{"id":"https://openalex.org/W2134425468","doi":"https://doi.org/10.1186/1471-2105-13-s10-s9","title":"Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes","display_name":"Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes","publication_year":2012,"publication_date":"2012-06-01","ids":{"openalex":"https://openalex.org/W2134425468","doi":"https://doi.org/10.1186/1471-2105-13-s10-s9","mag":"2134425468","pmid":"https://pubmed.ncbi.nlm.nih.gov/22759433","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3389459"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s10-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S10-S9","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_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S10-S9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":"funder","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 Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics University of 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":"funder","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 Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics University of Ottawa Canada","institution_ids":["https://openalex.org/I153718931"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.465,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":15,"citation_normalized_percentile":{"value":0.69901,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":87,"max":88},"biblio":{"volume":"13","issue":"S10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.996,"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":0.996,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9954,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9897,"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":[],"concepts":[{"id":"https://openalex.org/C178300618","wikidata":"https://www.wikidata.org/wiki/Q1898509","display_name":"Extant taxon","level":2,"score":0.73939776},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.73607427},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.63484937},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.6221852},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5950778},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.56546956},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5275048},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48359317},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.39718992},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38385558},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.15743175},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10438591},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10178387}],"mesh":[{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023061","descriptor_name":"Gene Order","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019684","descriptor_name":"Magnoliopsida","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018744","descriptor_name":"DNA, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018744","descriptor_name":"DNA, Plant","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019684","descriptor_name":"Magnoliopsida","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D019684","descriptor_name":"Magnoliopsida","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s10-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S10-S9","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_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389459","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_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22759433","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_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s10-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S10-S9","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_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[{"score":0.54,"id":"https://metadata.un.org/sdg/15","display_name":"Life on land"}],"grants":[],"datasets":[],"versions":[],"referenced_works_count":36,"referenced_works":["https://openalex.org/W102313747","https://openalex.org/W1530804984","https://openalex.org/W1972818612","https://openalex.org/W1979469999","https://openalex.org/W1990188370","https://openalex.org/W1994145712","https://openalex.org/W2008047531","https://openalex.org/W2013476107","https://openalex.org/W2024998162","https://openalex.org/W2056871145","https://openalex.org/W2064911343","https://openalex.org/W2067086660","https://openalex.org/W2070387787","https://openalex.org/W2084477034","https://openalex.org/W2091507729","https://openalex.org/W2092779913","https://openalex.org/W2097710447","https://openalex.org/W2101021876","https://openalex.org/W2104734478","https://openalex.org/W2115483901","https://openalex.org/W2120381562","https://openalex.org/W2125346198","https://openalex.org/W2130001957","https://openalex.org/W2130640131","https://openalex.org/W2132150084","https://openalex.org/W2136598303","https://openalex.org/W2145046927","https://openalex.org/W2146384771","https://openalex.org/W2149628296","https://openalex.org/W2157081150","https://openalex.org/W2161481677","https://openalex.org/W2168955735","https://openalex.org/W2169283658","https://openalex.org/W3191052428","https://openalex.org/W4251061433","https://openalex.org/W4388252998"],"related_works":["https://openalex.org/W4372354731","https://openalex.org/W4290948148","https://openalex.org/W4249944690","https://openalex.org/W3016239368","https://openalex.org/W2949152769","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2487162673","https://openalex.org/W2402755139","https://openalex.org/W1978228495"],"abstract_inverted_index":{"Ancestral":[0],"gene":[1,61,96,142,161],"order":[2,62,97,143,162,170],"reconstruction":[3,144,229],"for":[4,121,140],"flowering":[5],"plants":[6],"has":[7],"lagged":[8],"behind":[9],"developments":[10],"in":[11,92,145,197,230],"yeasts,":[12],"insects":[13],"and":[14,39,49,72,81,85,102,110,114,136,201,209],"higher":[15],"animals,":[16],"because":[17],"of":[18,21,41,53,63,98,104,155,185,222,233],"the":[19,50,60,94,99,108,118,133,137,160,166,169,174,182,234],"recency":[20],"widespread":[22],"plant":[23],"genome":[24,36],"sequencing,":[25],"sequencers'":[26],"embargoes":[27],"on":[28],"public":[29],"data":[30,131],"use,":[31],"paralogies":[32,205],"due":[33,206],"to":[34,164,173,181,207,218],"whole":[35],"duplication":[37],"(WGD)":[38],"fractionation":[40],"undeleted":[42],"duplicates,":[43],"extensive":[44],"paralogy":[45],"from":[46,89,127],"other":[47,210],"sources,":[48],"computational":[51],"cost":[52],"existing":[54],"methods.We":[55],"address":[56],"these":[57],"problems,":[58],"using":[59],"four":[64],"core":[65],"eudicot":[66,187],"genomes":[67,135,151],"(cacao,":[68],"castor":[69],"bean,":[70],"papaya":[71],"grapevine)":[73],"that":[74,87,168],"have":[75],"escaped":[76],"any":[77],"recent":[78],"WGD":[79,156,208],"events,":[80],"two":[82],"others":[83],"(poplar":[84],"cucumber)":[86],"descend":[88],"independent":[90],"WGDs,":[91],"inferring":[93],"ancestral":[95,141,186],"rosid":[100],"clade":[101],"those":[103],"its":[105],"main":[106],"subgroups,":[107],"fabids":[109],"malvids.":[111],"We":[112,158],"improve":[113],"adapt":[115],"techniques":[116],"including":[117],"OMG":[119],"method":[120],"extracting":[122],"large,":[123],"paralogy-free,":[124],"multiple":[125,223],"orthologies":[126],"conflated":[128],"pairwise":[129],"synteny":[130],"among":[132],"six":[134],"PATHGROUPS":[138],"approach":[139],"a":[146,219],"given":[147],"phylogeny,":[148],"where":[149],"some":[150],"may":[152],"be":[153,195],"descendants":[154],"events.":[157],"use":[159],"evidence":[163],"evaluate":[165],"hypothesis":[167],"Malpighiales":[171],"belongs":[172],"malvids":[175],"rather":[176],"than":[177],"as":[178],"traditionally":[179],"assigned":[180],"fabids.Gene":[183],"orders":[184],"species,":[188],"involving":[189],"10,000":[190],"or":[191],"more":[192],"genes":[193],"can":[194],"reconstructed":[196],"an":[198],"efficient,":[199],"parsimonious":[200],"consistent":[202],"way,":[203],"despite":[204],"processes.":[211],"Pairwise":[212],"genomic":[213],"syntenies":[214],"provide":[215],"appropriate":[216],"input":[217],"parameter-free":[220],"procedure":[221],"ortholog":[224],"identification":[225],"followed":[226],"by":[227],"gene-order":[228],"solving":[231],"instances":[232],"\"small":[235],"phylogeny\"":[236],"problem.":[237]},"abstract_inverted_index_v3":null,"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2134425468","counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2025-04-16T15:25:11.353129","created_date":"2016-06-24"}