{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T02:29:20Z","timestamp":1742956160436,"version":"3.40.3"},"publisher-location":"Cham","reference-count":13,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030181734"},{"type":"electronic","value":"9783030181741"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","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":[[2019]]},"DOI":"10.1007\/978-3-030-18174-1_15","type":"book-chapter","created":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T10:15:30Z","timestamp":1558347330000},"page":"203-211","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcript Abundance Estimation and the Laminar Packing Problem"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1805-3971","authenticated-orcid":false,"given":"Atif","family":"Rahman","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9164-6231","authenticated-orcid":false,"given":"Lior","family":"Pachter","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,4,13]]},"reference":[{"issue":"5","key":"15_CR1","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/nbt.3519","volume":"34","author":"NL Bray","year":"2016","unstructured":"Bray, N.L., Pimentel, H., Melsted, P., Pachter, L.: Near-optimal probabilistic RNA-Seq quantification. Nat. Biotechnol. 34(5), 525 (2016)","journal-title":"Nat. Biotechnol."},{"issue":"2","key":"15_CR2","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1089\/cmb.1996.3.275","volume":"3","author":"D Bryant","year":"1996","unstructured":"Bryant, D.: Hunting for trees in binary character sets: efficient algorithms for extraction, enumeration, and optimization. J. Comput. Biol. 3(2), 275\u2013288 (1996)","journal-title":"J. Comput. Biol."},{"issue":"2","key":"15_CR3","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1093\/sysbio\/35.2.224","volume":"35","author":"WH Day","year":"1986","unstructured":"Day, W.H., Sankoff, D.: Computational complexity of inferring phylogenies by compatibility. Syst. Biol. 35(2), 224\u2013229 (1986)","journal-title":"Syst. Biol."},{"key":"15_CR4","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/S0167-5060(08)70734-9","volume-title":"Studies in Integer Programming","author":"Jack Edmonds","year":"1977","unstructured":"Edmonds, J., Giles, R.: A min-max relation for submodular functions on graphs. In: Hammer, P.L., Johnson, E.L., Korte, B., Nemhauser, G. (eds.) Studies in Integer Programming Annals of Discrete Mathematics, vol. 1, pp. 185\u2013204. Elsevier (1977) \n                      https:\/\/doi.org\/10.1016\/S0167-5060(08)70734-9\n                      \n                    . \n                      http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0167506008707349"},{"issue":"1","key":"15_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.7155\/jgaa.00020","volume":"4","author":"MM Halld\u00f3rsson","year":"2000","unstructured":"Halld\u00f3rsson, M.M.: Approximations of weighted independent set and hereditary subset problems. J. Graph Algorithms Appl. 4(1), 1\u201316 (2000)","journal-title":"J. Graph Algorithms Appl."},{"issue":"1\u20133","key":"15_CR6","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/S0166-218X(99)00124-9","volume":"99","author":"MM Halld\u00f3rsson","year":"2000","unstructured":"Halld\u00f3rsson, M.M., Kratochv\u0131l, J., Telle, J.A.: Independent sets with domination constraints. Discrete Appl. Math. 99(1\u20133), 39\u201354 (2000). \n                      https:\/\/doi.org\/10.1016\/S0166-218X(99)00124-9\n                      \n                    . \n                      http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0166218X99001249","journal-title":"Discrete Appl. Math."},{"key":"15_CR7","unstructured":"H\u00e5stad, J.: Clique is hard to approximate within \n                      \n                        \n                      \n                      $$n^{(1-\\epsilon )}$$\n                    . In: Acta Mathematica, pp. 627\u2013636 (1996)"},{"key":"15_CR8","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/978-1-4684-2001-2_9","volume-title":"Complexity of Computer Computations","author":"RM Karp","year":"1972","unstructured":"Karp, R.M.: Reducibility among combinatorial problems. In: Miller, R.E., Thatcher, J.W., Bohlinger, J.D. (eds.) Complexity of Computer Computations, pp. 85\u2013103. Springer, Heidelberg (1972). \n                      https:\/\/doi.org\/10.1007\/978-1-4684-2001-2_9"},{"issue":"1","key":"15_CR9","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li, B., Dewey, C.N.: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 12(1), 323 (2011)","journal-title":"BMC Bioinform."},{"issue":"4","key":"15_CR10","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","volume":"14","author":"R Patro","year":"2017","unstructured":"Patro, R., Duggal, G., Love, M.I., Irizarry, R.A., Kingsford, C.: Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14(4), 417 (2017)","journal-title":"Nat. Methods"},{"issue":"5","key":"15_CR11","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1038\/nbt.2862","volume":"32","author":"R Patro","year":"2014","unstructured":"Patro, R., Mount, S.M., Kingsford, C.: Sailfish enables alignment-free isoform quantification from RNA-Seq reads using lightweight algorithms. Nat. Biotechnol. 32(5), 462 (2014)","journal-title":"Nat. Biotechnol."},{"issue":"1","key":"15_CR12","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nmeth.2251","volume":"10","author":"A Roberts","year":"2013","unstructured":"Roberts, A., Pachter, L.: Streaming fragment assignment for real-time analysis of sequencing experiments. Nat. Methods 10(1), 71 (2013)","journal-title":"Nat. Methods"},{"issue":"5","key":"15_CR13","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1038\/nbt.1621","volume":"28","author":"C Trapnell","year":"2010","unstructured":"Trapnell, C., et al.: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28(5), 511 (2010)","journal-title":"Nat. Biotechnol."}],"container-title":["Lecture Notes in Computer Science","Algorithms for Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-18174-1_15","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T16:11:58Z","timestamp":1558541518000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-18174-1_15"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9783030181734","9783030181741"],"references-count":13,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-18174-1_15","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2019]]},"assertion":[{"value":"13 April 2019","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":"Berkeley, CA","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"USA","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2019","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"28 May 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"30 May 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"alcob2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/alcob2019.irdta.eu\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"30","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"15","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"50% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"3","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"2","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"One paper of an invited talk is included.","order":10,"name":"additional_info_on_review_process","label":"Additional Info on Review Process","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}}]}}