{"id":"https://openalex.org/W2726414492","doi":"https://doi.org/10.1186/s13040-017-0141-9","title":"Arete \u2013 candidate gene prioritization using biological network topology with additional evidence types","display_name":"Arete \u2013 candidate gene prioritization using biological network topology with additional evidence types","publication_year":2017,"publication_date":"2017-07-06","ids":{"openalex":"https://openalex.org/W2726414492","doi":"https://doi.org/10.1186/s13040-017-0141-9","mag":"2726414492","pmid":"https://pubmed.ncbi.nlm.nih.gov/28694847"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-017-0141-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-017-0141-9","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-017-0141-9","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-017-0141-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068144584","display_name":"Artem Lysenko","orcid":"https://orcid.org/0000-0002-1441-0604"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Artem Lysenko","raw_affiliation_strings":["Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan","Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055624617","display_name":"Keith A. Boroevich","orcid":"https://orcid.org/0000-0001-7095-7332"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Keith Anthony Boroevich","raw_affiliation_strings":["Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan","Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049989071","display_name":"Tatsuhiko Tsunoda","orcid":"https://orcid.org/0000-0002-5439-7918"},"institutions":[{"id":"https://openalex.org/I125602781","display_name":"Tokyo Medical and Dental University","ror":"https://ror.org/051k3eh31","country_code":"JP","type":"education","lineage":["https://openalex.org/I125602781"]},{"id":"https://openalex.org/I4210086780","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19","country_code":"JP","type":"government","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210086780"]},{"id":"https://openalex.org/I4210102982","display_name":"Centre for Research in Engineering Surface Technology","ror":"https://ror.org/018q3fa22","country_code":"IE","type":"other","lineage":["https://openalex.org/I4210102982"]},{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["IE","JP"],"is_corresponding":true,"raw_author_name":"Tatsuhiko Tsunoda","raw_affiliation_strings":["CREST, JST, Tokyo, 113-8510 Japan","Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan","Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan","Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan","CREST, JST, Tokyo, 113-8510, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CREST, JST, Tokyo, 113-8510 Japan","institution_ids":["https://openalex.org/I4210086780","https://openalex.org/I4210102982"]},{"raw_affiliation_string":"Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510 Japan","institution_ids":["https://openalex.org/I125602781"]},{"raw_affiliation_string":"Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan","institution_ids":["https://openalex.org/I125602781"]},{"raw_affiliation_string":"CREST, JST, Tokyo, 113-8510, Japan","institution_ids":["https://openalex.org/I4210086780"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5049989071","https://openalex.org/A5068144584"],"corresponding_institution_ids":["https://openalex.org/I125602781","https://openalex.org/I4210086780","https://openalex.org/I4210102982","https://openalex.org/I4210150921"],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":0.3041,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.56091879,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"1","first_page":"22","last_page":"22"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9872999787330627,"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":0.9872999787330627,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0020000000949949026,"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/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.0013000000035390258,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/prioritization","display_name":"Prioritization","score":0.8002408146858215},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6705648899078369},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.5823913216590881},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.5334145426750183},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.43614447116851807},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37150484323501587},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3619534969329834},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.29966190457344055},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2523667514324188},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15191805362701416},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.06232699751853943}],"concepts":[{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.8002408146858215},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6705648899078369},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5823913216590881},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.5334145426750183},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.43614447116851807},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37150484323501587},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3619534969329834},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.29966190457344055},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2523667514324188},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15191805362701416},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.06232699751853943},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-017-0141-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-017-0141-9","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-017-0141-9","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:28694847","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28694847","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:5a84c7080809417181d60c31372b2853","is_oa":false,"landing_page_url":"https://doaj.org/article/5a84c7080809417181d60c31372b2853","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 10, Iss 1, Pp 1-12 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4350080","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5501438","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/s13040-017-0141-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-017-0141-9","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-017-0141-9","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6499999761581421}],"awards":[{"id":"https://openalex.org/G2521286739","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320334789","funder_display_name":"Japan Science and Technology Agency"}],"funders":[{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320335125","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2726414492.pdf","grobid_xml":"https://content.openalex.org/works/W2726414492.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W586739142","https://openalex.org/W1966841828","https://openalex.org/W1981637710","https://openalex.org/W1995443851","https://openalex.org/W2004393812","https://openalex.org/W2009018507","https://openalex.org/W2012034410","https://openalex.org/W2015799373","https://openalex.org/W2046831513","https://openalex.org/W2058722872","https://openalex.org/W2062340962","https://openalex.org/W2064585235","https://openalex.org/W2066325577","https://openalex.org/W2081038787","https://openalex.org/W2090247362","https://openalex.org/W2100471807","https://openalex.org/W2104622981","https://openalex.org/W2109555487","https://openalex.org/W2110553827","https://openalex.org/W2111974471","https://openalex.org/W2112543617","https://openalex.org/W2119220491","https://openalex.org/W2120051475","https://openalex.org/W2124649441","https://openalex.org/W2125256338","https://openalex.org/W2133001645","https://openalex.org/W2143965041","https://openalex.org/W2144086069","https://openalex.org/W2145632240","https://openalex.org/W2150951857","https://openalex.org/W2159675211","https://openalex.org/W2159946239","https://openalex.org/W2165428492","https://openalex.org/W2169374864","https://openalex.org/W2170866859","https://openalex.org/W2324728706","https://openalex.org/W4255852734"],"related_works":["https://openalex.org/W2506292322","https://openalex.org/W4283209547","https://openalex.org/W4367627632","https://openalex.org/W653452717","https://openalex.org/W2086397253","https://openalex.org/W2554445088","https://openalex.org/W3088013537","https://openalex.org/W2621003306","https://openalex.org/W2133122801","https://openalex.org/W2335661150"],"abstract_inverted_index":{"BACKGROUND:":[0],"Refinement":[1],"of":[2,27,37,46,57,62,93,101,108,146,155,174,183,196],"candidate":[3],"gene":[4,79,158,204],"lists":[5],"to":[6,186,216],"select":[7],"the":[8,25,32,53,58,94,102,114,126,137,169,194],"most":[9],"promising":[10],"candidates":[11],"for":[12,51,125,168],"further":[13,134],"experimental":[14],"verification":[15],"remains":[16],"an":[17,70,122],"essential":[18],"step":[19],"between":[20],"high-throughput":[21],"exploratory":[22],"analysis":[23,129,141],"and":[24,34,48,105,131,163,208],"discovery":[26],"specific":[28],"causal":[29],"genes.":[30],"Given":[31],"qualitative":[33],"semantic":[35],"complexity":[36],"biological":[38,103],"data,":[39],"successfully":[40],"addressing":[41],"this":[42,147],"challenge":[43],"requires":[44],"development":[45],"flexible":[47],"interoperable":[49],"solutions":[50],"making":[52],"best":[54],"possible":[55,60],"use":[56],"largest":[59],"fraction":[61],"all":[63],"available":[64,143],"data.":[65,191],"RESULTS:":[66],"We":[67,150],"have":[68],"developed":[69,179],"easily":[71],"accessible":[72],"framework":[73],"that":[74,97,180],"links":[75],"two":[76,156,201],"established":[77],"network-based":[78],"prioritization":[80,159,205],"approaches":[81],"with":[82,139,166,189],"a":[83],"supporting":[84],"isolation":[85],"forest-based":[86],"integrative":[87],"ranking":[88],"method.":[89],"The":[90,117],"defining":[91],"feature":[92],"method":[95],"is":[96],"both":[98],"topological":[99],"information":[100],"networks":[104],"additional":[106,190],"sources":[107],"evidence":[109],"can":[110,133,213],"be":[111,187,214],"considered":[112],"at":[113],"same":[115],"time.":[116],"implementation":[118],"was":[119,177],"realized":[120],"as":[121,144],"app":[123],"extension":[124,173],"Cytoscape":[127,170],"graph":[128],"suite,":[130],"therefore":[132],"benefit":[135],"from":[136],"synergy":[138],"other":[140],"methods":[142,176],"part":[145],"system.":[148,171],"CONCLUSIONS:":[149],"provide":[151],"efficient":[152],"reference":[153],"implementations":[154],"popular":[157],"algorithms":[160,185],"-":[161],"DIAMOnD":[162],"random":[164],"walk":[165],"restart":[167],"An":[172],"those":[175],"also":[178],"allows":[181],"outputs":[182],"these":[184,218],"combined":[188],"To":[192],"demonstrate":[193],"utility":[195],"our":[197,211],"software,":[198],"we":[199],"present":[200],"example":[202],"disease":[203],"application":[206],"cases":[207],"show":[209],"how":[210],"tool":[212],"used":[215],"evaluate":[217],"different":[219],"approaches.":[220]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
