{"id":"https://openalex.org/W2135984873","doi":"https://doi.org/10.1093/bioinformatics/bti723","title":"Inferring functional information from domain co-evolution","display_name":"Inferring functional information from domain co-evolution","publication_year":2005,"publication_date":"2005-11-13","ids":{"openalex":"https://openalex.org/W2135984873","doi":"https://doi.org/10.1093/bioinformatics/bti723","mag":"2135984873","pmid":"https://pubmed.ncbi.nlm.nih.gov/16301205"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti723","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti723","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/1/40/48838474/bioinformatics_22_1_40.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/1/40/48838474/bioinformatics_22_1_40.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101499793","display_name":"Yo-Han Kim","orcid":"https://orcid.org/0000-0002-2699-2496"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yohan Kim","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California at San Diego 1 \u00a0 1 \u00a0 \u00a0 La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California at San Diego 1 \u00a0 1 \u00a0 \u00a0 La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035558591","display_name":"Mehmet Koyut\u00fcrk","orcid":"https://orcid.org/0000-0002-3434-5512"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mehmet Koyut\u00fcrk","raw_affiliation_strings":["Department of Computer Sciences, Purdue University 2 \u00a0 2 \u00a0 \u00a0 West Lafayette, IN 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, Purdue University 2 \u00a0 2 \u00a0 \u00a0 West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014039394","display_name":"Umut Topkara","orcid":null},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Umut Topkara","raw_affiliation_strings":["Department of Computer Sciences, Purdue University 2 \u00a0 2 \u00a0 \u00a0 West Lafayette, IN 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, Purdue University 2 \u00a0 2 \u00a0 \u00a0 West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019202832","display_name":"Ananth Grama","orcid":"https://orcid.org/0000-0002-9378-9244"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ananth Grama","raw_affiliation_strings":["Department of Computer Sciences, Purdue University 2 \u00a0 2 \u00a0 \u00a0 West Lafayette, IN 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, Purdue University 2 \u00a0 2 \u00a0 \u00a0 West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063396453","display_name":"Shankar Subramaniam","orcid":"https://orcid.org/0000-0002-8059-4659"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shankar Subramaniam","raw_affiliation_strings":["Department of Bioengineering, University of California at San Diego 3 \u00a0 3 \u00a0 \u00a0 La Jolla, CA 92093, USA","Department of Chemistry and Biochemistry, University of California at San Diego 1 \u00a0 1 \u00a0 \u00a0 La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California at San Diego 3 \u00a0 3 \u00a0 \u00a0 La Jolla, CA 92093, USA","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California at San Diego 1 \u00a0 1 \u00a0 \u00a0 La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5063396453"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1371,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.7656453,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"22","issue":"1","first_page":"40","last_page":"49"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.3165999948978424,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.3165999948978424,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.24539999663829803,"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":0.23270000517368317,"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/domain","display_name":"Domain (mathematical analysis)","score":0.6695678234100342},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6315106153488159},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5965508818626404},{"id":"https://openalex.org/keywords/coevolution","display_name":"Coevolution","score":0.5346020460128784},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5261028409004211},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.515687108039856},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.4985082149505615},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4559429883956909},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43444889783859253},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.43377017974853516},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.37510204315185547},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3152374029159546},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.28085440397262573},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18171045184135437},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17010024189949036},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16331765055656433}],"concepts":[{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.6695678234100342},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6315106153488159},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5965508818626404},{"id":"https://openalex.org/C33009525","wikidata":"https://www.wikidata.org/wiki/Q208841","display_name":"Coevolution","level":2,"score":0.5346020460128784},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5261028409004211},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.515687108039856},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.4985082149505615},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4559429883956909},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43444889783859253},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.43377017974853516},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37510204315185547},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3152374029159546},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.28085440397262573},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18171045184135437},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17010024189949036},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16331765055656433},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000072236","descriptor_name":"Methyl-Accepting Chemotaxis Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072236","descriptor_name":"Methyl-Accepting Chemotaxis Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072236","descriptor_name":"Methyl-Accepting Chemotaxis Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti723","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti723","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/1/40/48838474/bioinformatics_22_1_40.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16301205","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16301205","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti723","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti723","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/1/40/48838474/bioinformatics_22_1_40.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6499999761581421}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1567209750","https://openalex.org/W1966421023","https://openalex.org/W1980578041","https://openalex.org/W1991071802","https://openalex.org/W1995117714","https://openalex.org/W2008630890","https://openalex.org/W2009391447","https://openalex.org/W2014090222","https://openalex.org/W2037036397","https://openalex.org/W2046618236","https://openalex.org/W2057885377","https://openalex.org/W2065304353","https://openalex.org/W2065970966","https://openalex.org/W2084619201","https://openalex.org/W2088480418","https://openalex.org/W2099279481","https://openalex.org/W2104315543","https://openalex.org/W2107424557","https://openalex.org/W2108407398","https://openalex.org/W2111361043","https://openalex.org/W2113654464","https://openalex.org/W2116543222","https://openalex.org/W2141885858","https://openalex.org/W2142237411","https://openalex.org/W2146312020","https://openalex.org/W2158714788","https://openalex.org/W2167869241","https://openalex.org/W4210400672","https://openalex.org/W4237572013","https://openalex.org/W4252706339","https://openalex.org/W6677582213"],"related_works":["https://openalex.org/W4385298573","https://openalex.org/W2105859129","https://openalex.org/W2093176106","https://openalex.org/W3165639034","https://openalex.org/W2374348541","https://openalex.org/W2119296079","https://openalex.org/W2896674752","https://openalex.org/W2767173479","https://openalex.org/W2952660917","https://openalex.org/W401507264"],"abstract_inverted_index":{"MOTIVATION:":[0],"Co-evolution":[1],"is":[2,67,80],"a":[3,61,71,93],"powerful":[4],"mechanism":[5],"for":[6,83,141],"understanding":[7],"protein":[8,58],"function.":[9],"Prior":[10],"work":[11],"in":[12,75],"this":[13,43,78],"area":[14],"has":[15],"shown":[16],"that":[17,30,55,70,98,121,129],"co-evolving":[18,119,155],"proteins":[19,145,158],"are":[20,46,175],"more":[21],"likely":[22],"to":[23,117,124,165],"share":[24],"the":[25,39,48,56,112,130,142],"same":[26],"function":[27],"than":[28],"those":[29],"do":[31],"not":[32,81],"because":[33],"of":[34,38,50,103,107,137,151,157,173],"functional":[35,139],"constraints.":[36],"Many":[37],"efforts":[40],"founded":[41],"on":[42],"observation,":[44],"however,":[45],"at":[47],"level":[49],"entire":[51],"sequences,":[52],"implicitly":[53],"assuming":[54],"complete":[57],"sequence":[59],"follows":[60],"single":[62],"evolutionary":[63],"trajectory.":[64],"Since":[65],"it":[66],"well":[68],"known":[69,138],"domain":[72,110],"can":[73,133],"exist":[74],"various":[76],"contexts,":[77],"assumption":[79],"valid":[82],"numerous":[84],"multi-domain":[85],"proteins.":[86,105],"Motivated":[87],"by":[88,160,177],"these":[89],"observations,":[90],"we":[91],"introduce":[92],"novel":[94],"technique":[95],"called":[96],"Coevolutionary-Matrix":[97,131],"captures":[99],"co-evolution":[100],"between":[101],"regions":[102,120,156],"two":[104],"Instead":[106],"using":[108],"existing":[109,178],"information,":[111],"method":[113,132,162],"exploits":[114],"residue-level":[115],"conservation":[116],"identify":[118],"might":[122],"correspond":[123],"domains.":[125],"RESULTS:":[126],"We":[127],"show":[128],"detect":[134],"greater":[135],"number":[136],"associations":[140],"Escherichia":[143],"coli":[144],"when":[146],"compared":[147],"with":[148],"earlier":[149],"implementations":[150],"phylogenetic":[152],"profiles.":[153],"Furthermore,":[154],"detected":[159],"our":[161],"enable":[163],"us":[164],"make":[166],"hypotheses":[167],"about":[168],"their":[169],"specific":[170],"functions,":[171],"many":[172],"which":[174],"supported":[176],"biochemical":[179],"studies.":[180]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}