{"id":"https://openalex.org/W2418732050","doi":"https://doi.org/10.1109/tcbb.2016.2576442","title":"An Algorithm for Motif-Based Network Design","display_name":"An Algorithm for Motif-Based Network Design","publication_year":2016,"publication_date":"2016-06-07","ids":{"openalex":"https://openalex.org/W2418732050","doi":"https://doi.org/10.1109/tcbb.2016.2576442","mag":"2418732050"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2016.2576442","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2016.2576442","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1607.08472","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011473530","display_name":"Tuomo M\u00e4ki\u2010Marttunen","orcid":"https://orcid.org/0000-0002-7082-2507"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]},{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI","NO"],"is_corresponding":true,"raw_author_name":"Tuomo Maki-Marttunen","raw_affiliation_strings":["Department of Signal Processing, Tampere University of Technology, Tampere, Pirkanmaa, FI","Institute of Clinical Medicine, University of Oslo, Oslo, Norway","Department of Signal Processing, Tampere University of Technology Tampere, Finland"],"affiliations":[{"raw_affiliation_string":"Department of Signal Processing, Tampere University of Technology, Tampere, Pirkanmaa, FI","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Clinical Medicine, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Signal Processing, Tampere University of Technology Tampere, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5011473530"],"corresponding_institution_ids":["https://openalex.org/I166825849","https://openalex.org/I184942183","https://openalex.org/I4210133110"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03393166,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"14","issue":"5","first_page":"1181","last_page":"1186"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.996399998664856,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.996399998664856,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.996399998664856,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/modularity","display_name":"Modularity (biology)","score":0.6662065386772156},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.6501016020774841},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6124823689460754},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5298250317573547},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5221163034439087},{"id":"https://openalex.org/keywords/degree-distribution","display_name":"Degree distribution","score":0.4969065487384796},{"id":"https://openalex.org/keywords/network-motif","display_name":"Network motif","score":0.4431701898574829},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.42814093828201294},{"id":"https://openalex.org/keywords/complex-network","display_name":"Complex network","score":0.42170020937919617},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.061255186796188354}],"concepts":[{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.6662065386772156},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6501016020774841},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6124823689460754},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5298250317573547},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5221163034439087},{"id":"https://openalex.org/C87414783","wikidata":"https://www.wikidata.org/wiki/Q1002603","display_name":"Degree distribution","level":3,"score":0.4969065487384796},{"id":"https://openalex.org/C60723933","wikidata":"https://www.wikidata.org/wiki/Q7001080","display_name":"Network motif","level":3,"score":0.4431701898574829},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.42814093828201294},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.42170020937919617},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.061255186796188354},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","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},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2016.2576442","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2016.2576442","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:1607.08472","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1607.08472","pdf_url":"https://arxiv.org/pdf/1607.08472","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"mag:2418732050","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1607.08472.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1607.08472","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1607.08472","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1607.08472","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1607.08472","pdf_url":"https://arxiv.org/pdf/1607.08472","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311269","display_name":"KAUTE-S\u00e4\u00e4ti\u00f6","ror":"https://ror.org/00zwv5854"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2418732050.pdf","grobid_xml":"https://content.openalex.org/works/W2418732050.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W165295313","https://openalex.org/W261461018","https://openalex.org/W1965499304","https://openalex.org/W1971421925","https://openalex.org/W1992107140","https://openalex.org/W1994801733","https://openalex.org/W2008620264","https://openalex.org/W2012529953","https://openalex.org/W2035372517","https://openalex.org/W2048324994","https://openalex.org/W2057993765","https://openalex.org/W2063310557","https://openalex.org/W2075156939","https://openalex.org/W2084573744","https://openalex.org/W2112090702","https://openalex.org/W2120092772","https://openalex.org/W2124953625","https://openalex.org/W2130776740","https://openalex.org/W2135838082","https://openalex.org/W2147654946","https://openalex.org/W2148072853","https://openalex.org/W2148606196","https://openalex.org/W2151936673","https://openalex.org/W2153624566","https://openalex.org/W2164727176","https://openalex.org/W2165922980","https://openalex.org/W2167822639","https://openalex.org/W2169768989","https://openalex.org/W2171895829","https://openalex.org/W3143219376","https://openalex.org/W6654396940"],"related_works":["https://openalex.org/W2896890240","https://openalex.org/W3147893811","https://openalex.org/W2168331307","https://openalex.org/W2963381982","https://openalex.org/W2616249495","https://openalex.org/W2886459569","https://openalex.org/W2840335614","https://openalex.org/W3154973012","https://openalex.org/W2104131585","https://openalex.org/W3162080762","https://openalex.org/W3203576334","https://openalex.org/W2055073892","https://openalex.org/W2776324202","https://openalex.org/W2409979763","https://openalex.org/W3048250178","https://openalex.org/W2077294208","https://openalex.org/W3081408878","https://openalex.org/W2046559008","https://openalex.org/W2913345427","https://openalex.org/W3012659934"],"abstract_inverted_index":{"A":[0],"determinant":[1],"property":[2],"of":[3,6,13,35,59,67,88,95,103],"the":[4,11,51,57,68,89,107],"structure":[5],"a":[7,23,32],"biological":[8],"network":[9,18,41,117],"is":[10,37,77],"distribution":[12,66],"local":[14],"connectivity":[15],"patterns,":[16],"i.e.,":[17],"motifs.":[19,61],"In":[20],"this":[21],"work,":[22],"method":[24],"for":[25],"creating":[26],"directed,":[27],"unweighted":[28],"networks":[29,70,84],"while":[30],"promoting":[31],"certain":[33],"combination":[34],"motifs":[36],"presented.":[38],"This":[39],"motif-based":[40],"algorithm":[42,76,108],"starts":[43],"with":[44,85],"an":[45],"empty":[46],"graph":[47],"and":[48,127],"randomly":[49],"connects":[50],"nodes":[52,97],"by":[53],"advancing":[54],"or":[55,64],"discouraging":[56],"formation":[58],"chosen":[60],"The":[62,75],"in-":[63],"out-degree":[65],"generated":[69],"can":[71,109],"be":[72,111],"explicitly":[73],"chosen.":[74],"shown":[78],"to":[79,113],"perform":[80],"well":[81,99],"in":[82,120],"producing":[83],"high":[86],"occurrences":[87],"targeted":[90],"motifs,":[91],"both":[92],"ones":[93,101],"consisting":[94,102],"three":[96],"as":[98,100,125],"four":[104],"nodes.":[105],"Moreover,":[106],"also":[110],"tuned":[112],"bring":[114],"about":[115],"global":[116],"characteristics":[118],"found":[119],"many":[121],"natural":[122],"networks,":[123],"such":[124],"small-worldness":[126],"modularity.":[128]},"counts_by_year":[],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
