{"id":"https://openalex.org/W2149505266","doi":"https://doi.org/10.1186/1752-0509-5-28","title":"Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans","display_name":"Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans","publication_year":2011,"publication_date":"2011-02-15","ids":{"openalex":"https://openalex.org/W2149505266","doi":"https://doi.org/10.1186/1752-0509-5-28","mag":"2149505266","pmid":"https://pubmed.ncbi.nlm.nih.gov/21324125"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-5-28","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-28","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-28","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":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-28","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100460647","display_name":"Vinay Kumar","orcid":"https://orcid.org/0000-0003-0077-0956"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]},{"id":"https://openalex.org/I53012624","display_name":"Joint BioEnergy Institute","ror":"https://ror.org/03ww55028","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I53012624"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vinay Satish Kumar","raw_affiliation_strings":["Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA","Joint BioEnergy Institute, 5885 Hollis street, Emeryville, California, 94608, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Joint BioEnergy Institute, 5885 Hollis street, Emeryville, California, 94608, USA","institution_ids":["https://openalex.org/I53012624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023972342","display_name":"James G. Ferry","orcid":"https://orcid.org/0000-0003-2642-1711"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James G Ferry","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083581014","display_name":"Costas D. Maranas","orcid":"https://orcid.org/0000-0002-1508-1398"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Costas D Maranas","raw_affiliation_strings":["Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5083581014"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":8.1328,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.97065146,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"5","issue":"1","first_page":"28","last_page":"28"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10284","display_name":"Anaerobic Digestion and Biogas Production","score":0.4803999960422516,"subfield":{"id":"https://openalex.org/subfields/2215","display_name":"Building and Construction"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10284","display_name":"Anaerobic Digestion and Biogas Production","score":0.4803999960422516,"subfield":{"id":"https://openalex.org/subfields/2215","display_name":"Building and Construction"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.28380000591278076,"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/T12688","display_name":"Microbial metabolism and enzyme function","score":0.1462000012397766,"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/methanogen","display_name":"Methanogen","score":0.9543219208717346},{"id":"https://openalex.org/keywords/methanosarcina","display_name":"Methanosarcina","score":0.7182544469833374},{"id":"https://openalex.org/keywords/methanogenesis","display_name":"Methanogenesis","score":0.6466109752655029},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6086781024932861},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.556267499923706},{"id":"https://openalex.org/keywords/archaea","display_name":"Archaea","score":0.5007309913635254},{"id":"https://openalex.org/keywords/methanomicrobiales","display_name":"Methanomicrobiales","score":0.4992411136627197},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.33150702714920044},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3249586224555969},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29143381118774414},{"id":"https://openalex.org/keywords/methane","display_name":"Methane","score":0.2121933102607727},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.20019569993019104}],"concepts":[{"id":"https://openalex.org/C2777438225","wikidata":"https://www.wikidata.org/wiki/Q1169785","display_name":"Methanogen","level":3,"score":0.9543219208717346},{"id":"https://openalex.org/C2778563749","wikidata":"https://www.wikidata.org/wiki/Q1942715","display_name":"Methanosarcina","level":4,"score":0.7182544469833374},{"id":"https://openalex.org/C2778589620","wikidata":"https://www.wikidata.org/wiki/Q22275999","display_name":"Methanogenesis","level":3,"score":0.6466109752655029},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6086781024932861},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.556267499923706},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.5007309913635254},{"id":"https://openalex.org/C2780148642","wikidata":"https://www.wikidata.org/wiki/Q4044130","display_name":"Methanomicrobiales","level":5,"score":0.4992411136627197},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.33150702714920044},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3249586224555969},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29143381118774414},{"id":"https://openalex.org/C516920438","wikidata":"https://www.wikidata.org/wiki/Q37129","display_name":"Methane","level":2,"score":0.2121933102607727},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.20019569993019104}],"mesh":[{"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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017020","descriptor_name":"Methanosarcina","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017020","descriptor_name":"Methanosarcina","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017020","descriptor_name":"Methanosarcina","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017020","descriptor_name":"Methanosarcina","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017020","descriptor_name":"Methanosarcina","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017020","descriptor_name":"Methanosarcina","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":3,"locations":[{"id":"doi:10.1186/1752-0509-5-28","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-28","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-28","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:21324125","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21324125","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3048526","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3048526","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"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-5-28","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-28","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-28","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/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149505266.pdf","grobid_xml":"https://content.openalex.org/works/W2149505266.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W564414355","https://openalex.org/W611589739","https://openalex.org/W1562957825","https://openalex.org/W1579893055","https://openalex.org/W1966394322","https://openalex.org/W1980672599","https://openalex.org/W1983693177","https://openalex.org/W1985517408","https://openalex.org/W1986656046","https://openalex.org/W1992985911","https://openalex.org/W1996039824","https://openalex.org/W2007467553","https://openalex.org/W2011427396","https://openalex.org/W2012481059","https://openalex.org/W2022012525","https://openalex.org/W2037080719","https://openalex.org/W2040858974","https://openalex.org/W2045780029","https://openalex.org/W2066870045","https://openalex.org/W2066900019","https://openalex.org/W2072013780","https://openalex.org/W2073837631","https://openalex.org/W2078244178","https://openalex.org/W2083011190","https://openalex.org/W2084305298","https://openalex.org/W2085993965","https://openalex.org/W2093826349","https://openalex.org/W2103536675","https://openalex.org/W2111381495","https://openalex.org/W2113622844","https://openalex.org/W2114034054","https://openalex.org/W2115901152","https://openalex.org/W2119269408","https://openalex.org/W2119828149","https://openalex.org/W2120445312","https://openalex.org/W2123060905","https://openalex.org/W2126175129","https://openalex.org/W2127872845","https://openalex.org/W2130364940","https://openalex.org/W2140860400","https://openalex.org/W2148750928","https://openalex.org/W2149534614","https://openalex.org/W2153223562","https://openalex.org/W2156162633","https://openalex.org/W2156382259","https://openalex.org/W2156481615","https://openalex.org/W2157635835","https://openalex.org/W2158714788","https://openalex.org/W2161062388","https://openalex.org/W2170085970","https://openalex.org/W2170124846","https://openalex.org/W2728021558","https://openalex.org/W4232868252","https://openalex.org/W4236541940","https://openalex.org/W4239545644","https://openalex.org/W4239838272","https://openalex.org/W4254415287","https://openalex.org/W4299159762","https://openalex.org/W4300607473"],"related_works":["https://openalex.org/W3126204815","https://openalex.org/W2150501288","https://openalex.org/W3176439267","https://openalex.org/W4387706892","https://openalex.org/W1484221008","https://openalex.org/W2500331995","https://openalex.org/W4232710487","https://openalex.org/W2919344833","https://openalex.org/W4206450708","https://openalex.org/W4205598697"],"abstract_inverted_index":{"BACKGROUND:":[0],"Methanogens":[1],"are":[2,6],"ancient":[3],"organisms":[4],"that":[5],"key":[7],"players":[8],"in":[9,44,71,80,88,112,191],"the":[10,34,42,89,137,150,162,165,177],"carbon":[11,157],"cycle":[12],"accounting":[13],"for":[14,59,97,143],"about":[15],"one":[16],"billion":[17],"tones":[18],"of":[19,30,132,139,164,171],"biological":[20],"methane":[21],"produced":[22],"annually.":[23],"Methanosarcina":[24],"acetivorans,":[25],"with":[26,79,111],"a":[27,50,55],"genome":[28],"size":[29,163],"~5.7":[31],"mb,":[32],"is":[33,189],"largest":[35],"sequenced":[36],"archaeon":[37],"methanogen":[38],"and":[39,84,102,119,147,149,169,193],"unique":[40,151],"amongst":[41],"methanogens":[43],"its":[45],"biochemical":[46,152],"characteristics.":[47],"By":[48],"following":[49],"systematic":[51],"workflow":[52],"we":[53],"reconstruct":[54],"genome-scale":[56,166],"metabolic":[57,128,167],"model":[58,94,106,124,175,188],"M.":[60,133],"acetivorans.":[61],"This":[62],"process":[63],"relies":[64],"on":[65,145,156,161],"previously":[66],"developed":[67,70],"computational":[68],"tools":[69],"our":[72],"group":[73],"to":[74,182,196],"correct":[75],"growth":[76,114,144,155],"prediction":[77,109],"inconsistencies":[78,87],"vivo":[81,113],"data":[82,115],"sets":[83],"rectify":[85],"topological":[86],"model.":[90],"RESULTS:":[91],"The":[92,105,123,186],"generated":[93],"iVS941":[95],"accounts":[96],"941":[98],"genes,":[99],"705":[100],"reactions":[101],"708":[103],"metabolites.":[104],"achieves":[107],"93.3%":[108],"agreement":[110],"across":[116],"different":[117],"substrates":[118],"multiple":[120],"gene":[121],"deletions.":[122],"also":[125],"correctly":[126],"recapitulates":[127],"pathway":[129],"usage":[130],"patterns":[131],"acetivorans":[134],"such":[135],"as":[136],"indispensability":[138],"flux":[140],"through":[141],"methanogenesis":[142],"acetate":[146],"methanol":[148],"characteristics":[153],"under":[154],"monoxide.":[158],"CONCLUSIONS:":[159],"Based":[160],"reconstruction":[168],"extent":[170],"validated":[172],"predictions":[173],"this":[174],"represents":[176],"most":[178],"comprehensive":[179],"up-to-date":[180],"effort":[181],"catalogue":[183],"methanogenic":[184],"metabolism.":[185],"reconstructed":[187],"available":[190],"spreadsheet":[192],"SBML":[194],"formats":[195],"enable":[197],"dissemination.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":6}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}