{"id":"https://openalex.org/W2215639193","doi":"https://doi.org/10.1109/bibe.2015.7367733","title":"SIMBio: Searching and inferring colorful motifs in biological networks","display_name":"SIMBio: Searching and inferring colorful motifs in biological networks","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2215639193","doi":"https://doi.org/10.1109/bibe.2015.7367733","mag":"2215639193"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2015.7367733","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2015.7367733","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5041224517","display_name":"Diego P. Rubert","orcid":"https://orcid.org/0000-0002-4131-7309"},"institutions":[{"id":"https://openalex.org/I122558511","display_name":"Universidade Federal de Mato Grosso do Sul","ror":"https://ror.org/0366d2847","country_code":"BR","type":"education","lineage":["https://openalex.org/I122558511"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Diego P. Rubert","raw_affiliation_strings":["Faculdade de Computacao, Universidade Federal de Mato Grosso do Sul, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculdade de Computacao, Universidade Federal de Mato Grosso do Sul, Brazil","institution_ids":["https://openalex.org/I122558511"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073102002","display_name":"El\u00f3i Ara\u00fajo","orcid":"https://orcid.org/0000-0002-8015-6237"},"institutions":[{"id":"https://openalex.org/I122558511","display_name":"Universidade Federal de Mato Grosso do Sul","ror":"https://ror.org/0366d2847","country_code":"BR","type":"education","lineage":["https://openalex.org/I122558511"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Eloi Araujo","raw_affiliation_strings":["Faculdade de Computacao, Universidade Federal de Mato Grosso do Sul, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculdade de Computacao, Universidade Federal de Mato Grosso do Sul, Brazil","institution_ids":["https://openalex.org/I122558511"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044775293","display_name":"Marco A. Stefanes","orcid":"https://orcid.org/0000-0002-7155-6597"},"institutions":[{"id":"https://openalex.org/I122558511","display_name":"Universidade Federal de Mato Grosso do Sul","ror":"https://ror.org/0366d2847","country_code":"BR","type":"education","lineage":["https://openalex.org/I122558511"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Marco A. Stefanes","raw_affiliation_strings":["Faculdade de Computacao, Universidade Federal de Mato Grosso do Sul, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculdade de Computacao, Universidade Federal de Mato Grosso do Sul, Brazil","institution_ids":["https://openalex.org/I122558511"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.07307662,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"100","issue":null,"first_page":"1","last_page":"6"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.993399977684021,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9929999709129333,"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/inference","display_name":"Inference","score":0.7710962891578674},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.7354360818862915},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6553452610969543},{"id":"https://openalex.org/keywords/network-motif","display_name":"Network motif","score":0.6255390644073486},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.6220598220825195},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5896856784820557},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.5410507917404175},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.4893612265586853},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45819291472435},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4267008900642395},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3452156186103821},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20571628212928772},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1795743703842163}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7710962891578674},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.7354360818862915},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6553452610969543},{"id":"https://openalex.org/C60723933","wikidata":"https://www.wikidata.org/wiki/Q7001080","display_name":"Network motif","level":3,"score":0.6255390644073486},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6220598220825195},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5896856784820557},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.5410507917404175},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.4893612265586853},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45819291472435},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4267008900642395},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3452156186103821},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20571628212928772},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1795743703842163},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibe.2015.7367733","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2015.7367733","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","raw_type":"proceedings-article"},{"id":"pmh:oai:pub.uni-bielefeld.de:2965063","is_oa":false,"landing_page_url":"https://pub.uni-bielefeld.de/record/2965063","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"http://purl.org/coar/resource_type/c_5794"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W22881454","https://openalex.org/W1565474750","https://openalex.org/W1600301286","https://openalex.org/W1825216778","https://openalex.org/W1966893452","https://openalex.org/W1970110893","https://openalex.org/W2028843648","https://openalex.org/W2078542889","https://openalex.org/W2086133268","https://openalex.org/W2104009289","https://openalex.org/W2106202847","https://openalex.org/W2109488005","https://openalex.org/W2110699703","https://openalex.org/W2128601422","https://openalex.org/W2139343285","https://openalex.org/W2142678478","https://openalex.org/W2153624566","https://openalex.org/W2739999456","https://openalex.org/W4230770774","https://openalex.org/W4243777566","https://openalex.org/W6600940479","https://openalex.org/W6635962089","https://openalex.org/W6638601623","https://openalex.org/W6657954829"],"related_works":["https://openalex.org/W15348386","https://openalex.org/W4385510321","https://openalex.org/W2142272337","https://openalex.org/W2077895977","https://openalex.org/W782572168","https://openalex.org/W2215639193","https://openalex.org/W2123854512","https://openalex.org/W4389148664","https://openalex.org/W2098027521","https://openalex.org/W3087406311"],"abstract_inverted_index":{"The":[0],"study":[1],"of":[2,10,82,160],"motifs":[3,32,53,86,99,161],"plays":[4],"a":[5,36,56,88,94,111],"central":[6],"role":[7],"in":[8,14,43,72,87,144],"recognition":[9],"relations":[11,28],"among":[12],"components":[13],"biological":[15,64,73,89],"networks":[16],"such":[17],"that":[18,134],"gene":[19],"regulation,":[20],"protein":[21],"interaction,":[22],"and":[23,66,115,120,124,154],"metabolic":[24],"networks.":[25,74],"Since":[26],"these":[27],"are":[29],"not":[30],"well-known,":[31],"inference":[33],"appears":[34],"as":[35],"way":[37],"for":[38,59,96,113,140],"understanding":[39],"the":[40,44,50,80,145,163],"principles":[41],"involved":[42],"relationship":[45],"between":[46],"cellular":[47],"components.":[48],"On":[49],"other":[51],"hand,":[52],"search":[54],"is":[55,136],"basic":[57],"step":[58],"constructing":[60],"models":[61],"which":[62,100],"represent":[63],"behavior":[65],"explain":[67],"functional":[68],"and/or":[69],"structural":[70],"effects":[71],"In":[75],"this":[76],"work":[77],"we":[78,121],"address":[79],"problem":[81],"infer":[83],"all":[84],"relevant":[85],"network.":[90],"We":[91,109,148],"also":[92,149],"provide":[93],"solution":[95],"searching":[97,114],"colorful":[98],"can":[101],"be":[102],"topological-free":[103],"or":[104],"have":[105,132],"an":[106],"acyclic":[107],"topology.":[108],"developed":[110],"tool":[112],"inferring":[116,141],"motifs,":[117,142],"named":[118],"SIMBio,":[119],"implemented":[122],"sequential":[123,146],"parallel":[125],"versions.":[126],"When":[127],"comparing":[128],"performance,":[129],"our":[130],"experiments":[131],"showed":[133],"SIMBio":[135,155],"faster":[137],"than":[138],"MOTUS":[139],"even":[143],"version.":[147],"compared":[150],"it":[151],"to":[152],"Torque,":[153],"has":[156],"found":[157],"more":[158],"occurrences":[159],"under":[162],"same":[164],"experiments.":[165]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
