{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T08:20:24Z","timestamp":1771662024393,"version":"3.50.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2017,10,3]],"date-time":"2017-10-03T00:00:00Z","timestamp":1506988800000},"content-version":"vor","delay-in-days":4,"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","award":["NRF-2012R1A1A3012428, NRF-2015R1A1A3A04001269, NRF-2015R1A2A2A01006885"],"award-info":[{"award-number":["NRF-2012R1A1A3012428, NRF-2015R1A1A3A04001269, NRF-2015R1A2A2A01006885"]}],"id":[{"id":"10.13039\/100007431","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["MOP-84287"],"award-info":[{"award-number":["MOP-84287"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Big-LD, a block partition method based on interval graph modeling of LD bins which are clusters of strong pairwise LD SNPs, not necessarily physically consecutive. Big-LD uses an agglomerative approach that starts by identifying small communities of SNPs, i.e. the SNPs in each LD bin region, and proceeds by merging these communities. We determine the number of blocks using a method to find maximum-weight independent set. Big-LD produces larger LD blocks compared to existing methods such as MATILDE, Haploview, MIG\u2009++, or S-MIG\u2009++ and the LD blocks better agree with recombination hotspot locations determined by sperm-typing experiments. The observed average runtime of Big-LD for 13\u2009288\u2009240 non-monomorphic SNPs from 1000 Genomes Project autosome data (286 East Asians) is about 5.83\u2009h, which is a significant improvement over the existing methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code and documentation are available for download at http:\/\/github.com\/sunnyeesl\/BigLD.<\/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\/btx609","type":"journal-article","created":{"date-parts":[[2017,9,28]],"date-time":"2017-09-28T19:13:34Z","timestamp":1506626014000},"page":"388-397","source":"Crossref","is-referenced-by-count":62,"title":["A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs"],"prefix":"10.1093","volume":"34","author":[{"given":"Sun Ah","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Statistics, Seoul National University, Seoul, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chang-Sung","family":"Cho","sequence":"additional","affiliation":[{"name":"Department of Mathematics Education, Seoul National University, Seoul, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suh-Ryung","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Mathematics Education, Seoul National University, Seoul, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shelley B","family":"Bull","sequence":"additional","affiliation":[{"name":"Prosserman Centre for Health Research, The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada"},{"name":"Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yun Joo","family":"Yoo","sequence":"additional","affiliation":[{"name":"Department of Mathematics Education, Seoul National University, Seoul, South Korea"},{"name":"Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,9,29]]},"reference":[{"key":"2023012712273899700_btx609-B2","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","article-title":"Haploview: analysis and visualization of LD and haplotype maps","volume":"21","author":"Barrett","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012712273899700_btx609-B3","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1145\/362342.362367","article-title":"Algorithm 457: finding all cliques of an undirected graph","volume":"16","author":"Bron","year":"1973","journal-title":"Commun. 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