{"id":"https://openalex.org/W2145149978","doi":"https://doi.org/10.1093/bioinformatics/btr637","title":"Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter","display_name":"Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter","publication_year":2011,"publication_date":"2011-12-06","ids":{"openalex":"https://openalex.org/W2145149978","doi":"https://doi.org/10.1093/bioinformatics/btr637","mag":"2145149978","pmid":"https://pubmed.ncbi.nlm.nih.gov/22155862"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr637","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr637","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/2/290/48867640/bioinformatics_28_2_290.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/28/2/290/48867640/bioinformatics_28_2_290.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000113086","display_name":"Christopher W. Whelan","orcid":"https://orcid.org/0000-0001-8446-8468"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I4210164117","display_name":"Walker (United States)","ror":"https://ror.org/05hgh7849","country_code":"US","type":"company","lineage":["https://openalex.org/I4210164117"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christopher Whelan","raw_affiliation_strings":["Biomedical Engineering, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR 97006, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Engineering, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR 97006, USA","institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210164117"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023103090","display_name":"Kemal S\u00f6nmez","orcid":"https://orcid.org/0000-0002-2816-6438"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]},{"id":"https://openalex.org/I4210164117","display_name":"Walker (United States)","ror":"https://ror.org/05hgh7849","country_code":"US","type":"company","lineage":["https://openalex.org/I4210164117"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kemal S\u00f6nmez","raw_affiliation_strings":["Biomedical Engineering, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR 97006, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Engineering, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR 97006, USA","institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210164117"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5000113086"],"corresponding_institution_ids":["https://openalex.org/I165690674","https://openalex.org/I4210164117"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6557,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.69122074,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"28","issue":"2","first_page":"290","last_page":"291"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9886000156402588,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9868000149726868,"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/workflow","display_name":"Workflow","score":0.7949792146682739},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.789899468421936},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7285484075546265},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6690297722816467},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6471909284591675},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5158459544181824},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.5025746822357178},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46991080045700073},{"id":"https://openalex.org/keywords/software-tool","display_name":"Software tool","score":0.4426212012767792},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.43510860204696655},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23711365461349487},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2217230498790741},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.21432247757911682}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7949792146682739},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.789899468421936},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7285484075546265},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6690297722816467},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6471909284591675},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5158459544181824},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.5025746822357178},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46991080045700073},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.4426212012767792},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.43510860204696655},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23711365461349487},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2217230498790741},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.21432247757911682},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"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":"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":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btr637","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr637","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/2/290/48867640/bioinformatics_28_2_290.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:22155862","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22155862","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/btr637","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr637","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/2/290/48867640/bioinformatics_28_2_290.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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1849803292","https://openalex.org/W1966638085","https://openalex.org/W2049966951","https://openalex.org/W2104812688","https://openalex.org/W2120063363","https://openalex.org/W2124533460","https://openalex.org/W2148762636","https://openalex.org/W2153624566","https://openalex.org/W2159675211","https://openalex.org/W2898709021","https://openalex.org/W4293282039"],"related_works":["https://openalex.org/W2924735795","https://openalex.org/W2141346699","https://openalex.org/W2083975137","https://openalex.org/W2901655697","https://openalex.org/W2727283706","https://openalex.org/W4238786050","https://openalex.org/W1525985997","https://openalex.org/W108107911","https://openalex.org/W2161626927","https://openalex.org/W118100147"],"abstract_inverted_index":{"UNLABELLED:":[0],"Biological":[1],"network":[2,47,65],"analysis":[3,48],"can":[4,36,68,89,107],"be":[5,69,108],"enhanced":[6],"by":[7,71,74],"examining":[8],"the":[9,14,17,46,61,75,111],"connections":[10],"between":[11],"nodes":[12],"and":[13,88,115],"rest":[15],"of":[16,54,64],"network.":[18],"For":[19],"this":[20],"purpose":[21],"we":[22],"have":[23],"developed":[24],"GraphletCounter,":[25],"an":[26],"open-source":[27],"software":[28],"tool":[29,77],"for":[30,83,93],"computing":[31],"graphlet":[32,62,81,91],"degree":[33],"signatures":[34,63,82],"that":[35],"operate":[37],"on":[38],"its":[39,57],"own":[40],"or":[41],"as":[42],"a":[43],"plug-in":[44],"to":[45,59],"environment":[49],"Cytoscape.":[50],"A":[51],"unique":[52],"characteristic":[53],"GraphletCounter":[55,79,101],"is":[56,102,116],"ability":[58],"compute":[60],"motifs,":[66],"which":[67],"specified":[70],"files":[72],"generated":[73],"motif-finding":[76],"mfinder.":[78],"displays":[80],"visual":[84],"inspection":[85],"within":[86],"Cytoscape,":[87],"output":[90],"data":[92],"integration":[94],"with":[95],"larger":[96],"workflows.":[97],"AVAILABILITY":[98],"AND":[99],"IMPLEMENTATION:":[100],"implemented":[103],"in":[104],"Java.":[105],"It":[106],"downloaded":[109],"from":[110],"Cytoscape":[112],"plugin":[113],"repository,":[114],"also":[117],"available":[118],"at":[119],"http://sonmezsysbio.org/software/":[120],"graphletcounter.":[121]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2016-06-24T00:00:00"}
