{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,6]],"date-time":"2024-09-06T00:45:10Z","timestamp":1725583510367},"publisher-location":"Berlin, Heidelberg","reference-count":84,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642163449"},{"type":"electronic","value":"9783642163456"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011]]},"DOI":"10.1007\/978-3-642-16345-6_2","type":"book-chapter","created":{"date-parts":[[2011,5,16]],"date-time":"2011-05-16T12:31:03Z","timestamp":1305549063000},"page":"31-53","source":"Crossref","is-referenced-by-count":3,"title":["Statistical and Computational Studies on Alternative Splicing"],"prefix":"10.1007","author":[{"given":"Liang","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,4,9]]},"reference":[{"key":"2_CR1_2","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/nature07509","volume":"456","author":"ET Wang","year":"2008","unstructured":"Wang, E.\u00a0T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.\u00a0F., Schroth, G.\u00a0P., & Burge, C.\u00a0B. (2008). Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470\u2013476.","journal-title":"Nature"},{"key":"2_CR2_2","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.1038\/ng.259","volume":"40","author":"Q Pan","year":"2008","unstructured":"Pan, Q., Shai, O., Lee, L.\u00a0J., Frey, B.\u00a0J., & Blencowe, B.\u00a0J. (2008). Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics, 40, 1413\u20131415.","journal-title":"Nature Genetics"},{"key":"2_CR3_2","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1038\/271501a0","volume":"271","author":"W Gilbert","year":"1978","unstructured":"Gilbert, W. (1978). Why genes in pieces? Nature, 271, 501.","journal-title":"Nature"},{"key":"2_CR4_2","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1146\/annurev.bi.56.070187.002343","volume":"56","author":"RE Breitbart","year":"1987","unstructured":"Breitbart, R.\u00a0E., Andreadis, A., & Nadal-Ginard, B. (1987). Alternative splicing: A ubiquitous mechanism for the generation of multiple protein isoforms from single genes. Annual Review of Biochemistry, 56, 467\u2013495.","journal-title":"Annual Review of Biochemistry"},{"key":"2_CR5_2","doi-asserted-by":"publisher","first-page":"2141","DOI":"10.1126\/science.1090100","volume":"302","author":"JM Johnson","year":"2003","unstructured":"Johnson, J.\u00a0M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P.\u00a0M., Armour, C.\u00a0D., Santos,\u00a0R., Schadt, E.\u00a0E., Stoughton, R., & Shoemaker, D.\u00a0D. (2003). Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science, 302, 2141\u20132144.","journal-title":"Science"},{"key":"2_CR6_2","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1101\/gr.155001","volume":"11","author":"Z Kan","year":"2001","unstructured":"Kan, Z., Rouchka, E.\u00a0C., Gish, W.\u00a0R., & States, D.\u00a0J. (2001). Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Research, 11, 889\u2013900.","journal-title":"Genome Research"},{"key":"2_CR7_2","doi-asserted-by":"publisher","first-page":"1288","DOI":"10.1101\/gr.9.12.1288","volume":"9","author":"AA Mironov","year":"1999","unstructured":"Mironov, A.\u00a0A., Fickett, J.\u00a0W., & Gelfand, M.\u00a0S. (1999). Frequent alternative splicing of human genes. Genome Research, 9, 1288\u20131293.","journal-title":"Genome Research"},{"key":"2_CR8_2","doi-asserted-by":"publisher","first-page":"2850","DOI":"10.1093\/nar\/29.13.2850","volume":"29","author":"B Modrek","year":"2001","unstructured":"Modrek, B., Resch, A., Grasso, C., & Lee, C. (2001). Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Research, 29, 2850\u20132859.","journal-title":"Nucleic Acids Research"},{"key":"2_CR9_2","doi-asserted-by":"publisher","first-page":"1499","DOI":"10.1261\/rna.7105504","volume":"10","author":"BR Graveley","year":"2004","unstructured":"Graveley, B.\u00a0R., Kaur, A., Gunning, D., Zipursky, S.\u00a0L., Rowen, L., & Clemens, J.\u00a0C. (2004). The organization and evolution of the dipteran and hymenopteran Down syndrome cell adhesion molecule (Dscam) genes. RNA, 10, 1499\u20131506.","journal-title":"RNA"},{"key":"2_CR10_2","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/S0168-9525(97)01324-3","volume":"14","author":"M Missler","year":"1998","unstructured":"Missler, M., & Sudhof, T.\u00a0C. (1998). Neurexins: Three genes and 1001 products. Trends in Genetics, 14, 20\u201326.","journal-title":"Trends in Genetics"},{"key":"2_CR11_2","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1126\/science.1077061","volume":"298","author":"EM Zdobnov","year":"2002","unstructured":"Zdobnov, E.\u00a0M., von\u00a0Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.\u00a0R., Christophides, G.\u00a0K., Thomasova, D., Holt, R.\u00a0A., Subramanian, G.\u00a0M., Mueller, H.\u00a0M., Dimopoulos, G., Law, J.\u00a0H., Wells, M.\u00a0A., Birney, E., Charlab, R., Halpern, A.\u00a0L., Kokoza, E., Kraft, C.\u00a0L., Lai, Z., Lewis, S., Louis, C., Barillas-Mury, C., Nusskern, D., Rubin, G.\u00a0M., Salzberg, S.\u00a0L., Sutton, G.\u00a0G., Topalis, P., Wides, R., Wincker, P., Yandell, M., Collins, F.\u00a0H., Ribeiro, J., Gelbart, W.\u00a0M., Kafatos, F.\u00a0C., & Bork, P. (2002). Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science, 298, 149\u2013159.","journal-title":"Science"},{"key":"2_CR12_2","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1101\/gr.229202","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent, W.\u00a0J. (2002). BLAT \u2013 the BLAST-like alignment tool. Genome Research, 12, 656\u2013664.","journal-title":"Genome Research"},{"key":"2_CR13_2","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1101\/gr.8.9.967","volume":"8","author":"L Florea","year":"1998","unstructured":"Florea, L., Hartzell, G., Zhang, Z., Rubin, G.\u00a0M., & Miller, W. (1998). A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Research, 8, 967\u2013974.","journal-title":"Genome Research"},{"key":"2_CR14_2","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1093\/bioinformatics\/bti310","volume":"21","author":"TD Wu","year":"2005","unstructured":"Wu, T.\u00a0D., & Watanabe, C.\u00a0K. (2005). GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859\u20131875.","journal-title":"Bioinformatics"},{"key":"2_CR15_2","doi-asserted-by":"publisher","first-page":"e24","DOI":"10.1371\/journal.pgen.0020024","volume":"2","author":"E Nimwegen van","year":"2006","unstructured":"van\u00a0Nimwegen, E., Paul, N., Sheridan, R., & Zavolan, M. (2006). SPA: A probabilistic algorithm for spliced alignment. PLoS Genetics, 2, e24.","journal-title":"PLoS Genetics"},{"key":"2_CR16_2","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1101\/gr.2889405","volume":"15","author":"L Florea","year":"2005","unstructured":"Florea, L., Di Francesco, V., Miller, J., Turner, R., Yao, A., Harris, M., Walenz, B., Mobarry, C., Merkulov, G.\u00a0V., Charlab, R., Dew, I., Deng, Z., Istrail, S., Li, P., & Sutton, G. (2005). Gene and alternative splicing annotation with AIR. Genome Research, 15, 54\u201366.","journal-title":"Genome Research"},{"issue":"Suppl 1","key":"2_CR17_2","doi-asserted-by":"publisher","first-page":"S181","DOI":"10.1093\/bioinformatics\/18.suppl_1.S181","volume":"18","author":"S Heber","year":"2002","unstructured":"Heber, S., Alekseyev, M., Sze, S.\u00a0H., Tang, H., & Pevzner, P.\u00a0A. (2002). Splicing graphs and EST assembly problem. Bioinformatics, 18(Suppl 1), S181\u2013S188.","journal-title":"Bioinformatics"},{"key":"2_CR18_2","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1101\/gr.3030405","volume":"15","author":"N Kim","year":"2005","unstructured":"Kim, N., Shin, S., & Lee, S. (2005). ECgene: Genome-based EST clustering and gene modeling for alternative splicing. Genome Research, 15, 566\u2013576.","journal-title":"Genome Research"},{"key":"2_CR19_2","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/nar\/gkl396","volume":"34","author":"Y Xing","year":"2006","unstructured":"Xing, Y., Yu, T., Wu, Y.\u00a0N., Roy, M., Kim, J., & Lee, C. (2006). An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Research, 34, 3150\u20133160.","journal-title":"Nucleic Acids Research"},{"key":"2_CR20_2","doi-asserted-by":"publisher","first-page":"3192","DOI":"10.1093\/nar\/gkm187","volume":"35","author":"GG Leparc","year":"2007","unstructured":"Leparc, G.\u00a0G., & Mitra, R.\u00a0D. (2007). Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Nucleic Acids Research, 35, 3192\u20133202.","journal-title":"Nucleic Acids Research"},{"key":"2_CR21_2","doi-asserted-by":"publisher","first-page":"1631","DOI":"10.1101\/gr.1208803","volume":"13","author":"R Sorek","year":"2003","unstructured":"Sorek, R., & Ast, G. (2003). Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Research, 13, 1631\u20131637.","journal-title":"Genome Research"},{"key":"2_CR22_2","doi-asserted-by":"publisher","first-page":"1617","DOI":"10.1101\/gr.2572604","volume":"14","author":"R Sorek","year":"2004","unstructured":"Sorek, R., Shemesh, R., Cohen, Y., Basechess, O., Ast, G., & Shamir, R. (2004). A non-EST-based method for exon-skipping prediction. Genome Research, 14, 1617\u20131623.","journal-title":"Genome Research"},{"key":"2_CR23_2","doi-asserted-by":"publisher","first-page":"2850","DOI":"10.1073\/pnas.0409742102","volume":"102","author":"GW Yeo","year":"2005","unstructured":"Yeo, G.\u00a0W., Van\u00a0Nostrand, E., Holste, D., Poggio, T., & Burge, C.\u00a0B. (2005). Identification and analysis of alternative splicing events conserved in human and mouse. Proceedings of the National Academy of Sciences of the United States of America, 102, 2850\u20132855.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2_CR24_2","doi-asserted-by":"publisher","first-page":"e2806","DOI":"10.1371\/journal.pone.0002806","volume":"3","author":"L Chen","year":"2008","unstructured":"Chen, L., & Zheng, S. (2008). Identify alternative splicing events based on position-specific evolutionary conservation. PLoS One, 3, e2806.","journal-title":"PLoS One"},{"key":"2_CR25_2","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1023\/A:1010933404324","volume":"45","author":"L Breiman","year":"2001","unstructured":"Breiman, L. (2001). Random forests. Machine Learning, 45, 5\u201332.","journal-title":"Machine Learning"},{"key":"2_CR26_2","doi-asserted-by":"publisher","first-page":"e14","DOI":"10.1371\/journal.pbio.0050014","volume":"5","author":"JL Parmley","year":"2007","unstructured":"Parmley, J.\u00a0L., Urrutia, A.\u00a0O., Potrzebowski, L., Kaessmann, H., & Hurst, L.\u00a0D. (2007). Splicing and the evolution of proteins in mammals. PLoS Biology, 5, e14.","journal-title":"PLoS Biology"},{"key":"2_CR27_2","doi-asserted-by":"publisher","first-page":"e268","DOI":"10.1371\/journal.pbio.0020268","volume":"2","author":"WG Fairbrother","year":"2004","unstructured":"Fairbrother, W.\u00a0G., Holste, D., Burge, C.\u00a0B., & Sharp, P.\u00a0A. (2004). Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biology, 2, e268.","journal-title":"PLoS Biology"},{"key":"2_CR28_2","doi-asserted-by":"publisher","first-page":"1636","DOI":"10.1101\/gad.1558107","volume":"21","author":"PL Boutz","year":"2007","unstructured":"Boutz, P.\u00a0L., Stoilov, P., Li, Q., Lin, C.\u00a0H., Chawla, G., Ostrow, K., Shiue, L., Ares, M., Jr., & Black, D.\u00a0L. (2007). A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes & Development, 21, 1636\u20131652.","journal-title":"Genes & Development"},{"key":"2_CR29_2","doi-asserted-by":"publisher","first-page":"R64","DOI":"10.1186\/gb-2007-8-4-r64","volume":"8","author":"TA Clark","year":"2007","unstructured":"Clark, T.\u00a0A., Schweitzer, A.\u00a0C., Chen, T.\u00a0X., Staples, M.\u00a0K., Lu, G., Wang, H., Williams, A.,\u00a0& Blume, J.\u00a0E. (2007). Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biology, 8, R64.","journal-title":"Genome Biology"},{"key":"2_CR30_2","doi-asserted-by":"publisher","first-page":"1951","DOI":"10.1371\/journal.pcbi.0030196","volume":"3","author":"GW Yeo","year":"2007","unstructured":"Yeo, G.\u00a0W., Xu, X., Liang, T.\u00a0Y., Muotri, A.\u00a0R., Carson, C.\u00a0T., Coufal, N.\u00a0G., & Gage, F.\u00a0H. (2007). Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Computational Biology, 3, 1951\u20131967.","journal-title":"PLoS Computational Biology"},{"key":"2_CR31_2","doi-asserted-by":"publisher","first-page":"1416","DOI":"10.1038\/ng.264","volume":"40","author":"JC Castle","year":"2008","unstructured":"Castle, J.\u00a0C., Zhang, C., Shah, J.\u00a0K., Kulkarni, A.\u00a0V., Kalsotra, A., Cooper, T.\u00a0A., & Johnson, J.\u00a0M. (2008). Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nature Genetics, 40, 1416\u20131425.","journal-title":"Nature Genetics"},{"key":"2_CR32_2","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1126\/science.1069415","volume":"296","author":"TA Clark","year":"2002","unstructured":"Clark, T.\u00a0A., Sugnet, C.\u00a0W., & Ares, M., Jr. (2002). Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science, 296, 907\u2013910.","journal-title":"Science"},{"issue":"Suppl. 1","key":"2_CR33_2","doi-asserted-by":"publisher","first-page":"i107","DOI":"10.1093\/bioinformatics\/bti1010","volume":"21","author":"MS Cline","year":"2005","unstructured":"Cline, M.\u00a0S., Blume, J., Cawley, S., Clark, T.\u00a0A., Hu, J.\u00a0S., Lu, G., Salomonis, N., Wang, H.,\u00a0& Williams, A. (2005). ANOSVA: A statistical method for detecting splice variation from expression data. Bioinformatics, 21(Suppl. 1), i107\u2013i115.","journal-title":"Bioinformatics"},{"key":"2_CR34_2","doi-asserted-by":"publisher","first-page":"1707","DOI":"10.1093\/bioinformatics\/btn284","volume":"24","author":"E Purdom","year":"2008","unstructured":"Purdom, E., Simpson, K.\u00a0M., Robinson, M.\u00a0D., Conboy, J.\u00a0G., Lapuk, A.\u00a0V., & Speed, T.\u00a0P. (2008). FIRMA: A method for detection of alternative splicing from exon array data. Bioinformatics, 24, 1707\u20131714.","journal-title":"Bioinformatics"},{"issue":"Suppl. 1","key":"2_CR35_2","doi-asserted-by":"publisher","first-page":"i315","DOI":"10.1093\/bioinformatics\/btg1044","volume":"19","author":"H Wang","year":"2003","unstructured":"Wang, H., Hubbell, E., Hu, J.\u00a0S., Mei, G., Cline, M., Lu, G., Clark, T., Siani-Rose, M.\u00a0A., Ares, M., Kulp, D.\u00a0C., & Haussler, D. (2003). Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics, 19(Suppl. 1), i315\u2013i322.","journal-title":"Bioinformatics"},{"key":"2_CR36_2","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1073\/pnas.98.1.31","volume":"98","author":"C Li","year":"2001","unstructured":"Li, C., & Wong, W.\u00a0H. (2001). Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proceedings of the National Academy of Sciences of the United States of America, 98, 31\u201336.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2_CR37_2","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2008-9-2-r46","volume":"9","author":"MA Anton","year":"2008","unstructured":"Anton, M.\u00a0A., Gorostiaga, D., Guruceaga, E., Segura, V., Carmona-Saez, P., Pascual-Montano,\u00a0A., Pio, R., Montuenga, L.\u00a0M., & Rubio, A. (2008). SPACE: An algorithm to predict and quantify alternatively spliced isoforms using microarrays. Genome Biology, 9, R46.","journal-title":"Genome Biology"},{"key":"2_CR38_2","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1093\/bioinformatics\/btk028","volume":"22","author":"O Shai","year":"2006","unstructured":"Shai, O., Morris, Q.\u00a0D., Blencowe, B.\u00a0J., & Frey, B.\u00a0J. (2006). Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics, 22, 606\u2013613.","journal-title":"Bioinformatics"},{"key":"2_CR39_2","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1016\/j.molcel.2004.12.004","volume":"16","author":"Q Pan","year":"2004","unstructured":"Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A.\u00a0L., Mohammad, N., Babak, T., Siu,\u00a0H., Hughes, T.\u00a0R., Morris, Q.\u00a0D., Frey, B.\u00a0J., & Blencowe, B.\u00a0J. (2004). Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Molecular Cell, 16, 929\u2013941.","journal-title":"Molecular Cell"},{"key":"2_CR40_2","doi-asserted-by":"publisher","first-page":"R108","DOI":"10.1186\/gb-2007-8-6-r108","volume":"8","author":"M Fagnani","year":"2007","unstructured":"Fagnani, M., Barash, Y., Ip, J.\u00a0Y., Misquitta, C., Pan, Q., Saltzman, A.\u00a0L., Shai, O., Lee, L., Rozenhek, A., Mohammad, N., Willaime-Morawek, S., Babak, T., Zhang, W., Hughes, T.\u00a0R., van\u00a0der\u00a0Kooy, D., Frey, B.\u00a0J., & Blencowe, B.\u00a0J. (2007). Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biology, 8, R108.","journal-title":"Genome Biology"},{"key":"2_CR41_2","doi-asserted-by":"publisher","first-page":"1344","DOI":"10.1126\/science.1158441","volume":"320","author":"U Nagalakshmi","year":"2008","unstructured":"Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., & Snyder, M. (2008). The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344\u20131349.","journal-title":"Science"},{"key":"2_CR42_2","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1038\/nature07002","volume":"453","author":"BT Wilhelm","year":"2008","unstructured":"Wilhelm, B.\u00a0T., Marguerat, S., Watt, S., Schubert, F., Wood, V., Goodhead, I., Penkett, C.\u00a0J., Rogers, J., & Bahler, J. (2008). Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature, 453, 1239\u20131243.","journal-title":"Nature"},{"key":"2_CR43_2","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1016\/j.cell.2008.03.029","volume":"133","author":"R Lister","year":"2008","unstructured":"Lister, R., O\u2019Malley, R.\u00a0C., Tonti-Filippini, J., Gregory, B.\u00a0D., Berry, C.\u00a0C., Millar, A.\u00a0H.,\u00a0& Ecker, J.\u00a0R. (2008). Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523\u2013536.","journal-title":"Cell"},{"key":"2_CR44_2","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1038\/nmeth.1223","volume":"5","author":"N Cloonan","year":"2008","unstructured":"Cloonan, N., Forrest, A.\u00a0R., Kolle, G., Gardiner, B.\u00a0B., Faulkner, G.\u00a0J., Brown, M.\u00a0K., Taylor, D.\u00a0F., Steptoe, A.\u00a0L., Wani, S., Bethel, G., Robertson, A.\u00a0J., Perkins, A.\u00a0C., Bruce, S.\u00a0J., Lee, C.\u00a0C., Ranade, S.\u00a0S., Peckham, H.\u00a0E., Manning, J.\u00a0M., McKernan, K.\u00a0J., & Grimmond, S.\u00a0M. (2008). Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods, 5, 613\u2013619.","journal-title":"Nature Methods"},{"key":"2_CR45_2","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/nmeth.1226","volume":"5","author":"A Mortazavi","year":"2008","unstructured":"Mortazavi, A., Williams, B.\u00a0A., McCue, K., Schaeffer, L., & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5, 621\u2013628.","journal-title":"Nature Methods"},{"key":"2_CR46_2","doi-asserted-by":"publisher","first-page":"1509","DOI":"10.1101\/gr.079558.108","volume":"18","author":"JC Marioni","year":"2008","unstructured":"Marioni, J.\u00a0C., Mason, C.\u00a0E., Mane, S.\u00a0M., Stephens, M., & Gilad, Y. (2008). RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research, 18, 1509\u20131517.","journal-title":"Genome Research"},{"key":"2_CR47_2","doi-asserted-by":"publisher","first-page":"956","DOI":"10.1126\/science.1160342","volume":"321","author":"M Sultan","year":"2008","unstructured":"Sultan, M., Schulz, M.\u00a0H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., Schmidt, D., O\u2019Keeffe, S., Haas, S., Vingron, M., Lehrach, H., & Yaspo, M.\u00a0L. (2008). A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 321, 956\u2013960.","journal-title":"Science"},{"key":"2_CR48_2","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/bioinformatics\/btp113","volume":"25","author":"H. Jiang","year":"2009","unstructured":"Jiang, H., & Wong, W.\u00a0H. (2009). Statistical inferences for isoform expression in RNA-Seq. Bioinformatics,25, 1026\u20131032.","journal-title":"Bioinformatics"},{"key":"2_CR49_2","doi-asserted-by":"publisher","first-page":"e75","DOI":"10.1093\/nar\/gkp282","volume":"37","author":"S Zheng","year":"2009","unstructured":"Zheng, S., & Chen, L. (2009). A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Research, 37,e75.","journal-title":"Nucleic Acids Research"},{"key":"2_CR50_2","doi-asserted-by":"publisher","first-page":"D46","DOI":"10.1093\/nar\/gkj031","volume":"34","author":"S Stamm","year":"2006","unstructured":"Stamm, S., Riethoven, J.\u00a0J., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Tang, Y., Barbosa-Morais, N.\u00a0L., & Thanaraj, T.\u00a0A. (2006). ASD: A bioinformatics resource on alternative splicing. Nucleic Acids Research, 34, D46\u2013D55.","journal-title":"Nucleic Acids Research"},{"key":"2_CR51_2","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1038\/nature01031","volume":"419","author":"Z Zhou","year":"2002","unstructured":"Zhou, Z., Licklider, L.\u00a0J., Gygi, S.\u00a0P., & Reed, R. (2002). Comprehensive proteomic analysis of the human spliceosome. Nature, 419, 182\u2013185.","journal-title":"Nature"},{"key":"2_CR52_2","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/S1097-2765(03)00270-3","volume":"12","author":"MS Jurica","year":"2003","unstructured":"Jurica, M.\u00a0S., & Moore, M.\u00a0J. (2003). Pre-mRNA splicing: Awash in a sea of proteins. Molecular Cell, 12, 5\u201314.","journal-title":"Molecular Cell"},{"key":"2_CR53_2","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1261\/rna.876308","volume":"14","author":"Z Wang","year":"2008","unstructured":"Wang, Z., & Burge, C.\u00a0B. (2008). Splicing regulation: From a parts list of regulatory elements to an integrated splicing code. RNA, 14, 802\u2013813.","journal-title":"RNA"},{"key":"2_CR54_2","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1101\/gad.8.13.1561","volume":"8","author":"GS Huh","year":"1994","unstructured":"Huh, G.\u00a0S., & Hynes, R.\u00a0O. (1994). Regulation of alternative pre-mRNA splicing by a novel repeated hexanucleotide element. Genes & Development, 8, 1561\u20131574.","journal-title":"Genes & Development"},{"key":"2_CR55_2","doi-asserted-by":"crossref","first-page":"4562","DOI":"10.1128\/MCB.17.8.4562","volume":"17","author":"AJ McCullough","year":"1997","unstructured":"McCullough, A.\u00a0J., & Berget, S.\u00a0M. (1997). G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Molecular Cell Biology, 17, 4562\u20134571.","journal-title":"Molecular Cell Biology"},{"key":"2_CR56_2","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1016\/S1097-2765(00)80260-9","volume":"5","author":"MY Chou","year":"2000","unstructured":"Chou, M.\u00a0Y., Underwood, J.\u00a0G., Nikolic, J., Luu, M.\u00a0H., & Black, D.\u00a0L. (2000). Multisite RNA binding and release of polypyrimidine tract binding protein during the regulation of c-src neural-specific splicing. Molecular Cell, 5, 949\u2013957.","journal-title":"Molecular Cell"},{"key":"2_CR57_2","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1016\/j.cell.2004.11.010","volume":"119","author":"Z Wang","year":"2004","unstructured":"Wang, Z., Rolish, M.\u00a0E., Yeo, G., Tung, V., Mawson, M., & Burge, C.\u00a0B. (2004). Systematic identification and analysis of exonic splicing silencers. Cell, 119, 831\u2013845.","journal-title":"Cell"},{"key":"2_CR58_2","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1101\/gad.1195304","volume":"18","author":"XH Zhang","year":"2004","unstructured":"Zhang, X.\u00a0H., & Chasin, L.\u00a0A. (2004). Computational definition of sequence motifs governing constitutive exon splicing. Genes & Development, 18, 1241\u20131250.","journal-title":"Genes & Development"},{"key":"2_CR59_2","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1146\/annurev.biochem.72.121801.161720","volume":"72","author":"DL Black","year":"2003","unstructured":"Black, D.\u00a0L. (2003). Mechanisms of alternative pre-messenger RNA splicing. Annual Review of Biochemistry, 72, 291\u2013336.","journal-title":"Annual Review of Biochemistry"},{"key":"2_CR60_2","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1038\/nrm1645","volume":"6","author":"AJ Matlin","year":"2005","unstructured":"Matlin, A.\u00a0J., Clark, F., & Smith, C.\u00a0W. (2005). Understanding alternative splicing: Towards a cellular code. Nature Review. Molecular Cell Biology, 6, 386\u2013398.","journal-title":"Nature Review. Molecular Cell Biology"},{"key":"2_CR61_2","doi-asserted-by":"publisher","first-page":"736","DOI":"10.1016\/j.cell.2004.11.039","volume":"119","author":"XD Fu","year":"2004","unstructured":"Fu, X.\u00a0D. (2004). Towards a splicing code. Cell, 119, 736\u2013738.","journal-title":"Cell"},{"key":"2_CR62_2","doi-asserted-by":"publisher","first-page":"R3","DOI":"10.1186\/gb-2009-10-1-r3","volume":"10","author":"L Chen","year":"2009","unstructured":"Chen, L., & Zheng, S. (2009). Studying alternative splicing regulatory networks through partial correlation analysis. Genome Biology, 10, R3.","journal-title":"Genome Biology"},{"key":"2_CR63_2","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1198\/016214506000001211","volume":"102","author":"B Efron","year":"2007","unstructured":"Efron, B. (2007). Correlation and large-scale simultaneous significance testing. Journal of the American Statistical Association, 102, 93\u2013103.","journal-title":"Journal of the American Statistical Association"},{"key":"2_CR64_2","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1101\/gad.1048803","volume":"17","author":"NA Faustino","year":"2003","unstructured":"Faustino, N.\u00a0A., & Cooper, T.\u00a0A. (2003). Pre-mRNA splicing and human disease. Genes & Development, 17, 419\u2013437.","journal-title":"Genes & Development"},{"key":"2_CR65_2","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1038\/nbt964","volume":"22","author":"MA Garcia-Blanco","year":"2004","unstructured":"Garcia-Blanco, M.\u00a0A., Baraniak, A.\u00a0P., & Lasda, E.\u00a0L. (2004). Alternative splicing in disease and therapy. Nature Biotechnology, 22, 535\u2013546.","journal-title":"Nature Biotechnology"},{"key":"2_CR66_2","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1016\/S0968-0004(00)01549-8","volume":"25","author":"BJ Blencowe","year":"2000","unstructured":"Blencowe, B.\u00a0J. (2000). Exonic splicing enhancers: Mechanism of action, diversity and role in human genetic diseases. Trends in Biochemical Sciences, 25, 106\u2013110.","journal-title":"Trends in Biochemical Sciences"},{"key":"2_CR67_2","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1002\/humu.20400","volume":"28","author":"M Krawczak","year":"2007","unstructured":"Krawczak, M., Thomas, N.\u00a0S., Hundrieser, B., Mort, M., Wittig, M., Hampe, J., & Cooper, D.\u00a0N. (2007). Single base-pair substitutions in exon-intron junctions of human genes: Nature, distribution, and consequences for mRNA splicing. Human Mutation, 28, 150\u2013158.","journal-title":"Human Mutation"},{"key":"2_CR68_2","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/j.cell.2006.06.023","volume":"126","author":"BJ Blencowe","year":"2006","unstructured":"Blencowe, B.\u00a0J. (2006). Alternative splicing: New insights from global analyses. Cell, 126, 37\u201347.","journal-title":"Cell"},{"key":"2_CR69_2","doi-asserted-by":"publisher","first-page":"4079","DOI":"10.1158\/0008-5472.CAN-05-4264","volume":"66","author":"HR Li","year":"2006","unstructured":"Li, H.\u00a0R., Wang-Rodriguez, J., Nair, T.\u00a0M., Yeakley, J.\u00a0M., Kwon, Y.\u00a0S., Bibikova, M., Zheng, C., Zhou, L., Zhang, K., Downs, T., Fu, X.\u00a0D., & Fan, J.\u00a0B. (2006). Two-dimensional transcriptome profiling: Identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. Cancer Research, 66, 4079\u20134088.","journal-title":"Cancer Research"},{"key":"2_CR70_2","doi-asserted-by":"publisher","first-page":"1990","DOI":"10.1158\/0008-5472.CAN-05-2593","volume":"66","author":"C Li","year":"2006","unstructured":"Li, C., Kato, M., Shiue, L., Shively, J.\u00a0E., Ares, M., Jr., & Lin, R.\u00a0J. Cell type and culture condition-dependent alternative splicing in human breast cancer cells revealed by splicing-sensitive microarrays. Cancer Research, 66, 1990\u20131999 (2006).","journal-title":"Cancer Research"},{"key":"2_CR71_2","doi-asserted-by":"publisher","first-page":"4779","DOI":"10.1074\/jbc.M411976200","volume":"280","author":"A Relogio","year":"2005","unstructured":"Relogio, A., Ben-Dov, C., Baum, M., Ruggiu, M., Gemund, C., Benes, V., Darnell, R.\u00a0B., & Valcarcel, J. (2005). Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells. The Journal of Biological Chemistry, 280, 4779\u20134784.","journal-title":"The Journal of Biological Chemistry"},{"key":"2_CR72_2","doi-asserted-by":"publisher","first-page":"1210","DOI":"10.1101\/gr.6281007","volume":"17","author":"T Kwan","year":"2007","unstructured":"Kwan, T., Benovoy, D., Dias, C., Gurd, S., Serre, D., Zuzan, H., Clark, T.\u00a0A., Schweitzer, A., Staples, M.\u00a0K., Wang, H., Blume, J.\u00a0E., Hudson, T.\u00a0J., Sladek, R., & Majewski, J. (2007). Heritability of alternative splicing in the human genome. Genome Research, 17, 1210\u20131218.","journal-title":"Genome Research"},{"key":"2_CR73_2","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1093\/nar\/30.1.186","volume":"30","author":"YH Huang","year":"2002","unstructured":"Huang, Y.\u00a0H., Chen, Y.\u00a0T., Lai, J.\u00a0J., Yang, S.\u00a0T., & Yang, U.\u00a0C. (2002). PALS db: Putative Alternative Splicing database. Nucleic Acids Research, 30, 186\u2013190.","journal-title":"Nucleic Acids Research"},{"key":"2_CR74_2","doi-asserted-by":"publisher","first-page":"D80","DOI":"10.1093\/nar\/gki129","volume":"33","author":"HD Huang","year":"2005","unstructured":"Huang, H.\u00a0D., Horng, J.\u00a0T., Lin, F.\u00a0M., Chang, Y.\u00a0C., & Huang, C.\u00a0C. (2005). SpliceInfo: An information repository for mRNA alternative splicing in human genome. Nucleic Acids Research, 33, D80\u2013D85.","journal-title":"Nucleic Acids Research"},{"key":"2_CR75_2","doi-asserted-by":"publisher","first-page":"W181","DOI":"10.1093\/nar\/gkh404","volume":"32","author":"N Kim","year":"2004","unstructured":"Kim, N., Shin, S., & Lee, S. (2004). ASmodeler: Gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences. Nucleic Acids Research, 32,W181\u2013W186.","journal-title":"Nucleic Acids Research"},{"key":"2_CR76_2","doi-asserted-by":"publisher","first-page":"D75","DOI":"10.1093\/nar\/gki118","volume":"33","author":"P Kim","year":"2005","unstructured":"Kim, P., Kim, N., Lee, Y., Kim, B., Shin, Y., & Lee, S. (2005). ECgene: Genome annotation for alternative splicing. Nucleic Acids Research, 33, D75\u2013D79.","journal-title":"Nucleic Acids Research"},{"key":"2_CR77_2","doi-asserted-by":"publisher","first-page":"3977","DOI":"10.1093\/nar\/gkh731","volume":"32","author":"J Leipzig","year":"2004","unstructured":"Leipzig, J., Pevzner, P., & Heber, S. (2004). The Alternative Splicing Gallery (ASG): Bridging the gap between genome and transcriptome. Nucleic Acids Research, 32, 3977\u20133983.","journal-title":"Nucleic Acids Research"},{"key":"2_CR78_2","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1186\/1471-2105-5-189","volume":"5","author":"BT Lee","year":"2004","unstructured":"Lee, B.\u00a0T., Tan, T.\u00a0W., & Ranganathan, S. (2004). DEDB: A database of Drosophila melanogaster exons in splicing graph form. BMC Bioinformatics, 5, 189.","journal-title":"BMC Bioinformatics"},{"key":"2_CR79_2","doi-asserted-by":"publisher","first-page":"1815","DOI":"10.1093\/bioinformatics\/btm084","volume":"23","author":"A Bhasi","year":"2007","unstructured":"Bhasi, A., Pandey, R.\u00a0V., Utharasamy, S.\u00a0P., & Senapathy, P. (2007). EuSplice: A unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. Bioinformatics, 23, 1815\u20131823.","journal-title":"Bioinformatics"},{"key":"2_CR80_2","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1093\/bioinformatics\/btn113","volume":"24","author":"T Castrignano","year":"2008","unstructured":"Castrignano, T., D\u2019Antonio, M., Anselmo, A., Carrabino, D., D\u2019Onorio De\u00a0Meo, A., D\u2019Erchia, A.\u00a0M., Licciulli, F., Mangiulli, M., Mignone, F., Pavesi, G., Picardi, E., Riva, A., Rizzi, R., Bonizzoni, P., & Pesole, G. (2008). ASPicDB: A database resource for alternative splicing analysis. Bioinformatics, 24, 1300\u20131304.","journal-title":"Bioinformatics"},{"key":"2_CR81_2","doi-asserted-by":"publisher","first-page":"D56","DOI":"10.1093\/nar\/gkj048","volume":"34","author":"D Holste","year":"2006","unstructured":"Holste, D., Huo, G., Tung, V., & Burge, C.\u00a0B. (2006). HOLLYWOOD: A comparative relational database of alternative splicing. Nucleic Acids Research, 34, D56\u2013D62.","journal-title":"Nucleic Acids Research"},{"key":"2_CR82_2","doi-asserted-by":"publisher","first-page":"D305","DOI":"10.1093\/nar\/gkn869","volume":"37","author":"M Shionyu","year":"2009","unstructured":"Shionyu, M., Yamaguchi, A., Shinoda, K., Takahashi, K., & Go, M. (2009). AS-ALPS: A database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. Nucleic Acids Research, 37, D305\u2013D309.","journal-title":"Nucleic Acids Research"},{"key":"2_CR83_2","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1186\/1471-2105-9-313","volume":"9","author":"MC Ryan","year":"2008","unstructured":"Ryan, M.\u00a0C., Zeeberg, B.\u00a0R., Caplen, N.\u00a0J., Cleland, J.\u00a0A., Kahn, A.\u00a0B., Liu, H., & Weinstein, J.\u00a0N. (2008). SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinformatics, 9, 313.","journal-title":"BMC Bioinformatics"},{"key":"2_CR84_2","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1186\/1471-2164-9-453","volume":"9","author":"M Floris","year":"2008","unstructured":"Floris, M., Orsini, M., & Thanaraj, T.\u00a0A. (2008). Splice-mediated Variants of Proteins (SpliVaP)\u00a0\u2013 data and characterization of changes in signatures among protein isoforms due to alternative splicing. BMC Genomics, 9, 453.","journal-title":"BMC Genomics"}],"container-title":["Handbook of Statistical Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-16345-6_2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,23]],"date-time":"2019-05-23T04:12:59Z","timestamp":1558584779000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-16345-6_2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011]]},"ISBN":["9783642163449","9783642163456"],"references-count":84,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-16345-6_2","relation":{},"subject":[],"published":{"date-parts":[[2011]]}}}