{"id":"https://openalex.org/W3003029563","doi":"https://doi.org/10.1109/tcbb.2020.2968310","title":"The Impact of Self-Loops on Boolean Networks Attractor Landscape and Implications for Cell Differentiation Modelling","display_name":"The Impact of Self-Loops on Boolean Networks Attractor Landscape and Implications for Cell Differentiation Modelling","publication_year":2020,"publication_date":"2020-01-22","ids":{"openalex":"https://openalex.org/W3003029563","doi":"https://doi.org/10.1109/tcbb.2020.2968310","mag":"3003029563","pmid":"https://pubmed.ncbi.nlm.nih.gov/31985435"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.2968310","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.2968310","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":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://ieeexplore.ieee.org/abstract/document/8966265","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019839016","display_name":"Sara Montagna","orcid":"https://orcid.org/0000-0001-5390-4319"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Sara Montagna","raw_affiliation_strings":["Computer Science and Engineering Department (DISI), Alma Mater Studiorum Universit\u00e0 di Bologna, Cesena, FC, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science and Engineering Department (DISI), Alma Mater Studiorum Universit\u00e0 di Bologna, Cesena, FC, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030984151","display_name":"Michele Braccini","orcid":"https://orcid.org/0000-0002-2335-2514"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Michele Braccini","raw_affiliation_strings":["Computer Science and Engineering Department (DISI), Alma Mater Studiorum Universit\u00e0 di Bologna, Cesena, FC, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science and Engineering Department (DISI), Alma Mater Studiorum Universit\u00e0 di Bologna, Cesena, FC, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045128977","display_name":"Andrea Roli","orcid":"https://orcid.org/0000-0001-9891-5441"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Roli","raw_affiliation_strings":["Computer Science and Engineering Department (DISI), Alma Mater Studiorum Universit\u00e0 di Bologna, Cesena, FC, Italy"],"affiliations":[{"raw_affiliation_string":"Computer Science and Engineering Department (DISI), Alma Mater Studiorum Universit\u00e0 di Bologna, Cesena, FC, Italy","institution_ids":["https://openalex.org/I9360294"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5019839016"],"corresponding_institution_ids":["https://openalex.org/I9360294"],"apc_list":null,"apc_paid":null,"fwci":0.5004,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.616443,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"18","issue":"6","first_page":"2702","last_page":"2713"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":1.0,"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":1.0,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9857000112533569,"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/boolean-network","display_name":"Boolean network","score":0.9118301272392273},{"id":"https://openalex.org/keywords/attractor","display_name":"Attractor","score":0.834004282951355},{"id":"https://openalex.org/keywords/autoregulation","display_name":"Autoregulation","score":0.825475811958313},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.7003154754638672},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6359937191009521},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4747629165649414},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33745574951171875},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33699363470077515},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3048092722892761},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24551615118980408},{"id":"https://openalex.org/keywords/boolean-function","display_name":"Boolean function","score":0.21962666511535645},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12379425764083862},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10899579524993896},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.1080365777015686}],"concepts":[{"id":"https://openalex.org/C134444547","wikidata":"https://www.wikidata.org/wiki/Q585230","display_name":"Boolean network","level":3,"score":0.9118301272392273},{"id":"https://openalex.org/C164380108","wikidata":"https://www.wikidata.org/wiki/Q507187","display_name":"Attractor","level":2,"score":0.834004282951355},{"id":"https://openalex.org/C111774379","wikidata":"https://www.wikidata.org/wiki/Q1364253","display_name":"Autoregulation","level":3,"score":0.825475811958313},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.7003154754638672},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6359937191009521},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4747629165649414},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33745574951171875},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33699363470077515},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3048092722892761},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24551615118980408},{"id":"https://openalex.org/C187455244","wikidata":"https://www.wikidata.org/wiki/Q942353","display_name":"Boolean function","level":2,"score":0.21962666511535645},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12379425764083862},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10899579524993896},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.1080365777015686},{"id":"https://openalex.org/C84393581","wikidata":"https://www.wikidata.org/wiki/Q82642","display_name":"Blood pressure","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C134018914","wikidata":"https://www.wikidata.org/wiki/Q162606","display_name":"Endocrinology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2020.2968310","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.2968310","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":"pmid:31985435","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31985435","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:cris.unibo.it:11585/742391","is_oa":true,"landing_page_url":"https://ieeexplore.ieee.org/abstract/document/8966265","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:ora.uniurb.it:11576/2690128","is_oa":false,"landing_page_url":"https://ieeexplore.ieee.org/document/8966265","pdf_url":null,"source":{"id":"https://openalex.org/S4377196377","display_name":"CINECA IRIS Institutional Research information system (University of Urbino)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I190397597","host_organization_name":"University of Urbino","host_organization_lineage":["https://openalex.org/I190397597"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:cris.unibo.it:11585/742391","is_oa":true,"landing_page_url":"https://ieeexplore.ieee.org/abstract/document/8966265","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.6000000238418579,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320311030","display_name":"Istituto Nazionale di Alta Matematica \"Francesco Severi\"","ror":"https://ror.org/01vx64p53"},{"id":"https://openalex.org/F4320334079","display_name":"Gruppo Nazionale per il Calcolo Scientifico","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W899419236","https://openalex.org/W1493053380","https://openalex.org/W1551490917","https://openalex.org/W1599839677","https://openalex.org/W1599969036","https://openalex.org/W1959710399","https://openalex.org/W1966954598","https://openalex.org/W1969547738","https://openalex.org/W1971224531","https://openalex.org/W1978178057","https://openalex.org/W1978217382","https://openalex.org/W1979302584","https://openalex.org/W1986373777","https://openalex.org/W2000982470","https://openalex.org/W2005486846","https://openalex.org/W2025037494","https://openalex.org/W2029991507","https://openalex.org/W2030925300","https://openalex.org/W2044890688","https://openalex.org/W2058221907","https://openalex.org/W2058942402","https://openalex.org/W2061425021","https://openalex.org/W2077720193","https://openalex.org/W2081466838","https://openalex.org/W2108120899","https://openalex.org/W2110612987","https://openalex.org/W2130324073","https://openalex.org/W2132886043","https://openalex.org/W2141545875","https://openalex.org/W2142400903","https://openalex.org/W2142956218","https://openalex.org/W2153624566","https://openalex.org/W2167031279","https://openalex.org/W2246730411","https://openalex.org/W2625475375","https://openalex.org/W2794783882","https://openalex.org/W2795055646","https://openalex.org/W2800423704","https://openalex.org/W2886310122","https://openalex.org/W2887007872","https://openalex.org/W2894827346","https://openalex.org/W2963796328","https://openalex.org/W4210551050","https://openalex.org/W4211017114","https://openalex.org/W4242024146","https://openalex.org/W4388252848","https://openalex.org/W4388299828","https://openalex.org/W6679598573"],"related_works":["https://openalex.org/W2101472055","https://openalex.org/W2061235113","https://openalex.org/W2808998548","https://openalex.org/W1968124963","https://openalex.org/W3003029563","https://openalex.org/W2789889436","https://openalex.org/W2963357480","https://openalex.org/W4302620569","https://openalex.org/W2509811556","https://openalex.org/W1883363587"],"abstract_inverted_index":{"Boolean":[0,48,92,97],"networks":[1,9,93],"are":[2,84],"a":[3,87,131],"notable":[4],"model":[5,66],"of":[6,41,45,75,110,119],"gene":[7,26],"regulatory":[8,27],"and,":[10],"particularly,":[11],"prominent":[12],"theories":[13],"discuss":[14],"how":[15,72],"they":[16,83],"can":[17],"capture":[18],"cellular":[19],"differentiation":[20,141],"processes.":[21,142],"One":[22],"frequent":[23],"motif":[24],"in":[25,30,34,58,86,107,140],"networks,":[28],"especially":[29],"those":[31],"circuits":[32],"involved":[33],"cell":[35,137],"differentiation,":[36],"is":[37,130],"autoregulation.":[38],"In":[39,60],"spite":[40],"this,":[42],"the":[43,73,126],"impact":[44],"autoregulation":[46,67,129],"on":[47],"network":[49],"attractor":[50],"landscape":[51],"has":[52],"not":[53],"yet":[54],"been":[55],"extensively":[56],"discussed":[57],"literature.":[59],"this":[61],"paper":[62],"we":[63],"propose":[64],"to":[65,125,135],"as":[68],"self-loops,":[69],"and":[70,77,89,116],"analyse":[71],"number":[74,115],"attractors":[76],"their":[78],"robustness":[79,118],"may":[80],"change":[81],"once":[82],"introduced":[85],"well-known":[88],"widely":[90],"used":[91],"model,":[94],"namely":[95],"random":[96],"networks.":[98],"Results":[99],"show":[100],"that":[101,128],"self-loops":[102],"provide":[103,123],"an":[104],"evolutionary":[105],"advantage":[106],"dynamic":[108],"mechanisms":[109],"cells,":[111],"by":[112],"increasing":[113],"both":[114],"maximal":[117],"attractors.":[120],"These":[121],"results":[122],"evidence":[124],"hypothesis":[127],"straightforward":[132],"functional":[133],"component":[134],"consolidate":[136],"dynamics,":[138],"mainly":[139]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-17T09:09:15.849793","created_date":"2025-10-10T00:00:00"}
