{"id":"https://openalex.org/W2142215982","doi":"https://doi.org/10.1007/s00453-011-9494-5","title":"An Efficient Algorithm for Haplotype Inference on\u00a0Pedigrees with a Small Number of Recombinants","display_name":"An Efficient Algorithm for Haplotype Inference on\u00a0Pedigrees with a Small Number of Recombinants","publication_year":2011,"publication_date":"2011-02-08","ids":{"openalex":"https://openalex.org/W2142215982","doi":"https://doi.org/10.1007/s00453-011-9494-5","mag":"2142215982"},"language":"en","primary_location":{"id":"doi:10.1007/s00453-011-9494-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00453-011-9494-5","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00453-011-9494-5.pdf","source":{"id":"https://openalex.org/S89324355","display_name":"Algorithmica","issn_l":"0178-4617","issn":["0178-4617","1432-0541"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithmica","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s00453-011-9494-5.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070173803","display_name":"Jing Xiao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210126794","display_name":"IBM Research (China)","ror":"https://ror.org/02yg1pf55","country_code":"CN","type":"company","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210126794"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jing Xiao","raw_affiliation_strings":["IBM China Research Lab, Beijing, China","IBM China Research Lab, BeiJing, China"],"affiliations":[{"raw_affiliation_string":"IBM China Research Lab, Beijing, China","institution_ids":["https://openalex.org/I4210126794"]},{"raw_affiliation_string":"IBM China Research Lab, BeiJing, China","institution_ids":["https://openalex.org/I4210126794"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041348628","display_name":"Tiancheng Lou","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tiancheng Lou","raw_affiliation_strings":["Department of Computer Science and Technology, Tsinghua University, Beijing, China","Tsinghua University, Dept. of Computer Science and Technology, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University, Dept. of Computer Science and Technology, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101911266","display_name":"Tao Jiang","orcid":"https://orcid.org/0000-0003-3833-4498"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]},{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Tao Jiang","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California, Riverside, CA, USA","Department of Computer Science and Technology, Tsinghua University, Beijing, China","Tsinghua University, Department of Computer Science and Technology, Beijing, China and University of California, Department of Computer Science and Engineering, Riverside, CA, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, Riverside, CA, USA","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University, Department of Computer Science and Technology, Beijing, China and University of California, Department of Computer Science and Engineering, Riverside, CA, USA#TAB#","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5070173803"],"corresponding_institution_ids":["https://openalex.org/I4210126794"],"apc_list":{"value":2290,"currency":"EUR","value_usd":2890},"apc_paid":{"value":2290,"currency":"EUR","value_usd":2890},"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.14402265,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"62","issue":"3-4","first_page":"951","last_page":"981"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9966999888420105,"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":0.9955000281333923,"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":0.7304209470748901},{"id":"https://openalex.org/keywords/pedigree-chart","display_name":"Pedigree chart","score":0.6780698895454407},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.6501562595367432},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4740076959133148},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4271862208843231},{"id":"https://openalex.org/keywords/bounded-function","display_name":"Bounded function","score":0.42262423038482666},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4051234722137451},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3460993766784668},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.19261011481285095},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08827030658721924}],"concepts":[{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.7304209470748901},{"id":"https://openalex.org/C22593422","wikidata":"https://www.wikidata.org/wiki/Q3242583","display_name":"Pedigree chart","level":3,"score":0.6780698895454407},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.6501562595367432},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4740076959133148},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4271862208843231},{"id":"https://openalex.org/C34388435","wikidata":"https://www.wikidata.org/wiki/Q2267362","display_name":"Bounded function","level":2,"score":0.42262423038482666},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4051234722137451},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3460993766784668},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.19261011481285095},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08827030658721924},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s00453-011-9494-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00453-011-9494-5","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00453-011-9494-5.pdf","source":{"id":"https://openalex.org/S89324355","display_name":"Algorithmica","issn_l":"0178-4617","issn":["0178-4617","1432-0541"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithmica","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s00453-011-9494-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00453-011-9494-5","pdf_url":"https://link.springer.com/content/pdf/10.1007/s00453-011-9494-5.pdf","source":{"id":"https://openalex.org/S89324355","display_name":"Algorithmica","issn_l":"0178-4617","issn":["0178-4617","1432-0541"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithmica","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.5}],"awards":[{"id":"https://openalex.org/G5553661940","display_name":null,"funder_award_id":"LM008991","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2142215982.pdf","grobid_xml":"https://content.openalex.org/works/W2142215982.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W605092692","https://openalex.org/W617260339","https://openalex.org/W1484216542","https://openalex.org/W1541888433","https://openalex.org/W1594138279","https://openalex.org/W1891283710","https://openalex.org/W1912294093","https://openalex.org/W1979077551","https://openalex.org/W1981876302","https://openalex.org/W1989681157","https://openalex.org/W1993063013","https://openalex.org/W1998158007","https://openalex.org/W2024112606","https://openalex.org/W2030148262","https://openalex.org/W2040152649","https://openalex.org/W2058401000","https://openalex.org/W2059476414","https://openalex.org/W2078778189","https://openalex.org/W2088353637","https://openalex.org/W2091383090","https://openalex.org/W2091708844","https://openalex.org/W2105306382","https://openalex.org/W2107871825","https://openalex.org/W2111771950","https://openalex.org/W2128357262","https://openalex.org/W2129731347","https://openalex.org/W2142659700","https://openalex.org/W2152236186","https://openalex.org/W2152664025","https://openalex.org/W2206749611","https://openalex.org/W2521813346","https://openalex.org/W2913688336","https://openalex.org/W4248237286","https://openalex.org/W4292230561"],"related_works":["https://openalex.org/W2279490262","https://openalex.org/W2473551174","https://openalex.org/W3146762847","https://openalex.org/W1965396974","https://openalex.org/W2038331681","https://openalex.org/W1998686087","https://openalex.org/W1981169569","https://openalex.org/W2369420545","https://openalex.org/W2044943383","https://openalex.org/W2152033571"],"abstract_inverted_index":{"Combinatorial":[0],"(or":[1],"rule-based)":[2],"methods":[3,21],"for":[4,107,161,264],"inferring":[5],"haplotypes":[6,27,76,238,292],"from":[7,122,239],"genotypes":[8,240],"on":[9,77,163,241,281],"a":[10,57,78,89,103,115,123,126,197,228,254,272,294],"pedigree":[11,80],"have":[12,144,249],"been":[13],"studied":[14],"extensively":[15],"in":[16,40,56,150,246,306],"the":[17,26,33,41,52,69,82,93,110,118,133,151,172,179,182,192,203,251,302,307],"recent":[18],"literature.":[19,308],"These":[20],"generally":[22],"try":[23],"to":[24,73,125,131,143,236],"reconstruct":[25,291],"of":[28,36,54,71,84,114,174,181,206,227,275],"each":[29],"individual":[30],"so":[31,94],"that":[32,51,187,201,288],"total":[34],"number":[35,53,83,173,274],"recombinants":[37,55,85,214,276],"is":[38,45,49,60,86,171,178,222,226,298],"minimized":[39],"pedigree.":[42,152],"The":[43,220,259],"problem":[44],"NP-hard,":[46],"although":[47],"it":[48],"known":[50],"practical":[58],"dataset":[59],"usually":[61],"very":[62],"small.":[63],"In":[64],"this":[65],"paper,":[66],"we":[67],"consider":[68],"question":[70],"how":[72],"efficiently":[74,245],"infer":[75,237],"large":[79,242,273],"when":[81,188,224],"bounded":[87],"by":[88],"small":[90],"constant,":[91],"i.e.":[92],"called":[95],"k-recombinant":[96],"haplotype":[97,112,119,199],"configuration":[98,200],"(k-RHC)":[99],"problem.":[100],"We":[101,153,248],"introduce":[102],"simple":[104],"probabilistic":[105],"model":[106],"k-RHC":[108,162],"where":[109,169],"prior":[111],"probability":[113,121,216],"founder":[116],"and":[117,136,148,176,185,208,231,269,284,297],"transmission":[120],"parent":[124],"child":[127],"are":[128,141],"all":[129],"assumed":[130,142],"follow":[132],"uniform":[134],"distribution":[135],"k":[137,213,225],"random":[138],"recombination":[139],"events":[140],"taken":[145],"place":[146],"uniformly":[147],"independently":[149],"present":[154],"an":[155],"O(mnlog":[156],"k+1":[157],"n)":[158],"time":[159],"algorithm":[160,193,221,252],"tree":[164,243],"pedigrees":[165,244],"without":[166],"mating":[167],"loops,":[168],"m":[170],"loci":[175],"n":[177],"size":[180],"input":[183],"pedigree,":[184],"prove":[186],"90log":[189],"n<m<n":[190],"3,":[191],"can":[194,290],"correctly":[195],"find":[196],"feasible":[198],"obeys":[202],"Mendelian":[204],"law":[205],"inheritance":[207],"requires":[209],"no":[210],"more":[211],"than":[212,301],"with":[215,266,271,293],"$1":[217],"-O(k^{2}\\frac{\\log^{2}n}{mn}+\\frac{1}{n^{2}})$":[218],".":[219],"efficient":[223],"moderate":[229],"value":[230],"could":[232],"thus":[233],"be":[234],"used":[235],"practice.":[247],"implemented":[250],"as":[253],"C++":[255],"program":[256],"named":[257],"Tree-k-RHC.":[258],"implementation":[260],"incorporates":[261],"several":[262],"ideas":[263],"dealing":[265],"missing":[267],"data":[268,270],"effectively.":[277],"Our":[278],"experimental":[279],"results":[280],"both":[282],"simulated":[283],"real":[285],"datasets":[286],"show":[287],"Tree-k-RHC":[289],"high":[295],"accuracy":[296],"much":[299],"faster":[300],"best":[303],"combinatorial":[304],"method":[305]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
