{"id":"https://openalex.org/W1592034947","doi":"https://doi.org/10.1186/1471-2105-16-s8-a6","title":"Using coevolution to improve protein subfamily classification","display_name":"Using coevolution to improve protein subfamily classification","publication_year":2015,"publication_date":"2015-04-30","ids":{"openalex":"https://openalex.org/W1592034947","doi":"https://doi.org/10.1186/1471-2105-16-s8-a6","mag":"1592034947"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-16-s8-a6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s8-a6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S8-A6","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S8-A6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069445871","display_name":"Franco L. Simonetti","orcid":"https://orcid.org/0000-0002-6472-9998"},"institutions":[{"id":"https://openalex.org/I2801749607","display_name":"Fundaci\u00f3n Instituto Leloir","ror":"https://ror.org/0431v7h69","country_code":"AR","type":"facility","lineage":["https://openalex.org/I2801749607"]}],"countries":["AR"],"is_corresponding":true,"raw_author_name":"Franco Simonetti","raw_affiliation_strings":["Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina","Fundaci\u00f3n Instituto Leloir, , Buenos Aires, Argentina"],"affiliations":[{"raw_affiliation_string":"Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina","institution_ids":["https://openalex.org/I2801749607"]},{"raw_affiliation_string":"Fundaci\u00f3n Instituto Leloir, , Buenos Aires, Argentina","institution_ids":["https://openalex.org/I2801749607"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031009447","display_name":"Martin Banchero","orcid":null},"institutions":[{"id":"https://openalex.org/I2801749607","display_name":"Fundaci\u00f3n Instituto Leloir","ror":"https://ror.org/0431v7h69","country_code":"AR","type":"facility","lineage":["https://openalex.org/I2801749607"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Martin Banchero","raw_affiliation_strings":["Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina","Fundaci\u00f3n Instituto Leloir, , Buenos Aires, Argentina"],"affiliations":[{"raw_affiliation_string":"Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina","institution_ids":["https://openalex.org/I2801749607"]},{"raw_affiliation_string":"Fundaci\u00f3n Instituto Leloir, , Buenos Aires, Argentina","institution_ids":["https://openalex.org/I2801749607"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068676336","display_name":"Ariel Berenstein","orcid":"https://orcid.org/0000-0001-8540-5389"},"institutions":[{"id":"https://openalex.org/I24354313","display_name":"University of Buenos Aires","ror":"https://ror.org/0081fs513","country_code":"AR","type":"education","lineage":["https://openalex.org/I24354313"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Ariel J Berenstein","raw_affiliation_strings":["Universidad de Buenos Aires, Buenos Aires, Argentina"],"affiliations":[{"raw_affiliation_string":"Universidad de Buenos Aires, Buenos Aires, Argentina","institution_ids":["https://openalex.org/I24354313"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005988020","display_name":"Ariel Chernomoretz","orcid":"https://orcid.org/0000-0003-2675-353X"},"institutions":[{"id":"https://openalex.org/I24354313","display_name":"University of Buenos Aires","ror":"https://ror.org/0081fs513","country_code":"AR","type":"education","lineage":["https://openalex.org/I24354313"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Ariel Chernomoretz","raw_affiliation_strings":["Universidad de Buenos Aires, Buenos Aires, Argentina"],"affiliations":[{"raw_affiliation_string":"Universidad de Buenos Aires, Buenos Aires, Argentina","institution_ids":["https://openalex.org/I24354313"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000071168","display_name":"Cristina Marino\u2010Buslje","orcid":"https://orcid.org/0000-0002-6564-1920"},"institutions":[{"id":"https://openalex.org/I2801749607","display_name":"Fundaci\u00f3n Instituto Leloir","ror":"https://ror.org/0431v7h69","country_code":"AR","type":"facility","lineage":["https://openalex.org/I2801749607"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Cristina Marino Buslje","raw_affiliation_strings":["Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina","Fundaci\u00f3n Instituto Leloir, , Buenos Aires, Argentina"],"affiliations":[{"raw_affiliation_string":"Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina","institution_ids":["https://openalex.org/I2801749607"]},{"raw_affiliation_string":"Fundaci\u00f3n Instituto Leloir, , Buenos Aires, Argentina","institution_ids":["https://openalex.org/I2801749607"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5069445871"],"corresponding_institution_ids":["https://openalex.org/I2801749607"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.205,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.78027965,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"16","issue":"S8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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":0.9987999796867371,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9979000091552734,"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":0.9898999929428101,"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/subfamily","display_name":"Subfamily","score":0.8138957023620605},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6627165079116821},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.5082266330718994},{"id":"https://openalex.org/keywords/coevolution","display_name":"Coevolution","score":0.49517741799354553},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4866860508918762},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4860458970069885},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.44757795333862305},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4441399872303009},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.43911564350128174},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4342799484729767},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.4156586527824402},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39154431223869324},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.327064573764801},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2534497380256653},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.18677249550819397},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1512460708618164}],"concepts":[{"id":"https://openalex.org/C50929876","wikidata":"https://www.wikidata.org/wiki/Q164280","display_name":"Subfamily","level":3,"score":0.8138957023620605},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6627165079116821},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.5082266330718994},{"id":"https://openalex.org/C33009525","wikidata":"https://www.wikidata.org/wiki/Q208841","display_name":"Coevolution","level":2,"score":0.49517741799354553},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4866860508918762},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4860458970069885},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.44757795333862305},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4441399872303009},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.43911564350128174},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4342799484729767},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.4156586527824402},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39154431223869324},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.327064573764801},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2534497380256653},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.18677249550819397},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1512460708618164},{"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/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1471-2105-16-s8-a6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s8-a6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S8-A6","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":"pmh:oai:europepmc.org:3389585","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4423731","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:10.1186/1471-2105-16-s8-a6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s8-a6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S8-A6","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":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.7200000286102295}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1592034947.pdf","grobid_xml":"https://content.openalex.org/works/W1592034947.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1554866783","https://openalex.org/W1673546563","https://openalex.org/W2047437886","https://openalex.org/W2093176106","https://openalex.org/W2765585254","https://openalex.org/W2075451741","https://openalex.org/W2070693796","https://openalex.org/W2139240863","https://openalex.org/W2036521446","https://openalex.org/W2053803793"],"abstract_inverted_index":{"Background":[0],"The":[1,96],"common":[2,121],"approach":[3],"for":[4,27],"protein":[5,11,67],"subfamily":[6,35],"classification":[7,36],"relies":[8],"on":[9],"grouping":[10,29],"sequences":[12,30,108],"according":[13],"to":[14,41,55,102],"their":[15],"degree":[16],"of":[17,87,98,105,135],"similarity.":[18],"However,":[19],"there":[20],"is":[21,101],"no":[22],"single":[23,58],"sequence":[24,68],"similarity":[25],"threshold":[26],"accurately":[28],"into":[31],"isofunctional":[32],"groups.":[33],"Current":[34],"methods":[37,61],"use":[38],"bottom-up":[39],"clustering":[40],"construct":[42],"a":[43,57,84,110,117,120,133],"cluster":[44],"hierarchy,":[45],"then":[46],"cut":[47],"the":[48,51],"hierarchy":[49],"at":[50],"most":[52],"appropriate":[53],"locations":[54],"obtain":[56],"partitioning.":[59],"These":[60],"usually":[62,82],"integrate":[63],"data":[64],"such":[65],"as":[66],"similarity,":[69],"residue":[70],"conservation":[71],"within":[72,109,116,128],"groups":[73],"and":[74,92],"HMM":[75],"profiles.":[76],"Despite":[77],"this":[78,99],"straightforward":[79],"approach,":[80],"results":[81],"predict":[83],"great":[85],"number":[86],"subfamilies":[88],"with":[89],"few":[90],"members":[91],"limited":[93],"biological":[94],"meaning.":[95],"goal":[97],"study":[100],"identify":[103],"subsets":[104],"functionally":[106],"related":[107],"given":[111],"superfamily.":[112],"Since":[113],"all":[114],"proteins":[115],"superfamily":[118],"share":[119],"ancestor,":[122],"we":[123],"hypothesize":[124],"that":[125,138],"functional":[126],"diversity":[127],"superfamilies":[129],"has":[130],"arisen":[131],"through":[132],"series":[134],"concerted":[136],"changes":[137],"must":[139],"have":[140],"left":[141],"an":[142],"identifiable":[143],"coevolutionary":[144],"signal.":[145]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}