{"id":"https://openalex.org/W4388599466","doi":"https://doi.org/10.1093/bioinformatics/btad678","title":"Exploiting the structure of biochemical pathways to investigate dynamical properties with neural networks for graphs","display_name":"Exploiting the structure of biochemical pathways to investigate dynamical properties with neural networks for graphs","publication_year":2023,"publication_date":"2023-11-01","ids":{"openalex":"https://openalex.org/W4388599466","doi":"https://doi.org/10.1093/bioinformatics/btad678","pmid":"https://pubmed.ncbi.nlm.nih.gov/37951586"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad678","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad678","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad678/53267807/btad678.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/btad678/53267807/btad678.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078841880","display_name":"Michele Fontanesi","orcid":"https://orcid.org/0009-0004-7566-903X"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Michele Fontanesi","raw_affiliation_strings":["Department of Computer Science, University of Pisa , 56127 Pisa, Italy","Department of Computer Science, University of Pisa, Pisa, 56127, Italy ()"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Pisa , 56127 Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]},{"raw_affiliation_string":"Department of Computer Science, University of Pisa, Pisa, 56127, Italy ()","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010923663","display_name":"Alessio Micheli","orcid":"https://orcid.org/0000-0001-5764-5238"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessio Micheli","raw_affiliation_strings":["Department of Computer Science, University of Pisa , 56127 Pisa, Italy","Department of Computer Science, University of Pisa, Pisa, 56127, Italy ()"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Pisa , 56127 Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]},{"raw_affiliation_string":"Department of Computer Science, University of Pisa, Pisa, 56127, Italy ()","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038730637","display_name":"Paolo Milazzo","orcid":"https://orcid.org/0000-0002-7309-6424"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Milazzo","raw_affiliation_strings":["Department of Computer Science, University of Pisa , 56127 Pisa, Italy","Department of Computer Science, University of Pisa, Pisa, 56127, Italy ()"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Pisa , 56127 Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]},{"raw_affiliation_string":"Department of Computer Science, University of Pisa, Pisa, 56127, Italy ()","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027095496","display_name":"Marco Podda","orcid":"https://orcid.org/0000-0003-1497-9515"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Podda","raw_affiliation_strings":["Department of Computer Science, University of Pisa , 56127 Pisa, Italy","Department of Computer Science, University of Pisa, Pisa, 56127, Italy ()"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Pisa , 56127 Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]},{"raw_affiliation_string":"Department of Computer Science, University of Pisa, Pisa, 56127, Italy ()","institution_ids":["https://openalex.org/I108290504"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5078841880"],"corresponding_institution_ids":["https://openalex.org/I108290504"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.609,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.70921053,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"39","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9975000023841858,"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":0.9934999942779541,"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":0.7374669909477234},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7284631729125977},{"id":"https://openalex.org/keywords/dynamical-systems-theory","display_name":"Dynamical systems theory","score":0.7093770503997803},{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.683668851852417},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.6009097099304199},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5308096408843994},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5118715167045593},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.491072416305542},{"id":"https://openalex.org/keywords/dynamical-system","display_name":"Dynamical system (definition)","score":0.4707762897014618},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4413468539714813},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.437669038772583},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32879143953323364},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.26485496759414673},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.16508299112319946},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09997421503067017},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08643355965614319}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.7374669909477234},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7284631729125977},{"id":"https://openalex.org/C79379906","wikidata":"https://www.wikidata.org/wiki/Q3174497","display_name":"Dynamical systems theory","level":2,"score":0.7093770503997803},{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.683668851852417},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6009097099304199},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5308096408843994},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5118715167045593},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.491072416305542},{"id":"https://openalex.org/C33962884","wikidata":"https://www.wikidata.org/wiki/Q378637","display_name":"Dynamical system (definition)","level":3,"score":0.4707762897014618},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4413468539714813},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.437669038772583},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32879143953323364},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26485496759414673},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.16508299112319946},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09997421503067017},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08643355965614319},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad678","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad678","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad678/53267807/btad678.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:37951586","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37951586","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:arpi.unipi.it:11568/1214152","is_oa":true,"landing_page_url":"https://academic.oup.com/bioinformatics/article/39/11/btad678/7407341","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/11/btad678/53453457/btad678.pdf","source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10651430","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10651430","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10651430/pdf/btad678.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"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/btad678","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad678","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad678/53267807/btad678.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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6600000262260437}],"awards":[{"id":"https://openalex.org/G1016895160","display_name":null,"funder_award_id":"PNRR-M4C2","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G1115267702","display_name":null,"funder_award_id":"ECS00000017","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4508289328","display_name":null,"funder_award_id":"PE00000013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5376833654","display_name":null,"funder_award_id":"I53C22000780001","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8409961469","display_name":null,"funder_award_id":"Spoke 1","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8471708736","display_name":null,"funder_award_id":"CUP I53C22000780001","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8893660128","display_name":null,"funder_award_id":"PE0000001","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388599466.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W100464641","https://openalex.org/W133158124","https://openalex.org/W999207820","https://openalex.org/W1756205400","https://openalex.org/W1970661255","https://openalex.org/W1996074994","https://openalex.org/W2011923356","https://openalex.org/W2021713927","https://openalex.org/W2050341914","https://openalex.org/W2053145248","https://openalex.org/W2139906443","https://openalex.org/W2141755357","https://openalex.org/W2150908245","https://openalex.org/W2155418451","https://openalex.org/W2159807606","https://openalex.org/W2295288655","https://openalex.org/W2903545591","https://openalex.org/W2907492528","https://openalex.org/W2970119293","https://openalex.org/W2980427985","https://openalex.org/W2988361147","https://openalex.org/W2997785591","https://openalex.org/W4210257598","https://openalex.org/W4211017114","https://openalex.org/W6625977169","https://openalex.org/W6756925018","https://openalex.org/W6770460946"],"related_works":["https://openalex.org/W2045478141","https://openalex.org/W4250831671","https://openalex.org/W2230606337","https://openalex.org/W2118803783","https://openalex.org/W2129999614","https://openalex.org/W2089869689","https://openalex.org/W4388681848","https://openalex.org/W2078952919","https://openalex.org/W2945666329","https://openalex.org/W2617651062"],"abstract_inverted_index":{"https://github.com/marcopodda/petri-bio":[0],"(code),":[1],"https://zenodo.org/record/7610382":[2],"(data).":[3]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
