{"id":"https://openalex.org/W2256388145","doi":"https://doi.org/10.1093/bib/bbv044","title":"Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification","display_name":"Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification","publication_year":2015,"publication_date":"2015-07-02","ids":{"openalex":"https://openalex.org/W2256388145","doi":"https://doi.org/10.1093/bib/bbv044","mag":"2256388145","pmid":"https://pubmed.ncbi.nlm.nih.gov/26141830"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv044","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv044","pdf_url":"https://academic.oup.com/bib/article-pdf/17/3/440/6685577/bbv044.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/17/3/440/6685577/bbv044.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059437341","display_name":"Enrico Glaab","orcid":"https://orcid.org/0000-0003-3977-7469"},"institutions":[{"id":"https://openalex.org/I4210091800","display_name":"Pathways Behavioral Services","ror":"https://ror.org/00frxwd04","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210091800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Enrico Glaab","raw_affiliation_strings":["Enrico Glaab is a research associate in bioinformatics at the Luxembourg Centre for Systems Biomedicine. He develops and applies machine learning approaches to analyze disease-related omics data, with a focus on pathway- and network-based sample classification methods"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Enrico Glaab is a research associate in bioinformatics at the Luxembourg Centre for Systems Biomedicine. He develops and applies machine learning approaches to analyze disease-related omics data, with a focus on pathway- and network-based sample classification methods","institution_ids":["https://openalex.org/I4210091800"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5059437341"],"corresponding_institution_ids":["https://openalex.org/I4210091800"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":1.3874,"has_fulltext":true,"cited_by_count":41,"citation_normalized_percentile":{"value":0.81310959,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"3","first_page":"440","last_page":"452"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9991999864578247,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.9143161773681641},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.7383679747581482},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.667062520980835},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.6208052635192871},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5516788959503174},{"id":"https://openalex.org/keywords/biomarker-discovery","display_name":"Biomarker discovery","score":0.5464932918548584},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5180032849311829},{"id":"https://openalex.org/keywords/diagnostic-biomarker","display_name":"Diagnostic biomarker","score":0.502851665019989},{"id":"https://openalex.org/keywords/biomarker","display_name":"Biomarker","score":0.40228182077407837},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3846915662288666},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.336603581905365},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3285086154937744},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.1785036027431488},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1614638864994049}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.9143161773681641},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.7383679747581482},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.667062520980835},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.6208052635192871},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5516788959503174},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.5464932918548584},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5180032849311829},{"id":"https://openalex.org/C3017616150","wikidata":"https://www.wikidata.org/wiki/Q1069330","display_name":"Diagnostic biomarker","level":3,"score":0.502851665019989},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.40228182077407837},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3846915662288666},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.336603581905365},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3285086154937744},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.1785036027431488},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1614638864994049},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbv044","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv044","pdf_url":"https://academic.oup.com/bib/article-pdf/17/3/440/6685577/bbv044.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26141830","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26141830","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:3846363","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4870394","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":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bib:17/3/440","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/3/440","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:orbilu.uni.lu:10993/21843","is_oa":true,"landing_page_url":"http://orbilu.uni.lu/handle/10993/21843","pdf_url":null,"source":{"id":"https://openalex.org/S4306401815","display_name":"Open Repository and Bibliography (University of Luxembourg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I186903577","host_organization_name":"University of Luxembourg","host_organization_lineage":["https://openalex.org/I186903577"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 1-13 (2015-07-02)","raw_type":"http://purl.org/coar/resource_type/c_6501"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv044","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv044","pdf_url":"https://academic.oup.com/bib/article-pdf/17/3/440/6685577/bbv044.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2256388145.pdf","grobid_xml":"https://content.openalex.org/works/W2256388145.grobid-xml"},"referenced_works_count":116,"referenced_works":["https://openalex.org/W41479188","https://openalex.org/W1489191308","https://openalex.org/W1543415010","https://openalex.org/W1680622244","https://openalex.org/W1864299022","https://openalex.org/W1906461790","https://openalex.org/W1965335625","https://openalex.org/W1970594207","https://openalex.org/W1976022788","https://openalex.org/W1986348445","https://openalex.org/W1990212480","https://openalex.org/W1992045522","https://openalex.org/W1995515386","https://openalex.org/W1995576455","https://openalex.org/W2008161741","https://openalex.org/W2010502047","https://openalex.org/W2010754117","https://openalex.org/W2013520054","https://openalex.org/W2017920242","https://openalex.org/W2020999234","https://openalex.org/W2023250031","https://openalex.org/W2029445248","https://openalex.org/W2036568936","https://openalex.org/W2039366890","https://openalex.org/W2039473152","https://openalex.org/W2042396829","https://openalex.org/W2043484763","https://openalex.org/W2045030989","https://openalex.org/W2058087313","https://openalex.org/W2058237157","https://openalex.org/W2058532211","https://openalex.org/W2060880575","https://openalex.org/W2063576864","https://openalex.org/W2064901349","https://openalex.org/W2068648124","https://openalex.org/W2073241381","https://openalex.org/W2080182143","https://openalex.org/W2093194558","https://openalex.org/W2096410350","https://openalex.org/W2096766502","https://openalex.org/W2098607364","https://openalex.org/W2098979213","https://openalex.org/W2100025044","https://openalex.org/W2100714130","https://openalex.org/W2101567517","https://openalex.org/W2102074241","https://openalex.org/W2103017472","https://openalex.org/W2104369007","https://openalex.org/W2105882193","https://openalex.org/W2105924489","https://openalex.org/W2105981176","https://openalex.org/W2106248311","https://openalex.org/W2106336008","https://openalex.org/W2106391842","https://openalex.org/W2108456088","https://openalex.org/W2110336366","https://openalex.org/W2113582979","https://openalex.org/W2115580179","https://openalex.org/W2116063398","https://openalex.org/W2116531018","https://openalex.org/W2116709840","https://openalex.org/W2119910794","https://openalex.org/W2120449613","https://openalex.org/W2120973253","https://openalex.org/W2121507105","https://openalex.org/W2122264952","https://openalex.org/W2124537635","https://openalex.org/W2125508691","https://openalex.org/W2129560785","https://openalex.org/W2130410032","https://openalex.org/W2130639106","https://openalex.org/W2131987814","https://openalex.org/W2134555649","https://openalex.org/W2135950914","https://openalex.org/W2137304236","https://openalex.org/W2139027526","https://openalex.org/W2139329624","https://openalex.org/W2140468511","https://openalex.org/W2141690840","https://openalex.org/W2142890842","https://openalex.org/W2146791205","https://openalex.org/W2146995322","https://openalex.org/W2147554928","https://openalex.org/W2147714160","https://openalex.org/W2148172612","https://openalex.org/W2148606196","https://openalex.org/W2150452800","https://openalex.org/W2153684756","https://openalex.org/W2154947819","https://openalex.org/W2155330008","https://openalex.org/W2156673479","https://openalex.org/W2158384363","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2161775803","https://openalex.org/W2164105194","https://openalex.org/W2164683872","https://openalex.org/W2165133998","https://openalex.org/W2168264491","https://openalex.org/W2171029115","https://openalex.org/W2178225550","https://openalex.org/W2268004891","https://openalex.org/W2330647671","https://openalex.org/W2404039572","https://openalex.org/W2410771640","https://openalex.org/W2418424626","https://openalex.org/W2798323364","https://openalex.org/W4205350350","https://openalex.org/W4237171445","https://openalex.org/W4239017824","https://openalex.org/W4242404314","https://openalex.org/W4256409604","https://openalex.org/W6601688574","https://openalex.org/W6628864390","https://openalex.org/W6661634902","https://openalex.org/W6681667737"],"related_works":["https://openalex.org/W4229079080","https://openalex.org/W4206534706","https://openalex.org/W4200027074","https://openalex.org/W3006943036","https://openalex.org/W4200511449","https://openalex.org/W2414440007","https://openalex.org/W4211177414","https://openalex.org/W2017409119","https://openalex.org/W4299487748","https://openalex.org/W2035719588"],"abstract_inverted_index":{"For":[0],"many":[1],"complex":[2],"diseases,":[3],"an":[4,89],"earlier":[5],"and":[6,45,79,95,98,113,130],"more":[7,17],"reliable":[8],"diagnosis":[9],"is":[10,134],"considered":[11],"a":[12,131],"key":[13],"prerequisite":[14],"for":[15,30,47,60,108],"developing":[16],"effective":[18],"therapies":[19],"to":[20,82,118],"prevent":[21],"or":[22,52],"delay":[23],"disease":[24],"progression.":[25],"Classical":[26],"statistical":[27],"learning":[28],"approaches":[29,59,102],"specimen":[31,100],"classification":[32,101],"using":[33],"omics":[34,66],"data,":[35],"however,":[36],"often":[37],"cannot":[38],"provide":[39],"diagnostic":[40,126],"models":[41,64,123],"with":[42],"sufficient":[43],"accuracy":[44,112],"robustness":[46],"heterogeneous":[48],"diseases":[49],"like":[50],"cancers":[51],"neurodegenerative":[53],"disorders.":[54],"In":[55],"recent":[56,93],"years,":[57],"new":[58],"building":[61],"multivariate":[62],"biomarker":[63,122],"on":[65],"data":[67],"have":[68],"been":[69],"proposed,":[70],"which":[71],"exploit":[72],"prior":[73],"biological":[74,114],"knowledge":[75],"from":[76],"molecular":[77],"networks":[78],"cellular":[80],"pathways":[81],"address":[83],"these":[84,92],"limitations.":[85],"This":[86],"survey":[87],"provides":[88],"overview":[90],"of":[91,105],"developments":[94],"compares":[96],"pathway-":[97],"network-based":[99],"in":[103],"terms":[104],"their":[106],"utility":[107],"improving":[109],"model":[110],"robustness,":[111],"interpretability.":[115],"Different":[116],"routes":[117],"translate":[119],"omics-based":[120],"multifactorial":[121],"into":[124],"clinical":[125],"tests":[127],"are":[128],"discussed,":[129],"previous":[132],"study":[133],"presented":[135],"as":[136],"example.":[137]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-29T07:29:34.045763","created_date":"2025-10-10T00:00:00"}
