{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T14:59:30Z","timestamp":1786978770639,"version":"build-2736575974"},"publisher-location":"New York, NY","reference-count":21,"publisher":"Springer New York","isbn-type":[{"value":"9781493965373","type":"print"},{"value":"9781493965397","type":"electronic"}],"license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017]]},"DOI":"10.1007\/978-1-4939-6539-7_11","type":"book-chapter","created":{"date-parts":[[2016,11,2]],"date-time":"2016-11-02T05:19:44Z","timestamp":1478063984000},"page":"163-170","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Computational Methods and Correlation of Exon-skipping Events with Splicing, Transcription, and Epigenetic Factors"],"prefix":"10.1007","author":[{"given":"Jianbo","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenqing","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim H.","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huidong","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor X.","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,11,3]]},"reference":[{"key":"11_CR1","doi-asserted-by":"crossref","first-page":"188","DOI":"10.12688\/f1000research.2-188.v1","volume":"2","author":"L Florea","year":"2013","unstructured":"Florea L, Song L, Salberg SL et al (2013) Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues [v2; ref status: indexed, \n                  http:\/\/f1000r.es\/2dl\n                  \n                ]. F1000Research 2:188","journal-title":"F1000Research"},{"key":"11_CR2","doi-asserted-by":"publisher","first-page":"e39","DOI":"10.1093\/nar\/gks1026","volume":"41","author":"Y Hu","year":"2013","unstructured":"Hu Y, Huang Y, Du Y et al (2013) DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. Nucleic Acids Res 41:e39. doi:\n                  10.1093\/nar\/gks1026","journal-title":"Nucleic Acids Res"},{"key":"11_CR3","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1016\/j.gene.2012.11.045","volume":"518","author":"W Wang","year":"2013","unstructured":"Wang W, Qin Z, Feng Z et al (2013) Identifying differentially spliced genes from two groups of RNA-seq samples. Gene 518:164\u2013170","journal-title":"Gene"},{"key":"11_CR4","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1101\/gr.101907.109","volume":"20","author":"L Laurent","year":"2010","unstructured":"Laurent L, Wong E, Li G et al (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20:320\u2013331","journal-title":"Genome Res"},{"key":"11_CR5","doi-asserted-by":"publisher","first-page":"2856","DOI":"10.1093\/nar\/gkt1338","volume":"42","author":"Z Ye","year":"2014","unstructured":"Ye Z, Chen Z, Lan X et al (2014) Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. Nucleic Acids Res 42:2856\u20132869","journal-title":"Nucleic Acids Res"},{"key":"11_CR6","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1038\/nbt.1561","volume":"27","author":"D Pushkarev","year":"2009","unstructured":"Pushkarev D, Neff NF, Quake SR (2009) Single-molecule sequencing of an individual human genome. Nat Biotechnol 27:847\u2013850","journal-title":"Nat Biotechnol"},{"issue":"Web Server issu","key":"11_CR7","doi-asserted-by":"publisher","first-page":"W297","DOI":"10.1093\/nar\/gkm311","volume":"35","author":"S Foissac","year":"2007","unstructured":"Foissac S, Sammeth M (2007) ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res 35(Web Server issue):W297\u2013W299","journal-title":"Nucleic Acids Res"},{"key":"11_CR8","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","volume":"25","author":"C Trapnell","year":"2009","unstructured":"Trapnell C, Pachter L, Salberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105\u20131111","journal-title":"Bioinformatics"},{"key":"11_CR9","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1038\/nmeth.1528","volume":"7","author":"Y Katz","year":"2010","unstructured":"Katz Y, Wang ET, Airoldi EM, Burge CB (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7:1009\u20131015","journal-title":"Nat Methods"},{"key":"11_CR10","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1038\/nbt.1621","volume":"28","author":"C Trapnell","year":"2010","unstructured":"Trapnell C, Williams BA, Pertea G et al (2010) Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nat Biotechnol 28:511\u2013515","journal-title":"Nat Biotechnol"},{"key":"11_CR11","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nature11247","volume":"489","author":"The ENCODE Project Consortium","year":"2012","unstructured":"The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57\u201374","journal-title":"Nature"},{"key":"11_CR12","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1016\/S0090-4295(99)00185-5","volume":"54","author":"WJ Catalona","year":"1999","unstructured":"Catalona WJ, Partin AW, Finlay JA et al (1999) Use of percentage of free prostate-specific antigen to identify men at high risk of prostate cancer when psa levels are 2.51 to 4 ng\/mL and digital rectal examination is not suspicious for prostate cancer: an alternative model. Urology 54:220\u2013224","journal-title":"Urology"},{"key":"11_CR13","doi-asserted-by":"publisher","first-page":"69","DOI":"10.3322\/caac.20107","volume":"61","author":"A Jemal","year":"2011","unstructured":"Jemal A, Bray F, Center MM et al (2011) Global cancer statistics. CA Cancer J Clin 61:69\u201390","journal-title":"CA Cancer J Clin"},{"key":"11_CR14","doi-asserted-by":"publisher","first-page":"1967","DOI":"10.1101\/gad.1965810","volume":"24","author":"MM Shen","year":"2010","unstructured":"Shen MM, Abate-Shen C (2010) Molecular genetics of prostate cancer: new prospects for old challenges. Genes Dev 24:1967\u20132000","journal-title":"Genes Dev"},{"key":"11_CR15","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.3390\/cancers2021125","volume":"2","author":"RA Clarke","year":"2010","unstructured":"Clarke RA, Schirra HJ, Catto JW et al (2010) Markers for detection of prostate cancer. Cancers (Basel) 2:1125\u20131154","journal-title":"Cancers (Basel)"},{"key":"11_CR16","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1038\/nature09744","volume":"470","author":"MF Berger","year":"2011","unstructured":"Berger MF, Lawrence MS, Demichelis F et al (2011) The genomic complexity of primary human prostate cancer. Nature 470:214\u2013220","journal-title":"Nature"},{"key":"11_CR17","doi-asserted-by":"publisher","first-page":"1489","DOI":"10.1261\/rna.7100104","volume":"10","author":"AR Kornblihtt","year":"2004","unstructured":"Kornblihtt AR, de la Mata M, Fededa JP et al (2004) Multiple links between transcription and splicing. RNA 10:1489\u20131498","journal-title":"RNA"},{"key":"11_CR18","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1016\/j.cell.2013.03.021","volume":"153","author":"SC Baca","year":"2013","unstructured":"Baca SC, Prandi D, Lawrence MS et al (2013) Punctuated evolution of prostate cancer genomes. Cell 153:666\u2013677","journal-title":"Cell"},{"key":"11_CR19","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1038\/ni0710-549","volume":"11","author":"JA Goodrich","year":"2010","unstructured":"Goodrich JA, Tjian R (2010) Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nat Rev Genet 11:549\u2013558","journal-title":"Nat Rev Genet"},{"key":"11_CR20","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","volume":"129","author":"A Barski","year":"2007","unstructured":"Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823\u2013837","journal-title":"Cell"},{"key":"11_CR21","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/nature07509","volume":"456","author":"ET Wang","year":"2008","unstructured":"Wang ET, Sandberg R, Luo S et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470\u2013476","journal-title":"Nature"}],"container-title":["Methods in Molecular Biology","Cancer Gene Networks"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-4939-6539-7_11","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T00:59:34Z","timestamp":1558054774000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-1-4939-6539-7_11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,11,3]]},"ISBN":["9781493965373","9781493965397"],"references-count":21,"URL":"https:\/\/doi.org\/10.1007\/978-1-4939-6539-7_11","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,11,3]]},"assertion":[{"value":"3 November 2016","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}