{"id":"https://openalex.org/W1964012101","doi":"https://doi.org/10.1186/1471-2105-9-90","title":"Modularization of biochemical networks based on classification of Petri net t-invariants","display_name":"Modularization of biochemical networks based on classification of Petri net t-invariants","publication_year":2008,"publication_date":"2008-02-08","ids":{"openalex":"https://openalex.org/W1964012101","doi":"https://doi.org/10.1186/1471-2105-9-90","mag":"1964012101","pmid":"https://pubmed.ncbi.nlm.nih.gov/18257938"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-90","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-90","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-90","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-90","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077536951","display_name":"Eva Grafahrend\u2010Belau","orcid":"https://orcid.org/0000-0002-1938-3908"},"institutions":[{"id":"https://openalex.org/I129643931","display_name":"Berliner Hochschule f\u00fcr Technik","ror":"https://ror.org/00w7whj55","country_code":"DE","type":"education","lineage":["https://openalex.org/I129643931"]},{"id":"https://openalex.org/I90812881","display_name":"Steinbeis University Berlin","ror":"https://ror.org/03efsge90","country_code":"DE","type":"education","lineage":["https://openalex.org/I90812881"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Eva Grafahrend-Belau","raw_affiliation_strings":["Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr, 64, 13347 Berlin, Germany. grafahr@ipk-gatersleben.de","Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr. 64, 13347, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr, 64, 13347 Berlin, Germany. grafahr@ipk-gatersleben.de","institution_ids":["https://openalex.org/I90812881"]},{"raw_affiliation_string":"Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr. 64, 13347, Berlin, Germany","institution_ids":["https://openalex.org/I129643931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109343398","display_name":"Falk Schreiber","orcid":null},"institutions":[{"id":"https://openalex.org/I4210127902","display_name":"Leibniz Institute of Plant Genetics and Crop Plant Research","ror":"https://ror.org/02skbsp27","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210127902"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Falk Schreiber","raw_affiliation_strings":["Dept. of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany","institution_ids":["https://openalex.org/I4210127902"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002026696","display_name":"Monika Heiner","orcid":"https://orcid.org/0000-0003-1815-1205"},"institutions":[{"id":"https://openalex.org/I51783024","display_name":"Brandenburg University of Technology Cottbus-Senftenberg","ror":"https://ror.org/02wxx3e24","country_code":"DE","type":"education","lineage":["https://openalex.org/I51783024"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Monika Heiner","raw_affiliation_strings":["Dept. of Computer Science, Brandendenburg University of Technology at Cottbus, Postbox 10 13 44, 03013, Cottbus, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Brandendenburg University of Technology at Cottbus, Postbox 10 13 44, 03013, Cottbus, Germany","institution_ids":["https://openalex.org/I51783024"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020560256","display_name":"Andrea Sackmann","orcid":null},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Andrea Sackmann","raw_affiliation_strings":["Pozna\u0144 University of Technology, Institute of Computing Science, ul. Piotrowo 2, 60-965, Pozna\u0144, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pozna\u0144 University of Technology, Institute of Computing Science, ul. Piotrowo 2, 60-965, Pozna\u0144, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068201400","display_name":"Bj\u00f6rn H. Junker","orcid":"https://orcid.org/0000-0001-5818-9764"},"institutions":[{"id":"https://openalex.org/I4210127902","display_name":"Leibniz Institute of Plant Genetics and Crop Plant Research","ror":"https://ror.org/02skbsp27","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210127902"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bj\u00f6rn H Junker","raw_affiliation_strings":["Dept. of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany","institution_ids":["https://openalex.org/I4210127902"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001922122","display_name":"Stefanie Grunwald","orcid":"https://orcid.org/0000-0002-3899-5424"},"institutions":[{"id":"https://openalex.org/I129643931","display_name":"Berliner Hochschule f\u00fcr Technik","ror":"https://ror.org/00w7whj55","country_code":"DE","type":"education","lineage":["https://openalex.org/I129643931"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stefanie Grunwald","raw_affiliation_strings":["Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr. 64, 13347, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr. 64, 13347, Berlin, Germany","institution_ids":["https://openalex.org/I129643931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103408024","display_name":"Astrid Speer","orcid":null},"institutions":[{"id":"https://openalex.org/I129643931","display_name":"Berliner Hochschule f\u00fcr Technik","ror":"https://ror.org/00w7whj55","country_code":"DE","type":"education","lineage":["https://openalex.org/I129643931"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Astrid Speer","raw_affiliation_strings":["Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr. 64, 13347, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr. 64, 13347, Berlin, Germany","institution_ids":["https://openalex.org/I129643931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002744164","display_name":"Katja Winder","orcid":null},"institutions":[{"id":"https://openalex.org/I51783024","display_name":"Brandenburg University of Technology Cottbus-Senftenberg","ror":"https://ror.org/02wxx3e24","country_code":"DE","type":"education","lineage":["https://openalex.org/I51783024"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Katja Winder","raw_affiliation_strings":["Dept. of Computer Science, Brandendenburg University of Technology at Cottbus, Postbox 10 13 44, 03013, Cottbus, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Brandendenburg University of Technology at Cottbus, Postbox 10 13 44, 03013, Cottbus, Germany","institution_ids":["https://openalex.org/I51783024"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015346451","display_name":"Ina Koch","orcid":"https://orcid.org/0000-0002-3621-003X"},"institutions":[{"id":"https://openalex.org/I129643931","display_name":"Berliner Hochschule f\u00fcr Technik","ror":"https://ror.org/00w7whj55","country_code":"DE","type":"education","lineage":["https://openalex.org/I129643931"]},{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ina Koch","raw_affiliation_strings":["Dept. Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany","Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr. 64, 13347, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr. 64, 13347, Berlin, Germany","institution_ids":["https://openalex.org/I129643931"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5015346451","https://openalex.org/A5077536951"],"corresponding_institution_ids":["https://openalex.org/I129643931","https://openalex.org/I4210142260","https://openalex.org/I90812881"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":4.6272,"has_fulltext":true,"cited_by_count":86,"citation_normalized_percentile":{"value":0.95361812,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"90","last_page":"90"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4032999873161316,"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":0.4032999873161316,"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":0.3749000132083893,"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":0.026000000536441803,"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/petri-net","display_name":"Petri net","score":0.8133124113082886},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7088823318481445},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5584532618522644},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5534826517105103},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5361032485961914},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5185242891311646},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.47358375787734985},{"id":"https://openalex.org/keywords/associative-property","display_name":"Associative property","score":0.456814169883728},{"id":"https://openalex.org/keywords/subnetwork","display_name":"Subnetwork","score":0.45349180698394775},{"id":"https://openalex.org/keywords/invariant","display_name":"Invariant (physics)","score":0.42585939168930054},{"id":"https://openalex.org/keywords/experimental-data","display_name":"Experimental data","score":0.4194682240486145},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4164705276489258},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37799710035324097},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2687148153781891},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.22292062640190125},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1666181981563568},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1556636393070221},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13459008932113647}],"concepts":[{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.8133124113082886},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7088823318481445},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5584532618522644},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5534826517105103},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5361032485961914},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5185242891311646},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.47358375787734985},{"id":"https://openalex.org/C159423971","wikidata":"https://www.wikidata.org/wiki/Q177251","display_name":"Associative property","level":2,"score":0.456814169883728},{"id":"https://openalex.org/C2780186347","wikidata":"https://www.wikidata.org/wiki/Q11414","display_name":"Subnetwork","level":2,"score":0.45349180698394775},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.42585939168930054},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.4194682240486145},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4164705276489258},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37799710035324097},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2687148153781891},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.22292062640190125},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1666181981563568},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1556636393070221},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13459008932113647},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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":"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":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"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":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-9-90","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-90","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-90","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18257938","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18257938","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:62efac4377114d1794712912fabb99fd","is_oa":false,"landing_page_url":"https://doaj.org/article/62efac4377114d1794712912fabb99fd","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"BMC Bioinformatics, Vol 9, Iss 1, p 90 (2008)","raw_type":"article"},{"id":"pmh:oai:edoc.mpg.de:403156","is_oa":true,"landing_page_url":"http://edoc.mpg.de/403156","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, v.9, 90-90 (2008)","raw_type":"Article"},{"id":"pmh:oai:kops.uni-konstanz.de:123456789/40278","is_oa":true,"landing_page_url":"http://nbn-resolving.de/urn:nbn:de:bsz:352-0-427720","pdf_url":null,"source":{"id":"https://openalex.org/S4306401487","display_name":"KOPS (University of Konstanz)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189712700","host_organization_name":"University of Konstanz","host_organization_lineage":["https://openalex.org/I189712700"],"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":"","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2277402","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2277402","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-90","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-90","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-90","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7456479604","display_name":null,"funder_award_id":"0312705D","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1964012101.pdf","grobid_xml":"https://content.openalex.org/works/W1964012101.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W14215981","https://openalex.org/W94183112","https://openalex.org/W143456117","https://openalex.org/W249159571","https://openalex.org/W1505489763","https://openalex.org/W1514247755","https://openalex.org/W1544455702","https://openalex.org/W1573621493","https://openalex.org/W1740816575","https://openalex.org/W1780605602","https://openalex.org/W1807981783","https://openalex.org/W1814244002","https://openalex.org/W1963547452","https://openalex.org/W1963678392","https://openalex.org/W1987971958","https://openalex.org/W1993980414","https://openalex.org/W1994188141","https://openalex.org/W1996109622","https://openalex.org/W2000184633","https://openalex.org/W2009570821","https://openalex.org/W2011835017","https://openalex.org/W2028912942","https://openalex.org/W2029064186","https://openalex.org/W2037614307","https://openalex.org/W2042605932","https://openalex.org/W2051224630","https://openalex.org/W2063465221","https://openalex.org/W2067958620","https://openalex.org/W2084202592","https://openalex.org/W2088842371","https://openalex.org/W2097706568","https://openalex.org/W2102740981","https://openalex.org/W2103170157","https://openalex.org/W2108654339","https://openalex.org/W2112332161","https://openalex.org/W2128276963","https://openalex.org/W2131429754","https://openalex.org/W2133098435","https://openalex.org/W2134784304","https://openalex.org/W2148190806","https://openalex.org/W2149640111","https://openalex.org/W2153373497","https://openalex.org/W2157390113","https://openalex.org/W2161621619","https://openalex.org/W2169810918","https://openalex.org/W2172251739","https://openalex.org/W2320309238","https://openalex.org/W2412839122","https://openalex.org/W2500342052","https://openalex.org/W2612166593","https://openalex.org/W2911260754","https://openalex.org/W2914082976","https://openalex.org/W4240119503","https://openalex.org/W4245668478","https://openalex.org/W4299438414","https://openalex.org/W4301808069"],"related_works":["https://openalex.org/W2478888221","https://openalex.org/W2095452756","https://openalex.org/W2155492529","https://openalex.org/W4252504573","https://openalex.org/W15348386","https://openalex.org/W2158714033","https://openalex.org/W2767183729","https://openalex.org/W2521885831","https://openalex.org/W2099991711","https://openalex.org/W78967844"],"abstract_inverted_index":{"BACKGROUND:":[0],"Structural":[1],"analysis":[2],"of":[3,17,21,38,43,54,73,75,86,114,120,122,150,182,196,226,230,288,330,360,373,378,423,440,445,454],"biochemical":[4,190,456],"networks":[5,27],"is":[6,47,65,93,143,206,300],"a":[7,29,83,179,239,311,323,374,416],"growing":[8,48],"field":[9],"in":[10,219,265,319,351,357],"bioinformatics":[11],"and":[12,134,222,262,322,399,438],"systems":[13],"biology.":[14],"The":[15,41],"availability":[16],"an":[18,211],"increasing":[19,168],"amount":[20,42,53,85],"biological":[22,26,198,233,411,421],"data":[23,46,71,115,436],"from":[24],"molecular":[25],"promises":[28],"deeper":[30],"understanding":[31,225],"but":[32,95,111],"confronts":[33],"researchers":[34],"with":[35,248,267,407],"the":[36,52,112,118,123,148,151,164,171,193,197,224,227,231,285,294,337,352,358,361,368,380,386,393,410,420,433],"problem":[37],"combinatorial":[39],"explosion.":[40],"qualitative":[44,87,136,455],"network":[45,249,327,441],"much":[49],"faster":[50],"than":[51],"quantitative":[55,70],"data,":[56,88,92],"such":[57,89,255],"as":[58,90,256,281,309,348,365,367],"enzyme":[59],"kinetics.":[60],"In":[61,371],"many":[62,121],"cases":[63],"it":[64,96,129],"even":[66],"impossible":[67],"to":[68,131,160,185,242,246,271,290,409,432,465],"measure":[69],"because":[72],"limitations":[74],"experimental":[76],"methods,":[77,392],"or":[78],"for":[79,101,189,292,404,419,451],"ethical":[80],"reasons.":[81],"Thus,":[82,210],"huge":[84,180],"interaction":[91],"available,":[94],"was":[97],"not":[98,207],"sufficiently":[99],"used":[100],"modeling":[102],"purposes,":[103],"until":[104],"now.":[105],"New":[106],"approaches":[107],"have":[108],"been":[109],"developed,":[110],"complexity":[113],"often":[116],"limits":[117],"application":[119],"methods.":[124,370],"Biochemical":[125],"Petri":[126,140,191,424,457],"nets":[127],"make":[128],"possible":[130,208],"explore":[132],"static":[133],"dynamic":[135],"system":[137,166,169],"properties.":[138],"One":[139],"net":[141,425],"approach":[142,241,418,460],"model":[144,452],"validation":[145,187,453],"based":[146,427],"on":[147,156,428],"computation":[149],"system's":[152],"invariant":[153],"properties,":[154],"focusing":[155],"t-invariants.":[157,183],"T-invariants":[158],"correspond":[159],"subnetworks,":[161],"which":[162,277,343],"describe":[163],"basic":[165,172,228],"behavior.With":[167],"complexity,":[170],"behavior":[173,229],"can":[174,278,447,461],"only":[175],"be":[176,217,279,345,448,463],"expressed":[177],"by":[178,200],"number":[181,287],"According":[184],"our":[186],"criteria":[188],"nets,":[192],"necessary":[194],"verification":[195],"meaning,":[199],"interpreting":[201],"each":[202],"subnetwork":[203],"(t-invariant)":[204],"manually,":[205],"anymore.":[209],"automated,":[212],"biologically":[213,273,347,375,434],"meaningful":[214,274,376,435],"classification":[215,377,422],"would":[216],"helpful":[218],"analyzing":[220],"t-invariants,":[221,379],"supporting":[223],"considered":[232,304],"system.":[234],"METHODS:":[235],"Here,":[236],"we":[237],"introduce":[238],"new":[240,417],"automatically":[243,335],"classify":[244],"t-invariants":[245,338,406,426,446],"cope":[247],"complexity.":[250],"We":[251,303,334,354,414],"apply":[252],"clustering":[253,369,391,405],"techniques":[254],"UPGMA,":[257],"Complete":[258,400],"Linkage,":[259,261],"Single":[260],"Neighbor":[263],"Joining":[264],"combination":[266],"different":[268,306],"distance":[269,363,388],"measures":[270,364],"get":[272],"clusters":[275],"(t-clusters),":[276],"interpreted":[280,346],"modules.":[282],"To":[283],"find":[284],"optimal":[286],"t-clusters":[289],"consider":[291],"interpretation,":[293],"cluster":[295,429],"validity":[296],"measure,":[297],"Silhouette":[298],"Width,":[299],"applied.":[301],"RESULTS:":[302],"two":[305],"case":[307],"studies":[308],"examples:":[310],"small":[312],"signal":[313],"transduction":[314],"pathway":[315,318],"(pheromone":[316],"response":[317],"Saccharomyces":[320],"cerevisiae)":[321],"medium-sized":[324],"gene":[325],"regulatory":[326],"(gene":[328],"regulation":[329],"Duchenne":[331],"muscular":[332],"dystrophy).":[333],"classified":[336],"into":[339],"functionally":[340],"distinct":[341],"t-clusters,":[342],"could":[344],"functional":[349],"modules":[350],"network.":[353],"found":[355],"differences":[356],"suitability":[359],"various":[362],"well":[366],"terms":[372],"best":[381],"results":[382,395],"are":[383,402],"obtained":[384,394],"using":[385],"Tanimoto":[387],"measure.":[389],"Considering":[390],"suggest":[396],"that":[397],"UPGMA":[398],"Linkage":[401],"suitable":[403],"respect":[408],"interpretability.":[412],"CONCLUSION:":[413],"propose":[415],"analysis.":[430,468],"Due":[431],"reduction":[437],"structuring":[439],"processes,":[442],"large":[443],"sets":[444],"evaluated,":[449],"allowing":[450],"nets.":[458],"This":[459],"also":[462],"applied":[464],"elementary":[466],"mode":[467]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":5}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}