{"id":"https://openalex.org/W4390970753","doi":"https://doi.org/10.1109/bibm58861.2023.10385622","title":"Inference of subgenomes resulting from polyploid events using synteny based dynamic linking and maximum neighbourhood","display_name":"Inference of subgenomes resulting from polyploid events using synteny based dynamic linking and maximum neighbourhood","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390970753","doi":"https://doi.org/10.1109/bibm58861.2023.10385622"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385622","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385622","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093735736","display_name":"Thulani Hewavithana","orcid":"https://orcid.org/0000-0002-2579-0470"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Thulani Hewavithana","raw_affiliation_strings":["University of Saskatchewan,Department of Computer Science,Saskatoon,Canada","Department of Computer Science, University of Saskatchewan, Saskatoon, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Saskatchewan,Department of Computer Science,Saskatoon,Canada","institution_ids":["https://openalex.org/I32625721"]},{"raw_affiliation_string":"Department of Computer Science, University of Saskatchewan, Saskatoon, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048575722","display_name":"ChuShin Koh","orcid":"https://orcid.org/0000-0001-7313-2125"},"institutions":[{"id":"https://openalex.org/I4210161576","display_name":"Global Institute for Water Security","ror":"https://ror.org/05997db74","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210161576"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Chu Shin Koh","raw_affiliation_strings":["Global Institute for Food Security,Saskatoon,Canada","Global Institute for Food Security, Saskatoon, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Institute for Food Security,Saskatoon,Canada","institution_ids":["https://openalex.org/I4210161576"]},{"raw_affiliation_string":"Global Institute for Food Security, Saskatoon, Canada","institution_ids":["https://openalex.org/I4210161576"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014928674","display_name":"Avleen Kaur","orcid":"https://orcid.org/0000-0002-8689-9242"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Avleen Kaur","raw_affiliation_strings":["University of Saskatchewan,Department of Computer Science,Saskatoon,Canada","Department of Computer Science, University of Saskatchewan, Saskatoon, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Saskatchewan,Department of Computer Science,Saskatoon,Canada","institution_ids":["https://openalex.org/I32625721"]},{"raw_affiliation_string":"Department of Computer Science, University of Saskatchewan, Saskatoon, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084076822","display_name":"Raymond J. Spiteri","orcid":"https://orcid.org/0000-0002-3513-6237"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Raymond Spiteri","raw_affiliation_strings":["University of Saskatchewan,Department of Computer Science,Saskatoon,Canada","Department of Computer Science, University of Saskatchewan, Saskatoon, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Saskatchewan,Department of Computer Science,Saskatoon,Canada","institution_ids":["https://openalex.org/I32625721"]},{"raw_affiliation_string":"Department of Computer Science, University of Saskatchewan, Saskatoon, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073738872","display_name":"Isobel A. P. Parkin","orcid":"https://orcid.org/0000-0002-5807-9466"},"institutions":[{"id":"https://openalex.org/I1331897569","display_name":"Agriculture and Agri-Food Canada","ror":"https://ror.org/051dzs374","country_code":"CA","type":"government","lineage":["https://openalex.org/I1331897569","https://openalex.org/I2802286613"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Isobel Parkin","raw_affiliation_strings":["Agriculture and Agri-Food Canada,Saskatoon,Canada","Agriculture and Agri-Food Canada, Saskatoon, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Agriculture and Agri-Food Canada,Saskatoon,Canada","institution_ids":["https://openalex.org/I1331897569"]},{"raw_affiliation_string":"Agriculture and Agri-Food Canada, Saskatoon, Canada","institution_ids":["https://openalex.org/I1331897569"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089050646","display_name":"Lingling Jin","orcid":"https://orcid.org/0000-0002-4586-2347"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Lingling Jin","raw_affiliation_strings":["University of Saskatchewan,Department of Computer Science,Saskatoon,Canada","Department of Computer Science, University of Saskatchewan, Saskatoon, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Saskatchewan,Department of Computer Science,Saskatoon,Canada","institution_ids":["https://openalex.org/I32625721"]},{"raw_affiliation_string":"Department of Computer Science, University of Saskatchewan, Saskatoon, Canada","institution_ids":["https://openalex.org/I32625721"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.3332808,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"104","last_page":"109"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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"}},{"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/T10240","display_name":"Plant tissue culture and regeneration","score":0.9817000031471252,"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/synteny","display_name":"Synteny","score":0.9324150681495667},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7868210673332214},{"id":"https://openalex.org/keywords/polyploid","display_name":"Polyploid","score":0.7786313891410828},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5683662295341492},{"id":"https://openalex.org/keywords/brassica-rapa","display_name":"Brassica rapa","score":0.47236424684524536},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45982077717781067},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3925180733203888},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27747851610183716}],"concepts":[{"id":"https://openalex.org/C53702515","wikidata":"https://www.wikidata.org/wiki/Q971246","display_name":"Synteny","level":4,"score":0.9324150681495667},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7868210673332214},{"id":"https://openalex.org/C2776626444","wikidata":"https://www.wikidata.org/wiki/Q213410","display_name":"Polyploid","level":4,"score":0.7786313891410828},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5683662295341492},{"id":"https://openalex.org/C2993030687","wikidata":"https://www.wikidata.org/wiki/Q3384","display_name":"Brassica rapa","level":3,"score":0.47236424684524536},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45982077717781067},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3925180733203888},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27747851610183716}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385622","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385622","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Sustainable cities and communities","id":"https://metadata.un.org/sdg/11","score":0.4000000059604645}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1991552254","https://openalex.org/W2005713653","https://openalex.org/W2020134788","https://openalex.org/W2066125076","https://openalex.org/W2095645518","https://openalex.org/W2100874222","https://openalex.org/W2112995167","https://openalex.org/W2128996483","https://openalex.org/W2141550398","https://openalex.org/W2149517531","https://openalex.org/W2164567186","https://openalex.org/W2167963418","https://openalex.org/W2385435022","https://openalex.org/W2914560485","https://openalex.org/W2952105401","https://openalex.org/W2957163358","https://openalex.org/W2977811825","https://openalex.org/W3047959744","https://openalex.org/W3083715203","https://openalex.org/W3089783097","https://openalex.org/W3110970855","https://openalex.org/W3156232775","https://openalex.org/W3165217178","https://openalex.org/W4220742195","https://openalex.org/W4285727773"],"related_works":["https://openalex.org/W4237022323","https://openalex.org/W4393189113","https://openalex.org/W1969010119","https://openalex.org/W2131180151","https://openalex.org/W2042640523","https://openalex.org/W2037172645","https://openalex.org/W4243565069","https://openalex.org/W2995164487","https://openalex.org/W2106726141","https://openalex.org/W2119233950"],"abstract_inverted_index":{"Polyploidy":[0],"is":[1],"common":[2],"in":[3,7,19,71,76,172,195],"flowering":[4,210],"plants,":[5],"resulting":[6],"extra":[8],"sets":[9],"of":[10,25,83,120,209],"chromosomes,":[11],"known":[12],"as":[13],"subgenomes.":[14],"These":[15],"events":[16],"are":[17,44],"widespread":[18],"plant":[20],"evolution,":[21],"making":[22],"the":[23,57,81,104,109,114,169,183,206],"assignment":[24],"synteny":[26,65,77,90],"blocks":[27,78,91],"to":[28,32,146,158,167],"subgenomes":[29,101,119,171,194],"challenging":[30],"due":[31,157],"gene":[33,36,84],"fractionation":[34,74,161],"and":[35,46,73,79,94,129,150,175,189,212],"order":[37],"rearrangements.":[38],"Current":[39],"methods":[40],"for":[41,138,192,204],"subgenome":[42,62,139],"identification":[43],"labor-intensive":[45],"require":[47],"expertise,":[48],"lacking":[49],"automation.":[50],"To":[51],"address":[52],"this":[53],"challenge,":[54],"we":[55,164],"introduce":[56],"SyntenyLink":[58,86,115,166,184],"algorithm,":[59],"which":[60],"automates":[61],"reconstruction":[63],"from":[64,144],"blocks.":[66],"This":[67,199],"algorithm":[68,116,185],"considers":[69],"differences":[70],"substitution":[72],"patterns":[75],"maintains":[80],"continuity":[82],"order.":[85],"starts":[87],"by":[88,102],"identifying":[89],"using":[92,117],"BLASTP":[93],"DAGchainer,":[95],"then":[96],"Automatically":[97],"partitions":[98],"them":[99],"into":[100],"traversing":[103],"maximum":[105],"weighted":[106],"path":[107],"on":[108],"\"super-synteny":[110],"graph\".":[111],"We":[112],"validated":[113],"verified":[118],"Brassica":[121,123,125,127,173,176],"rapa,":[122],"oleracea,":[124],"nigra,":[126],"napus,":[128],"Sinapis":[130],"alba.":[131],"The":[132],"results":[133],"demonstrate":[134],"its":[135,179],"effectiveness,":[136],"especially":[137],"1,":[140],"with":[141],"accuracy":[142,155],"ranging":[143],"82%":[145],"88%.":[147],"Subgenomes":[148],"2":[149],"3":[151],"showed":[152],"slightly":[153],"lower":[154],"(60%-85%)":[156],"their":[159],"similar":[160],"patterns.":[162],"Furthermore,":[163],"applied":[165],"separate":[168],"six":[170],"juncea":[174],"carinata,":[177],"illustrating":[178],"versatility.":[180],"In":[181],"summary,":[182],"offers":[186],"a":[187],"powerful":[188],"automated":[190],"approach":[191],"reconstructing":[193],"complex":[196],"polyploid":[197,214],"genomes.":[198],"advancement":[200],"has":[201],"significant":[202],"implications":[203],"studying":[205],"evolutionary":[207],"history":[208],"plants":[211],"other":[213],"organisms.":[215]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}