{"id":"https://openalex.org/W2163493106","doi":"https://doi.org/10.1093/bioinformatics/bth378","title":"BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains","display_name":"BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains","publication_year":2004,"publication_date":"2004-06-24","ids":{"openalex":"https://openalex.org/W2163493106","doi":"https://doi.org/10.1093/bioinformatics/bth378","mag":"2163493106","pmid":"https://pubmed.ncbi.nlm.nih.gov/15217809"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth378","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth378","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/17/3289/48906373/bioinformatics_20_17_3289.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":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/20/17/3289/48906373/bioinformatics_20_17_3289.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107139754","display_name":"Michael L. Blinov","orcid":"https://orcid.org/0000-0002-9363-9705"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael L. Blinov","raw_affiliation_strings":["Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"],"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020336186","display_name":"James R. Faeder","orcid":"https://orcid.org/0000-0001-8127-609X"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James R. Faeder","raw_affiliation_strings":["Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"],"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111966793","display_name":"Byron Goldstein","orcid":null},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Byron Goldstein","raw_affiliation_strings":["Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"],"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016126519","display_name":"William S. Hlavacek","orcid":"https://orcid.org/0000-0003-4383-8711"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William S. Hlavacek","raw_affiliation_strings":["Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"],"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5107139754"],"corresponding_institution_ids":["https://openalex.org/I1343871089"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.4435,"has_fulltext":false,"cited_by_count":440,"citation_normalized_percentile":{"value":0.95419066,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"20","issue":"17","first_page":"3289","last_page":"3291"},"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":0.9970999956130981,"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":0.9927999973297119,"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/signal-transduction","display_name":"Signal transduction","score":0.6316497921943665},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6273182034492493},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.554781436920166},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.5421098470687866},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5052188038825989},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.47831061482429504},{"id":"https://openalex.org/keywords/transduction","display_name":"Transduction (biophysics)","score":0.46812501549720764},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.40239349007606506},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3145267367362976},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2863491177558899},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.18290334939956665},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.132407546043396}],"concepts":[{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.6316497921943665},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6273182034492493},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.554781436920166},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.5421098470687866},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5052188038825989},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.47831061482429504},{"id":"https://openalex.org/C15152581","wikidata":"https://www.wikidata.org/wiki/Q7833966","display_name":"Transduction (biophysics)","level":2,"score":0.46812501549720764},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.40239349007606506},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3145267367362976},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2863491177558899},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.18290334939956665},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.132407546043396},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bth378","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth378","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/17/3289/48906373/bioinformatics_20_17_3289.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:15217809","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15217809","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bth378","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth378","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/17/3289/48906373/bioinformatics_20_17_3289.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":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2163493106.pdf","grobid_xml":"https://content.openalex.org/works/W2163493106.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2034492556","https://openalex.org/W2042321087","https://openalex.org/W2044784465","https://openalex.org/W2044889656","https://openalex.org/W2082621456","https://openalex.org/W2109975391","https://openalex.org/W2111682035","https://openalex.org/W2139609157","https://openalex.org/W2139941949","https://openalex.org/W2149999958","https://openalex.org/W2150908245"],"related_works":["https://openalex.org/W2890433954","https://openalex.org/W2053366384","https://openalex.org/W4246428841","https://openalex.org/W2369434682","https://openalex.org/W1981686597","https://openalex.org/W2966233672","https://openalex.org/W2332505650","https://openalex.org/W4210978881","https://openalex.org/W2030055732","https://openalex.org/W2015238087"],"abstract_inverted_index":{"BioNetGen":[0],"allows":[1],"a":[2,6,14],"user":[3],"to":[4,61],"create":[5],"computational":[7],"model":[8,59],"that":[9,19,49,57,67],"characterizes":[10],"the":[11,34,44],"dynamics":[12],"of":[13,33,36,46,64,78,84],"signal":[15,85],"transduction":[16],"system,":[17],"and":[18,22,31,42,54,81],"accounts":[20],"comprehensively":[21],"precisely":[23],"for":[24,73],"specified":[25],"enzymatic":[26],"activities,":[27],"potential":[28],"post-translational":[29],"modifications":[30],"interactions":[32],"domains":[35],"signaling":[37,53],"molecules.":[38],"The":[39],"output":[40],"defines":[41],"parameterizes":[43],"network":[45],"molecular":[47],"species":[48],"can":[50,68],"arise":[51],"during":[52],"provides":[55],"functions":[56],"relate":[58],"variables":[60],"experimental":[62],"readouts":[63],"interest.":[65],"Models":[66],"be":[69],"generated":[70],"are":[71],"relevant":[72],"rational":[74],"drug":[75],"discovery,":[76],"analysis":[77],"proteomic":[79],"data":[80],"mechanistic":[82],"studies":[83],"transduction.":[86]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":18},{"year":2019,"cited_by_count":34},{"year":2018,"cited_by_count":20},{"year":2017,"cited_by_count":44},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":19},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":27},{"year":2012,"cited_by_count":21}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}
