{"id":"https://openalex.org/W2135857985","doi":"https://doi.org/10.1093/bioinformatics/btm553","title":"BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks","display_name":"BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks","publication_year":2007,"publication_date":"2007-11-16","ids":{"openalex":"https://openalex.org/W2135857985","doi":"https://doi.org/10.1093/bioinformatics/btm553","mag":"2135857985","pmid":"https://pubmed.ncbi.nlm.nih.gov/18024474"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm553","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm553","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/876/49045923/bioinformatics_24_6_876.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/24/6/876/49045923/bioinformatics_24_6_876.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077253721","display_name":"Andre\u00ef Zinovyev","orcid":"https://orcid.org/0000-0002-9517-7284"},"institutions":[{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Andrei Zinovyev","raw_affiliation_strings":["Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, F-75248 Paris Cedex 05, France","Institut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, F-75248 Paris Cedex 05, France","institution_ids":["https://openalex.org/I80043"]},{"raw_affiliation_string":"Institut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France","institution_ids":["https://openalex.org/I80043"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091579624","display_name":"Eric Viara","orcid":null},"institutions":[{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Eric Viara","raw_affiliation_strings":["Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, F-75248 Paris Cedex 05, France","Institut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, F-75248 Paris Cedex 05, France","institution_ids":["https://openalex.org/I80043"]},{"raw_affiliation_string":"Institut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France","institution_ids":["https://openalex.org/I80043"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061154457","display_name":"Laurence Calzone","orcid":"https://orcid.org/0000-0002-7835-1148"},"institutions":[{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurence Calzone","raw_affiliation_strings":["Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, F-75248 Paris Cedex 05, France","Institut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, F-75248 Paris Cedex 05, France","institution_ids":["https://openalex.org/I80043"]},{"raw_affiliation_string":"Institut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France","institution_ids":["https://openalex.org/I80043"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062067186","display_name":"Emmanuel Barillot","orcid":"https://orcid.org/0000-0003-2724-2002"},"institutions":[{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Emmanuel Barillot","raw_affiliation_strings":["Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, F-75248 Paris Cedex 05, France","Institut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Curie, Service de Bioinformatique, 26 rue d\u2019Ulm, F-75248 Paris Cedex 05, France","institution_ids":["https://openalex.org/I80043"]},{"raw_affiliation_string":"Institut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France","institution_ids":["https://openalex.org/I80043"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5077253721"],"corresponding_institution_ids":["https://openalex.org/I80043"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.288,"has_fulltext":false,"cited_by_count":102,"citation_normalized_percentile":{"value":0.88223914,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"24","issue":"6","first_page":"876","last_page":"877"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.3982999920845032,"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":0.3982999920845032,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.23019999265670776,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.1881999969482422,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/plug-in","display_name":"Plug-in","score":0.8137272596359253},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.7883996367454529},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6513548493385315},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5947153568267822},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5923096537590027},{"id":"https://openalex.org/keywords/marie-curie","display_name":"Marie curie","score":0.4615253508090973},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.35546088218688965},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32158440351486206},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2637968063354492},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.061997562646865845}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.8137272596359253},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.7883996367454529},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6513548493385315},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5947153568267822},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5923096537590027},{"id":"https://openalex.org/C2993243194","wikidata":"https://www.wikidata.org/wiki/Q7186","display_name":"Marie curie","level":3,"score":0.4615253508090973},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.35546088218688965},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32158440351486206},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2637968063354492},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.061997562646865845},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0},{"id":"https://openalex.org/C105639569","wikidata":"https://www.wikidata.org/wiki/Q582577","display_name":"Economic policy","level":1,"score":0.0},{"id":"https://openalex.org/C2910001868","wikidata":"https://www.wikidata.org/wiki/Q458","display_name":"European union","level":2,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm553","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm553","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/876/49045923/bioinformatics_24_6_876.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:18024474","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18024474","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":{"id":"doi:10.1093/bioinformatics/btm553","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm553","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/876/49045923/bioinformatics_24_6_876.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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5199999809265137}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135857985.pdf"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1987242421","https://openalex.org/W2045478141","https://openalex.org/W2069162648","https://openalex.org/W2147714160","https://openalex.org/W2159675211","https://openalex.org/W2172102555"],"related_works":["https://openalex.org/W1833372769","https://openalex.org/W2128782793","https://openalex.org/W1994518768","https://openalex.org/W104010570","https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W4385891864","https://openalex.org/W4321472021","https://openalex.org/W2118851895","https://openalex.org/W1991339919"],"abstract_inverted_index":{"UNLABELLED:":[0],"BiNoM":[1,29,44,60,76,116],"(Biological":[2],"Network":[3],"Manager)":[4],"is":[5,45],"a":[6,31,36,79,83,88],"new":[7],"bioinformatics":[8],"software":[9,69],"that":[10],"significantly":[11],"facilitates":[12],"the":[13,16,62,119],"usage":[14],"and":[15,35,70,81,98,110,127],"analysis":[17,63],"of":[18,38,64,91,104,115],"biological":[19],"networks":[20,65],"in":[21],"standard":[22],"systems":[23],"biology":[24],"formats":[25],"(SBML,":[26],"SBGN,":[27],"BioPAX).":[28],"implements":[30],"full-featured":[32],"BioPAX":[33,42,51,74],"editor":[34],"method":[37],"'interfaces'":[39],"for":[40],"accessing":[41],"content.":[43],"able":[46],"to":[47,93],"work":[48],"with":[49,67,123],"huge":[50],"files":[52],"such":[53,95],"as":[54,78,82,96],"whole":[55],"pathway":[56],"databases.":[57],"In":[58],"addition,":[59],"allows":[61],"created":[66],"CellDesigner":[68],"their":[71],"conversion":[72],"into":[73,106],"format.":[75],"comes":[77],"library":[80],"Cytoscape":[84,94],"plugin":[85],"which":[86],"adds":[87],"rich":[89],"set":[90],"operations":[92,109],"path":[97],"cycle":[99],"analysis,":[100],"clustering":[101],"sub-networks,":[102],"decomposition":[103],"network":[105],"modules,":[107],"clipboard":[108],"others.":[111],"AVAILABILITY:":[112],"Last":[113],"version":[114],"distributed":[117],"under":[118],"LGPL":[120],"licence":[121],"together":[122],"documentation,":[124],"source":[125],"code":[126],"API":[128],"are":[129],"available":[130],"at":[131],"http://bioinfo.curie.fr/projects/binom":[132]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":13},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":14},{"year":2012,"cited_by_count":18}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
