{"id":"https://openalex.org/W2104803510","doi":"https://doi.org/10.1186/1752-0509-2-111","title":"Metabolic pathway alignment between species using a comprehensive and flexible similarity measure","display_name":"Metabolic pathway alignment between species using a comprehensive and flexible similarity measure","publication_year":2008,"publication_date":"2008-12-01","ids":{"openalex":"https://openalex.org/W2104803510","doi":"https://doi.org/10.1186/1752-0509-2-111","mag":"2104803510","pmid":"https://pubmed.ncbi.nlm.nih.gov/19108747"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-2-111","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-2-111","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-2-111","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-2-111","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102862614","display_name":"Yunlei Li","orcid":"https://orcid.org/0000-0002-5697-1602"},"institutions":[{"id":"https://openalex.org/I2801582894","display_name":"Netherlands Bioinformatics Centre","ror":"https://ror.org/01r0k6965","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I2801582894"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Yunlei Li","raw_affiliation_strings":["Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, the Netherlands. y.li@tudelft.nl","Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands","Netherlands Bioinformatics Centre, 260 NBIC, Nijmegen, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, the Netherlands. y.li@tudelft.nl","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Netherlands Bioinformatics Centre, 260 NBIC, Nijmegen, the Netherlands","institution_ids":["https://openalex.org/I2801582894"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080533789","display_name":"Dick de Ridder","orcid":"https://orcid.org/0000-0002-4944-4310"},"institutions":[{"id":"https://openalex.org/I2801582894","display_name":"Netherlands Bioinformatics Centre","ror":"https://ror.org/01r0k6965","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I2801582894"]},{"id":"https://openalex.org/I4210127603","display_name":"Cancer Genomics Centre","ror":"https://ror.org/02y9qjz38","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210127603"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Dick de Ridder","raw_affiliation_strings":["Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, Delft, CD, 2628, the Netherlands","Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 9101, Julianalaan 67, Delft, BC, 2628, the Netherlands","Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, Mekelweg 4, Nijmegen, HB, 6500, the Netherlands","Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands","Netherlands Bioinformatics Centre, 260 NBIC, Nijmegen, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, Delft, CD, 2628, the Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 9101, Julianalaan 67, Delft, BC, 2628, the Netherlands","institution_ids":["https://openalex.org/I4210127603"]},{"raw_affiliation_string":"Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, Mekelweg 4, Nijmegen, HB, 6500, the Netherlands","institution_ids":["https://openalex.org/I2801582894"]},{"raw_affiliation_string":"Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Netherlands Bioinformatics Centre, 260 NBIC, Nijmegen, the Netherlands","institution_ids":["https://openalex.org/I2801582894"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113839595","display_name":"Marco J. L. de Groot","orcid":null},"institutions":[{"id":"https://openalex.org/I4210127603","display_name":"Cancer Genomics Centre","ror":"https://ror.org/02y9qjz38","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210127603"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Marco JL de Groot","raw_affiliation_strings":["Department of Biotechnology, Bioprocess Technology Group, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 67, P.O. Box 9101, Julianalaan 67, Delft, BC, 2628, the Netherlands","Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, Delft, CD, 2628, the Netherlands","Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 9101, Julianalaan 67, Delft, BC, 2628, the Netherlands","Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, Bioprocess Technology Group, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 67, P.O. Box 9101, Julianalaan 67, Delft, BC, 2628, the Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, Delft, CD, 2628, the Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 9101, Julianalaan 67, Delft, BC, 2628, the Netherlands","institution_ids":["https://openalex.org/I4210127603"]},{"raw_affiliation_string":"Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052699801","display_name":"Marcel Reinders","orcid":"https://orcid.org/0000-0002-1148-1562"},"institutions":[{"id":"https://openalex.org/I2801582894","display_name":"Netherlands Bioinformatics Centre","ror":"https://ror.org/01r0k6965","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I2801582894"]},{"id":"https://openalex.org/I4210127603","display_name":"Cancer Genomics Centre","ror":"https://ror.org/02y9qjz38","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210127603"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Marcel JT Reinders","raw_affiliation_strings":["Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, Delft, CD, 2628, the Netherlands","Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 9101, Julianalaan 67, Delft, BC, 2628, the Netherlands","Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, Mekelweg 4, Nijmegen, HB, 6500, the Netherlands","Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands","Netherlands Bioinformatics Centre, 260 NBIC, Nijmegen, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, Delft, CD, 2628, the Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 9101, Julianalaan 67, Delft, BC, 2628, the Netherlands","institution_ids":["https://openalex.org/I4210127603"]},{"raw_affiliation_string":"Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, Mekelweg 4, Nijmegen, HB, 6500, the Netherlands","institution_ids":["https://openalex.org/I2801582894"]},{"raw_affiliation_string":"Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Netherlands Bioinformatics Centre, 260 NBIC, Nijmegen, the Netherlands","institution_ids":["https://openalex.org/I2801582894"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102862614"],"corresponding_institution_ids":["https://openalex.org/I2801582894","https://openalex.org/I98358874"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":1.5601,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.82225811,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2","issue":"1","first_page":"111","last_page":"111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.883899986743927,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.883899986743927,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.06120000034570694,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.023099999874830246,"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/metabolic-pathway","display_name":"Metabolic pathway","score":0.7126877903938293},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6861326694488525},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.6665258407592773},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.6291379928588867},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6082439422607422},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5663471817970276},{"id":"https://openalex.org/keywords/metabolic-engineering","display_name":"Metabolic engineering","score":0.5276345610618591},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.48723307251930237},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4580255448818207},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.4533301591873169},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.41761332750320435},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4172452688217163},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.41022735834121704},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3592901825904846},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2939800024032593},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2800253629684448},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.23679843544960022},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21767351031303406},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12241283059120178},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.07786807417869568},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.07640686631202698}],"concepts":[{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.7126877903938293},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6861326694488525},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.6665258407592773},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6291379928588867},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6082439422607422},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5663471817970276},{"id":"https://openalex.org/C6350086","wikidata":"https://www.wikidata.org/wiki/Q6822347","display_name":"Metabolic engineering","level":3,"score":0.5276345610618591},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.48723307251930237},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4580255448818207},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.4533301591873169},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.41761332750320435},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4172452688217163},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.41022735834121704},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3592901825904846},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2939800024032593},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2800253629684448},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.23679843544960022},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21767351031303406},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12241283059120178},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.07786807417869568},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.07640686631202698},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","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":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1752-0509-2-111","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-2-111","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-2-111","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:19108747","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19108747","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 systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2677397","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2677397","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 Syst Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:39aa8a299a3944989901966af26003a0","is_oa":false,"landing_page_url":"https://doaj.org/article/39aa8a299a3944989901966af26003a0","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 Systems Biology, Vol 2, Iss 1, p 111 (2008)","raw_type":"article"},{"id":"pmh:oai:tudelft.nl:uuid:f1b98a46-15cd-470c-8052-a763d441a71d","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:f1b98a46-15cd-470c-8052-a763d441a71d","pdf_url":null,"source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"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":"journal article"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-2-111","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-2-111","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-2-111","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.5199999809265137}],"awards":[],"funders":[{"id":"https://openalex.org/F4320328786","display_name":"Norwegian Biodiversity Information Centre","ror":"https://ror.org/04jnzhb65"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2104803510.pdf","grobid_xml":"https://content.openalex.org/works/W2104803510.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W601739477","https://openalex.org/W1524662923","https://openalex.org/W1788277699","https://openalex.org/W1970737407","https://openalex.org/W1984249061","https://openalex.org/W1985051299","https://openalex.org/W1999649023","https://openalex.org/W2015705446","https://openalex.org/W2018045523","https://openalex.org/W2033719772","https://openalex.org/W2047496194","https://openalex.org/W2081622831","https://openalex.org/W2092899907","https://openalex.org/W2100438221","https://openalex.org/W2106202847","https://openalex.org/W2108859156","https://openalex.org/W2119497586","https://openalex.org/W2121773288","https://openalex.org/W2135445920","https://openalex.org/W2144885342","https://openalex.org/W2155254562","https://openalex.org/W2156721528","https://openalex.org/W2156966633","https://openalex.org/W2160648174","https://openalex.org/W2161062388","https://openalex.org/W2167065750","https://openalex.org/W2168157737","https://openalex.org/W2168491690","https://openalex.org/W2347998626","https://openalex.org/W3103786587","https://openalex.org/W4211054902","https://openalex.org/W4298226842"],"related_works":["https://openalex.org/W2402358048","https://openalex.org/W3022000530","https://openalex.org/W2991154838","https://openalex.org/W2338895903","https://openalex.org/W2126646394","https://openalex.org/W2966631026","https://openalex.org/W2556443379","https://openalex.org/W2148121172","https://openalex.org/W1992844569","https://openalex.org/W2072067873"],"abstract_inverted_index":{"BACKGROUND:":[0],"Comparative":[1],"analysis":[2],"of":[3,80,137,156],"metabolic":[4,21,70,78],"networks":[5,79],"in":[6,20,40,76,144,181,202],"multiple":[7],"species":[8,82,139,163],"yields":[9],"important":[10],"information":[11],"on":[12,48,110,196],"their":[13,44],"evolution,":[14],"and":[15,46,62,67,83,91,129,132,164,199,211],"has":[16],"great":[17],"practical":[18],"value":[19],"engineering,":[22],"human":[23],"disease":[24],"analysis,":[25],"drug":[26],"design":[27],"etc.":[28],"In":[29],"this":[30],"work,":[31],"we":[32,107,119],"aim":[33],"to":[34,167,193],"systematically":[35],"search":[36],"for":[37,65,209],"conserved":[38,69,125,147,169,204],"pathways":[39,112,123,176],"two":[41,81],"species,":[42,166],"quantify":[43],"similarities,":[45],"focus":[47,109],"the":[49,154],"variations":[50],"between":[51,126,162],"them.":[52],"RESULTS:":[53],"We":[54,171],"present":[55],"an":[56],"efficient":[57],"framework,":[58],"Metabolic":[59],"Pathway":[60],"Alignment":[61],"Scoring":[63],"(M-PAS),":[64],"identifying":[66],"ranking":[68],"pathways.":[71,148,170],"M-PAS":[72],"aligns":[73],"all":[74],"reactions":[75,198],"entire":[77],"assembles":[84],"them":[85],"into":[86,93],"pathways,":[87,205],"taking":[88],"mismatches,":[89],"gaps":[90],"crossovers":[92],"account.":[94],"It":[95],"uses":[96],"a":[97,138,141],"comprehensive":[98],"scoring":[99],"function,":[100],"which":[101,206],"quantifies":[102],"pathway":[103,187],"similarity":[104],"such":[105,177],"that":[106],"can":[108,191],"different":[111,114],"given":[113],"biological":[115],"motivations.":[116],"Using":[117],"M-PAS,":[118],"detected":[120],"1198":[121],"length-four":[122],"fully":[124],"Saccharomyces":[127],"cerevisiae":[128],"Escherichia":[130],"coli,":[131],"also":[133,184],"revealed":[134],"1399":[135],"cases":[136],"using":[140],"unique":[142],"route":[143],"otherwise":[145],"highly":[146,203],"CONCLUSION:":[149],"Our":[150,189],"method":[151],"efficiently":[152],"automates":[153],"process":[155],"exploring":[157],"reaction":[158],"arrangement":[159],"possibilities,":[160],"both":[161],"within":[165],"find":[168],"not":[172],"only":[173],"reconstruct":[174],"conventional":[175],"as":[178],"those":[179],"found":[180],"KEGG,":[182],"but":[183],"discover":[185],"new":[186],"possibilities.":[188],"results":[190],"help":[192],"generate":[194],"hypotheses":[195],"missing":[197],"manifest":[200],"differences":[201],"is":[207],"useful":[208],"biology":[210],"life":[212],"science":[213],"applications.":[214]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
