{"id":"https://openalex.org/W4396526543","doi":"https://doi.org/10.1093/bioinformatics/btae266","title":"BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities","display_name":"BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities","publication_year":2024,"publication_date":"2024-04-29","ids":{"openalex":"https://openalex.org/W4396526543","doi":"https://doi.org/10.1093/bioinformatics/btae266","pmid":"https://pubmed.ncbi.nlm.nih.gov/38688585"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae266","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae266","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btae266","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059311338","display_name":"Telmo Blasco","orcid":"https://orcid.org/0000-0001-7819-8668"},"institutions":[{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Telmo Blasco","raw_affiliation_strings":["Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain"],"raw_orcid":"https://orcid.org/0000-0001-7819-8668","affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain","institution_ids":["https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067155110","display_name":"Francesco Balzerani","orcid":"https://orcid.org/0000-0002-5608-5766"},"institutions":[{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Francesco Balzerani","raw_affiliation_strings":["Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain","institution_ids":["https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040584996","display_name":"Luis V. Valc\u00e1rcel","orcid":"https://orcid.org/0000-0003-3769-5419"},"institutions":[{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Luis V Valc\u00e1rcel","raw_affiliation_strings":["Biomedical Engineering Center, Campus Universitario, University of Navarra , Pamplona, Navarra 31009, Spain","Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain","Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), Campus Universitario, University of Navarra , Pamplona 31080, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Engineering Center, Campus Universitario, University of Navarra , Pamplona, Navarra 31009, Spain","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), Campus Universitario, University of Navarra , Pamplona 31080, Spain","institution_ids":["https://openalex.org/I88155538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049812833","display_name":"Pedro Larra\u00f1aga","orcid":"https://orcid.org/0000-0003-0652-9872"},"institutions":[{"id":"https://openalex.org/I88060688","display_name":"Universidad Polit\u00e9cnica de Madrid","ror":"https://ror.org/03n6nwv02","country_code":"ES","type":"education","lineage":["https://openalex.org/I88060688"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Pedro Larra\u00f1aga","raw_affiliation_strings":["Departamento de Inteligencia Artificial, Universidad Polit\u00e9cnica de Madrid , Madrid 28660, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Inteligencia Artificial, Universidad Polit\u00e9cnica de Madrid , Madrid 28660, Spain","institution_ids":["https://openalex.org/I88060688"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010920098","display_name":"Concha Bielza","orcid":"https://orcid.org/0000-0001-7109-2668"},"institutions":[{"id":"https://openalex.org/I88060688","display_name":"Universidad Polit\u00e9cnica de Madrid","ror":"https://ror.org/03n6nwv02","country_code":"ES","type":"education","lineage":["https://openalex.org/I88060688"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Concha Bielza","raw_affiliation_strings":["Departamento de Inteligencia Artificial, Universidad Polit\u00e9cnica de Madrid , Madrid 28660, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Inteligencia Artificial, Universidad Polit\u00e9cnica de Madrid , Madrid 28660, Spain","institution_ids":["https://openalex.org/I88060688"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021297859","display_name":"M. Pilar Francino","orcid":"https://orcid.org/0000-0002-4510-5653"},"institutions":[{"id":"https://openalex.org/I2801357902","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886","country_code":"ES","type":"funder","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210097149","display_name":"Fundaci\u00f3n para el Fomento de la Investigaci\u00f3n Sanitaria y Biom\u00e9dica de la Comunitat Valenciana","ror":"https://ror.org/0116vew40","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210097149"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Mar\u00eda Pilar Francino","raw_affiliation_strings":["Area de Gen\u00f3mica y Salud, Fundaci\u00f3n para el Fomento de la Investigaci\u00f3n Sanitaria y Biom\u00e9dica de la Comunitat Valenciana-Salud P\u00fablica , Valencia 46020, Spain","CIBER en Epidemiolog\u00eda y Salud P\u00fablica, Instituto de Salud Carlos III , Madrid 28029, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Area de Gen\u00f3mica y Salud, Fundaci\u00f3n para el Fomento de la Investigaci\u00f3n Sanitaria y Biom\u00e9dica de la Comunitat Valenciana-Salud P\u00fablica , Valencia 46020, Spain","institution_ids":["https://openalex.org/I4210097149"]},{"raw_affiliation_string":"CIBER en Epidemiolog\u00eda y Salud P\u00fablica, Instituto de Salud Carlos III , Madrid 28029, Spain","institution_ids":["https://openalex.org/I2801357902"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024132001","display_name":"Jos\u00e9 \u00c1ngel Rufi\u00e1n\u2010Henares","orcid":"https://orcid.org/0000-0002-1428-4353"},"institutions":[{"id":"https://openalex.org/I173304897","display_name":"Universidad de Granada","ror":"https://ror.org/04njjy449","country_code":"ES","type":"education","lineage":["https://openalex.org/I173304897"]},{"id":"https://openalex.org/I4210113665","display_name":"Instituto de Investigaci\u00f3n Biosanitaria de Granada","ror":"https://ror.org/026yy9j15","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210113665"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 \u00c1ngel Rufi\u00e1n-Henares","raw_affiliation_strings":["Departamento de Nutrici\u00f3n y Bromatolog\u00eda, Centro de Investigaci\u00f3n Biom\u00e9dica, Instituto de Nutrici\u00f3n y Tecnolog\u00eda de los Alimentos, Universidad de Granada , Granada 18016, Spain","Instituto de Investigaci\u00f3n Biosanitaria ibs. GRANADA, Universidad de Granada , Granada 18012, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Nutrici\u00f3n y Bromatolog\u00eda, Centro de Investigaci\u00f3n Biom\u00e9dica, Instituto de Nutrici\u00f3n y Tecnolog\u00eda de los Alimentos, Universidad de Granada , Granada 18016, Spain","institution_ids":["https://openalex.org/I173304897"]},{"raw_affiliation_string":"Instituto de Investigaci\u00f3n Biosanitaria ibs. GRANADA, Universidad de Granada , Granada 18012, Spain","institution_ids":["https://openalex.org/I173304897","https://openalex.org/I4210113665"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010754980","display_name":"Francisco J. Planes","orcid":"https://orcid.org/0000-0003-1155-3105"},"institutions":[{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Francisco J Planes","raw_affiliation_strings":["Biomedical Engineering Center, Campus Universitario, University of Navarra , Pamplona, Navarra 31009, Spain","Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain","Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), Campus Universitario, University of Navarra , Pamplona 31080, Spain"],"raw_orcid":"https://orcid.org/0000-0003-1155-3105","affiliations":[{"raw_affiliation_string":"Biomedical Engineering Center, Campus Universitario, University of Navarra , Pamplona, Navarra 31009, Spain","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), Campus Universitario, University of Navarra , Pamplona 31080, Spain","institution_ids":["https://openalex.org/I88155538"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056014601","display_name":"Sergio P\u00e9rez-Burillo","orcid":"https://orcid.org/0000-0001-6398-7496"},"institutions":[{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Sergio P\u00e9rez-Burillo","raw_affiliation_strings":["Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain","institution_ids":["https://openalex.org/I88155538"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6238,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.8288302,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"40","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.967199981212616,"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/T10066","display_name":"Gut microbiota and health","score":0.967199981212616,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.007899999618530273,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13984","display_name":"Nutrition, Genetics, and Disease","score":0.003000000026077032,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/computational-biology","display_name":"Computational biology","score":0.5433638095855713},{"id":"https://openalex.org/keywords/ascorbic-acid","display_name":"Ascorbic acid","score":0.532353401184082},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.4668598473072052},{"id":"https://openalex.org/keywords/microbial-metabolism","display_name":"Microbial metabolism","score":0.4642323851585388},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4541754424571991},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4495191276073456},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.44782555103302},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.43745455145835876},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.38709962368011475},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32876068353652954},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26188135147094727},{"id":"https://openalex.org/keywords/food-science","display_name":"Food science","score":0.24350610375404358},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21710336208343506},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21227014064788818},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1707746982574463},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10666346549987793}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5433638095855713},{"id":"https://openalex.org/C2986274086","wikidata":"https://www.wikidata.org/wiki/Q199678","display_name":"Ascorbic acid","level":2,"score":0.532353401184082},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.4668598473072052},{"id":"https://openalex.org/C101014631","wikidata":"https://www.wikidata.org/wiki/Q4889568","display_name":"Microbial metabolism","level":3,"score":0.4642323851585388},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4541754424571991},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4495191276073456},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.44782555103302},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.43745455145835876},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.38709962368011475},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32876068353652954},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26188135147094727},{"id":"https://openalex.org/C31903555","wikidata":"https://www.wikidata.org/wiki/Q1637030","display_name":"Food science","level":1,"score":0.24350610375404358},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21710336208343506},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21227014064788818},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1707746982574463},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10666346549987793}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btae266","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae266","pdf_url":null,"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:38688585","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38688585","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:dadun.unav.edu:10171/70158","is_oa":true,"landing_page_url":"https://hdl.handle.net/10171/70158","pdf_url":"https://dadun.unav.edu/bitstream/10171/70158/1/btae266.pdf","source":{"id":"https://openalex.org/S4306401514","display_name":"Deposito Adademico Digital Universidad De Navarra (University of Navarra)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I88155538","host_organization_name":"Universidad de Navarra","host_organization_lineage":["https://openalex.org/I88155538"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:digibug.ugr.es:10481/93218","is_oa":true,"landing_page_url":"https://hdl.handle.net/10481/93218","pdf_url":"https://digibug.ugr.es/bitstream/10481/93218/1/btae266.pdf","source":{"id":"https://openalex.org/S4306400567","display_name":"Institutional Repository of the University of Granada (University of Granada)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173304897","host_organization_name":"Universidad de Granada","host_organization_lineage":["https://openalex.org/I173304897"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:riuma.uma.es:10630/38629","is_oa":true,"landing_page_url":"https://hdl.handle.net/10630/38629","pdf_url":"https://riuma.uma.es/xmlui/bitstream/10630/38629/1/49%20BN_BacArena.pdf","source":{"id":"https://openalex.org/S4306401385","display_name":"Repositorio Institucional de la Universidad de M\u00e1laga (University of M\u00e1laga)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I82767444","host_organization_name":"Universidad de M\u00e1laga","host_organization_lineage":["https://openalex.org/I82767444"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11082422","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11082422","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"},{"id":"pmh:oai:dadun.unav.edu:10171/70204","is_oa":true,"landing_page_url":"https://hdl.handle.net/10171/70204","pdf_url":null,"source":{"id":"https://openalex.org/S4306401514","display_name":"Deposito Adademico Digital Universidad De Navarra (University of Navarra)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I88155538","host_organization_name":"Universidad de Navarra","host_organization_lineage":["https://openalex.org/I88155538"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae266","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae266","pdf_url":null,"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":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.7300000190734863}],"awards":[{"id":"https://openalex.org/G5515204682","display_name":"Smart Technologies for personAlised Nutrition and Consumer Engagement","funder_award_id":"816303","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"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320323834","display_name":"Universidad de Granada","ror":"https://ror.org/04njjy449"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1933114814","https://openalex.org/W2034285706","https://openalex.org/W2070495282","https://openalex.org/W2078355959","https://openalex.org/W2110065044","https://openalex.org/W2115701239","https://openalex.org/W2128088446","https://openalex.org/W2159080219","https://openalex.org/W2168175751","https://openalex.org/W2170551349","https://openalex.org/W2283457166","https://openalex.org/W2375532565","https://openalex.org/W2401404581","https://openalex.org/W2559597060","https://openalex.org/W2617261748","https://openalex.org/W2762019694","https://openalex.org/W2900697674","https://openalex.org/W2920925854","https://openalex.org/W2941179678","https://openalex.org/W2949418748","https://openalex.org/W3164249831","https://openalex.org/W3190067671","https://openalex.org/W3206959204","https://openalex.org/W4285093271","https://openalex.org/W4381951907"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W2085044184","https://openalex.org/W3135997498","https://openalex.org/W4290258708","https://openalex.org/W2239919633","https://openalex.org/W3139084279"],"abstract_inverted_index":{"MOTIVATION:":[0],"Simulating":[1],"gut":[2,149,171],"microbial":[3,23],"dynamics":[4],"is":[5],"extremely":[6],"challenging.":[7],"Several":[8],"computational":[9,69],"tools,":[10],"notably":[11],"the":[12,22,50,64,67,98,108,139,148,163,169],"widely":[13],"used":[14],"BacArena,":[15],"enable":[16],"modeling":[17,165],"of":[18,60,71,95,110,143,168],"dynamic":[19,164],"changes":[20],"in":[21,45,49,84,147,183],"environment.":[24],"These":[25],"methods,":[26],"however,":[27],"do":[28],"not":[29],"comprehensively":[30],"account":[31],"for":[32,39,78,162],"microbe-microbe":[33,79],"stimulant":[34],"or":[35,38],"inhibitory":[36,41],"effects":[37],"nutrient-microbe":[40,81],"effects,":[42],"typically":[43],"observed":[44],"different":[46,152],"compounds":[47,111],"present":[48,56],"daily":[51],"diet.":[52],"RESULTS:":[53],"Here,":[54],"we":[55],"BN-BacArena,":[57],"an":[58],"extension":[59],"BacArena":[61,136],"consisting":[62],"on":[63],"incorporation":[65],"within":[66],"native":[68],"framework":[70],"a":[72,131,156],"Bayesian":[73,100],"network":[74,101],"model":[75],"that":[76],"accounts":[77],"and":[80,92,118,121,166,178],"interactions.":[82],"Using":[83],"vitro":[85],"experiments,":[86],"16S":[87],"rRNA":[88],"gene":[89],"sequencing":[90],"data":[91],"nutritional":[93,153],"composition":[94],"55":[96],"foods,":[97],"output":[99],"showed":[102],"23":[103],"significant":[104,124,133],"nutrient-bacteria":[105],"interactions,":[106],"suggesting":[107],"importance":[109],"such":[112],"as":[113],"polyols,":[114],"ascorbic":[115],"acid,":[116],"polyphenols":[117],"other":[119],"phytochemicals,":[120],"40":[122],"bacteria-bacteria":[123],"relationships.":[125],"With":[126],"test":[127],"data,":[128],"BN-BacArena":[129,158],"demonstrates":[130],"statistically":[132],"improvement":[134],"over":[135],"to":[137],"predict":[138],"time-dependent":[140],"relative":[141],"abundance":[142],"bacterial":[144],"species":[145],"involved":[146],"microbiota":[150,172],"upon":[151],"interventions.":[154],"As":[155],"result,":[157],"opens":[159],"new":[160],"avenues":[161],"simulation":[167],"human":[170],"metabolism.":[173],"AVAILABILITY":[174],"AND":[175],"IMPLEMENTATION:":[176],"MATLAB":[177],"R":[179],"code":[180],"are":[181],"available":[182],"https://github.com/PlanesLab/BN-BacArena.":[184]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
