{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:18Z","timestamp":1740185118952,"version":"3.37.3"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,1,12]],"date-time":"2018-01-12T00:00:00Z","timestamp":1515715200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007431","name":"NRF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007431","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007431","name":"NRF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007431","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009950","name":"Ministry of Education","doi-asserted-by":"publisher","award":["2017R1D1A1B03029451"],"award-info":[{"award-number":["2017R1D1A1B03029451"]}],"id":[{"id":"10.13039\/100009950","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single-individual haplotyping (SIH) is critical in genomic association studies and genetic diseases analysis. However, most genomic analysis studies do not perform haplotype-phasing analysis due to its complexity. Several computational methods have been developed to solve the SIH problem, but these approaches have not generated sufficiently reliable haplotypes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we propose a novel SIH algorithm, called PEATH (Probabilistic Evolutionary Algorithm with Toggling for Haplotyping), to achieve more accurate and reliable haplotyping. The proposed PEATH method was compared to the most recent algorithms in terms of the phased length, N50 length, switch error rate and minimum error correction. The PEATH algorithm consistently provides the best phase and N50 lengths, as long as possible, given datasets. In addition, verification of the simulation data demonstrated that the PEATH method outperforms other methods on high noisy data. Additionally, the experimental results of a real dataset confirmed that the PEATH method achieved comparable or better accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code of PEATH is available at https:\/\/github.com\/jcna99\/PEATH.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty012","type":"journal-article","created":{"date-parts":[[2018,1,10]],"date-time":"2018-01-10T12:35:06Z","timestamp":1515587706000},"page":"1801-1807","source":"Crossref","is-referenced-by-count":5,"title":["PEATH: single-individual haplotyping by a probabilistic evolutionary algorithm with toggling"],"prefix":"10.1093","volume":"34","author":[{"given":"Joong Chae","family":"Na","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, Sejong University, Seoul, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jong-Chan","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Sejong University, Seoul, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Je-Keun","family":"Rhee","sequence":"additional","affiliation":[{"name":"Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soo-Yong","family":"Shin","sequence":"additional","affiliation":[{"name":"Department of Digital Health, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,1,12]]},"reference":[{"key":"2023012713535748800_bty012-B1","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1756-0381-1-6","article-title":"A review of estimation of distribution algorithms in bioinformatics","volume":"1","author":"Armananzas","year":"2008","journal-title":"BioData Min"},{"key":"2023012713535748800_bty012-B2","doi-asserted-by":"crossref","first-page":"i153","DOI":"10.1093\/bioinformatics\/btn298","article-title":"HapCUT: an efficient and accurate algorithm for the haplotype assembly problem","volume":"24","author":"Bansal","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012713535748800_bty012-B3","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.1101\/gr.077065.108","article-title":"An MCMC algorithm for haplotype assembly from whole-genome sequence data","volume":"18","author":"Bansal","year":"2008","journal-title":"Genome Res"},{"key":"2023012713535748800_bty012-B4","doi-asserted-by":"crossref","first-page":"260.","DOI":"10.1186\/s12864-015-1408-5","article-title":"SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming","volume":"16","author":"Das","year":"2015","journal-title":"BMC Genomics"},{"key":"2023012713535748800_bty012-B5","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1093\/nar\/gkr1042","article-title":"Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques","volume":"40","author":"Duitama","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023012713535748800_bty012-B6","doi-asserted-by":"crossref","first-page":"i183","DOI":"10.1093\/bioinformatics\/btq215","article-title":"Optimal algorithms for haplotype assembly from whole-genome sequence data","volume":"26","author":"He","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012713535748800_bty012-B7","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nbt.1740","article-title":"Haplotype-resolved genome sequencing of a Gujarati Indian individual","volume":"29","author":"Kitzman","year":"2011","journal-title":"Nat. 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