{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:32:48Z","timestamp":1773275568001,"version":"3.50.1"},"publisher-location":"Cham","reference-count":20,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783319581620","type":"print"},{"value":"9783319581637","type":"electronic"}],"license":[{"start":{"date-parts":[[2017,1,1]],"date-time":"2017-01-01T00:00:00Z","timestamp":1483228800000},"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\/978-3-319-58163-7_3","type":"book-chapter","created":{"date-parts":[[2017,4,24]],"date-time":"2017-04-24T06:59:25Z","timestamp":1493017165000},"page":"49-61","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext"],"prefix":"10.1007","author":[{"given":"Stefano","family":"Beretta","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paola","family":"Bonizzoni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luca","family":"Denti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Previtali","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raffaella","family":"Rizzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,4,25]]},"reference":[{"issue":"1","key":"3_CR1","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1006\/jagm.1999.1063","volume":"35","author":"A Amir","year":"2000","unstructured":"Amir, A., Lewenstein, M., Lewenstein, N.: Pattern matching in hypertext. J. Algorithms 35(1), 82\u201399 (2000)","journal-title":"J. Algorithms"},{"issue":"1","key":"3_CR2","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1089\/cmb.2013.0112","volume":"21","author":"S Beretta","year":"2014","unstructured":"Beretta, S., Bonizzoni, P., Della Vedova, G., Pirola, Y., Rizzi, R.: Modeling alternative splicing variants from RNA-seq data with isoform graphs. J. Comput. Biol. 21(1), 16\u201340 (2014)","journal-title":"J. Comput. Biol."},{"issue":"3","key":"3_CR3","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1089\/cmb.2015.0172","volume":"23","author":"P Bonizzoni","year":"2016","unstructured":"Bonizzoni, P., Della Vedova, G., Pirola, Y., Previtali, M., Rizzi, R.: LSG: an external-memory tool to compute string graphs for next-generation sequencing data assembly. J. Comput. Biol. 23(3), 137\u2013149 (2016)","journal-title":"J. Comput. Biol."},{"key":"3_CR4","unstructured":"Cormen, T.H., Leiserson, C.E., Rivest, R.L., Stein, C.: Introduction to Algorithms. MIT Press, 2nd edn. (2001)"},{"issue":"6","key":"3_CR5","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1038\/ng.3257","volume":"47","author":"A Dilthey","year":"2015","unstructured":"Dilthey, A., Cox, C., Iqbal, Z., Nelson, M.R., McVean, G.: Improved genome inference in the MHC using a population reference graph. Nat. Genet. 47(6), 682\u2013688 (2015)","journal-title":"Nat. Genet."},{"issue":"1","key":"3_CR6","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T.R.: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1), 15\u201321 (2013)","journal-title":"Bioinformatics"},{"issue":"suppl. 1","key":"3_CR7","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.H., Tang, H., Pevzner, P.A.: Splicing graphs and EST assembly problem. Bioinformatics 18(suppl. 1), S181\u2013S188 (2002)","journal-title":"Bioinformatics"},{"issue":"2","key":"3_CR8","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1093\/bib\/bbp046","volume":"11","author":"DS Horner","year":"2010","unstructured":"Horner, D.S., Pavesi, G., Castrignan\u00f2, T., De Meo, P.D., Liuni, S., Sammeth, M., Picardi, E., Pesole, G.: Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Briefings Bioinf. 11(2), 181\u2013197 (2010)","journal-title":"Briefings Bioinf."},{"issue":"4","key":"3_CR9","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.3317","volume":"12","author":"D Kim","year":"2015","unstructured":"Kim, D., Langmead, B., Salzberg, S.L.: HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12(4), 357\u2013360 (2015)","journal-title":"Nat. Methods"},{"issue":"4","key":"3_CR10","doi-asserted-by":"publisher","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","volume":"14","author":"D Kim","year":"2013","unstructured":"Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S.L.: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14(4), R36 (2013)","journal-title":"Genome Biol."},{"issue":"16","key":"3_CR11","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G.T., Abecasis, G.R., Durbin, R.: The sequence alignment\/map format and SAMtools. Bioinformatics 25(16), 2078\u20132079 (2009)","journal-title":"Bioinformatics"},{"key":"3_CR12","doi-asserted-by":"crossref","unstructured":"Manber, U., Wu, S.: Approximate string matching with arbitrary costs for text and hypertext. In: Proceedings of the IAPR International Workshop on Structural and Syntactic Pattern Recognition, pp. 22\u201333 (1993)","DOI":"10.1142\/9789812797919_0002"},{"issue":"1","key":"3_CR13","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1016\/S0304-3975(99)00333-3","volume":"237","author":"G Navarro","year":"2000","unstructured":"Navarro, G.: Improved approximate pattern matching on hypertext. Theoret. Comput. Sci. 237(1), 455\u2013463 (2000)","journal-title":"Theoret. Comput. Sci."},{"key":"3_CR14","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1007\/978-3-642-16321-0_36","volume-title":"String Processing and Information Retrieval","author":"E Ohlebusch","year":"2010","unstructured":"Ohlebusch, E., Gog, S., K\u00fcgel, A.: Computing matching statistics and maximal exact matches on compressed full-text indexes. In: Chavez, E., Lonardi, S. (eds.) SPIRE 2010. LNCS, vol. 6393, pp. 347\u2013358. Springer, Heidelberg (2010). doi:10.1007\/978-3-642-16321-0_36"},{"key":"3_CR15","doi-asserted-by":"crossref","unstructured":"Rhoads, A., Au, K.F.: PacBio sequencing and its applications. Genomics Proteomics Bioinform. 13(5), 278\u2013289 (2015). sI: Metagenomics of Marine Environments","DOI":"10.1016\/j.gpb.2015.08.002"},{"key":"3_CR16","doi-asserted-by":"crossref","unstructured":"Sir\u00e9n, J.: Indexing variation graphs. CoRR abs\/1604.06605 (2016)","DOI":"10.1137\/1.9781611974768.2"},{"key":"3_CR17","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.jda.2012.10.001","volume":"18","author":"C Thachuk","year":"2013","unstructured":"Thachuk, C.: Indexing hypertext. J. Discrete Algorithms 18, 113\u2013122 (2013)","journal-title":"J. Discrete Algorithms"},{"issue":"9","key":"3_CR18","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","volume":"25","author":"C Trapnell","year":"2009","unstructured":"Trapnell, C., Pachter, L., Salzberg, S.L.: TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25(9), 1105\u20131111 (2009)","journal-title":"Bioinformatics"},{"issue":"6","key":"3_CR19","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1093\/bioinformatics\/btt042","volume":"29","author":"M Vyverman","year":"2013","unstructured":"Vyverman, M., De Baets, B., Fack, V., Dawyndt, P.: essaMEM: finding maximal exact matches using enhanced sparse suffix arrays. Bioinformatics 29(6), 802\u2013804 (2013)","journal-title":"Bioinformatics"},{"issue":"9","key":"3_CR20","doi-asserted-by":"publisher","first-page":"4661","DOI":"10.1093\/nar\/gkv311","volume":"43","author":"LM Yeoh","year":"2015","unstructured":"Yeoh, L.M., Goodman, C.D., Hall, N.E., van Dooren, G.G., McFadden, G.I., Ralph, S.A.: A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii. Nucleic Acids Res. 43(9), 4661\u20134675 (2015)","journal-title":"Nucleic Acids Res."}],"container-title":["Lecture Notes in Computer Science","Algorithms for Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-58163-7_3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,11]],"date-time":"2024-03-11T14:16:47Z","timestamp":1710166607000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-319-58163-7_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017]]},"ISBN":["9783319581620","9783319581637"],"references-count":20,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-58163-7_3","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017]]},"assertion":[{"value":"25 April 2017","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"AlCoB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Algorithms for Computational Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Aveiro","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Portugal","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2017","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"5 June 2017","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6 June 2017","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"4","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"alcob2017","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/grammars.grlmc.com\/AlCoB2017\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}