{"id":"https://openalex.org/W2303100661","doi":"https://doi.org/10.1093/bioinformatics/btw469","title":"BioNetGen 2.2: advances in rule-based modeling","display_name":"BioNetGen 2.2: advances in rule-based modeling","publication_year":2016,"publication_date":"2016-07-08","ids":{"openalex":"https://openalex.org/W2303100661","doi":"https://doi.org/10.1093/bioinformatics/btw469","mag":"2303100661","pmid":"https://pubmed.ncbi.nlm.nih.gov/27402907"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw469","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw469","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3366/7889722/btw469.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":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3366/7889722/btw469.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010400772","display_name":"Leonard A. Harris","orcid":"https://orcid.org/0000-0003-2112-6940"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leonard A. Harris","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086482091","display_name":"Justin Hogg","orcid":"https://orcid.org/0009-0005-9329-606X"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin S. Hogg","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018022441","display_name":"Jos\u00e9-Juan Tapia","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jos\u00e9-Juan Tapia","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039014269","display_name":"John A. P. Sekar","orcid":"https://orcid.org/0000-0002-1605-8130"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John A. P. Sekar","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102781502","display_name":"Sanjana Gupta","orcid":"https://orcid.org/0000-0002-3440-0075"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sanjana Gupta","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049625162","display_name":"Ilya Korsunsky","orcid":"https://orcid.org/0000-0003-4848-3948"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ilya Korsunsky","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082707379","display_name":"Arshi Arora","orcid":"https://orcid.org/0000-0002-4040-1787"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arshi Arora","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086143636","display_name":"Dipak Barua","orcid":"https://orcid.org/0000-0001-8394-1233"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dipak Barua","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109064854","display_name":"Robert P. Sheehan","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert P. Sheehan","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020336186","display_name":"James R. Faeder","orcid":"https://orcid.org/0000-0001-8127-609X"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"James R. Faeder","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5020336186"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":10.6173,"has_fulltext":false,"cited_by_count":241,"citation_normalized_percentile":{"value":0.98672736,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"32","issue":"21","first_page":"3366","last_page":"3368"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9975000023841858,"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":0.9940000176429749,"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/computer-science","display_name":"Computer science","score":0.7492507696151733},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5578914284706116},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5292669534683228},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.485965371131897},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.44008103013038635},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3865669071674347}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7492507696151733},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5578914284706116},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5292669534683228},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.485965371131897},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.44008103013038635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3865669071674347}],"mesh":[{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btw469","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw469","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3366/7889722/btw469.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:27402907","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27402907","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},{"id":"pmh:oai:pubmedcentral.nih.gov:5079481","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5079481","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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","raw_type":"Text"},{"id":"pmh:oai:arXiv.org:1507.03572","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1507.03572","pdf_url":"https://arxiv.org/pdf/1507.03572","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":null,"raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/21/3366","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/21/3366","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw469","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw469","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3366/7889722/btw469.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":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2303100661.pdf","grobid_xml":"https://content.openalex.org/works/W2303100661.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W9952812","https://openalex.org/W1563071114","https://openalex.org/W1996444666","https://openalex.org/W1997483622","https://openalex.org/W2015500070","https://openalex.org/W2039639568","https://openalex.org/W2057485245","https://openalex.org/W2082221311","https://openalex.org/W2097240335","https://openalex.org/W2097319997","https://openalex.org/W2111483953","https://openalex.org/W2114124738","https://openalex.org/W2121490181","https://openalex.org/W2129629935","https://openalex.org/W2130611503","https://openalex.org/W2132302738","https://openalex.org/W2144063122","https://openalex.org/W2150908245","https://openalex.org/W2155306598","https://openalex.org/W2163493106","https://openalex.org/W2164554210","https://openalex.org/W2167154952","https://openalex.org/W2170171286","https://openalex.org/W2175715045","https://openalex.org/W2184251399","https://openalex.org/W2228538196","https://openalex.org/W2241238536","https://openalex.org/W2242773492","https://openalex.org/W2611943439","https://openalex.org/W3098919389","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2124842464","https://openalex.org/W2382657549","https://openalex.org/W4376877853","https://openalex.org/W75565505","https://openalex.org/W4214847518","https://openalex.org/W3200575725","https://openalex.org/W4242732953","https://openalex.org/W1535063848","https://openalex.org/W2186225517","https://openalex.org/W1153144596"],"abstract_inverted_index":{"Stable":[0],"BioNetGen":[1],"releases":[2],"(Linux,":[3],"Mac":[4],"OS/X":[5],"and":[6],"Windows),":[7],"with":[8],"documentation,":[9],"are":[10,25],"available":[11,17,26],"at":[12,18,27],"http://bionetgen.org":[13],"Source":[14],"code":[15],"is":[16],"http://github.com/RuleWorld/bionetgen":[19],"CONTACT:":[20],"bionetgen.help@gmail.comSupplementary":[21],"information:":[22],"Supplementary":[23],"data":[24],"Bioinformatics":[28],"online.":[29]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":28},{"year":2023,"cited_by_count":26},{"year":2022,"cited_by_count":35},{"year":2021,"cited_by_count":28},{"year":2020,"cited_by_count":37},{"year":2019,"cited_by_count":30},{"year":2018,"cited_by_count":19},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}
