{"id":"https://openalex.org/W4414003066","doi":"https://doi.org/10.1093/bioinformatics/btaf482","title":"Discovering subnetworks in SBML models","display_name":"Discovering subnetworks in SBML models","publication_year":2025,"publication_date":"2025-08-29","ids":{"openalex":"https://openalex.org/W4414003066","doi":"https://doi.org/10.1093/bioinformatics/btaf482","pmid":"https://pubmed.ncbi.nlm.nih.gov/40905951"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf482","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf482","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf482/64211186/btaf482.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_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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf482/64211186/btaf482.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038863305","display_name":"Joseph L. Hellerstein","orcid":"https://orcid.org/0000-0003-0802-4069"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210100791","display_name":"Paul G. Allen Family Foundation","ror":"https://ror.org/01degd278","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210100791"]},{"id":"https://openalex.org/I4210145583","display_name":"Bioengineering Center","ror":"https://ror.org/04f0ydx59","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210145583"]}],"countries":["RU","US"],"is_corresponding":true,"raw_author_name":"Joseph L Hellerstein","raw_affiliation_strings":["Department of Bioengineering, University of Washington , Seattle, WA, 98195,","Paul G. Allen School of Computer Science, University of Washington , Seattle, WA, 98195,","eScience Institute, University of Washington , Seattle, WA, 98195,","Department of Bioengineering, University of Washington, Seattle, WA United States","Paul G. Allen School of Computer Science, University of Washington, Seattle, WA United States","eScience Institute, University of Washington, Seattle, WA United States"],"raw_orcid":"https://orcid.org/0000-0003-0802-4069","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA, 98195,","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Paul G. Allen School of Computer Science, University of Washington , Seattle, WA, 98195,","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210100791"]},{"raw_affiliation_string":"eScience Institute, University of Washington , Seattle, WA, 98195,","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, WA United States","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210145583"]},{"raw_affiliation_string":"Paul G. Allen School of Computer Science, University of Washington, Seattle, WA United States","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210100791"]},{"raw_affiliation_string":"eScience Institute, University of Washington, Seattle, WA United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067339679","display_name":"Lucian P. Smith","orcid":"https://orcid.org/0000-0001-7002-6386"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210100791","display_name":"Paul G. Allen Family Foundation","ror":"https://ror.org/01degd278","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210100791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lucian P Smith","raw_affiliation_strings":["Paul G. Allen School of Computer Science, University of Washington , Seattle, WA, 98195,","Paul G. Allen School of Computer Science, University of Washington, Seattle, WA United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science, University of Washington , Seattle, WA, 98195,","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210100791"]},{"raw_affiliation_string":"Paul G. Allen School of Computer Science, University of Washington, Seattle, WA United States","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210100791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001501221","display_name":"Lillian T. Tatka","orcid":"https://orcid.org/0000-0001-7847-7747"},"institutions":[{"id":"https://openalex.org/I4210097616","display_name":"TRIA Bioscience (United States)","ror":"https://ror.org/00dh4zq96","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lillian T Tatka","raw_affiliation_strings":["Talus Bioscience , Seattle, WA, 98122,","Talus Bioscience, Seattle, WA United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Talus Bioscience , Seattle, WA, 98122,","institution_ids":["https://openalex.org/I4210097616"]},{"raw_affiliation_string":"Talus Bioscience, Seattle, WA United States","institution_ids":["https://openalex.org/I4210097616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079267168","display_name":"Steven S. Andrews","orcid":"https://orcid.org/0000-0002-4576-8107"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210145583","display_name":"Bioengineering Center","ror":"https://ror.org/04f0ydx59","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210145583"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Steven S Andrews","raw_affiliation_strings":["Department of Bioengineering, University of Washington , Seattle, WA, 98195,","Department of Bioengineering, University of Washington, Seattle, WA United States"],"raw_orcid":"https://orcid.org/0000-0002-4576-8107","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA, 98195,","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, WA United States","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210145583"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042926954","display_name":"Michael A. Kochen","orcid":"https://orcid.org/0000-0002-3379-1529"},"institutions":[{"id":"https://openalex.org/I4210146378","display_name":"Applications Research (United States)","ror":"https://ror.org/048kv9325","country_code":"US","type":"company","lineage":["https://openalex.org/I4210146378"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael A Kochen","raw_affiliation_strings":["Software Applications and Technology, Rocky Mountain Division, Applied Research Associates, Inc , Bentonville, AR, 72212,","Software Applications and Technology, Rocky Mountain Division, Applied Research Associates, Inc, Bentonville, AR United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Software Applications and Technology, Rocky Mountain Division, Applied Research Associates, Inc , Bentonville, AR, 72212,","institution_ids":["https://openalex.org/I4210146378"]},{"raw_affiliation_string":"Software Applications and Technology, Rocky Mountain Division, Applied Research Associates, Inc, Bentonville, AR United States","institution_ids":["https://openalex.org/I4210146378"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210145583","display_name":"Bioengineering Center","ror":"https://ror.org/04f0ydx59","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210145583"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Herbert M Sauro","raw_affiliation_strings":["Department of Bioengineering, University of Washington , Seattle, WA, 98195,","eScience Institute, University of Washington , Seattle, WA, 98195,","Department of Bioengineering, University of Washington, Seattle, WA United States","eScience Institute, University of Washington, Seattle, WA United States"],"raw_orcid":"https://orcid.org/0000-0002-3659-6817","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA, 98195,","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"eScience Institute, University of Washington , Seattle, WA, 98195,","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, WA United States","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210145583"]},{"raw_affiliation_string":"eScience Institute, University of Washington, Seattle, WA United States","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5038863305"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210100791","https://openalex.org/I4210145583"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13103802,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5095000267028809,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5095000267028809,"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":0.22030000388622284,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.18299999833106995,"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":0.9620194435119629},{"id":"https://openalex.org/keywords/subnet","display_name":"Subnet","score":0.7839582562446594},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7232682108879089},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6458821296691895},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5756075978279114},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5533803701400757},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5128017067909241},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4749184548854828},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.4169044494628906},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3296464681625366},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1891528069972992},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.11158913373947144},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.10943040251731873}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9620194435119629},{"id":"https://openalex.org/C21099817","wikidata":"https://www.wikidata.org/wiki/Q7631721","display_name":"Subnet","level":2,"score":0.7839582562446594},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7232682108879089},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6458821296691895},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5756075978279114},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5533803701400757},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5128017067909241},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4749184548854828},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.4169044494628906},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3296464681625366},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1891528069972992},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.11158913373947144},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.10943040251731873},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf482","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf482","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf482/64211186/btaf482.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_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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40905951","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40905951","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:11289299","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12478697","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12478697","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12478697/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf482","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf482","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf482/64211186/btaf482.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_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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G114059409","display_name":null,"funder_award_id":"P41EB023912","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G4536393517","display_name":"Center for Reproducible Systems for Biomedical Modeling","funder_award_id":"2p41eb023912-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414003066.pdf","grobid_xml":"https://content.openalex.org/works/W4414003066.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1644749979","https://openalex.org/W1984249061","https://openalex.org/W2061344791","https://openalex.org/W2061425021","https://openalex.org/W2103148772","https://openalex.org/W2109294083","https://openalex.org/W2114124738","https://openalex.org/W2115184421","https://openalex.org/W2125615370","https://openalex.org/W2147405597","https://openalex.org/W2150908245","https://openalex.org/W2161311439","https://openalex.org/W2764023277","https://openalex.org/W3094492244","https://openalex.org/W3167460727","https://openalex.org/W4284894508","https://openalex.org/W4315643551","https://openalex.org/W4380484857"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4225469991","https://openalex.org/W4226134703","https://openalex.org/W4206318408","https://openalex.org/W2157092888","https://openalex.org/W3157390305","https://openalex.org/W1546880839","https://openalex.org/W2122529434","https://openalex.org/W2509769281"],"abstract_inverted_index":{"MOTIVATION:":[0],"Many":[1],"advances":[2],"in":[3,16,33,106,111,127,135,184,213,231,234],"biomedical":[4],"research":[5],"are":[6,109,155],"driven":[7],"by":[8],"structural":[9,20],"analysis,":[10],"which":[11],"investigates":[12],"interconnections":[13],"between":[14],"elements":[15],"biological":[17],"systems":[18],"(e.g.":[19,69,86],"analysis":[21,52],"of":[22,40,137,177,191,210,228,240],"proteins":[23],"to":[24,47,162],"infer":[25],"their":[26],"function).":[27],"Herein,":[28],"we":[29,181],"consider":[30],"subnet":[31,76,131,178,204],"discovery":[32,77,205],"chemical":[34],"reaction":[35],"networks":[36,141],"(CRNs)-discovering":[37],"a":[38,41,48,147,163,170,200,241],"subset":[39],"target":[42,140,194,215],"CRN,":[43],"i.e.":[44],"structurally":[45],"identical":[46],"reference":[49,149,192,201],"CRN.":[50],"Structural":[51],"techniques":[53],"such":[54],"as":[55],"motif":[56],"finding":[57],"and":[58,65,82,193,236,258],"graph":[59],"mining":[60],"look":[61],"for":[62,79,103,130,172,186,199,244],"small,":[63],"arbitrary,":[64],"commonly":[66],"occurring":[67,84],"substructures":[68,85],"three":[70],"gene":[71],"feedforward":[72],"loops).":[73],"In":[74],"contrast,":[75],"looks":[78],"larger,":[80],"specific,":[81],"infrequently":[83],"10":[87],"reactions":[88,144],"mitogen-activated":[89],"protein":[90],"kinase":[91],"(MAPK)":[92],"pathway).":[93],"RESULTS:":[94],"We":[95,120,168,196],"introduce":[96],"pySubnetSB,":[97,257],"an":[98,158],"open":[99],"source":[100],"Python":[101],"package":[102],"discovering":[104],"subnets":[105,183],"CRNs":[107],"that":[108,122,198],"represented":[110],"the":[112,174,208,225,238],"Systems":[113],"Biology":[114],"Markup":[115],"Language":[116],"(SBML)":[117],"community":[118],"standard.":[119],"show":[121,197],"pySubnetSB":[123,251],"achieves":[124],"large":[125],"reductions":[126],"computational":[128],"complexity":[129],"discovery.":[132,179],"For":[133],"example,":[134],"studies":[136,218],"randomly":[138],"selected":[139],"with":[142,146,151],"100":[143],"each":[145],"random":[148],"network":[150],"20":[152],"reactions,":[153],"computations":[154],"reduced":[156],"from":[157],"infeasible":[159],"1078":[160],"evaluations":[161],"more":[164],"practical":[165],"108":[166],"evaluations.":[167],"develop":[169],"methodology":[171],"assessing":[173],"statistical":[175],"significance":[176],"Last,":[180],"study":[182],"BioModels":[185],"approximately":[187],"200":[188],"000":[189],"pairs":[190],"models.":[195,216],"MAPK":[202,211],"pathway,":[203],"correctly":[206],"indicates":[207],"presence":[209,227],"function":[212],"several":[214,232],"The":[217],"also":[219],"suggest":[220],"two":[221],"interesting":[222],"hypotheses:":[223],"(a)":[224],"potential":[226],"hidden":[229],"oscillators":[230],"models":[233],"BioModels,":[235],"(b)":[237],"possibility":[239],"conserved":[242],"mechanism":[243],"intracellular":[245],"immune":[246],"response.":[247],"AVAILABILITY":[248],"AND":[249],"IMPLENETATION:":[250],"is":[252,259],"installed":[253],"using":[254],"pip":[255],"install":[256],"hosted":[260],"at":[261],"https://github.com/ModelEngineering/pySubnetSB/.":[262]},"counts_by_year":[],"updated_date":"2026-08-23T07:36:19.812096","created_date":"2025-10-10T00:00:00"}
