{"id":"https://openalex.org/W2952115624","doi":"https://doi.org/10.1093/bioinformatics/btz060","title":"Haplotype assembly of autotetraploid potato using integer linear programing","display_name":"Haplotype assembly of autotetraploid potato using integer linear programing","publication_year":2019,"publication_date":"2019-01-23","ids":{"openalex":"https://openalex.org/W2952115624","doi":"https://doi.org/10.1093/bioinformatics/btz060","mag":"2952115624","pmid":"https://pubmed.ncbi.nlm.nih.gov/30689725"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz060","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3279/48975356/bioinformatics_35_18_3279.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3279/48975356/bioinformatics_35_18_3279.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053167866","display_name":"Enrico Siragusa","orcid":"https://orcid.org/0000-0002-5943-7544"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Enrico Siragusa","raw_affiliation_strings":["IBM T J Watson Research Center, Yorktown Heights , NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM T J Watson Research Center, Yorktown Heights , NY, USA","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054652878","display_name":"Niina Haiminen","orcid":"https://orcid.org/0000-0002-8663-1019"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niina Haiminen","raw_affiliation_strings":["IBM T J Watson Research Center, Yorktown Heights , NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM T J Watson Research Center, Yorktown Heights , NY, USA","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091360374","display_name":"Richard Finkers","orcid":"https://orcid.org/0000-0002-4368-8058"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Richard Finkers","raw_affiliation_strings":["Wageningen UR Plant Breeding , Wageningen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wageningen UR Plant Breeding , Wageningen, The Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009497765","display_name":"Richard G. F. Visser","orcid":"https://orcid.org/0000-0002-0213-4016"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Richard Visser","raw_affiliation_strings":["Wageningen UR Plant Breeding , Wageningen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wageningen UR Plant Breeding , Wageningen, The Netherlands","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025497346","display_name":"Laxmi Parida","orcid":"https://orcid.org/0000-0002-7872-5074"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Laxmi Parida","raw_affiliation_strings":["IBM T J Watson Research Center, Yorktown Heights , NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM T J Watson Research Center, Yorktown Heights , NY, USA","institution_ids":["https://openalex.org/I4210114115"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5025497346"],"corresponding_institution_ids":["https://openalex.org/I4210114115"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":2.8097,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.90485801,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"35","issue":"18","first_page":"3279","last_page":"3286"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11771","display_name":"Plant Pathogens and Resistance","score":0.5227000117301941,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11771","display_name":"Plant Pathogens and Resistance","score":0.5227000117301941,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.09960000216960907,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.06300000101327896,"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/integer","display_name":"Integer (computer science)","score":0.6392549872398376},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.5653678774833679},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.5630274415016174},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.5183842778205872},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3938252627849579},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39087361097335815},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35563284158706665},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3472152054309845},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27031147480010986},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11288616061210632},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10450363159179688},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.09180253744125366}],"concepts":[{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.6392549872398376},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.5653678774833679},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.5630274415016174},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.5183842778205872},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3938252627849579},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39087361097335815},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35563284158706665},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3472152054309845},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27031147480010986},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11288616061210632},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10450363159179688},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.09180253744125366}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011198","descriptor_name":"Solanum tuberosum","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011198","descriptor_name":"Solanum tuberosum","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011198","descriptor_name":"Solanum tuberosum","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011198","descriptor_name":"Solanum tuberosum","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btz060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz060","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3279/48975356/bioinformatics_35_18_3279.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30689725","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30689725","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmid:31280288","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31280288","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:library.wur.nl:wurpubs/554546","is_oa":true,"landing_page_url":"https://research.wur.nl/en/publications/haplotype-assembly-of-autotetraploid-potato-using-integer-linear-","pdf_url":null,"source":{"id":"https://openalex.org/S4210201231","display_name":"Socio-Environmental Systems Modeling","issn_l":"2663-3027","issn":["2663-3027"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"ISSN: 1367-4803","raw_type":"Article/Letter to editor"},{"id":"pmh:oai:pubmedcentral.nih.gov:6821310","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821310","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:9887466","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9887466","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz060","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3279/48975356/bioinformatics_35_18_3279.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2952115624.pdf","grobid_xml":"https://content.openalex.org/works/W2952115624.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W26356079","https://openalex.org/W418523852","https://openalex.org/W2053294845","https://openalex.org/W2067677152","https://openalex.org/W2088012127","https://openalex.org/W2110417468","https://openalex.org/W2117400776","https://openalex.org/W2129326667","https://openalex.org/W2150056019","https://openalex.org/W2157205588","https://openalex.org/W2160853127","https://openalex.org/W2164971951","https://openalex.org/W2472873926","https://openalex.org/W2511086505","https://openalex.org/W2563785056","https://openalex.org/W2583064351","https://openalex.org/W2730543825","https://openalex.org/W2753396470","https://openalex.org/W2763587271","https://openalex.org/W2789954089","https://openalex.org/W2884520208","https://openalex.org/W2950519676","https://openalex.org/W6601068097","https://openalex.org/W6639095687","https://openalex.org/W6731223309","https://openalex.org/W6745189765"],"related_works":["https://openalex.org/W3146762847","https://openalex.org/W2398263405","https://openalex.org/W2056886854","https://openalex.org/W2025446304","https://openalex.org/W1925942709","https://openalex.org/W2047683846","https://openalex.org/W2044902158","https://openalex.org/W2082154838","https://openalex.org/W2109912052","https://openalex.org/W1711527768"],"abstract_inverted_index":{"SUMMARY:":[0],"Haplotype":[1],"assembly":[2],"of":[3,40,55,83,125],"polyploids":[4,43],"is":[5,50],"an":[6,34],"open":[7],"issue":[8],"in":[9,30],"plant":[10],"genomics.":[11],"Recent":[12],"experimental":[13,90,116],"studies":[14],"on":[15,52,67,87,93,101,115],"highly":[16,41,109],"heterozygous":[17,42],"autotetraploid":[18,97],"potato":[19,98],"have":[20],"shown":[21],"that":[22,105],"available":[23,142],"methods":[24,79,107],"do":[25],"not":[26],"deliver":[27],"satisfying":[28],"results":[29,114],"practice.":[31],"We":[32,76],"propose":[33],"optimal":[35,74],"method":[36,49],"to":[37,62,72],"assemble":[38],"haplotypes":[39],"from":[44],"Illumina":[45],"short-sequencing":[46],"reads.":[47],"Our":[48],"based":[51,92],"a":[53,84,119],"generalization":[54],"the":[56,63,123,126],"existing":[57],"minimum":[58],"fragment":[59],"removal":[60],"model":[61],"polyploid":[64],"case":[65],"and":[66,89],"new":[68],"integer":[69],"linear":[70],"programs":[71],"reconstruct":[73],"haplotypes.":[75],"validate":[77],"our":[78,106],"experimentally":[80],"by":[81],"means":[82],"combined":[85],"evaluation":[86],"simulated":[88,102],"data":[91,103,117,140],"83":[94],"previously":[95],"sequenced":[96],"cultivars.":[99],"Results":[100],"show":[104],"produce":[108],"accurate":[110],"haplotype":[111],"assemblies,":[112],"while":[113],"confirm":[118],"sensible":[120],"improvement":[121],"over":[122],"state":[124],"art.":[127],"AVAILABILITY":[128],"AND":[129],"IMPLEMENTATION:":[130],"Executables":[131],"for":[132],"Linux":[133],"at":[134,143],"http://github.com/Computational":[135],"Genomics/HaplotypeAssembler.":[136],"SUPPLEMENTARY":[137],"INFORMATION:":[138],"Supplementary":[139],"are":[141],"Bioinformatics":[144],"online.":[145]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":7}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2019-06-27T00:00:00"}
