{"id":"https://openalex.org/W2314976248","doi":"https://doi.org/10.1109/tcbb.2015.2456897","title":"Fast Sampling-Based Whole-Genome Haplotype Block Recognition","display_name":"Fast Sampling-Based Whole-Genome Haplotype Block Recognition","publication_year":2015,"publication_date":"2015-07-15","ids":{"openalex":"https://openalex.org/W2314976248","doi":"https://doi.org/10.1109/tcbb.2015.2456897","mag":"2314976248","pmid":"https://pubmed.ncbi.nlm.nih.gov/27045830"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2015.2456897","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2456897","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075177958","display_name":"Daniel Taliun","orcid":"https://orcid.org/0000-0002-8874-5044"},"institutions":[{"id":"https://openalex.org/I171543936","display_name":"Free University of Bozen-Bolzano","ror":"https://ror.org/012ajp527","country_code":"IT","type":"education","lineage":["https://openalex.org/I171543936"]},{"id":"https://openalex.org/I4210118299","display_name":"Institute for Biomedicine","ror":"https://ror.org/02hsggv49","country_code":"IT","type":"facility","lineage":["https://openalex.org/I1319360392","https://openalex.org/I4210118299"]},{"id":"https://openalex.org/I1319360392","display_name":"Eurac Research","ror":"https://ror.org/01xt1w755","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1319360392"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Daniel Taliun","raw_affiliation_strings":["Center for Biomedicine, EURAC Research","Faculty of Computer Science, Free University of Bozen-Bolzano, Italy"],"affiliations":[{"raw_affiliation_string":"Center for Biomedicine, EURAC Research","institution_ids":["https://openalex.org/I4210118299","https://openalex.org/I1319360392"]},{"raw_affiliation_string":"Faculty of Computer Science, Free University of Bozen-Bolzano, Italy","institution_ids":["https://openalex.org/I171543936"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043864804","display_name":"Johann Gamper","orcid":"https://orcid.org/0000-0002-7128-507X"},"institutions":[{"id":"https://openalex.org/I171543936","display_name":"Free University of Bozen-Bolzano","ror":"https://ror.org/012ajp527","country_code":"IT","type":"education","lineage":["https://openalex.org/I171543936"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Johann Gamper","raw_affiliation_strings":["Faculty of Computer Science, Free University of Bozen-Bolzano, Italy"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science, Free University of Bozen-Bolzano, Italy","institution_ids":["https://openalex.org/I171543936"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055236937","display_name":"Ulf Leser","orcid":"https://orcid.org/0000-0003-2166-9582"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ulf Leser","raw_affiliation_strings":["Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010058481","display_name":"Cristian Pattaro","orcid":"https://orcid.org/0000-0002-4119-0109"},"institutions":[{"id":"https://openalex.org/I1319360392","display_name":"Eurac Research","ror":"https://ror.org/01xt1w755","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1319360392"]},{"id":"https://openalex.org/I4210118299","display_name":"Institute for Biomedicine","ror":"https://ror.org/02hsggv49","country_code":"IT","type":"facility","lineage":["https://openalex.org/I1319360392","https://openalex.org/I4210118299"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Cristian Pattaro","raw_affiliation_strings":["Center for Biomedicine, EURAC Research, Italy"],"affiliations":[{"raw_affiliation_string":"Center for Biomedicine, EURAC Research, Italy","institution_ids":["https://openalex.org/I4210118299","https://openalex.org/I1319360392"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5075177958"],"corresponding_institution_ids":["https://openalex.org/I1319360392","https://openalex.org/I171543936","https://openalex.org/I4210118299"],"apc_list":null,"apc_paid":null,"fwci":0.957,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.80444313,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"13","issue":"2","first_page":"315","last_page":"325"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.6988304853439331},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.5286222696304321},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5009050369262695},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.4929201602935791},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49146974086761475},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4251348376274109},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4043443500995636},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3419375717639923},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18745753169059753},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1466125249862671},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.10761767625808716},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.05815011262893677},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.05496165156364441}],"concepts":[{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.6988304853439331},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.5286222696304321},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5009050369262695},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.4929201602935791},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49146974086761475},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4251348376274109},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4043443500995636},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3419375717639923},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18745753169059753},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1466125249862671},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.10761767625808716},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.05815011262893677},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.05496165156364441},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2015.2456897","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2456897","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27045830","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27045830","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:alma.39UBZ_INST:11234994900001241","is_oa":false,"landing_page_url":"http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7159051\u2260wsearch=true&queryText=10.1109%2FTCBB.2015.2456897","pdf_url":null,"source":{"id":"https://openalex.org/S4210197018","display_name":"View","issn_l":"2688-268X","issn":["2688-268X","2688-3988"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"pmh:oai:alma.39UBZ_INST:11235014480001241","is_oa":false,"landing_page_url":"https://bia.unibz.it/esploro/outputs/journalArticle/Fast-Sampling-Based-Whole-Genome-Haplotype-Block-Recognition/991005772650101241","pdf_url":null,"source":{"id":"https://openalex.org/S4210197018","display_name":"View","issn_l":"2688-268X","issn":["2688-268X","2688-3988"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1508985588","https://openalex.org/W1971943467","https://openalex.org/W1994407979","https://openalex.org/W1994920627","https://openalex.org/W2007175522","https://openalex.org/W2025306791","https://openalex.org/W2030760029","https://openalex.org/W2037454239","https://openalex.org/W2037586880","https://openalex.org/W2053169778","https://openalex.org/W2069435832","https://openalex.org/W2071420702","https://openalex.org/W2096791516","https://openalex.org/W2099085143","https://openalex.org/W2106031386","https://openalex.org/W2133857505","https://openalex.org/W2135732313","https://openalex.org/W2140716217","https://openalex.org/W2152664025","https://openalex.org/W2156341632","https://openalex.org/W2159372288","https://openalex.org/W2160828516","https://openalex.org/W2162530578","https://openalex.org/W4230727657","https://openalex.org/W4234628562"],"related_works":["https://openalex.org/W3146762847","https://openalex.org/W2398263405","https://openalex.org/W2056886854","https://openalex.org/W2025446304","https://openalex.org/W2166354960","https://openalex.org/W2131321814","https://openalex.org/W1888102361","https://openalex.org/W2171251480","https://openalex.org/W1492100763","https://openalex.org/W4237549798"],"abstract_inverted_index":{"Scaling":[0],"linkage":[1],"disequilibrium":[2],"(LD)":[3],"based":[4],"haplotype":[5,64,107,121],"block":[6],"recognition":[7,105],"to":[8,55,167,188],"the":[9,51,57,80,86,90,97,104,117,136,143,155,175,183],"entire":[10],"human":[11],"genome":[12],"has":[13,21],"always":[14],"been":[15],"a":[16,43,68,127,161,171],"challenge.":[17],"The":[18],"best-known":[19],"algorithm":[20,151,178],"quadratic":[22],"runtime":[23,162,184],"complexity":[24],"and,":[25],"even":[26],"when":[27],"sophisticated":[28],"search":[29],"space":[30],"pruning":[31],"is":[32,54],"applied,":[33],"still":[34],"requires":[35],"several":[36],"days":[37],"of":[38,72,99,106,131,174],"computations.":[39],"Here,":[40],"we":[41,147],"propose":[42],"novel":[44],"sampling-based":[45],"algorithm,":[46],"called":[47],"S-MIG":[48,157,176],"(++),":[49],"where":[50],"main":[52],"idea":[53],"estimate":[56],"area":[58,118],"that":[59,116],"most":[60],"likely":[61],"contains":[62],"all":[63,120],"blocks":[65,82,108,122],"by":[66,83],"sampling":[67],"very":[69,109,128],"small":[70],"number":[71,98],"SNP":[73,87],"pairs.":[74],"A":[75],"subsequent":[76],"refinement":[77],"step":[78],"computes":[79],"exact":[81],"considering":[84],"only":[85],"pairs":[88],"within":[89],"estimated":[91,125],"area.":[92],"This":[93],"approach":[94],"significantly":[95],"reduces":[96],"computed":[100],"LD":[101],"statistics,":[102],"making":[103],"fast.":[110],"We":[111],"theoretically":[112],"and":[113,159],"empirically":[114],"prove":[115],"containing":[119],"can":[123],"be":[124],"with":[126,154],"high":[129],"degree":[130],"certainty.":[132],"Through":[133],"experiments":[134],"on":[135,139],"243,080":[137],"SNPs":[138],"chromosome":[140],"20":[141],"from":[142,164],"1,000":[144],"Genomes":[145],"Project,":[146],"compared":[148],"our":[149],"previous":[150],"MIG":[152],"(++)":[153,158,177],"new":[156],"observed":[160],"reduction":[163],"2.8":[165],"weeks":[166],"34.8":[168],"hours.":[169,190],"In":[170],"parallelized":[172],"version":[173],"using":[179],"32":[180],"parallel":[181],"processes,":[182],"was":[185],"further":[186],"reduced":[187],"5.1":[189]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}