{"id":"https://openalex.org/W2004237294","doi":"https://doi.org/10.1145/1353343.1353423","title":"OrthoCluster","display_name":"OrthoCluster","publication_year":2008,"publication_date":"2008-03-25","ids":{"openalex":"https://openalex.org/W2004237294","doi":"https://doi.org/10.1145/1353343.1353423","mag":"2004237294"},"language":"en","primary_location":{"id":"doi:10.1145/1353343.1353423","is_oa":true,"landing_page_url":"https://doi.org/10.1145/1353343.1353423","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/1353343.1353423","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th international conference on Extending database technology: Advances in database technology","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/1353343.1353423","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041803934","display_name":"Xinghuo Zeng","orcid":null},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Xinghuo Zeng","raw_affiliation_strings":["Simon Fraser University, Burnaby, BC Canada","[Simon Fraser University Burnaby, BC, Canada]"],"affiliations":[{"raw_affiliation_string":"Simon Fraser University, Burnaby, BC Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"[Simon Fraser University Burnaby, BC, Canada]","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066999136","display_name":"Matthew J. Nesbitt","orcid":null},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Matthew J. Nesbitt","raw_affiliation_strings":["Simon Fraser University, Burnaby, BC Canada","[Simon Fraser University Burnaby, BC, Canada]"],"affiliations":[{"raw_affiliation_string":"Simon Fraser University, Burnaby, BC Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"[Simon Fraser University Burnaby, BC, Canada]","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062247330","display_name":"Jian Pei","orcid":"https://orcid.org/0000-0002-2200-8711"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jian Pei","raw_affiliation_strings":["Simon Fraser University, Burnaby, BC Canada","[Simon Fraser University Burnaby, BC, Canada]"],"affiliations":[{"raw_affiliation_string":"Simon Fraser University, Burnaby, BC Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"[Simon Fraser University Burnaby, BC, Canada]","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100730995","display_name":"Ke Wang","orcid":"https://orcid.org/0000-0002-8272-455X"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ke Wang","raw_affiliation_strings":["Simon Fraser University, Burnaby, BC Canada","[Simon Fraser University Burnaby, BC, Canada]"],"affiliations":[{"raw_affiliation_string":"Simon Fraser University, Burnaby, BC Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"[Simon Fraser University Burnaby, BC, Canada]","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053029723","display_name":"Ismael A. Vergara","orcid":"https://orcid.org/0000-0002-2960-2967"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ismael A. Vergara","raw_affiliation_strings":["Simon Fraser University, Burnaby, BC Canada","[Simon Fraser University Burnaby, BC, Canada]"],"affiliations":[{"raw_affiliation_string":"Simon Fraser University, Burnaby, BC Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"[Simon Fraser University Burnaby, BC, Canada]","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101610338","display_name":"Nansheng Chen","orcid":"https://orcid.org/0000-0002-0615-7215"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nansheng Chen","raw_affiliation_strings":["Simon Fraser University, Burnaby, BC Canada","[Simon Fraser University Burnaby, BC, Canada]"],"affiliations":[{"raw_affiliation_string":"Simon Fraser University, Burnaby, BC Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"[Simon Fraser University Burnaby, BC, Canada]","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5041803934"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":null,"apc_paid":null,"fwci":1.2447,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.77927045,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"656","last_page":"667"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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":0.9983999729156494,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9979000091552734,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9959999918937683,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4889353811740875}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4889353811740875}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1353343.1353423","is_oa":true,"landing_page_url":"https://doi.org/10.1145/1353343.1353423","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/1353343.1353423","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th international conference on Extending database technology: Advances in database technology","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/1353343.1353423","is_oa":true,"landing_page_url":"https://doi.org/10.1145/1353343.1353423","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/1353343.1353423","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th international conference on Extending database technology: Advances in database technology","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.5099999904632568}],"awards":[{"id":"https://openalex.org/G5330548951","display_name":null,"funder_award_id":"Scholar","funder_id":"https://openalex.org/F4320319965","funder_display_name":"Michael Smith Health Research BC"}],"funders":[{"id":"https://openalex.org/F4320319965","display_name":"Michael Smith Health Research BC","ror":"https://ror.org/020x39229"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320335343","display_name":"SFU Community Trust Endowment Fund","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2004237294.pdf","grobid_xml":"https://content.openalex.org/works/W2004237294.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W185402263","https://openalex.org/W1263422348","https://openalex.org/W1509222088","https://openalex.org/W1510033442","https://openalex.org/W1635391495","https://openalex.org/W1966794959","https://openalex.org/W1971321176","https://openalex.org/W1971403296","https://openalex.org/W2011457803","https://openalex.org/W2041581620","https://openalex.org/W2045385587","https://openalex.org/W2048009853","https://openalex.org/W2088015737","https://openalex.org/W2088131236","https://openalex.org/W2090415636","https://openalex.org/W2096143996","https://openalex.org/W2096824423","https://openalex.org/W2100990361","https://openalex.org/W2102304447","https://openalex.org/W2104106326","https://openalex.org/W2127230663","https://openalex.org/W2131041596","https://openalex.org/W2135123683","https://openalex.org/W2137464714","https://openalex.org/W2141652419","https://openalex.org/W2141729174","https://openalex.org/W2142082312","https://openalex.org/W2142642738","https://openalex.org/W2143420603","https://openalex.org/W2145477956","https://openalex.org/W2149517531","https://openalex.org/W2150934173","https://openalex.org/W2151302772","https://openalex.org/W2153283265","https://openalex.org/W2158714788","https://openalex.org/W2168909179","https://openalex.org/W2981209166","https://openalex.org/W4229487902","https://openalex.org/W4229799243","https://openalex.org/W4230501579","https://openalex.org/W4248758183","https://openalex.org/W6607435448"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"By":[0],"comparing":[1],"genomes":[2,19,109],"among":[3],"both":[4,21],"closely":[5],"and":[6,15,23,75,110,116,139,198],"distally":[7],"related":[8,37],"species,":[9,38],"comparative":[10,43],"genomics":[11,44],"analysis":[12],"characterizes":[13],"structures":[14],"functions":[16],"of":[17,32,36,58,69,77,107,122,131,155,164],"different":[18],"in":[20,42,145,186],"conserved":[22,30],"divergent":[24],"regions.":[25],"Synteny":[26],"blocks,":[27,56],"which":[28,89],"are":[29],"blocks":[31],"genes":[33],"on":[34],"chromosomes":[35],"play":[39],"important":[40],"roles":[41],"analysis.":[45],"Although":[46],"a":[47,84,152,187],"few":[48],"tools":[49],"have":[50],"been":[51],"designed":[52],"to":[53,182],"identify":[54,183],"synteny":[55,123,160],"most":[57],"them":[59],"cannot":[60],"handle":[61,91],"some":[62,200],"challenging":[63],"application":[64,147],"requirements,":[65],"particularly":[66],"the":[67,103,119,159,168,194],"strandedness":[68,169],"genes,":[70],"gene":[71,73,105,173],"inversions,":[72],"duplications,":[74],"comparison":[76],"more":[78],"than":[79],"two":[80],"genomes.":[81],"We":[82],"developed":[83],"data":[85],"mining":[86],"tool,":[87],"Ortho-Cluster,":[88],"can":[90,179],"all":[92],"those":[93],"challenges.":[94],"It":[95],"is":[96,170,175],"publicly":[97],"available":[98],"at":[99],"http://genome.sfu.ca/projects/orthocluster.":[100],"OrthoCluster":[101,127,149,178],"takes":[102],"annotated":[104],"sets":[106],"candidate":[108],"pairwise":[111],"orthologous":[112],"relationships":[113],"as":[114,158],"input":[115],"efficiently":[117],"identifies":[118,128],"complete":[120],"set":[121,154],"blocks.":[124],"In":[125,189],"addition,":[126],"four":[129],"types":[130],"genome":[132],"rearrangement":[133],"events":[134],"namely":[135],"inversion,":[136],"transposition,":[137],"insertion/deletion,":[138],"reciprocal":[140],"translocation.":[141],"To":[142],"be":[143,180],"fleexible":[144],"various":[146],"scenarios,":[148],"comes":[150],"with":[151],"systematic":[153],"parameters":[156],"such":[157],"block":[161],"size,":[162],"number":[163],"mismatches":[165],"allowed,":[166],"whether":[167,172],"enforced,":[171],"ordering":[174],"preserved.":[176],"Furthermore,":[177],"used":[181],"segmental":[184],"duplication":[185],"genome.":[188],"this":[190],"paper,":[191],"we":[192],"introduce":[193],"major":[195],"technical":[196],"ideas,":[197],"present":[199],"interesting":[201],"findings":[202],"using":[203],"OrthoCluster.":[204]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}
