{"id":"https://openalex.org/W1596571240","doi":"https://doi.org/10.1007/978-3-642-02008-7_6","title":"Topology-Free Querying of Protein Interaction Networks","display_name":"Topology-Free Querying of Protein Interaction Networks","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W1596571240","doi":"https://doi.org/10.1007/978-3-642-02008-7_6","mag":"1596571240","pmid":"https://pubmed.ncbi.nlm.nih.gov/20377443"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-642-02008-7_6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-02008-7_6","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://acgt.cs.tau.ac.il/papers/torque_RECOMB.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002721305","display_name":"Sharon Bruckner","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Sharon Bruckner","raw_affiliation_strings":["School of Computer Science, Tel Aviv University, Tel Aviv, Israel","Tel Aviv University, School of Computer Science, 69978, Tel Aviv, Israel#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Tel Aviv University, School of Computer Science, 69978, Tel Aviv, Israel#TAB#","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063644073","display_name":"Falk H\u00fcffner","orcid":"https://orcid.org/0000-0003-0017-1881"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Falk H\u00fcffner","raw_affiliation_strings":["School of Computer Science, Tel Aviv University, Tel Aviv, Israel","Tel Aviv University, School of Computer Science, 69978, Tel Aviv, Israel#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Tel Aviv University, School of Computer Science, 69978, Tel Aviv, Israel#TAB#","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard M. Karp","raw_affiliation_strings":["International Computer Science Institute, Berkeley, California","International Computer Science Institute, 1947 Center St, Berkeley, CA 94704, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"International Computer Science Institute, Berkeley, California","institution_ids":["https://openalex.org/I1297971548"]},{"raw_affiliation_string":"International Computer Science Institute, 1947 Center St, Berkeley, CA 94704, USA#TAB#","institution_ids":["https://openalex.org/I1297971548"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038806020","display_name":"Ron Shamir","orcid":"https://orcid.org/0000-0003-1889-9870"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Ron Shamir","raw_affiliation_strings":["School of Computer Science, Tel Aviv University, Tel Aviv, Israel","Tel Aviv University, School of Computer Science, 69978, Tel Aviv, Israel#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Tel Aviv University, School of Computer Science, 69978, Tel Aviv, Israel#TAB#","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046958549","display_name":"Roded Sharan","orcid":"https://orcid.org/0000-0001-8363-4882"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Roded Sharan","raw_affiliation_strings":["School of Computer Science, Tel Aviv University, Tel Aviv, Israel","Tel Aviv University, School of Computer Science, 69978, Tel Aviv, Israel#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Tel Aviv University, School of Computer Science, 69978, Tel Aviv, Israel#TAB#","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5002721305"],"corresponding_institution_ids":["https://openalex.org/I16391192"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":0.1312,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.51186267,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"17","issue":"3","first_page":"237","last_page":"252"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983999729156494,"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":0.9983999729156494,"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":0.9843000173568726,"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":0.9736999869346619,"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/topology","display_name":"Topology (electrical circuits)","score":0.6302691698074341},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6098441481590271},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5735388994216919},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.5698384046554565},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5258477330207825},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4329388439655304},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3739166855812073},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3572532534599304},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20462533831596375},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.16399583220481873},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.12141886353492737}],"concepts":[{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.6302691698074341},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6098441481590271},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5735388994216919},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.5698384046554565},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5258477330207825},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4329388439655304},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3739166855812073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3572532534599304},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20462533831596375},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.16399583220481873},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.12141886353492737},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D006801","descriptor_name":"Humans","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1007/978-3-642-02008-7_6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-02008-7_6","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"doi:10.1089/cmb.2009.0170","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2009.0170","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:20377443","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20377443","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:10.1.1.155.3898","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.155.3898","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.math.tau.ac.il/~roded/torque.pdf","raw_type":"text"},{"id":"mag:1596571240","is_oa":true,"landing_page_url":"http://acgt.cs.tau.ac.il/papers/torque_RECOMB.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":null,"is_accepted":false,"is_published":null,"raw_source_name":"Nucleic Acids Research","raw_type":null}],"best_oa_location":{"id":"mag:1596571240","is_oa":true,"landing_page_url":"http://acgt.cs.tau.ac.il/papers/torque_RECOMB.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":null,"is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research","raw_type":null},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6600000262260437,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W107544894","https://openalex.org/W1517036688","https://openalex.org/W1565474750","https://openalex.org/W1602427246","https://openalex.org/W1876024155","https://openalex.org/W1966893452","https://openalex.org/W1970737407","https://openalex.org/W1994803330","https://openalex.org/W2003652380","https://openalex.org/W2029230311","https://openalex.org/W2040411864","https://openalex.org/W2042984464","https://openalex.org/W2045326192","https://openalex.org/W2050721857","https://openalex.org/W2061406919","https://openalex.org/W2068938373","https://openalex.org/W2080024158","https://openalex.org/W2101181377","https://openalex.org/W2102057828","https://openalex.org/W2103017472","https://openalex.org/W2104009289","https://openalex.org/W2104724853","https://openalex.org/W2106202847","https://openalex.org/W2106913956","https://openalex.org/W2109248504","https://openalex.org/W2110065044","https://openalex.org/W2112027455","https://openalex.org/W2116117181","https://openalex.org/W2121773288","https://openalex.org/W2125179362","https://openalex.org/W2132582966","https://openalex.org/W2133294187","https://openalex.org/W2134672568","https://openalex.org/W2139343285","https://openalex.org/W2148043260","https://openalex.org/W2148312898","https://openalex.org/W2149700511","https://openalex.org/W2152336513","https://openalex.org/W2159675211","https://openalex.org/W2166574880","https://openalex.org/W2167222948","https://openalex.org/W2296148711","https://openalex.org/W3145128584","https://openalex.org/W4233437719","https://openalex.org/W4409798803"],"related_works":["https://openalex.org/W2193000389","https://openalex.org/W2148312898","https://openalex.org/W2171038145","https://openalex.org/W1871425200","https://openalex.org/W3157049006","https://openalex.org/W2042984464","https://openalex.org/W2524167673","https://openalex.org/W2138756154","https://openalex.org/W1968340748","https://openalex.org/W2849719624","https://openalex.org/W2053238682","https://openalex.org/W1552512571","https://openalex.org/W2122961704","https://openalex.org/W1576019879","https://openalex.org/W2146529782","https://openalex.org/W2897734415","https://openalex.org/W2108881049","https://openalex.org/W2118656799","https://openalex.org/W3194156258","https://openalex.org/W3047995329"],"abstract_inverted_index":{"In":[0],"the":[1,24,36,52,56,59,107,116,135,153],"network":[2,20,60],"querying":[3,81],"problem,":[4,76],"one":[5],"is":[6,26,69],"given":[7],"a":[8,17,79,88,92,98,112],"protein":[9],"complex":[10],"or":[11,43],"pathway":[12],"of":[13,21,30,40,51,55,61,94,101,115],"species":[14,22,62],"A":[15],"and":[16,110,122,130,146,157],"protein-protein":[18],"interaction":[19,53],"B;":[23],"goal":[25],"to":[27,35,106,152],"identify":[28],"subnetworks":[29],"B":[31],"that":[32,103,179],"are":[33,104,180],"similar":[34],"query":[37,57,108],"in":[38,58,65],"terms":[39],"sequence,":[41],"topology,":[42],"both.":[44],"Existing":[45],"approaches":[46],"mostly":[47],"depend":[48],"on":[49],"knowledge":[50],"topology":[54,68],"A;":[63],"however,":[64],"practice,":[66],"this":[67,75],"often":[70],"not":[71],"known.":[72],"To":[73],"address":[74],"we":[77,84,149],"develop":[78],"topology-free":[80,166],"algorithm,":[82],"which":[83],"call":[85],"Torque.":[86],"Given":[87],"query,":[89],"represented":[90],"as":[91],"set":[93,100],"proteins,":[95],"Torque":[96,140,169],"seeks":[97],"matching":[99],"proteins":[102,109],"sequence-similar":[105],"span":[111],"connected":[113],"region":[114],"network,":[117],"while":[118,176],"allowing":[119],"both":[120],"insertions":[121],"deletions.":[123],"The":[124],"algorithm":[125],"uses":[126],"alternatively":[127],"dynamic":[128],"programming":[129,133],"integer":[131],"linear":[132],"for":[134],"search":[136],"task.":[137],"We":[138],"test":[139],"with":[141,158],"queries":[142,159],"from":[143,160],"yeast,":[144],"fly,":[145],"human,":[147],"where":[148,164],"compare":[150],"it":[151],"QNet":[154],"topology-based":[155],"approach,":[156],"less":[161],"studied":[162],"species,":[163],"only":[165],"algorithms":[167],"apply.":[168],"detects":[170],"many":[171],"more":[172],"matches":[173],"than":[174],"QNet,":[175],"giving":[177],"results":[178],"highly":[181],"functionally":[182],"coherent.":[183]},"counts_by_year":[{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
