{"id":"https://openalex.org/W2160581508","doi":"https://doi.org/10.1186/1752-0509-7-46","title":"Inferring ancient metabolism using ancestral core metabolic models of enterobacteria","display_name":"Inferring ancient metabolism using ancestral core metabolic models of enterobacteria","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2160581508","doi":"https://doi.org/10.1186/1752-0509-7-46","mag":"2160581508","pmid":"https://pubmed.ncbi.nlm.nih.gov/23758866"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-7-46","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-46","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-46","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-46","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060627525","display_name":"David J. Baumler","orcid":"https://orcid.org/0000-0002-7890-2843"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I4210127982","display_name":"Energy Center of Wisconsin","ror":"https://ror.org/02dzpb616","country_code":"US","type":"other","lineage":["https://openalex.org/I4210127982"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David J Baumler","raw_affiliation_strings":["Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA. dbaumler@wisc.edu","Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA"],"affiliations":[{"raw_affiliation_string":"Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA. dbaumler@wisc.edu","institution_ids":["https://openalex.org/I4210127982"]},{"raw_affiliation_string":"Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA","institution_ids":["https://openalex.org/I4210127982","https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047674427","display_name":"Bing Ma","orcid":"https://orcid.org/0000-0002-3488-2393"},"institutions":[{"id":"https://openalex.org/I4210127982","display_name":"Energy Center of Wisconsin","ror":"https://ror.org/02dzpb616","country_code":"US","type":"other","lineage":["https://openalex.org/I4210127982"]},{"id":"https://openalex.org/I108865366","display_name":"Human Genome Sciences (United States)","ror":"https://ror.org/05k1yyh03","country_code":"US","type":"company","lineage":["https://openalex.org/I108865366"]},{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]},{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bing Ma","raw_affiliation_strings":["Current affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA","Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA"],"affiliations":[{"raw_affiliation_string":"Current affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA","institution_ids":["https://openalex.org/I126744593","https://openalex.org/I108865366"]},{"raw_affiliation_string":"Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA","institution_ids":["https://openalex.org/I4210127982","https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059438505","display_name":"Jennifer L. Reed","orcid":"https://orcid.org/0000-0001-7854-6220"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer L Reed","raw_affiliation_strings":["Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028916575","display_name":"Nicole T. Perna","orcid":"https://orcid.org/0000-0001-8208-0929"},"institutions":[{"id":"https://openalex.org/I4210127982","display_name":"Energy Center of Wisconsin","ror":"https://ror.org/02dzpb616","country_code":"US","type":"other","lineage":["https://openalex.org/I4210127982"]},{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicole T Perna","raw_affiliation_strings":["Department of Genetics, University of Wisconsin-Madison, Madison, USA","Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, University of Wisconsin-Madison, Madison, USA","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA","institution_ids":["https://openalex.org/I4210127982","https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5060627525"],"corresponding_institution_ids":["https://openalex.org/I135310074","https://openalex.org/I4210127982"],"apc_list":null,"apc_paid":null,"fwci":0.7437,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.72452779,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"7","issue":"1","first_page":"46","last_page":"46"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9927999973297119,"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/T10066","display_name":"Gut microbiota and health","score":0.986299991607666,"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/computational-biology","display_name":"Computational biology","score":0.6338656544685364},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5975471138954163},{"id":"https://openalex.org/keywords/core","display_name":"Core (optical fiber)","score":0.5892700552940369},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5614973306655884},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.49495238065719604},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38165518641471863}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6338656544685364},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5975471138954163},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.5892700552940369},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5614973306655884},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.49495238065719604},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38165518641471863},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007501","descriptor_name":"Iron","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007501","descriptor_name":"Iron","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007501","descriptor_name":"Iron","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009584","descriptor_name":"Nitrogen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009584","descriptor_name":"Nitrogen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009584","descriptor_name":"Nitrogen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010758","descriptor_name":"Phosphorus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010758","descriptor_name":"Phosphorus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010758","descriptor_name":"Phosphorus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013455","descriptor_name":"Sulfur","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013455","descriptor_name":"Sulfur","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013455","descriptor_name":"Sulfur","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-7-46","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-46","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-46","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:23758866","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23758866","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:europepmc.org:2687310","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3694032","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3694032","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3694032","pdf_url":null,"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":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-7-46","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-46","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-46","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160581508.pdf","grobid_xml":"https://content.openalex.org/works/W2160581508.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1485044783","https://openalex.org/W1546639740","https://openalex.org/W1650035715","https://openalex.org/W1974760528","https://openalex.org/W1980965251","https://openalex.org/W1982309495","https://openalex.org/W1987148148","https://openalex.org/W1989277878","https://openalex.org/W1994750157","https://openalex.org/W1996835973","https://openalex.org/W1996912752","https://openalex.org/W1999746728","https://openalex.org/W2004964623","https://openalex.org/W2029403511","https://openalex.org/W2031319125","https://openalex.org/W2045765967","https://openalex.org/W2045780029","https://openalex.org/W2054506883","https://openalex.org/W2056305771","https://openalex.org/W2061334781","https://openalex.org/W2062018285","https://openalex.org/W2072613143","https://openalex.org/W2073234837","https://openalex.org/W2078355959","https://openalex.org/W2081050097","https://openalex.org/W2083011190","https://openalex.org/W2092784980","https://openalex.org/W2096245011","https://openalex.org/W2096974471","https://openalex.org/W2098824895","https://openalex.org/W2099836442","https://openalex.org/W2107459209","https://openalex.org/W2110384600","https://openalex.org/W2111211467","https://openalex.org/W2111967267","https://openalex.org/W2117509624","https://openalex.org/W2123966372","https://openalex.org/W2124737787","https://openalex.org/W2126175129","https://openalex.org/W2136861579","https://openalex.org/W2138127621","https://openalex.org/W2139553051","https://openalex.org/W2141181138","https://openalex.org/W2142402047","https://openalex.org/W2150618302","https://openalex.org/W2151645494","https://openalex.org/W2152164604","https://openalex.org/W2153139855","https://openalex.org/W2154767435","https://openalex.org/W2162237022","https://openalex.org/W2170427655","https://openalex.org/W2170681488","https://openalex.org/W3101308120","https://openalex.org/W3199943451"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2061542922","https://openalex.org/W5284979","https://openalex.org/W4245853730"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-03T08:47:05.690250","created_date":"2025-10-10T00:00:00"}