{"id":"https://openalex.org/W2169906287","doi":"https://doi.org/10.1093/bioinformatics/btl130","title":"Integrating multi-attribute similarity networks for robust representation of the protein space","display_name":"Integrating multi-attribute similarity networks for robust representation of the protein space","publication_year":2006,"publication_date":"2006-04-04","ids":{"openalex":"https://openalex.org/W2169906287","doi":"https://doi.org/10.1093/bioinformatics/btl130","mag":"2169906287","pmid":"https://pubmed.ncbi.nlm.nih.gov/16595556"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl130","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl130","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1585/16851509/btl130.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/22/13/1585/16851509/btl130.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056984579","display_name":"Orhan \u00c7amo\u01e7lu","orcid":null},"institutions":[{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Orhan \u00c7amo\u011flu","raw_affiliation_strings":["Department of Computer Science, University of California 1 \u00a0 1 \u00a0 \u00a0 Santa Barbara, CA 93106, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California 1 \u00a0 1 \u00a0 \u00a0 Santa Barbara, CA 93106, USA","institution_ids":["https://openalex.org/I154570441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045764563","display_name":"Tolga Can","orcid":"https://orcid.org/0000-0002-5532-0154"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Tolga Can","raw_affiliation_strings":["Department of Computer Engineering, Middle East Technical University 2 \u00a0 2 \u00a0 \u00a0 06531, Ankara, Turkey"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Middle East Technical University 2 \u00a0 2 \u00a0 \u00a0 06531, Ankara, Turkey","institution_ids":["https://openalex.org/I201799495"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036639779","display_name":"Ambuj K. Singh","orcid":"https://orcid.org/0000-0002-1997-7140"},"institutions":[{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ambuj K. Singh","raw_affiliation_strings":["Department of Computer Science, University of California 1 \u00a0 1 \u00a0 \u00a0 Santa Barbara, CA 93106, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California 1 \u00a0 1 \u00a0 \u00a0 Santa Barbara, CA 93106, USA","institution_ids":["https://openalex.org/I154570441"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5056984579"],"corresponding_institution_ids":["https://openalex.org/I154570441"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8139,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.71391976,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"22","issue":"13","first_page":"1585","last_page":"1592"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9990000128746033,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9990000128746033,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9976999759674072,"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":0.9966999888420105,"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/representation","display_name":"Representation (politics)","score":0.7462859749794006},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.7247698307037354},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6571992635726929},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.5798786282539368},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41023656725883484},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3948069214820862}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.7462859749794006},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7247698307037354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6571992635726929},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5798786282539368},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41023656725883484},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3948069214820862},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"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":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"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":"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, 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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btl130","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl130","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1585/16851509/btl130.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:16595556","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16595556","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},{"id":"pmh:oai:open.metu.edu.tr:11511/35619","is_oa":true,"landing_page_url":"https://hdl.handle.net/11511/35619","pdf_url":null,"source":{"id":"https://openalex.org/S4306402495","display_name":"OpenMETU (Middle East Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201799495","host_organization_name":"Middle East Technical University","host_organization_lineage":["https://openalex.org/I201799495"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl130","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl130","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1585/16851509/btl130.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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2169906287.pdf","grobid_xml":"https://content.openalex.org/works/W2169906287.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W648165475","https://openalex.org/W1504035679","https://openalex.org/W1514107797","https://openalex.org/W1542652324","https://openalex.org/W1576213419","https://openalex.org/W1755360231","https://openalex.org/W1973714307","https://openalex.org/W1996357466","https://openalex.org/W2007018477","https://openalex.org/W2013502943","https://openalex.org/W2021312899","https://openalex.org/W2022058405","https://openalex.org/W2023790301","https://openalex.org/W2041862730","https://openalex.org/W2050330741","https://openalex.org/W2080587643","https://openalex.org/W2082442678","https://openalex.org/W2085277871","https://openalex.org/W2095318832","https://openalex.org/W2097282516","https://openalex.org/W2107425660","https://openalex.org/W2108067237","https://openalex.org/W2109781945","https://openalex.org/W2121950477","https://openalex.org/W2122837498","https://openalex.org/W2127648442","https://openalex.org/W2128036349","https://openalex.org/W2128817214","https://openalex.org/W2130479394","https://openalex.org/W2133075481","https://openalex.org/W2133657429","https://openalex.org/W2139240863","https://openalex.org/W2141885858","https://openalex.org/W2144686793","https://openalex.org/W2149255331","https://openalex.org/W2151831732","https://openalex.org/W2152326664","https://openalex.org/W2153635508","https://openalex.org/W2170512680","https://openalex.org/W3120421331","https://openalex.org/W4210400672","https://openalex.org/W4299670631","https://openalex.org/W6630222208","https://openalex.org/W6630727257","https://openalex.org/W6634338208","https://openalex.org/W6653629126","https://openalex.org/W6676236601","https://openalex.org/W6678450398","https://openalex.org/W6684822707"],"related_works":["https://openalex.org/W2062195135","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/W2795079307"],"abstract_inverted_index":{"We":[0,85],"propose":[1],"a":[2,42,47,92,100,107,132],"novel":[3,108],"approach":[4],"for":[5,103],"analyzing":[6],"multi-attribute":[7,20],"similarity":[8,30,37,71],"networks":[9],"by":[10,24,129],"combining":[11,25],"random":[12,58],"walks":[13],"on":[14],"graphs":[15],"with":[16,131],"Bayesian":[17,93,101],"theory.":[18],"A":[19],"network":[21,56],"is":[22,78],"created":[23],"sequence":[26],"and":[27,73,115],"structure":[28],"based":[29],"measures.":[31],"For":[32],"each":[33],"attribute":[34,118],"of":[35,44,64,69,106,126],"the":[36,55,65,70,88,124],"network,":[38,72],"one":[39],"can":[40],"compute":[41],"measure":[43],"affinity":[45],"from":[46],"given":[48],"protein":[49,53],"to":[50,80],"every":[51],"other":[52],"in":[54],"using":[57,91],"walks.":[59],"This":[60],"process":[61],"makes":[62],"use":[63],"implicit":[66],"clustering":[67],"information":[68,135],"we":[74,98,110,122],"show":[75],"that":[76],"it":[77],"superior":[79],"naive,":[81],"local":[82],"ranking":[83],"methods.":[84],"then":[86],"combine":[87],"computed":[89],"affinities":[90],"framework.":[94],"In":[95,120],"particular,":[96],"when":[97],"train":[99],"model":[102],"automated":[104],"classification":[105,113],"protein,":[109],"achieve":[111],"high":[112],"accuracy":[114],"outperform":[116],"single":[117],"networks.":[119],"addition,":[121],"demonstrate":[123],"effectiveness":[125],"our":[127],"technique":[128],"comparison":[130],"competing":[133],"kernel-based":[134],"integration":[136],"approach.":[137]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}