{"id":"https://openalex.org/W4284973663","doi":"https://doi.org/10.1186/s12859-022-04801-z","title":"Integer programming for selecting set of informative markers in paternity inference","display_name":"Integer programming for selecting set of informative markers in paternity inference","publication_year":2022,"publication_date":"2022-07-08","ids":{"openalex":"https://openalex.org/W4284973663","doi":"https://doi.org/10.1186/s12859-022-04801-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/35804290"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04801-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04801-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04801-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04801-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071046874","display_name":"So\u2010ichiro Nishiyama","orcid":"https://orcid.org/0000-0002-3451-6166"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Soichiro Nishiyama","raw_affiliation_strings":["Graduate School of Agriculture, Kyoto University, Kyoto, Japan. nishiyama.soichiro.8e@kyoto-u.ac.jp","Graduate School of Agriculture, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Agriculture, Kyoto University, Kyoto, Japan. nishiyama.soichiro.8e@kyoto-u.ac.jp","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"Graduate School of Agriculture, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101608371","display_name":"Kengo Sato","orcid":"https://orcid.org/0009-0005-7677-3995"},"institutions":[{"id":"https://openalex.org/I165522056","display_name":"Tokyo Denki University","ror":"https://ror.org/01pa62v70","country_code":"JP","type":"education","lineage":["https://openalex.org/I165522056"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kengo Sato","raw_affiliation_strings":["School of System Design and Technology, Tokyo Denki University, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of System Design and Technology, Tokyo Denki University, Tokyo, Japan","institution_ids":["https://openalex.org/I165522056"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018454719","display_name":"Ryutaro Tao","orcid":"https://orcid.org/0000-0001-7811-5789"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryutaro Tao","raw_affiliation_strings":["Graduate School of Agriculture, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Agriculture, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071046874"],"corresponding_institution_ids":["https://openalex.org/I22299242"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1864,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.60289001,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"23","issue":"1","first_page":"265","last_page":"265"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.4821000099182129,"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/T10012","display_name":"Genetic diversity and population structure","score":0.4821000099182129,"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":0.07919999957084656,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.07209999859333038,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5882397294044495},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5345284938812256},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.48402851819992065},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.48273417353630066},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4762558937072754},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4621722102165222},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45699024200439453},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.41563665866851807},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.373150110244751},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35370177030563354},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31263333559036255},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28357189893722534},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.23060926795005798}],"concepts":[{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5882397294044495},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5345284938812256},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48402851819992065},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.48273417353630066},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4762558937072754},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4621722102165222},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45699024200439453},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.41563665866851807},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.373150110244751},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35370177030563354},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31263333559036255},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28357189893722534},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.23060926795005798},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","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":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010334","descriptor_name":"Paternity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010334","descriptor_name":"Paternity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010334","descriptor_name":"Paternity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-022-04801-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04801-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04801-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35804290","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35804290","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:irdb.nii.ac.jp:01221:0005888741","is_oa":true,"landing_page_url":"http://hdl.handle.net/2433/284492","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal article"},{"id":"pmh:oai:doaj.org/article:97f48e65e3bd4fc3ab4cf0a0d05fe639","is_oa":true,"landing_page_url":"https://doaj.org/article/97f48e65e3bd4fc3ab4cf0a0d05fe639","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-17 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9264695","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9264695","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04801-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04801-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04801-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G7467356850","display_name":null,"funder_award_id":"20K20454","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4284973663.pdf","grobid_xml":"https://content.openalex.org/works/W4284973663.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1582042412","https://openalex.org/W1902647886","https://openalex.org/W1975992505","https://openalex.org/W2053755275","https://openalex.org/W2070004305","https://openalex.org/W2071892703","https://openalex.org/W2075945757","https://openalex.org/W2084722705","https://openalex.org/W2091239497","https://openalex.org/W2099085143","https://openalex.org/W2107473082","https://openalex.org/W2120675904","https://openalex.org/W2120907314","https://openalex.org/W2129935545","https://openalex.org/W2325258195","https://openalex.org/W2488354499","https://openalex.org/W2549501493","https://openalex.org/W2593463317","https://openalex.org/W2617850113","https://openalex.org/W2906107948","https://openalex.org/W2929650387","https://openalex.org/W3003176383","https://openalex.org/W3014819096","https://openalex.org/W3041141216","https://openalex.org/W3116632215","https://openalex.org/W3135567871"],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W4205762803","https://openalex.org/W2535856026","https://openalex.org/W2265065644","https://openalex.org/W4321636575","https://openalex.org/W1986418932","https://openalex.org/W2357796999","https://openalex.org/W2045526782","https://openalex.org/W2741131631","https://openalex.org/W2415545834"],"abstract_inverted_index":{"BACKGROUND:":[0],"Parentage":[1],"information":[2],"is":[3,33,243,256],"fundamental":[4],"to":[5,18,119,128,152,212,232,245,247],"various":[6,220,251],"life":[7],"sciences.":[8],"Recent":[9],"advances":[10],"in":[11,23,92,219,225,236,250],"sequencing":[12,183],"technologies":[13],"have":[14],"made":[15],"it":[16],"possible":[17],"accurately":[19],"infer":[20],"parentage":[21,190],"even":[22],"non-model":[24],"species.":[25,221],"The":[26,75,222,254],"optimization":[27],"of":[28,30,43,50,65,86,100,114,122,132,142,194],"sets":[29],"genome-wide":[31],"markers":[32,145,171],"valuable":[34],"for":[35,47,56,168,189],"cost-effective":[36],"applications":[37],"but":[38],"requires":[39],"extremely":[40],"large":[41],"amounts":[42],"computation,":[44],"which":[45,109],"presses":[46],"the":[48,63,83,87,112,123,129,178,187,195,209],"development":[49],"new":[51],"efficient":[52,106],"algorithms.":[53],"RESULTS:":[54],"Here,":[55],"a":[57,70,97,140,153,157,165,192,213],"closed":[58],"half-sib":[59],"population,":[60,90],"we":[61,138],"generalized":[62],"process":[64],"marker":[66,80,197],"loci":[67],"selection":[68,198],"as":[69,204],"binary":[71,174],"integer":[72,175],"programming":[73],"problem.":[74],"proposed":[76,104],"systematic":[77,196],"formulation":[78],"considered":[79],"localization":[81],"and":[82,117,239,242],"family":[84],"structure":[85],"potential":[88,149],"parental":[89],"resulting":[91],"an":[93,105],"accurate":[94],"assignment":[95],"with":[96,156,199],"small":[98],"set":[99,141],"markers.":[101],"We":[102,163],"also":[103],"heuristic":[107],"approach,":[108],"effectively":[110],"improved":[111],"number":[113],"markers,":[115],"localization,":[116],"tolerance":[118],"missing":[120],"data":[121,179],"set.":[124],"Applying":[125],"this":[126,226],"method":[127,223],"actual":[130],"genotypes":[131],"apple":[133],"(Malus":[134],"\u00d7":[135],"domestica)":[136],"germplasm,":[137],"identified":[139],"34":[143],"SNP":[144,201],"that":[146,215],"distinguished":[147],"300":[148],"parents":[150],"crossed":[151],"particular":[154],"cultivar":[155],"greater":[158],"than":[159],"99%":[160],"accuracy.":[161],"CONCLUSIONS:":[162],"present":[164],"novel":[166,248],"approach":[167],"selecting":[169],"informative":[170],"based":[172],"on":[173],"programming.":[176],"Since":[177],"generated":[180],"by":[181],"high-throughput":[182],"technology":[184],"far":[185],"exceeds":[186],"requirement":[188],"assignment,":[191],"combination":[193],"targeted":[200],"genotyping,":[202],"such":[203],"KASP,":[205],"allows":[206],"flexibly":[207],"enlarging":[208],"analysis":[210],"up":[211],"scale":[214],"has":[216],"been":[217],"unrealistic":[218],"developed":[224],"study":[227],"can":[228],"be":[229],"directly":[230],"applied":[231],"unsolved":[233],"large-scale":[234],"problems":[235],"breeding,":[237],"reproduction,":[238],"ecological":[240],"research,":[241],"expected":[244],"lead":[246],"knowledge":[249],"biological":[252],"fields.":[253],"implementation":[255],"available":[257],"at":[258],"https://github.com/SoNishiyama/IP-SIMPAT":[259],".":[260]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
