{"id":"https://openalex.org/W2112381943","doi":"https://doi.org/10.1093/bioinformatics/btp297","title":"Structure discovery in PPI networks using pattern-based network decomposition","display_name":"Structure discovery in PPI networks using pattern-based network decomposition","publication_year":2009,"publication_date":"2009-05-15","ids":{"openalex":"https://openalex.org/W2112381943","doi":"https://doi.org/10.1093/bioinformatics/btp297","mag":"2112381943","pmid":"https://pubmed.ncbi.nlm.nih.gov/19447784"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp297","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp297","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058417675","display_name":"Philip Bachman","orcid":null},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Philip Bachman","raw_affiliation_strings":["1 Department of Computer Science and 2 Department of Molecular Biology, University of Texas at Dallas, Richardson, TX 75083-0688","Department of Computer Science and Department of Molecular Biology, University of Texas at Dallas, Richardson, TX 75083-0688, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and 2 Department of Molecular Biology, University of Texas at Dallas, Richardson, TX 75083-0688","institution_ids":["https://openalex.org/I162577319"]},{"raw_affiliation_string":"Department of Computer Science and Department of Molecular Biology, University of Texas at Dallas, Richardson, TX 75083-0688, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100414171","display_name":"Ying Liu","orcid":"https://orcid.org/0000-0002-2391-5970"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ying Liu","raw_affiliation_strings":["1 Department of Computer Science and 2 Department of Molecular Biology, University of Texas at Dallas, Richardson, TX 75083-0688"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and 2 Department of Molecular Biology, University of Texas at Dallas, Richardson, TX 75083-0688","institution_ids":["https://openalex.org/I162577319"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5058417675"],"corresponding_institution_ids":["https://openalex.org/I162577319"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0498,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.75993087,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"25","issue":"14","first_page":"1814","last_page":"1821"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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":0.9993000030517578,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9939000010490417,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9930999875068665,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7187509536743164},{"id":"https://openalex.org/keywords/modularity","display_name":"Modularity (biology)","score":0.6569104194641113},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.521960437297821},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5214868783950806},{"id":"https://openalex.org/keywords/graph-isomorphism","display_name":"Graph isomorphism","score":0.5104628801345825},{"id":"https://openalex.org/keywords/protein-interaction-networks","display_name":"Protein Interaction Networks","score":0.5035871863365173},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5023148059844971},{"id":"https://openalex.org/keywords/network-motif","display_name":"Network motif","score":0.4848438501358032},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.45355042815208435},{"id":"https://openalex.org/keywords/complex-network","display_name":"Complex network","score":0.45346322655677795},{"id":"https://openalex.org/keywords/network-structure","display_name":"Network structure","score":0.4404720962047577},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4250791370868683},{"id":"https://openalex.org/keywords/decomposition","display_name":"Decomposition","score":0.410244882106781},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33918434381484985},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.2917541265487671},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.1572551131248474},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11769753694534302}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7187509536743164},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.6569104194641113},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.521960437297821},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5214868783950806},{"id":"https://openalex.org/C61665672","wikidata":"https://www.wikidata.org/wiki/Q303100","display_name":"Graph isomorphism","level":4,"score":0.5104628801345825},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.5035871863365173},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5023148059844971},{"id":"https://openalex.org/C60723933","wikidata":"https://www.wikidata.org/wiki/Q7001080","display_name":"Network motif","level":3,"score":0.4848438501358032},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.45355042815208435},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.45346322655677795},{"id":"https://openalex.org/C2988224531","wikidata":"https://www.wikidata.org/wiki/Q20830730","display_name":"Network structure","level":2,"score":0.4404720962047577},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4250791370868683},{"id":"https://openalex.org/C124681953","wikidata":"https://www.wikidata.org/wiki/Q339062","display_name":"Decomposition","level":2,"score":0.410244882106781},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33918434381484985},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2917541265487671},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.1572551131248474},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11769753694534302},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C203776342","wikidata":"https://www.wikidata.org/wiki/Q1378376","display_name":"Line graph","level":3,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"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":"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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"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":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp297","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp297","pdf_url":null,"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:19447784","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19447784","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":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W135031542","https://openalex.org/W1553420678","https://openalex.org/W1556691015","https://openalex.org/W1579879095","https://openalex.org/W1973322735","https://openalex.org/W1990144966","https://openalex.org/W1999227640","https://openalex.org/W2023096047","https://openalex.org/W2040411864","https://openalex.org/W2047693963","https://openalex.org/W2057680921","https://openalex.org/W2065769502","https://openalex.org/W2066235893","https://openalex.org/W2066506515","https://openalex.org/W2069898971","https://openalex.org/W2081931663","https://openalex.org/W2086595847","https://openalex.org/W2097876388","https://openalex.org/W2098045561","https://openalex.org/W2099982459","https://openalex.org/W2104812688","https://openalex.org/W2124166542","https://openalex.org/W2130687290","https://openalex.org/W2136850043","https://openalex.org/W2137786672","https://openalex.org/W2139343285","https://openalex.org/W2141629057","https://openalex.org/W2144885342","https://openalex.org/W2148762636","https://openalex.org/W2152495216","https://openalex.org/W2153624566","https://openalex.org/W2161917555","https://openalex.org/W2164727176","https://openalex.org/W2164928285","https://openalex.org/W2166468869","https://openalex.org/W2168157678","https://openalex.org/W2899266716","https://openalex.org/W3103071483","https://openalex.org/W3103786587","https://openalex.org/W4236956086","https://openalex.org/W6605502080","https://openalex.org/W6633203230","https://openalex.org/W6643567790","https://openalex.org/W6674999918"],"related_works":["https://openalex.org/W2796517744","https://openalex.org/W2008014943","https://openalex.org/W2807926763","https://openalex.org/W2951915565","https://openalex.org/W15348386","https://openalex.org/W2090574217","https://openalex.org/W3119507950","https://openalex.org/W2113782798","https://openalex.org/W2323587325","https://openalex.org/W3175302423"],"abstract_inverted_index":{"In":[0],"this":[1,31],"article,":[2],"we":[3],"present":[4,26],"an":[5],"efficient":[6],"algorithm":[7],"for":[8,61],"performing":[9],"sub-graph":[10],"isomorphism":[11],"queries":[12],"on":[13],"a":[14,27,40,44],"network":[15,70],"and":[16,52],"show":[17],"its":[18],"computational":[19],"advantage":[20],"over":[21],"previous":[22],"methods.":[23],"We":[24],"also":[25],"novel":[28],"application":[29],"of":[30,33,39,48,54,64,71],"form":[32],"topological":[34],"search":[35],"which":[36],"permits":[37],"analysis":[38,58],"network's":[41],"structure":[42],"at":[43],"scale":[45],"between":[46],"that":[47,53],"individual":[49],"functional":[50],"modules":[51],"network-wide":[55],"properties.":[56],"This":[57],"provides":[59],"support":[60],"the":[62,68],"presence":[63],"hierarchical":[65],"modularity":[66],"in":[67],"PPI":[69],"Saccharomyces":[72],"cerevisiae.":[73]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
