{"id":"https://openalex.org/W2139251761","doi":"https://doi.org/10.1186/1471-2105-13-s19-s8","title":"A consolidation algorithm for genomes fractionated after higher order polyploidization","display_name":"A consolidation algorithm for genomes fractionated after higher order polyploidization","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W2139251761","doi":"https://doi.org/10.1186/1471-2105-13-s19-s8","mag":"2139251761","pmid":"https://pubmed.ncbi.nlm.nih.gov/23282012"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s19-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s19-s8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S19-S8","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/track/pdf/10.1186/1471-2105-13-S19-S8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102807386","display_name":"Katharina Jahn","orcid":"https://orcid.org/0000-0002-6983-4615"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Katharina Jahn","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada K1N 6N5. sankoff@uottawa.ca","Department of Mathematics and Statistics University of Ottawa Ottawa, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada K1N 6N5. sankoff@uottawa.ca","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Department of Mathematics and Statistics University of Ottawa Ottawa, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106265672","display_name":"Chunfang Zheng","orcid":"https://orcid.org/0000-0003-4205-4501"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Chunfang Zheng","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada, K1N 6N5","Department of Mathematics and Statistics University of Ottawa Ottawa, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada, K1N 6N5","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Department of Mathematics and Statistics University of Ottawa Ottawa, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103891614","display_name":"Jakub Kov\u00e1\u010d","orcid":null},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jakub Kov\u00e1\u010d","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada, K1N 6N5","Department of Mathematics and Statistics University of Ottawa Ottawa, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada, K1N 6N5","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Department of Mathematics and Statistics University of Ottawa Ottawa, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089707881","display_name":"David Sankoff","orcid":"https://orcid.org/0000-0001-8415-5189"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"David Sankoff","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada, K1N 6N5","Department of Mathematics and Statistics University of Ottawa Ottawa, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada, K1N 6N5","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Department of Mathematics and Statistics University of Ottawa Ottawa, Canada","institution_ids":["https://openalex.org/I153718931"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102807386"],"corresponding_institution_ids":["https://openalex.org/I153718931"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.2257,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.91786658,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"13","issue":"S19","first_page":"S8","last_page":"S8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9994999766349792,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9994999766349792,"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/T11247","display_name":"Plant nutrient uptake and metabolism","score":0.9972000122070312,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.995199978351593,"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/genome","display_name":"Genome","score":0.7803323268890381},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5201828479766846},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.4911019802093506},{"id":"https://openalex.org/keywords/consolidation","display_name":"Consolidation (business)","score":0.4722817838191986},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45285916328430176},{"id":"https://openalex.org/keywords/fractionation","display_name":"Fractionation","score":0.4378136396408081},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42453548312187195},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4226628839969635},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35567808151245117},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26154378056526184},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10597372055053711}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7803323268890381},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5201828479766846},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.4911019802093506},{"id":"https://openalex.org/C2776014549","wikidata":"https://www.wikidata.org/wiki/Q3050847","display_name":"Consolidation (business)","level":2,"score":0.4722817838191986},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45285916328430176},{"id":"https://openalex.org/C97428945","wikidata":"https://www.wikidata.org/wiki/Q15305109","display_name":"Fractionation","level":2,"score":0.4378136396408081},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42453548312187195},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4226628839969635},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35567808151245117},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26154378056526184},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10597372055053711},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C121955636","wikidata":"https://www.wikidata.org/wiki/Q4116214","display_name":"Accounting","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"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":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023061","descriptor_name":"Gene Order","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023061","descriptor_name":"Gene Order","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023061","descriptor_name":"Gene Order","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D027843","descriptor_name":"Vitis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027843","descriptor_name":"Vitis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027843","descriptor_name":"Vitis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-13-s19-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s19-s8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S19-S8","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:23282012","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23282012","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:europepmc.org:2543601","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3526428","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s19-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s19-s8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S19-S8","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":[],"awards":[{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G5784215521","display_name":null,"funder_award_id":"Chair","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320320875","display_name":"Deutscher Akademischer Austauschdienst","ror":"https://ror.org/039djdh30"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2139251761.pdf","grobid_xml":"https://content.openalex.org/works/W2139251761.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1506856932","https://openalex.org/W1641544182","https://openalex.org/W1994145712","https://openalex.org/W2064911343","https://openalex.org/W2081933515","https://openalex.org/W2082054947","https://openalex.org/W2116905253","https://openalex.org/W2124829311","https://openalex.org/W2137120608","https://openalex.org/W2139856280","https://openalex.org/W2145046927","https://openalex.org/W2152060876"],"related_works":["https://openalex.org/W4388014327","https://openalex.org/W2115382138","https://openalex.org/W1979058569","https://openalex.org/W1883409887","https://openalex.org/W2367076742","https://openalex.org/W2349742942","https://openalex.org/W4234514162","https://openalex.org/W2202284674","https://openalex.org/W4378782348","https://openalex.org/W2128467432"],"abstract_inverted_index":{"In":[0],"this":[1,33,45,73],"paper,":[2],"we":[3],"present":[4],"a":[5],"new":[6,39,46,92],"consolidation":[7,81],"algorithm":[8,40,74,93],"that":[9,62],"extends":[10],"and":[11,51,66,100],"improves":[12],"previous":[13],"work":[14,43],"in":[15,110],"several":[16],"directions.":[17],"We":[18],"extend":[19],"the":[20,23,76,88,106],"notion":[21],"of":[22,48,69,80,108],"fractionation":[24,49,109],"region":[25,50],"to":[26,54,84,97,101,104],"use":[27],"information":[28],"provided":[29],"by":[30],"regions":[31],"where":[32],"process":[34,55],"is":[35,52,94],"still":[36],"ongoing.":[37],"The":[38,91],"can":[41],"optionally":[42],"with":[44],"definition":[47],"able":[53],"not":[56],"only":[57],"tetraploids":[58],"but":[59],"also":[60],"genomes":[61,99],"have":[63],"undergone":[64],"hexaploidization":[65],"polyploidization":[67],"events":[68],"higher":[70],"order.":[71],"Finally,":[72],"reduces":[75],"asymptotic":[77],"time":[78],"complexity":[79],"from":[82],"quadratic":[83],"linear":[85],"dependence":[86],"on":[87],"genome":[89],"size.":[90],"applied":[95],"both":[96],"plant":[98],"simulated":[102],"data":[103],"study":[105],"effect":[107],"ancient":[111],"hexaploids.":[112]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
