{"id":"https://openalex.org/W2136185018","doi":"https://doi.org/10.1162/artl_a_00021","title":"In Silico Evolution of Early Metabolism","display_name":"In Silico Evolution of Early Metabolism","publication_year":2011,"publication_date":"2011-03-03","ids":{"openalex":"https://openalex.org/W2136185018","doi":"https://doi.org/10.1162/artl_a_00021","mag":"2136185018","pmid":"https://pubmed.ncbi.nlm.nih.gov/21370961"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1162/artl_a_00021","pdf_url":null,"source":{"id":"https://openalex.org/S2181302","display_name":"Artificial Life","issn_l":"1064-5462","issn":["1064-5462","1530-9185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315718","host_organization_name":"The MIT Press","host_organization_lineage":["https://openalex.org/P4310315718"],"host_organization_lineage_names":["The MIT Press"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://www.bioinf.uni-leipzig.de/Publications/PREPRINTS/10-016.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079624888","display_name":"Alexander Ullrich","orcid":"https://orcid.org/0000-0002-4894-6124"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alexander Ullrich","raw_affiliation_strings":["[Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany]"],"affiliations":[{"raw_affiliation_string":"[Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany]","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015299450","display_name":"Markus Rohrschneider","orcid":null},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Markus Rohrschneider","raw_affiliation_strings":["[Department of Computer Science, University of Leipzig, Leipzig, Germany]"],"affiliations":[{"raw_affiliation_string":"[Department of Computer Science, University of Leipzig, Leipzig, Germany]","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029336209","display_name":"Gerik Scheuermann","orcid":"https://orcid.org/0000-0001-5200-8870"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Gerik Scheuermann","raw_affiliation_strings":["[Department of Computer Science, University of Leipzig, Leipzig, Germany]"],"affiliations":[{"raw_affiliation_string":"[Department of Computer Science, University of Leipzig, Leipzig, Germany]","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"institutions":[{"id":"https://openalex.org/I4210091327","display_name":"Max Planck Institute for Mathematics in the Sciences","ror":"https://ror.org/00ez2he07","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210091327"]},{"id":"https://openalex.org/I4210119712","display_name":"Max Planck Institute for Mathematics","ror":"https://ror.org/02dh8ja68","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210119712"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Peter F. Stadler","raw_affiliation_strings":["Max Planck Institute for Mathematics in the Sciences"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Mathematics in the Sciences","institution_ids":["https://openalex.org/I4210091327","https://openalex.org/I4210119712"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005564950","display_name":"Christoph Flamm","orcid":"https://orcid.org/0000-0001-5500-2415"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Christoph Flamm","raw_affiliation_strings":["Department of Theoretical Chemistry, University of Vienna, Wien, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, Wien, Austria","institution_ids":["https://openalex.org/I129774422"]}]}],"institution_assertions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.907,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":12,"citation_normalized_percentile":{"value":0.643781,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":86,"max":87},"biblio":{"volume":"17","issue":"2","first_page":"87","last_page":"108"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9999,"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":0.9999,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9963,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9916,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.54144675},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.43395922}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7132335},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.54144675},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.51327705},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47593546},{"id":"https://openalex.org/C76346623","wikidata":"https://www.wikidata.org/wiki/Q205858","display_name":"Ribozyme","level":4,"score":0.4706663},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43903625},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.43395922},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.42133975},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3574865},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.28465778},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23041916},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15772921}],"mesh":[{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":"","qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1162/artl_a_00021","pdf_url":null,"source":{"id":"https://openalex.org/S2181302","display_name":"Artificial Life","issn_l":"1064-5462","issn":["1064-5462","1530-9185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315718","host_organization_name":"The MIT Press","host_organization_lineage":["https://openalex.org/P4310315718"],"host_organization_lineage_names":["The MIT Press"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.703.4700","pdf_url":"http://www.bioinf.uni-leipzig.de/Publications/PREPRINTS/10-016.pdf","source":{"id":"https://openalex.org/S4306400349","display_name":"CiteSeer X (The Pennsylvania State University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I130769515","host_organization_name":"Pennsylvania State University","host_organization_lineage":["https://openalex.org/I130769515"],"host_organization_lineage_names":["Pennsylvania State University"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21370961","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.703.4700","pdf_url":"http://www.bioinf.uni-leipzig.de/Publications/PREPRINTS/10-016.pdf","source":{"id":"https://openalex.org/S4306400349","display_name":"CiteSeer X (The Pennsylvania State University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I130769515","host_organization_name":"Pennsylvania State University","host_organization_lineage":["https://openalex.org/I130769515"],"host_organization_lineage_names":["Pennsylvania State University"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false},"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":57,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1552271991","https://openalex.org/W157941085","https://openalex.org/W1607668835","https://openalex.org/W1621975707","https://openalex.org/W1971399377","https://openalex.org/W1974232498","https://openalex.org/W1974272811","https://openalex.org/W1975113414","https://openalex.org/W1977940795","https://openalex.org/W1978992872","https://openalex.org/W1982583288","https://openalex.org/W1982940904","https://openalex.org/W1992625839","https://openalex.org/W1998238795","https://openalex.org/W2000118138","https://openalex.org/W2005188205","https://openalex.org/W2005603912","https://openalex.org/W2024872256","https://openalex.org/W2029403511","https://openalex.org/W2033788780","https://openalex.org/W2046585679","https://openalex.org/W2048395341","https://openalex.org/W2049827003","https://openalex.org/W2051147125","https://openalex.org/W2055006847","https://openalex.org/W2055993805","https://openalex.org/W2062345761","https://openalex.org/W2065800250","https://openalex.org/W2067087023","https://openalex.org/W2078355959","https://openalex.org/W2078880021","https://openalex.org/W2082616165","https://openalex.org/W2093929396","https://openalex.org/W2102678486","https://openalex.org/W2103731920","https://openalex.org/W2104125400","https://openalex.org/W2110198171","https://openalex.org/W2112492958","https://openalex.org/W2116968684","https://openalex.org/W2122640489","https://openalex.org/W2125859860","https://openalex.org/W2128312954","https://openalex.org/W2134441341","https://openalex.org/W2135900956","https://openalex.org/W2137266088","https://openalex.org/W2138199375","https://openalex.org/W2141327539","https://openalex.org/W2146405302","https://openalex.org/W2153123473","https://openalex.org/W2158247504","https://openalex.org/W2166930654","https://openalex.org/W2177127249","https://openalex.org/W2489959488","https://openalex.org/W2606226749","https://openalex.org/W2914728119","https://openalex.org/W3098195359"],"related_works":["https://openalex.org/W851314325","https://openalex.org/W4308449887","https://openalex.org/W2775873384","https://openalex.org/W2171305205","https://openalex.org/W2163823651","https://openalex.org/W2160381008","https://openalex.org/W2143424137","https://openalex.org/W2136185018","https://openalex.org/W2072067873","https://openalex.org/W2005673176"],"abstract_inverted_index":{"We":[0,79,101],"developed":[1],"a":[2,38,42,57,127,158],"simulation":[3,68,84],"tool":[4,85],"for":[5,71,91],"investigating":[6],"the":[7,17,28,73,96,124,140,164],"evolution":[8,97,125,135],"of":[9,19,30,37,51,98,126,144,161],"early":[10,142,165],"metabolism,":[11],"allowing":[12],"us":[13],"to":[14],"speculate":[15],"on":[16,27,95],"formation":[18],"metabolic":[20,77,99,128,137],"pathways":[21,162],"from":[22,163],"catalyzed":[23],"chemical":[24],"reactions":[25],"and":[26,47,65,148],"development":[29],"their":[31],"characteristic":[32],"properties.":[33],"Our":[34,130],"model":[35],"consists":[36],"protocellular":[39],"entity":[40],"with":[41],"simple":[43],"RNA-based":[44],"genetic":[45],"system":[46],"an":[48,62],"evolving":[49],"metabolism":[50],"catalytically":[52],"active":[53],"ribozymes":[54],"that":[55,103,117,133],"manipulate":[56],"rich":[58],"underlying":[59],"chemistry.":[60],"Ensuring":[61],"almost":[63],"open-ended":[64],"fairly":[66],"realistic":[67],"is":[69],"crucial":[70],"understanding":[72],"first":[74],"steps":[75,143],"in":[76,89,123,139],"evolution.":[78,145],"show":[80],"here":[81],"how":[82],"our":[83],"can":[86],"be":[87,110],"helpful":[88],"arguing":[90],"or":[92],"against":[93],"hypotheses":[94,107],"pathways.":[100],"demonstrate":[102],"seemingly":[104],"mutually":[105],"exclusive":[106],"may":[108],"well":[109],"compatible":[111],"when":[112],"we":[113],"take":[114],"into":[115],"account":[116],"different":[118,121],"processes":[119],"dominate":[120],"phases":[122],"system.":[129],"results":[131],"suggest":[132],"forward":[134,155],"shapes":[136],"network":[138],"very":[141],"In":[146],"later":[147],"more":[149],"complex":[150],"stages,":[151],"enzyme":[152],"recruitment":[153],"supersedes":[154],"evolution,":[156],"keeping":[157],"core":[159],"set":[160],"phase.":[166]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2136185018","counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2024-12-17T05:46:02.936506","created_date":"2016-06-24"}