1038/76469
- Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., Sementchenko, V., Piccolboni, A., Bekiranov, S., Bailey, D.K., Ganesh, M., Ghosh, S., Bell, I., Gerhard, D.S., and Gingeras, T.R. (2005). Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution. Science 308, 1149-1154 https://doi.org/10.1126/science.1108625
- Fehlbaum, P., Guihal, C., Bracco, L., and Cochet, O. (2005). A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucleic Acids Res. 33, e47 https://doi.org/10.1093/nar/gni047
- Hu,G.K., Madore,S.J., Moldover, B., Jatkoe, T., Balaban, D., Thomas, J., and Wang, Y. (2001). Predicting splice variant from DNA chip expression data. Genome Res. 11,1237-1245 https://doi.org/10.1101/gr.165501
- Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., and et al., (2004). Integrative annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLOS Bio. 2, 856-875
- Johnson, J.M., Castel, J., Garrett-Engele, P., Kan, Z., Loerch, P.M., Armour, C.o., Santos, R., Schadt, E.E., Stoughton, R., and Shoemaker,DD, (2003).Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302, 2141-2144 https://doi.org/10.1126/science.1090100
- Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., Tammana, H., and Gingeras, T.R. (2004). Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22. Genome Res. 14, 331-342 https://doi.org/10.1101/gr.2094104
- Kim, P., Kim, N., Lee, Y., Kim, B., Shin, Y., and Lee, S. (2005). ECgene: genome annotation for alternative splicing. Nucleic Acids Res. 33, D75-D79 https://doi.org/10.1093/nar/gni075
- Lawson, C.L. and Hanson, R.J. (1974). Solving Least Squares Problem, Prentice-Hall, Engelwood Cliffs, N.J
- Lee, D.O. and Seung, H.S. (1999). Learning the parts of objects by non-negative matrix factorization. Nature 401, 788-791 https://doi.org/10.1038/44565
- Modrek, B., Resch, A., Grasso C., and Lee, C. (2001). Genome-wide detection of alternative splicing in expressed sequences of human gene. Nucleic Acids Res. 29, 2850-2859 https://doi.org/10.1093/nar/29.13.2850
- Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A.L., Mohammad, N., Babak, T., Siu, H., Hughes, T., Morris, Q.D., Frey, B.J., and Blencowe, B.J. (2004). Revealing global regulatory features of mammalian altemative splicing using a quantitative microarray platform. Mol. Cell 16, 929-941 https://doi.org/10.1016/j.molcel.2004.12.004
- Shai. O., Morris. Q.D., Blencowe, B.J., and Frey, B.J. (2005). Inferring global leels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics 22, 606-613 https://doi.org/10.1093/bioinformatics/btk028
- Shoemaker,D.D., Schadt,E.E., Armour, C.D., He, Y.D., Garrett-Engele, P. et al. (2001). Experimental annotation of the human genome using microarray technology. Nature 409. 922-927 https://doi.org/10.1038/35057141
- Strausberg, L.R., Feingold, E.A, Klausner, R.D., and Collins, F.S. (1999). The mammalian gene collection. Science 286, 455-457 https://doi.org/10.1126/science.286.5439.455
- Ule, J., Ule, A., Spencer, J., Williams, A., Hu, J. Cline, M. Wang, H., Clark, T., Fraser, C., Ruggiu, M., Zeeberg, B.R., Kane, D., Weinstein, J.N., Blume, J., and Darnell, A.B. (2005). Nova regulates brain-specific splicing to shape the synapse. Nature Genet. 37, 844-852
- Wang, H., Hubbell, E., Hu, J., Mei, G., Cline, M., Lu, G., Clark,T., Siani-Rose, M.A., Ares, M., Kulp, D.C., and Haussler, D. (2003). Gene structure-based splice variant deconvolution using microarray platform. Bioinformatics 19, i315-i322 https://doi.org/10.1093/bioinformatics/19.2.315
- Xu, Q., Modrek, B., and Lee, C. (2002). Genome-wide detection of tissue-specific alternative splicing in the human transcriptome, Nucleic Acids Res. 30, 3754-3766 https://doi.org/10.1093/nar/gkf492