{"id":"https://openalex.org/W2042984464","doi":"https://doi.org/10.1089/cmb.2007.0025","title":"Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm","display_name":"Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm","publication_year":2007,"publication_date":"2007-09-01","ids":{"openalex":"https://openalex.org/W2042984464","doi":"https://doi.org/10.1089/cmb.2007.0025","mag":"2042984464","pmid":"https://pubmed.ncbi.nlm.nih.gov/17803369"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2007.0025","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2007.0025","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077782872","display_name":"Manikandan Narayanan","orcid":"https://orcid.org/0000-0002-8490-4087"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manikandan Narayanan","raw_affiliation_strings":["Computer Science Division, University of California, Berkeley, California","Computer Science Division University of California, Berkeley, California 94720, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Division, University of California, Berkeley, California","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Computer Science Division University of California, Berkeley, California 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068875104","display_name":"Richard M. Karp","orcid":null},"institutions":[{"id":"https://openalex.org/I1297971548","display_name":"International Computer Science Institute","ror":"https://ror.org/01ewh7m12","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1297971548"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard M. Karp","raw_affiliation_strings":["Computer Science Division, University of California, Berkeley, California","International Computer Science Institute, Berkeley, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Division, University of California, Berkeley, California","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"International Computer Science Institute, Berkeley, California","institution_ids":["https://openalex.org/I1297971548"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.2632,"has_fulltext":false,"cited_by_count":66,"citation_normalized_percentile":{"value":0.87818975,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"14","issue":"7","first_page":"892","last_page":"907"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9876999855041504,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9700000286102295,"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/correctness","display_name":"Correctness","score":0.6938419938087463},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.6524991989135742},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6107380390167236},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6107065081596375},{"id":"https://openalex.org/keywords/social-connectedness","display_name":"Social connectedness","score":0.6041924953460693},{"id":"https://openalex.org/keywords/protein-interaction-networks","display_name":"Protein Interaction Networks","score":0.5702661275863647},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.534583330154419},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.49825477600097656},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.45871901512145996},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4356954097747803},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4030688405036926},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35741573572158813},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3422502875328064},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3392694294452667},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2633136808872223},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21777763962745667},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.17008757591247559},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16029876470565796}],"concepts":[{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.6938419938087463},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6524991989135742},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6107380390167236},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6107065081596375},{"id":"https://openalex.org/C201943243","wikidata":"https://www.wikidata.org/wiki/Q7551008","display_name":"Social connectedness","level":2,"score":0.6041924953460693},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.5702661275863647},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.534583330154419},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.49825477600097656},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.45871901512145996},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4356954097747803},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4030688405036926},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35741573572158813},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3422502875328064},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3392694294452667},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2633136808872223},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21777763962745667},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.17008757591247559},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16029876470565796},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"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":"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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:10.1089/cmb.2007.0025","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2007.0025","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:17803369","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17803369","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.243.3849","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.243.3849","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arxiv.org/pdf/q-bio/0702001v1.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.5600000023841858}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W85880394","https://openalex.org/W1644749979","https://openalex.org/W1793943890","https://openalex.org/W1966833356","https://openalex.org/W1967638691","https://openalex.org/W1971421925","https://openalex.org/W1984209790","https://openalex.org/W1984249061","https://openalex.org/W1993384523","https://openalex.org/W2011039300","https://openalex.org/W2103017472","https://openalex.org/W2107705503","https://openalex.org/W2124354935","https://openalex.org/W2127874029","https://openalex.org/W2130687290","https://openalex.org/W2134672568","https://openalex.org/W2136316164","https://openalex.org/W2136850043","https://openalex.org/W2154139219","https://openalex.org/W2159675211","https://openalex.org/W2160167256","https://openalex.org/W2162551958","https://openalex.org/W2166574880","https://openalex.org/W2171081680","https://openalex.org/W2986989272","https://openalex.org/W3147056755"],"related_works":["https://openalex.org/W2072806201","https://openalex.org/W2044343925","https://openalex.org/W2353139202","https://openalex.org/W4323896988","https://openalex.org/W3208326136","https://openalex.org/W2971267355","https://openalex.org/W2945365184","https://openalex.org/W4312816440","https://openalex.org/W4383860413","https://openalex.org/W4312266567"],"abstract_inverted_index":{"We":[0,71,170],"present":[1],"a":[2,68,94,105,148,161],"method":[3,23,74,121,144],"that":[4,60],"compares":[5],"the":[6,79,84,111,158,172,188],"protein":[7,18,81,91,118],"interaction":[8],"networks":[9],"of":[10,78,110,160,163,174],"two":[11,36,63,129],"species":[12,141],"to":[13,31,75,183],"detect":[14],"functionally":[15],"similar":[16],"(conserved)":[17],"modules":[19,114,165],"between":[20,35],"them.":[21],"The":[22],"is":[24,193],"based":[25,97],"on":[26,48,98],"an":[27],"algorithm":[28,44,53],"we":[29,156],"developed":[30],"identify":[32],"matching":[33,101],"subgraphs":[34,64],"graphs.":[37],"Unlike":[38],"previous":[39,130],"network":[40,82,131,175],"comparison":[41,132,176],"methods,":[42],"our":[43,73,120,143,168],"has":[45],"provable":[46],"guarantees":[47],"correctness":[49],"and":[50,66,88,100,125,140,186],"efficiency.":[51],"Our":[52],"framework":[54],"also":[55],"admits":[56],"quite":[57],"general":[58],"criteria":[59],"define":[61],"when":[62],"match":[65],"constitute":[67],"conserved":[69,113,164],"module.":[70],"apply":[72],"pairwise":[76],"comparisons":[77],"yeast":[80,117,181],"with":[83,104,124],"human,":[85],"fruit":[86],"fly":[87],"nematode":[89],"worm":[90],"networks,":[92],"using":[93],"lenient":[95],"criterion":[96],"connectedness":[99],"edges,":[102],"coupled":[103],"clustering":[106,151],"heuristic.":[107],"In":[108],"evaluations":[109],"detected":[112,166],"against":[115],"reference":[116],"complexes,":[119],"performs":[122,145],"competitively":[123],"sometimes":[126],"better":[127,146],"than":[128,147],"methods.":[133],"Further,":[134],"under":[135],"some":[136],"conditions":[137],"(proper":[138],"homolog":[139],"selection),":[142],"popular":[149],"single-species":[150],"method.":[152,169],"Beyond":[153],"these":[154],"evaluations,":[155],"discuss":[157],"biology":[159],"couple":[162],"by":[167],"demonstrate":[171],"utility":[173],"for":[177],"transferring":[178],"annotations":[179],"from":[180],"proteins":[182],"human":[184],"ones,":[185],"validate":[187],"predicted":[189],"annotations.":[190],"Supplemental":[191],"text":[192],"available":[194],"at":[195],"www.cs.berkeley.edu/":[196],"approximately":[197],"nmani/M-and-S/supplement.pdf.":[198]},"counts_by_year":[{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":6}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
