{"id":"https://openalex.org/W2144352571","doi":"https://doi.org/10.1186/1752-0509-6-s1-s22","title":"BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity","display_name":"BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W2144352571","doi":"https://doi.org/10.1186/1752-0509-6-s1-s22","mag":"2144352571","pmid":"https://pubmed.ncbi.nlm.nih.gov/23046607"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-s1-s22","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s1-s22","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-6-S1-S22","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"conference-abstract","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-6-S1-S22","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060157739","display_name":"Melvin Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Melvin Zhang","raw_affiliation_strings":["School of Computing, National University of Singapore, 13 Computing Drive, Singapore, Republic of Singapore","School of Computing, National University of Singapore, Singapore, Republic of Singapore#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, National University of Singapore, 13 Computing Drive, Singapore, Republic of Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"School of Computing, National University of Singapore, Singapore, Republic of Singapore#TAB#","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":null,"display_name":"Hon Leong","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Hon Leong","raw_affiliation_strings":["School of Computing, National University of Singapore, Singapore, Republic of Singapore#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, National University of Singapore, Singapore, Republic of Singapore#TAB#","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I165932596"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":null,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"6","issue":"Suppl 1","first_page":"S22","last_page":"S22"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.913100004196167,"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"}},"topics":[{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.913100004196167,"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":0.02979999966919422,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.012299999594688416,"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/sequence","display_name":"Sequence (biology)","score":0.6675753593444824},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6642508506774902},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6214379072189331},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.577675461769104},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.546546220779419},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5077858567237854},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.45006904006004333},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34211164712905884},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32081592082977295},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21457165479660034}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6675753593444824},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6642508506774902},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6214379072189331},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.577675461769104},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.546546220779419},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5077858567237854},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.45006904006004333},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34211164712905884},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32081592082977295},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21457165479660034},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1752-0509-6-s1-s22","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s1-s22","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-6-S1-S22","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:23046607","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23046607","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 systems biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3403649","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3403649","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/77829","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/77829","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:7838b9ba3d05444c892eb82aad994c71","is_oa":false,"landing_page_url":"https://doaj.org/article/7838b9ba3d05444c892eb82aad994c71","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 6, Iss Suppl 1, p S22 (2012)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-s1-s22","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s1-s22","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-6-S1-S22","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144352571.pdf","grobid_xml":"https://content.openalex.org/works/W2144352571.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W173754913","https://openalex.org/W319819633","https://openalex.org/W602132365","https://openalex.org/W1479777405","https://openalex.org/W1492180884","https://openalex.org/W1494919299","https://openalex.org/W1532397568","https://openalex.org/W1971926406","https://openalex.org/W1989978323","https://openalex.org/W2008856488","https://openalex.org/W2009234149","https://openalex.org/W2038968181","https://openalex.org/W2044892321","https://openalex.org/W2080153599","https://openalex.org/W2082202339","https://openalex.org/W2088015737","https://openalex.org/W2089499735","https://openalex.org/W2093342565","https://openalex.org/W2096466922","https://openalex.org/W2097771645","https://openalex.org/W2109258478","https://openalex.org/W2119027485","https://openalex.org/W2125029076","https://openalex.org/W2143825552","https://openalex.org/W2145100181","https://openalex.org/W2162742404"],"related_works":["https://openalex.org/W2375480909","https://openalex.org/W2353314428","https://openalex.org/W2012019886","https://openalex.org/W2166090428","https://openalex.org/W2381021552","https://openalex.org/W2354749003","https://openalex.org/W2377121353","https://openalex.org/W2350529538","https://openalex.org/W2366015234","https://openalex.org/W2034625591"],"abstract_inverted_index":{"BACKGROUND:":[0],"Identifying":[1],"corresponding":[2],"genes":[3,21],"(orthologs)":[4],"in":[5,12,22,50,97],"different":[6,23],"species":[7,24],"is":[8,162],"an":[9],"important":[10],"step":[11],"genome-wide":[13],"comparative":[14,82],"analysis.":[15],"In":[16,63],"particular,":[17],"one-to-one":[18,60],"correspondences":[19],"between":[20],"greatly":[25],"simplify":[26],"certain":[27],"problems":[28],"such":[29,158],"as":[30,159],"transfer":[31],"of":[32,45,77,84,116],"function":[33],"annotation":[34],"and":[35,56,93,119,133,136,148],"genome":[36],"rearrangement":[37],"studies.":[38],"Positional":[39],"homologs":[40,79,168],"are":[41],"the":[42,51,75,81,108,130,141,155],"direct":[43],"descendants":[44],"a":[46,68,114],"single":[47],"ancestral":[48],"gene":[49,94,120,149],"most":[52],"recent":[53],"common":[54],"ancestor":[55],"by":[57],"definition":[58],"form":[59],"correspondence.":[61],"RESULTS:":[62],"this":[64],"work,":[65],"we":[66],"present":[67],"simple":[69],"yet":[70],"effective":[71],"method":[72,89,128],"(BBH-LS)":[73],"for":[74],"identification":[76],"positional":[78,167],"from":[80],"analysis":[83],"two":[85],"genomes.":[86],"Our":[87],"BBH-LS":[88,106,139,161],"integrates":[90],"sequence":[91,117,147],"similarity":[92,96,118,122],"context":[95,121,150],"order":[98],"to":[99,113,129,154,164],"get":[100],"more":[101,166],"accurate":[102],"ortholog":[103],"assignments.":[104],"Specifically,":[105],"applies":[107],"bidirectional":[109],"best":[110,142],"hit":[111],"heuristic":[112],"combination":[115],"scores.":[123],"CONCLUSION:":[124],"We":[125],"applied":[126],"our":[127],"human,":[131],"mouse,":[132],"rat":[134],"genomes":[135],"found":[137],"that":[138],"produced":[140],"results":[143],"when":[144],"using":[145],"both":[146],"information":[151],"equally.":[152],"Compared":[153],"state-of-the-art":[156],"algorithms,":[157],"MSOAR2,":[160],"able":[163],"identify":[165],"with":[169],"fewer":[170],"false":[171],"positives.":[172]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}