{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T11:21:34Z","timestamp":1772277694773,"version":"3.50.1"},"publisher-location":"New York, NY, USA","reference-count":39,"publisher":"ACM","license":[{"start":{"date-parts":[[2018,8,15]],"date-time":"2018-08-15T00:00:00Z","timestamp":1534291200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000098","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R15GM123487"],"award-info":[{"award-number":["1R15GM123487"]}],"id":[{"id":"10.13039\/100000098","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2018,8,15]]},"DOI":"10.1145\/3233547.3233592","type":"proceedings-article","created":{"date-parts":[[2018,8,24]],"date-time":"2018-08-24T12:05:17Z","timestamp":1535112317000},"page":"200-210","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Splice-Aware Multiple Sequence Alignment of Protein Isoforms"],"prefix":"10.1145","author":[{"given":"Alex","family":"Nord","sequence":"first","affiliation":[{"name":"University of Montana, Missoula, MT, USA"}]},{"given":"Peter","family":"Hornbeck","sequence":"additional","affiliation":[{"name":"Cell Signaling Technology, Inc., Danvers, MA, USA"}]},{"given":"Kaitlin","family":"Carey","sequence":"additional","affiliation":[{"name":"University of Montana, Missoula, MT, USA"}]},{"given":"Travis","family":"Wheeler","sequence":"additional","affiliation":[{"name":"University of Montana, Missoula, MT, USA"}]}],"member":"320","published-online":{"date-parts":[[2018,8,15]]},"reference":[{"key":"e_1_3_2_1_1_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2015-06-651034"},{"key":"e_1_3_2_1_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2010.10.012"},{"key":"e_1_3_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh340"},{"key":"e_1_3_2_1_4_1","volume-title":"Quality measures for protein alignment benchmarks. Nucleic acids research 38, 7","author":"Edgar Robert C","year":"2010","unstructured":"Robert C Edgar . 2010. Quality measures for protein alignment benchmarks. Nucleic acids research 38, 7 ( 2010 ), 2145--2153. Robert C Edgar. 2010. Quality measures for protein alignment benchmarks. Nucleic acids research 38, 7 (2010), 2145--2153."},{"key":"e_1_3_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2006.04.004"},{"key":"e_1_3_2_1_6_1","volume-title":"When orthologs diverge between human and mouse. Briefings in bioinformatics 12, 5","author":"Gharib Walid H","year":"2011","unstructured":"Walid H Gharib and Marc Robinson-Rechavi . 2011. When orthologs diverge between human and mouse. Briefings in bioinformatics 12, 5 ( 2011 ), 436--441. Walid H Gharib and Marc Robinson-Rechavi. 2011. When orthologs diverge between human and mouse. Briefings in bioinformatics 12, 5 (2011), 436--441."},{"key":"e_1_3_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-15-189"},{"key":"e_1_3_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/onc.2015.504"},{"key":"e_1_3_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.1042\/bj20040337"},{"key":"e_1_3_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20177728"},{"key":"e_1_3_2_1_11_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.22.10915"},{"key":"e_1_3_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(88)90330-7"},{"key":"e_1_3_2_1_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1267"},{"key":"e_1_3_2_1_14_1","volume-title":"Multiple Sequence Alignment Methods","author":"Iantorno Stefano","unstructured":"Stefano Iantorno , Kevin Gori , Nick Goldman , Manuel Gil , and Christophe Dessimoz . 2014. Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment . In Multiple Sequence Alignment Methods . Springer , 59--73. Stefano Iantorno, Kevin Gori, Nick Goldman, Manuel Gil, and Christophe Dessimoz. 2014. Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. In Multiple Sequence Alignment Methods. Springer, 59--73."},{"key":"e_1_3_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks708"},{"key":"e_1_3_2_1_16_1","volume-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research 30, 14","author":"Katoh Kazutaka","year":"2002","unstructured":"Kazutaka Katoh , Kazuharu Misawa , Kei-ichi Kuma, and Takashi Miyata . 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research 30, 14 ( 2002 ), 3059--3066. Kazutaka Katoh, Kazuharu Misawa, Kei-ichi Kuma, and Takashi Miyata. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research 30, 14 (2002), 3059--3066."},{"key":"e_1_3_2_1_17_1","doi-asserted-by":"publisher","DOI":"10.5555\/647817.738617"},{"key":"e_1_3_2_1_18_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229202"},{"key":"e_1_3_2_1_19_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1932072100"},{"key":"e_1_3_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229102"},{"key":"e_1_3_2_1_21_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0907841107"},{"key":"e_1_3_2_1_22_1","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M900030-MCP200"},{"key":"e_1_3_2_1_23_1","volume-title":"A genome-wide study of dual coding regions in human alternatively spliced genes. Genome research 16, 2","author":"Liang Han","year":"2006","unstructured":"Han Liang and Laura F Landweber . 2006. A genome-wide study of dual coding regions in human alternatively spliced genes. Genome research 16, 2 ( 2006 ), 190--196. Han Liang and Laura F Landweber. 2006. A genome-wide study of dual coding regions in human alternatively spliced genes. Genome research 16, 2 (2006), 190--196."},{"key":"e_1_3_2_1_24_1","volume-title":"Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics. Genome medicine 5, 2","author":"Liddy Kiersten A","year":"2013","unstructured":"Kiersten A Liddy , Melanie Y White , and Stuart J Cordwell . 2013. Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics. Genome medicine 5, 2 ( 2013 ), 20. Kiersten A Liddy, Melanie Y White, and Stuart J Cordwell. 2013. Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics. Genome medicine 5, 2 (2013), 20."},{"key":"e_1_3_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.R200025200"},{"key":"e_1_3_2_1_26_1","volume-title":"Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science 338, 6114","author":"Merkin Jason","year":"2012","unstructured":"Jason Merkin , Caitlin Russell , Ping Chen , and Christopher B Burge . 2012. Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science 338, 6114 ( 2012 ), 1593--1599. Jason Merkin, Caitlin Russell, Ping Chen, and Christopher B Burge. 2012. Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science 338, 6114 (2012), 1593--1599."},{"key":"e_1_3_2_1_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(70)90057-4"},{"key":"e_1_3_2_1_28_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.259"},{"key":"e_1_3_2_1_29_1","volume-title":"UniProt protein knowledgebase. Protein Bioinformatics: From Protein Modifications and Networks to Proteomics","author":"Pundir Sangya","year":"2017","unstructured":"Sangya Pundir , Maria J Martin , and Claire O'Donovan . 2017. UniProt protein knowledgebase. Protein Bioinformatics: From Protein Modifications and Networks to Proteomics ( 2017 ), 41--55. Sangya Pundir, Maria J Martin, and Claire O'Donovan. 2017. UniProt protein knowledgebase. Protein Bioinformatics: From Protein Modifications and Networks to Proteomics (2017), 41--55."},{"key":"e_1_3_2_1_30_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00595-09"},{"key":"e_1_3_2_1_31_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340090107"},{"key":"e_1_3_2_1_32_1","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2011.75"},{"key":"e_1_3_2_1_33_1","volume-title":"Automated generation of heuristics for biological sequence comparison. BMC bioinformatics 6, 1","author":"Slater Guy St C","year":"2005","unstructured":"Guy St C Slater and Ewan Birney . 2005. Automated generation of heuristics for biological sequence comparison. BMC bioinformatics 6, 1 ( 2005 ), 31. Guy St C Slater and Ewan Birney. 2005. Automated generation of heuristics for biological sequence comparison. BMC bioinformatics 6, 1 (2005), 31."},{"key":"e_1_3_2_1_34_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.113.113803"},{"key":"e_1_3_2_1_35_1","volume-title":"Alternative isoform regulation in human tissue transcriptomes. Nature 456, 7221","author":"Wang Eric T","year":"2008","unstructured":"Eric T Wang , Rickard Sandberg , Shujun Luo , Irina Khrebtukova , Lu Zhang , Christine Mayr , Stephen F Kingsmore , Gary P Schroth , and Christopher B Burge . 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 7221 ( 2008 ), 470. Eric T Wang, Rickard Sandberg, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen F Kingsmore, Gary P Schroth, and Christopher B Burge. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 7221 (2008), 470."},{"key":"e_1_3_2_1_36_1","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-81-7-1675"},{"key":"e_1_3_2_1_37_1","volume-title":"Linear motifs confer functional diversity onto splice variants. Nucleic acids research 40, 15","author":"Weatheritt Robert J","year":"2012","unstructured":"Robert J Weatheritt , Norman E Davey , and Toby J Gibson . 2012. Linear motifs confer functional diversity onto splice variants. Nucleic acids research 40, 15 ( 2012 ), 7123--7131. Robert J Weatheritt, Norman E Davey, and Toby J Gibson. 2012. Linear motifs confer functional diversity onto splice variants. Nucleic acids research 40, 15 (2012), 7123--7131."},{"key":"e_1_3_2_1_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm226"},{"key":"e_1_3_2_1_39_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx1098"}],"event":{"name":"BCB '18: 9th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","location":"Washington DC USA","acronym":"BCB '18","sponsor":["SIGBio ACM Special Interest Group on Bioinformatics"]},"container-title":["Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3233547.3233592","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3233547.3233592","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T02:13:13Z","timestamp":1750212793000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3233547.3233592"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,8,15]]},"references-count":39,"alternative-id":["10.1145\/3233547.3233592","10.1145\/3233547"],"URL":"https:\/\/doi.org\/10.1145\/3233547.3233592","relation":{},"subject":[],"published":{"date-parts":[[2018,8,15]]},"assertion":[{"value":"2018-08-15","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}