{"id":"https://openalex.org/W2103454055","doi":"https://doi.org/10.1093/bioinformatics/btq124","title":"BoolNet\u2014an R package for generation, reconstruction and analysis of Boolean networks","display_name":"BoolNet\u2014an R package for generation, reconstruction and analysis of Boolean networks","publication_year":2010,"publication_date":"2010-04-07","ids":{"openalex":"https://openalex.org/W2103454055","doi":"https://doi.org/10.1093/bioinformatics/btq124","mag":"2103454055","pmid":"https://pubmed.ncbi.nlm.nih.gov/20378558"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq124","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/10/1378/48851866/bioinformatics_26_10_1378.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/10/1378/48851866/bioinformatics_26_10_1378.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033625762","display_name":"Christoph M\u00fcssel","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155144","display_name":"University Hospital Ulm","ror":"https://ror.org/05emabm63","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210155144"]},{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"funder","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christoph M\u00fcssel","raw_affiliation_strings":["1 Institute of Neural Information Processing, University of Ulm and 2 Department of Internal Medicine I, University Hospital Ulm, 89081 Ulm, Germany"],"affiliations":[{"raw_affiliation_string":"1 Institute of Neural Information Processing, University of Ulm and 2 Department of Internal Medicine I, University Hospital Ulm, 89081 Ulm, Germany","institution_ids":["https://openalex.org/I4210155144","https://openalex.org/I196349391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048466051","display_name":"Martin Hopfensitz","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155144","display_name":"University Hospital Ulm","ror":"https://ror.org/05emabm63","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210155144"]},{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"funder","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Hopfensitz","raw_affiliation_strings":["1 Institute of Neural Information Processing, University of Ulm and 2 Department of Internal Medicine I, University Hospital Ulm, 89081 Ulm, Germany"],"affiliations":[{"raw_affiliation_string":"1 Institute of Neural Information Processing, University of Ulm and 2 Department of Internal Medicine I, University Hospital Ulm, 89081 Ulm, Germany","institution_ids":["https://openalex.org/I4210155144","https://openalex.org/I196349391"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023316486","display_name":"Hans A. Kestler","orcid":"https://orcid.org/0000-0002-4759-5254"},"institutions":[{"id":"https://openalex.org/I4210155144","display_name":"University Hospital Ulm","ror":"https://ror.org/05emabm63","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210155144"]},{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"funder","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hans A. Kestler","raw_affiliation_strings":["1 Institute of Neural Information Processing, University of Ulm and 2 Department of Internal Medicine I, University Hospital Ulm, 89081 Ulm, Germany"],"affiliations":[{"raw_affiliation_string":"1 Institute of Neural Information Processing, University of Ulm and 2 Department of Internal Medicine I, University Hospital Ulm, 89081 Ulm, Germany","institution_ids":["https://openalex.org/I4210155144","https://openalex.org/I196349391","https://openalex.org/I4210155144","https://openalex.org/I196349391"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":7.592,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":408,"citation_normalized_percentile":{"value":0.927725,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"26","issue":"10","first_page":"1378","last_page":"1380"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9999,"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":0.9999,"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":0.9961,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9942,"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/sbml","display_name":"SBML","score":0.5127955},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5022156},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.47964436},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness","score":0.4751601},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.43549448}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7906557},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5871626},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.57818234},{"id":"https://openalex.org/C151319957","wikidata":"https://www.wikidata.org/wiki/Q752739","display_name":"Asynchronous communication","level":2,"score":0.5529294},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5505571},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.5127955},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.50250125},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5022156},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.47964436},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4751601},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.461632},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.439386},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.43549448},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35113484},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32317942},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.30636492},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2761826},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.21420383},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.16063294},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","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/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.0},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq124","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/10/1378/48851866/bioinformatics_26_10_1378.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1031.9379","pdf_url":"http://bioinformatics.oxfordjournals.org/content/early/2010/04/07/bioinformatics.btq124.full.pdf","source":{"id":"https://openalex.org/S4306400349","display_name":"CiteSeer X (The Pennsylvania State University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_indexed_in_scopus":false,"is_core":false,"host_organization":"https://openalex.org/I130769515","host_organization_name":"Pennsylvania State University","host_organization_lineage":["https://openalex.org/I130769515"],"host_organization_lineage_names":["Pennsylvania State University"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20378558","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_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq124","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/10/1378/48851866/bioinformatics_26_10_1378.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/14","score":0.48,"display_name":"Life below water"}],"grants":[],"datasets":[],"versions":[],"referenced_works_count":21,"referenced_works":["https://openalex.org/W1256890642","https://openalex.org/W1481919380","https://openalex.org/W1600339875","https://openalex.org/W1606059141","https://openalex.org/W1640890183","https://openalex.org/W1677575702","https://openalex.org/W1970441315","https://openalex.org/W1971224531","https://openalex.org/W2037728288","https://openalex.org/W2053961182","https://openalex.org/W2058221907","https://openalex.org/W2070815798","https://openalex.org/W2103453943","https://openalex.org/W2103723044","https://openalex.org/W2108020239","https://openalex.org/W2109278577","https://openalex.org/W2127020923","https://openalex.org/W2132935366","https://openalex.org/W2160533336","https://openalex.org/W2944782266","https://openalex.org/W4388252848"],"related_works":["https://openalex.org/W4384009753","https://openalex.org/W4286531993","https://openalex.org/W4285209474","https://openalex.org/W4225089214","https://openalex.org/W2791776396","https://openalex.org/W2546377002","https://openalex.org/W22571951","https://openalex.org/W2046541848","https://openalex.org/W2045478141","https://openalex.org/W2036021480"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"As":[2],"the":[3,28,40,67,146],"study":[4],"of":[5,31,42,46,62,69,76,82,89,136],"information":[6],"processing":[7],"in":[8],"living":[9],"cells":[10],"moves":[11],"from":[12,119,145],"individual":[13],"pathways":[14],"to":[15,72],"complex":[16,29],"regulatory":[17],"networks,":[18,124],"mathematical":[19,60],"models":[20,61],"and":[21,34,92,112,132,134],"simulation":[22],"become":[23],"indispensable":[24],"tools":[25],"for":[26,49,96,109],"analyzing":[27],"behavior":[30],"such":[32],"networks":[33,56,118],"can":[35,51],"provide":[36],"deep":[37],"insights":[38],"into":[39,100],"functioning":[41],"cells.":[43],"The":[44,139],"dynamics":[45],"gene":[47],"expression,":[48],"example,":[50],"be":[52],"modeled":[53],"with":[54],"Boolean":[55],"(BNs).":[57],"These":[58],"are":[59,163],"low":[63],"complexity,":[64],"but":[65],"have":[66],"advantage":[68],"being":[70],"able":[71],"capture":[73],"essential":[74],"properties":[75],"gene-regulatory":[77],"networks.":[78],"However,":[79],"current":[80],"implementations":[81],"BNs":[83],"only":[84],"focus":[85],"on":[86],"different":[87],"sub-aspects":[88],"this":[90],"model":[91],"do":[93],"not":[94],"allow":[95],"a":[97],"seamless":[98],"integration":[99],"existing":[101],"preprocessing":[102],"pipelines.":[103],"Results:":[104],"BoolNet":[105,141],"efficiently":[106],"integrates":[107],"methods":[108],"synchronous,":[110],"asynchronous":[111],"probabilistic":[113],"BNs.":[114],"This":[115],"includes":[116],"reconstructing":[117],"time":[120],"series,":[121],"generating":[122],"random":[123],"robustness":[125],"analysis":[126],"via":[127],"perturbation,":[128],"Markov":[129],"chain":[130],"simulations,":[131],"identification":[133],"visualization":[135],"attractors.":[137],"Availability:":[138],"package":[140],"is":[142],"freely":[143],"available":[144,164],"R":[147],"project":[148],"at":[149,165],"http://cran.r-project.org/":[150],"or":[151],"http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/boolnet/":[152],"under":[153],"Artistic":[154],"License":[155],"2.0.":[156],"Contact:":[157],"hans.kestler@uni-ulm.de":[158],"Supplementary":[159,161],"information:":[160],"data":[162],"Bioinformatics":[166],"online.":[167]},"abstract_inverted_index_v3":null,"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2103454055","counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":33},{"year":2023,"cited_by_count":34},{"year":2022,"cited_by_count":44},{"year":2021,"cited_by_count":36},{"year":2020,"cited_by_count":33},{"year":2019,"cited_by_count":26},{"year":2018,"cited_by_count":37},{"year":2017,"cited_by_count":28},{"year":2016,"cited_by_count":22},{"year":2015,"cited_by_count":40},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":22},{"year":2012,"cited_by_count":27}],"updated_date":"2025-04-22T02:17:27.905833","created_date":"2016-06-24"}