{"id":"https://openalex.org/W2003402157","doi":"https://doi.org/10.1186/1471-2105-14-78","title":"AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures","display_name":"AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures","publication_year":2013,"publication_date":"2013-03-05","ids":{"openalex":"https://openalex.org/W2003402157","doi":"https://doi.org/10.1186/1471-2105-14-78","mag":"2003402157","pmid":"https://pubmed.ncbi.nlm.nih.gov/23496976"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-78","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-78","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-78","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-78","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071514791","display_name":"John C. Earls","orcid":"https://orcid.org/0000-0002-8239-911X"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John C Earls","raw_affiliation_strings":["Institute for Systems Biology, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA, USA","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058971932","display_name":"James A. Eddy","orcid":"https://orcid.org/0000-0001-9758-0176"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James A Eddy","raw_affiliation_strings":["Department of Bioengineering, University of Illinois, Urbana, IL, USA","Institute for Systems Biology, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Illinois, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA, USA","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085629786","display_name":"Cory C. Funk","orcid":"https://orcid.org/0000-0002-5229-9011"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cory C Funk","raw_affiliation_strings":["Institute for Systems Biology, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA, USA","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110511389","display_name":"Younhee Ko","orcid":"https://orcid.org/0000-0002-2843-2222"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Younhee Ko","raw_affiliation_strings":["Department of Computer Science, University of Illinois, Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035252203","display_name":"Andrew T. Magis","orcid":"https://orcid.org/0000-0003-0576-677X"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew T Magis","raw_affiliation_strings":["Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA","Institute for Systems Biology, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA, USA","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034589050","display_name":"Nathan D. Price","orcid":"https://orcid.org/0000-0002-4157-0267"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nathan D Price","raw_affiliation_strings":["Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA","Department of Bioengineering, University of Illinois, Urbana, IL, USA","Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA","Department of Computer Science, University of Illinois, Urbana, IL, USA","Institute for Systems Biology, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Bioengineering, University of Illinois, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Computer Science, University of Illinois, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, WA, USA","institution_ids":["https://openalex.org/I3148997608"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5034589050"],"corresponding_institution_ids":["https://openalex.org/I157725225","https://openalex.org/I201448701","https://openalex.org/I3148997608"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.4127,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.62139357,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"14","issue":"1","first_page":"78","last_page":"78"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.7276999950408936,"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/T10885","display_name":"Gene expression and cancer classification","score":0.7276999950408936,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.14020000398159027,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.03240000084042549,"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/identification","display_name":"Identification (biology)","score":0.6698747873306274},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.6478847861289978},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5713149309158325},{"id":"https://openalex.org/keywords/open-source-software","display_name":"Open source software","score":0.5550732612609863},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4939430356025696},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4892458915710449},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.46810030937194824},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4515950381755829},{"id":"https://openalex.org/keywords/user-friendly","display_name":"User Friendly","score":0.44180330634117126},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33608224987983704},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3309926390647888},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.29798200726509094},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.20165133476257324},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1383315622806549},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10552224516868591},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10040315985679626},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.06847363710403442}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6698747873306274},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.6478847861289978},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5713149309158325},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.5550732612609863},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4939430356025696},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4892458915710449},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.46810030937194824},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4515950381755829},{"id":"https://openalex.org/C61437842","wikidata":"https://www.wikidata.org/wiki/Q281291","display_name":"User Friendly","level":2,"score":0.44180330634117126},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33608224987983704},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3309926390647888},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.29798200726509094},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.20165133476257324},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1383315622806549},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10552224516868591},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10040315985679626},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.06847363710403442}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-14-78","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-78","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-78","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23496976","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23496976","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 bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2603565","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3599560","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-78","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-78","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-78","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2003402157.pdf","grobid_xml":"https://content.openalex.org/works/W2003402157.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1524141331","https://openalex.org/W1973097976","https://openalex.org/W2007615926","https://openalex.org/W2020541351","https://openalex.org/W2021790986","https://openalex.org/W2031100365","https://openalex.org/W2088477148","https://openalex.org/W2126874043","https://openalex.org/W2130410032","https://openalex.org/W2137920719","https://openalex.org/W2139319528","https://openalex.org/W2150459098","https://openalex.org/W2163244155","https://openalex.org/W2171528238"],"related_works":["https://openalex.org/W4376877853","https://openalex.org/W1493891899","https://openalex.org/W4250928611","https://openalex.org/W4232280318","https://openalex.org/W166480398","https://openalex.org/W167327709","https://openalex.org/W4387839566","https://openalex.org/W4210922265","https://openalex.org/W4319870556","https://openalex.org/W2084742289"],"abstract_inverted_index":{"BACKGROUND:":[0],"Public":[1],"databases":[2],"such":[3,34],"as":[4,36],"the":[5,61,111,115,122,201,214,261,275],"NCBI":[6],"Gene":[7],"Expression":[8,128],"Omnibus":[9],"contain":[10],"extensive":[11],"and":[12,59,71,93,113,149,161,184,196,212,236,252,260,286],"exponentially":[13],"increasing":[14],"amounts":[15,277],"of":[16,44,101,107,117,170,216,265,278],"high-throughput":[17],"data":[18,29,246,250,281],"that":[19,46,132,166,192],"can":[20,30,290],"be":[21,31,291],"applied":[22],"to":[23,187,273],"molecular":[24,88],"phenotype":[25,40],"characterization.":[26],"Collectively,":[27],"these":[28,118,194,205],"analyzed":[32],"for":[33,50,85,90,172,241],"purposes":[35],"disease":[37,51,91],"diagnosis":[38],"or":[39],"classification.":[41],"One":[42],"family":[43],"algorithms":[45,81,195,206,235],"has":[47,133],"proven":[48],"useful":[49],"classification":[52],"is":[53],"based":[54],"on":[55,98,200],"relative":[56,78,173,232],"expression":[57,79,174,233],"analysis":[58,80,234,254],"includes":[60],"Top-Scoring":[62,68],"Pair":[63],"(TSP),":[64],"k-Top-Scoring":[65],"Pairs":[66],"(k-TSP),":[67],"Triplet":[69],"(TST)":[70],"Differential":[72],"Rank":[73],"Conservation":[74],"(DIRAC)":[75],"algorithms.":[76],"These":[77],"hold":[82],"significant":[83],"advantages":[84],"identifying":[86],"interpretable":[87],"signatures":[89],"classification,":[92],"have":[94,229],"been":[95],"implemented":[96],"previously":[97],"a":[99,134,168,238],"variety":[100],"computational":[102],"platforms":[103],"with":[104],"varying":[105],"degrees":[106],"usability.":[108],"To":[109],"increase":[110],"user-base":[112],"maximize":[114],"utility":[116],"methods,":[119,179],"we":[120,155],"developed":[121],"program":[123],"AUREA":[124,176,266,289],"(Adaptive":[125],"Unified":[126],"Relative":[127],"Analyzer)-a":[129],"cross-platform":[130],"tool":[131],"consistent":[135,208],"application":[136],"programming":[137],"interface":[138,144,240,259],"(API),":[139],"an":[140,158,268],"easy-to-use":[141],"graphical":[142],"user":[143],"(GUI),":[145],"fast":[146],"running":[147],"times":[148],"automated":[150],"parameter":[151,219,248,263],"discovery.":[152],"RESULTS:":[153],"Herein,":[154],"describe":[156],"AUREA,":[157],"efficient,":[159],"cohesive,":[160],"user-friendly":[162],"open-source":[163],"software":[164],"system":[165],"comprises":[167],"suite":[169],"methods":[171],"analysis.":[175],"incorporates":[177],"existing":[178],"while":[180,244],"extending":[181],"their":[182,188,210,242],"capabilities":[183],"bringing":[185],"uniformity":[186],"interfaces.":[189],"We":[190,228],"demonstrate":[191,213],"combining":[193],"adaptively":[197],"tuning":[198,264],"parameters":[199],"training":[202],"sets":[203],"makes":[204],"more":[207],"in":[209,271],"performance":[211],"effectiveness":[215],"our":[217],"adaptive":[218,262],"tuner":[220],"by":[221,282],"comparing":[222],"accuracy":[223],"across":[224],"diverse":[225],"datasets.":[226],"CONCLUSIONS:":[227],"integrated":[230],"several":[231],"provided":[237],"unified":[239,258],"implementation":[243],"making":[245],"acquisition,":[247],"fixing,":[249],"merging,":[251],"results":[253],"'point-and-click'":[255],"simple.":[256],"The":[257],"provide":[267],"effective":[269],"framework":[270],"which":[272],"investigate":[274],"massive":[276],"publically":[279],"available":[280],"both":[283],"'in":[284],"silico'":[285],"'bench'":[287],"scientists.":[288],"found":[292],"at":[293],"http://price.systemsbiology.net/AUREA/.":[294]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
