{"id":"https://openalex.org/W2099693848","doi":"https://doi.org/10.1093/bioinformatics/btp066","title":"Simulation of large-scale rule-based models","display_name":"Simulation of large-scale rule-based models","publication_year":2009,"publication_date":"2009-02-11","ids":{"openalex":"https://openalex.org/W2099693848","doi":"https://doi.org/10.1093/bioinformatics/btp066","mag":"2099693848","pmid":"https://pubmed.ncbi.nlm.nih.gov/19213740"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp066","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp066","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/910/16891651/btp066.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/25/7/910/16891651/btp066.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061748422","display_name":"Joshua Colvin","orcid":"https://orcid.org/0000-0001-5938-3059"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]},{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]},{"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"]},{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joshua Colvin","raw_affiliation_strings":["1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA","institution_ids":["https://openalex.org/I1284308235","https://openalex.org/I169521973","https://openalex.org/I203172682","https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036070075","display_name":"Michael Monine","orcid":"https://orcid.org/0000-0001-8381-1594"},"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"]},{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]},{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]},{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael I. Monine","raw_affiliation_strings":["1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA","institution_ids":["https://openalex.org/I1284308235","https://openalex.org/I169521973","https://openalex.org/I203172682","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/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]},{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]},{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]},{"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":["1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA","institution_ids":["https://openalex.org/I1284308235","https://openalex.org/I169521973","https://openalex.org/I203172682","https://openalex.org/I1343871089"]}]},{"author_position":"middle","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"]},{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]},{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]},{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William S. Hlavacek","raw_affiliation_strings":["1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA","institution_ids":["https://openalex.org/I1284308235","https://openalex.org/I169521973","https://openalex.org/I203172682","https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080900202","display_name":"Daniel D. Von Hoff","orcid":"https://orcid.org/0000-0003-4723-7681"},"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"]},{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]},{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]},{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel D. Von Hoff","raw_affiliation_strings":["1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA","institution_ids":["https://openalex.org/I1284308235","https://openalex.org/I169521973","https://openalex.org/I203172682","https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064022214","display_name":"Richard G. Posner","orcid":"https://orcid.org/0000-0002-0489-9397"},"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"]},{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]},{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]},{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard G. Posner","raw_affiliation_strings":["1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA"],"affiliations":[{"raw_affiliation_string":"1 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, 2Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 4Department of Biology, University of New Mexico, Albuquerque, NM 87131, 5Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA","institution_ids":["https://openalex.org/I1284308235","https://openalex.org/I169521973","https://openalex.org/I203172682","https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5061748422"],"corresponding_institution_ids":["https://openalex.org/I1284308235","https://openalex.org/I1343871089","https://openalex.org/I169521973","https://openalex.org/I203172682"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.9091,"has_fulltext":true,"cited_by_count":60,"citation_normalized_percentile":{"value":0.94288962,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"7","first_page":"910","last_page":"917"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9984999895095825,"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":0.9984999895095825,"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":0.9983000159263611,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9955000281333923,"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":0.7473781704902649},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6380220651626587},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.495943158864975},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4281458258628845},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.40320998430252075},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3751002550125122},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3681885004043579},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32116806507110596},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14145228266716003}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7473781704902649},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6380220651626587},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.495943158864975},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4281458258628845},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.40320998430252075},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3751002550125122},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3681885004043579},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32116806507110596},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14145228266716003},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","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":"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":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":"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":"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":"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":"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"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},{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp066","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp066","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/910/16891651/btp066.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:19213740","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19213740","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:2660871","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2660871","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp066","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp066","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/910/16891651/btp066.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":[{"id":"https://openalex.org/G1059191547","display_name":null,"funder_award_id":"RR18754","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1872210597","display_name":null,"funder_award_id":"DE-AC52-06NA2539","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G359075050","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5657628048","display_name":null,"funder_award_id":"AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5713387433","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G928841278","display_name":null,"funder_award_id":"contract DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332140","display_name":"Arizona Biomedical Research Commission","ror":"https://ror.org/01smpj292"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2099693848.pdf","grobid_xml":"https://content.openalex.org/works/W2099693848.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1500381309","https://openalex.org/W1513962738","https://openalex.org/W1518407096","https://openalex.org/W1599936794","https://openalex.org/W1607824205","https://openalex.org/W1832276623","https://openalex.org/W1973641880","https://openalex.org/W1977290213","https://openalex.org/W1979063761","https://openalex.org/W1982679461","https://openalex.org/W1986649132","https://openalex.org/W1987003260","https://openalex.org/W1987129107","https://openalex.org/W2009772909","https://openalex.org/W2030709758","https://openalex.org/W2034492556","https://openalex.org/W2045478141","https://openalex.org/W2052246560","https://openalex.org/W2069941324","https://openalex.org/W2071523020","https://openalex.org/W2079704365","https://openalex.org/W2082874501","https://openalex.org/W2087354994","https://openalex.org/W2093179886","https://openalex.org/W2094179928","https://openalex.org/W2111682035","https://openalex.org/W2111696845","https://openalex.org/W2132300645","https://openalex.org/W2134923619","https://openalex.org/W2144063122","https://openalex.org/W2151251638","https://openalex.org/W2163493106","https://openalex.org/W2165714871","https://openalex.org/W2167154952","https://openalex.org/W2169193349","https://openalex.org/W2175715045","https://openalex.org/W2611943439","https://openalex.org/W2966257977","https://openalex.org/W4251538155","https://openalex.org/W4313333784"],"related_works":["https://openalex.org/W2774965289","https://openalex.org/W2073218260","https://openalex.org/W658175190","https://openalex.org/W2340360219","https://openalex.org/W762323262","https://openalex.org/W2589574832","https://openalex.org/W3011569429","https://openalex.org/W2046096535","https://openalex.org/W2060112755","https://openalex.org/W3005511719"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":8}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
