{"id":"https://openalex.org/W2148312898","doi":"https://doi.org/10.1093/nar/gkp474","title":"Torque: topology-free querying of protein interaction networks","display_name":"Torque: topology-free querying of protein interaction networks","publication_year":2009,"publication_date":"2009-06-02","ids":{"openalex":"https://openalex.org/W2148312898","doi":"https://doi.org/10.1093/nar/gkp474","mag":"2148312898","pmid":"https://pubmed.ncbi.nlm.nih.gov/19491310"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkp474","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp474","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W106/3971433/gkp474.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W106/3971433/gkp474.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063965880","display_name":"Stefan Br\u00fcckner","orcid":"https://orcid.org/0000-0002-0885-8402"},"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/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"S. Bruckner","raw_affiliation_strings":["The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel. bruckner@tau.ac.il","The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA"],"affiliations":[{"raw_affiliation_string":"The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel. bruckner@tau.ac.il","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA","institution_ids":["https://openalex.org/I1297971548","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"]},{"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":["IL","US"],"is_corresponding":false,"raw_author_name":"F. Huffner","raw_affiliation_strings":["The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA"],"affiliations":[{"raw_affiliation_string":"The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA","institution_ids":["https://openalex.org/I1297971548","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"]},{"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","US"],"is_corresponding":false,"raw_author_name":"R. M. Karp","raw_affiliation_strings":["The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA"],"affiliations":[{"raw_affiliation_string":"The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA","institution_ids":["https://openalex.org/I1297971548","https://openalex.org/I16391192"]}]},{"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/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/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL","US"],"is_corresponding":false,"raw_author_name":"R. Shamir","raw_affiliation_strings":["The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA"],"affiliations":[{"raw_affiliation_string":"The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA","institution_ids":["https://openalex.org/I1297971548","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"]},{"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":["IL","US"],"is_corresponding":true,"raw_author_name":"R. Sharan","raw_affiliation_strings":["The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and","The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA"],"affiliations":[{"raw_affiliation_string":"The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"The Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel and 2International Computer Science Institute, 1947 Center St., Berkeley, CA 94704, USA","institution_ids":["https://openalex.org/I1297971548","https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5046958549","https://openalex.org/A5063965880"],"corresponding_institution_ids":["https://openalex.org/I1297971548","https://openalex.org/I16391192"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.8307,"has_fulltext":true,"cited_by_count":39,"citation_normalized_percentile":{"value":0.91018333,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"Web Server","first_page":"W106","last_page":"W108"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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":0.9994000196456909,"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":0.992900013923645,"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":0.9919000267982483,"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/biology","display_name":"Biology","score":0.8707783222198486},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.48241910338401794},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.43896040320396423},{"id":"https://openalex.org/keywords/torque","display_name":"Torque","score":0.41420865058898926},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3924694061279297},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.1913546919822693},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1763293445110321},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.16797739267349243},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.08659738302230835}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8707783222198486},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.48241910338401794},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.43896040320396423},{"id":"https://openalex.org/C144171764","wikidata":"https://www.wikidata.org/wiki/Q48103","display_name":"Torque","level":2,"score":0.41420865058898926},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3924694061279297},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1913546919822693},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1763293445110321},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.16797739267349243},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.08659738302230835},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":"D020539","descriptor_name":"Sequence Analysis, Protein","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":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gkp474","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp474","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W106/3971433/gkp474.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:19491310","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19491310","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.155.2035","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.155.2035","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_nar.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.352.2952","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.352.2952","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.user.tu-berlin.de/hueffner/network-query-jcb10.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.358.9710","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.358.9710","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/b0/2b/Nucleic_Acids_Res_2009_Jul_1_37(Web_Server_issue)_W106-W108.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.366.5488","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.366.5488","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.tau.ac.il/~roded/jtorque.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2703961","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2703961","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkp474","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp474","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W106/3971433/gkp474.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2148312898.pdf","grobid_xml":"https://content.openalex.org/works/W2148312898.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1966893452","https://openalex.org/W2032680335","https://openalex.org/W2061406919","https://openalex.org/W2097917188","https://openalex.org/W2112027455","https://openalex.org/W2139343285","https://openalex.org/W2159675211","https://openalex.org/W2167222948","https://openalex.org/W2193000389"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":{"TORQUE":[0,85],"is":[1,111],"a":[2,19,24,28,34,53,68],"tool":[3],"for":[4,77,114],"cross-species":[5],"querying":[6],"of":[7,21,45,56,71,90,102],"protein-protein":[8],"interaction":[9],"networks.":[10],"It":[11,97],"aims":[12],"to":[13,62,104],"answer":[14],"the":[15,42,63,72,91,94],"following":[16],"question:":[17],"given":[18],"set":[20,55],"proteins":[22,57,65],"constituting":[23],"known":[25],"complex":[26,36],"or":[27,37],"pathway":[29,38],"in":[30,41],"one":[31],"species,":[32],"can":[33,98],"similar":[35,61],"be":[39],"found":[40],"protein":[43],"network":[44],"another":[46],"species?":[47],"To":[48],"this":[49],"end,":[50],"Torque":[51,108],"seeks":[52],"matching":[54],"that":[58],"are":[59],"sequence":[60],"query":[64,95],"and":[66,80],"span":[67],"connected":[69],"region":[70],"target":[73],"network,":[74],"while":[75],"allowing":[76],"both":[78],"insertions":[79],"deletions.":[81],"Unlike":[82],"existing":[83],"approaches,":[84],"does":[86],"not":[87],"require":[88],"knowledge":[89],"interconnections":[92],"among":[93],"proteins.":[96,106],"handle":[99],"large":[100],"queries":[101],"up":[103],"25":[105],"The":[107],"web":[109],"server":[110],"freely":[112],"available":[113],"use":[115],"at":[116],"http://www.cs.tau.ac.il/~bnet/torque.html.":[117]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":7}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
