{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,24]],"date-time":"2025-08-24T01:57:27Z","timestamp":1756000647825,"version":"3.41.0"},"publisher-location":"New York, NY, USA","reference-count":15,"publisher":"ACM","license":[{"start":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T00:00:00Z","timestamp":1668038400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"name":"JSPS KAKENHI","award":["JP21K19827"],"award-info":[{"award-number":["JP21K19827"]}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2022,11,10]]},"DOI":"10.1145\/3574198.3574212","type":"proceedings-article","created":{"date-parts":[[2023,3,15]],"date-time":"2023-03-15T09:24:43Z","timestamp":1678872283000},"page":"88-92","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["A Novel Method for Fusion Gene Detection using Both End-Fragment Sequences of Long Reads"],"prefix":"10.1145","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3644-3781","authenticated-orcid":false,"given":"Keigo","family":"Masuda","sequence":"first","affiliation":[{"name":"Graduate School of Information Science and Technology, Osaka University, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5963-652X","authenticated-orcid":false,"given":"Yoshiaki","family":"Sota","sequence":"additional","affiliation":[{"name":"Graduate School of Medicine, Osaka University, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4701-3779","authenticated-orcid":false,"given":"Hideo","family":"Matsuda","sequence":"additional","affiliation":[{"name":"Graduate School of Information Science and Technology, Osaka University, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2023,3,15]]},"reference":[{"key":"e_1_3_2_1_1_1","volume-title":"Continuous base identification for single-molecule nanopore DNA sequencing. Nature nanotechnology 4, 4","author":"Clarke James","year":"2009","unstructured":"James Clarke , Hai-Chen Wu , Lakmal Jayasinghe , Alpesh Patel , Stuart Reid , and Hagan Bayley . 2009. Continuous base identification for single-molecule nanopore DNA sequencing. Nature nanotechnology 4, 4 ( 2009 ), 265\u2013270. James Clarke, Hai-Chen Wu, Lakmal Jayasinghe, Alpesh Patel, Stuart Reid, and Hagan Bayley. 2009. Continuous base identification for single-molecule nanopore DNA sequencing. Nature nanotechnology 4, 4 (2009), 265\u2013270."},{"key":"e_1_3_2_1_2_1","volume-title":"JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome biology 23, 1","author":"Davidson M","year":"2022","unstructured":"Nadia\u00a0 M Davidson , Ying Chen , Teresa Sadras , Georgina\u00a0 L Ryland , Piers Blombery , Paul\u00a0 G Ekert , Jonathan G\u00f6ke , and Alicia Oshlack . 2022. JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome biology 23, 1 ( 2022 ), 1\u201320. Nadia\u00a0M Davidson, Ying Chen, Teresa Sadras, Georgina\u00a0L Ryland, Piers Blombery, Paul\u00a0G Ekert, Jonathan G\u00f6ke, and Alicia Oshlack. 2022. JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome biology 23, 1 (2022), 1\u201320."},{"key":"e_1_3_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM200104053441401"},{"key":"e_1_3_2_1_4_1","volume-title":"Real-time DNA sequencing from single polymerase molecules. Science 323, 5910","author":"Eid John","year":"2009","unstructured":"John Eid , Adrian Fehr , Jeremy Gray , Khai Luong , John Lyle , Geoff Otto , Paul Peluso , David Rank , Primo Baybayan , Brad Bettman , 2009. Real-time DNA sequencing from single polymerase molecules. Science 323, 5910 ( 2009 ), 133\u2013138. John Eid, Adrian Fehr, Jeremy Gray, Khai Luong, John Lyle, Geoff Otto, Paul Peluso, David Rank, Primo Baybayan, Brad Bettman, 2009. Real-time DNA sequencing from single polymerase molecules. Science 323, 5910 (2009), 133\u2013138."},{"key":"e_1_3_2_1_5_1","volume-title":"Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome biology 20, 1","author":"Haas J","year":"2019","unstructured":"Brian\u00a0 J Haas , Alexander Dobin , Bo Li , Nicolas Stransky , Nathalie Pochet , and Aviv Regev . 2019. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome biology 20, 1 ( 2019 ), 1\u201316. Brian\u00a0J Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet, and Aviv Regev. 2019. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome biology 20, 1 (2019), 1\u201316."},{"key":"e_1_3_2_1_6_1","volume-title":"GENCODE: the reference human genome annotation for The ENCODE Project. Genome research 22, 9","author":"Harrow Jennifer","year":"2012","unstructured":"Jennifer Harrow , Adam Frankish , Jose\u00a0 M Gonzalez , Electra Tapanari , Mark Diekhans , Felix Kokocinski , Bronwen\u00a0 L Aken , Daniel Barrell , Amonida Zadissa , Stephen Searle , 2012. GENCODE: the reference human genome annotation for The ENCODE Project. Genome research 22, 9 ( 2012 ), 1760\u20131774. Jennifer Harrow, Adam Frankish, Jose\u00a0M Gonzalez, Electra Tapanari, Mark Diekhans, Felix Kokocinski, Bronwen\u00a0L Aken, Daniel Barrell, Amonida Zadissa, Stephen Searle, 2012. GENCODE: the reference human genome annotation for The ENCODE Project. Genome research 22, 9 (2012), 1760\u20131774."},{"key":"e_1_3_2_1_7_1","doi-asserted-by":"crossref","first-page":"502","DOI":"10.3390\/ijms19020502","article-title":"Perspective insight into future potential fusion gene transcript biomarker candidates in breast cancer","volume":"19","author":"Kim Ryong\u00a0Nam","year":"2018","unstructured":"Ryong\u00a0Nam Kim , Hyeong-Gon Moon , Wonshik Han , and Dong-Young Noh . 2018 . Perspective insight into future potential fusion gene transcript biomarker candidates in breast cancer . International Journal of Molecular Sciences 19 , 2 (2018), 502 . Ryong\u00a0Nam Kim, Hyeong-Gon Moon, Wonshik Han, and Dong-Young Noh. 2018. Perspective insight into future potential fusion gene transcript biomarker candidates in breast cancer. International Journal of Molecular Sciences 19, 2 (2018), 502.","journal-title":"International Journal of Molecular Sciences"},{"key":"e_1_3_2_1_8_1","volume-title":"Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. Scientific reports 6, 1","author":"Kumar Shailesh","year":"2016","unstructured":"Shailesh Kumar , Angie\u00a0Duy Vo , Fujun Qin , and Hui Li. 2016. Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. Scientific reports 6, 1 ( 2016 ), 1\u201310. Shailesh Kumar, Angie\u00a0Duy Vo, Fujun Qin, and Hui Li. 2016. Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. Scientific reports 6, 1 (2016), 1\u201310."},{"key":"e_1_3_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_3_2_1_10_1","volume-title":"LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing. BMC genomics 21, 11","author":"Liu Qian","year":"2020","unstructured":"Qian Liu , Yu Hu , Andres Stucky , Li Fang , Jiang\u00a0 F Zhong , and Kai Wang . 2020. LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing. BMC genomics 21, 11 ( 2020 ), 1\u201312. Qian Liu, Yu Hu, Andres Stucky, Li Fang, Jiang\u00a0F Zhong, and Kai Wang. 2020. LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing. BMC genomics 21, 11 (2020), 1\u201312."},{"key":"e_1_3_2_1_11_1","volume-title":"From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome biology 19, 1","author":"Rang J","year":"2018","unstructured":"Franka\u00a0 J Rang , Wigard\u00a0 P Kloosterman , and Jeroen de Ridder . 2018. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome biology 19, 1 ( 2018 ), 1\u201311. Franka\u00a0J Rang, Wigard\u00a0P Kloosterman, and Jeroen de Ridder. 2018. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome biology 19, 1 (2018), 1\u201311."},{"key":"e_1_3_2_1_12_1","volume-title":"AERON: Transcript quantification and gene-fusion detection using long reads. BioRxiv","author":"Rautiainen Mikko","year":"2020","unstructured":"Mikko Rautiainen , Dilip\u00a0 A Durai , Ying Chen , Lixia Xin , Hwee\u00a0Meng Low , Jonathan G\u00f6ke , Tobias Marschall , and Marcel\u00a0 H Schulz . 2020 . AERON: Transcript quantification and gene-fusion detection using long reads. BioRxiv (2020). https:\/\/doi.org\/10.1101\/2020.01.27.921338 10.1101\/2020.01.27.921338 Mikko Rautiainen, Dilip\u00a0A Durai, Ying Chen, Lixia Xin, Hwee\u00a0Meng Low, Jonathan G\u00f6ke, Tobias Marschall, and Marcel\u00a0H Schulz. 2020. AERON: Transcript quantification and gene-fusion detection using long reads. BioRxiv (2020). https:\/\/doi.org\/10.1101\/2020.01.27.921338"},{"key":"e_1_3_2_1_13_1","volume-title":"PacBio sequencing and its applications. Genomics, proteomics & bioinformatics 13, 5","author":"Rhoads Anthony","year":"2015","unstructured":"Anthony Rhoads and Kin\u00a0Fai Au. 2015. PacBio sequencing and its applications. Genomics, proteomics & bioinformatics 13, 5 ( 2015 ), 278\u2013289. Anthony Rhoads and Kin\u00a0Fai Au. 2015. PacBio sequencing and its applications. Genomics, proteomics & bioinformatics 13, 5 (2015), 278\u2013289."},{"key":"e_1_3_2_1_14_1","doi-asserted-by":"crossref","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen Wei","year":"2016","unstructured":"Wei Shen , Shuai Le , Yan Li , and Fuquan Hu . 2016 . SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation . PloS one 11 , 10 (2016), e0163962 . Wei Shen, Shuai Le, Yan Li, and Fuquan Hu. 2016. SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation. PloS one 11, 10 (2016), e0163962.","journal-title":"PloS one"},{"key":"e_1_3_2_1_15_1","volume-title":"Identification of the transforming EML4\u2013ALK fusion gene in non-small-cell lung cancer. Nature 448, 7153","author":"Soda Manabu","year":"2007","unstructured":"Manabu Soda , Young\u00a0Lim Choi , Munehiro Enomoto , Shuji Takada , Yoshihiro Yamashita , Shunpei Ishikawa , Shin-ichiro Fujiwara, Hideki Watanabe , Kentaro Kurashina , Hisashi Hatanaka , 2007. Identification of the transforming EML4\u2013ALK fusion gene in non-small-cell lung cancer. Nature 448, 7153 ( 2007 ), 561\u2013566. Manabu Soda, Young\u00a0Lim Choi, Munehiro Enomoto, Shuji Takada, Yoshihiro Yamashita, Shunpei Ishikawa, Shin-ichiro Fujiwara, Hideki Watanabe, Kentaro Kurashina, Hisashi Hatanaka, 2007. Identification of the transforming EML4\u2013ALK fusion gene in non-small-cell lung cancer. Nature 448, 7153 (2007), 561\u2013566."}],"event":{"name":"ICBBE 2022: 2022 9th International Conference on Biomedical and Bioinformatics Engineering","acronym":"ICBBE 2022","location":"Kyoto Japan"},"container-title":["Proceedings of the 2022 9th International Conference on Biomedical and Bioinformatics Engineering"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3574198.3574212","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3574198.3574212","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T18:08:25Z","timestamp":1750183705000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3574198.3574212"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,10]]},"references-count":15,"alternative-id":["10.1145\/3574198.3574212","10.1145\/3574198"],"URL":"https:\/\/doi.org\/10.1145\/3574198.3574212","relation":{},"subject":[],"published":{"date-parts":[[2022,11,10]]},"assertion":[{"value":"2023-03-15","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}