{"id":"https://openalex.org/W2523771784","doi":"https://doi.org/10.1371/journal.pcbi.1005125","title":"Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction","display_name":"Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction","publication_year":2016,"publication_date":"2016-09-27","ids":{"openalex":"https://openalex.org/W2523771784","doi":"https://doi.org/10.1371/journal.pcbi.1005125","mag":"2523771784","pmid":"https://pubmed.ncbi.nlm.nih.gov/27673682"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005125","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005125","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005125&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005125&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102836745","display_name":"Noam Auslander","orcid":null},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Noam Auslander","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology and the Department of Computer Science, University of Maryland, College Park, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology and the Department of Computer Science, University of Maryland, College Park, Maryland, United States of America","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089647811","display_name":"Allon Wagner","orcid":"https://orcid.org/0000-0001-5095-6009"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Allon Wagner","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028671382","display_name":"Matthew Oberhardt","orcid":"https://orcid.org/0000-0001-6491-6315"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Oberhardt","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology and the Department of Computer Science, University of Maryland, College Park, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology and the Department of Computer Science, University of Maryland, College Park, Maryland, United States of America","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063492133","display_name":"Eytan Ruppin","orcid":"https://orcid.org/0000-0002-7862-3940"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"Eytan Ruppin","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology and the Department of Computer Science, University of Maryland, College Park, Maryland, United States of America","The Blavatnik School of Computer Science and the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology and the Department of Computer Science, University of Maryland, College Park, Maryland, United States of America","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"The Blavatnik School of Computer Science and the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5063492133","https://openalex.org/A5102836745"],"corresponding_institution_ids":["https://openalex.org/I16391192","https://openalex.org/I66946132"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6407,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.72652798,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"9","first_page":"e1005125","last_page":"e1005125"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9965999722480774,"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":0.6991326212882996},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.6790178418159485},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6230552792549133},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5633054375648499},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.5153824687004089},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5074486136436462},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4730207920074463},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3687879145145416},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29591041803359985}],"concepts":[{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.6991326212882996},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.6790178418159485},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6230552792549133},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5633054375648499},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.5153824687004089},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5074486136436462},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4730207920074463},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3687879145145416},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29591041803359985}],"mesh":[],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1005125","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005125","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005125&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:27673682","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27673682","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5038951","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5038951","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:ark:/13030/qt5rq9r247","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:ca322d652e1e4ee88d2d8a03dc151962","is_oa":true,"landing_page_url":"https://doaj.org/article/ca322d652e1e4ee88d2d8a03dc151962","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 12, Iss 9, p e1005125 (2016)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt5rq9r247","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5rq9r247","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"PLOS Computational Biology, vol 12, iss 9","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/3968937","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Data-Driven_Metabolic_Pathway_Compositions_Enhance_Cancer_Survival_Prediction/3968937","pdf_url":null,"source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"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":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005125","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005125","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005125&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7099999785423279,"display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332613","display_name":"Graduate School, University of Maryland","ror":"https://ror.org/047s2c258"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2523771784.pdf","grobid_xml":"https://content.openalex.org/works/W2523771784.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W1546862091","https://openalex.org/W1782873782","https://openalex.org/W1935838690","https://openalex.org/W1967482096","https://openalex.org/W1970620631","https://openalex.org/W1979300931","https://openalex.org/W1984283136","https://openalex.org/W1990445837","https://openalex.org/W1992045522","https://openalex.org/W2003605385","https://openalex.org/W2005895632","https://openalex.org/W2014058353","https://openalex.org/W2020541351","https://openalex.org/W2022101765","https://openalex.org/W2022397091","https://openalex.org/W2022899908","https://openalex.org/W2028561804","https://openalex.org/W2037931983","https://openalex.org/W2043398720","https://openalex.org/W2045599972","https://openalex.org/W2052543023","https://openalex.org/W2056633943","https://openalex.org/W2057626690","https://openalex.org/W2059736685","https://openalex.org/W2062725167","https://openalex.org/W2093255090","https://openalex.org/W2097259163","https://openalex.org/W2098421151","https://openalex.org/W2099787654","https://openalex.org/W2100980426","https://openalex.org/W2101039596","https://openalex.org/W2104108767","https://openalex.org/W2112660220","https://openalex.org/W2114972221","https://openalex.org/W2117692326","https://openalex.org/W2120261416","https://openalex.org/W2128014041","https://openalex.org/W2129925362","https://openalex.org/W2132969874","https://openalex.org/W2138040987","https://openalex.org/W2141360045","https://openalex.org/W2145378054","https://openalex.org/W2152027903","https://openalex.org/W2153178365","https://openalex.org/W2154947819","https://openalex.org/W2163578961","https://openalex.org/W2165967770","https://openalex.org/W2168264491","https://openalex.org/W2168941598","https://openalex.org/W2172290661","https://openalex.org/W2234115940","https://openalex.org/W2322921974","https://openalex.org/W2345381093","https://openalex.org/W2419474496","https://openalex.org/W3004540582","https://openalex.org/W3145128584","https://openalex.org/W4293241248"],"related_works":["https://openalex.org/W2151866902","https://openalex.org/W2378339845","https://openalex.org/W2087715585","https://openalex.org/W2102850238","https://openalex.org/W2394833619","https://openalex.org/W2157193718","https://openalex.org/W3129154869","https://openalex.org/W3116780334","https://openalex.org/W2806907921","https://openalex.org/W2028890121"],"abstract_inverted_index":{"Altered":[0],"cellular":[1,52],"metabolism":[2,53],"is":[3],"an":[4,159],"important":[5],"characteristic":[6],"and":[7,35,63,104],"driver":[8],"of":[9,30,38,119,153,180],"cancer.":[10],"Surprisingly,":[11],"however,":[12],"we":[13,58],"find":[14],"here":[15],"that":[16,46,82],"aggregating":[17],"individual":[18,101,181],"gene":[19,68,102,143],"expression":[20,69,103,144],"using":[21,163],"canonical":[22,106,165,217],"metabolic":[23,47,74,109,167,210],"pathways":[24,127,147,168,183,199,218],"fails":[25],"to":[26,76,130,133,149,207],"enhance":[27,83],"the":[28,36,44,120,125,137,164,176,216],"classification":[29,89],"noncancerous":[31,87,193],"vs.":[32,85,172,192],"cancerous":[33],"tissues":[34],"prediction":[37],"cancer":[39,50,84,93,122,140,155,191,214],"patient":[40],"survival.":[41],"This":[42],"supports":[43],"notion":[45],"alterations":[48,211],"in":[49,158,189,213],"rewire":[51],"through":[54,145],"unconventional":[55],"pathways.":[56,110],"Here":[57],"present":[59],"MCF":[60,95,126,146,182,202],"(Metabolic":[61],"classifier":[62],"feature":[64],"generator),":[65],"which":[66],"incorporates":[67],"measurements":[70],"into":[71],"a":[72],"human":[73,107,166,221],"network":[75],"infer":[77],"new":[78],"cancer-mediated":[79],"pathway":[80],"compositions":[81],"adjacent":[86],"tissue":[88],"across":[90],"five":[91],"different":[92,117],"types.":[94,141],"outperforms":[96],"standard":[97],"classifiers":[98,115],"based":[99],"on":[100,105],"curated":[108],"It":[111],"successfully":[112],"builds":[113],"robust":[114],"integrating":[116],"datasets":[118],"same":[121],"type.":[123],"Reassuringly,":[124],"identified":[128,200],"lead":[129],"metabolites":[131],"known":[132],"be":[134],"associated":[135],"with":[136,186],"pertaining":[138],"specific":[139],"Aggregating":[142],"leads":[148],"markedly":[150],"better":[151],"predictions":[152],"breast":[154],"patients'":[156],"survival":[157,177],"independent":[160],"cohort":[161],"than":[162,215],"(C-index":[169],"=":[170],"0.69":[171],"0.52,":[173],"respectively).":[174],"Notably,":[175],"predictive":[178,197],"power":[179,188],"strongly":[184],"correlates":[185],"their":[187],"predicting":[190],"samples.":[194],"The":[195],"more":[196,205],"composite":[198],"via":[201],"are":[203],"hence":[204],"likely":[206],"capture":[208],"key":[209],"occurring":[212],"characterizing":[219],"healthy":[220],"metabolism.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
