{"id":"https://openalex.org/W2570972025","doi":"https://doi.org/10.1093/bioinformatics/btw737","title":"Context-sensitive network-based disease genetics prediction and its implications in drug discovery","display_name":"Context-sensitive network-based disease genetics prediction and its implications in drug discovery","publication_year":2016,"publication_date":"2016-11-19","ids":{"openalex":"https://openalex.org/W2570972025","doi":"https://doi.org/10.1093/bioinformatics/btw737","mag":"2570972025","pmid":"https://pubmed.ncbi.nlm.nih.gov/28062449"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw737","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw737","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/1031/25149859/btw737.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/1031/25149859/btw737.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100350382","display_name":"Yang Chen","orcid":"https://orcid.org/0000-0001-9406-8273"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Chen","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050134236","display_name":"Rong Xu","orcid":"https://orcid.org/0000-0003-3127-4795"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rong Xu","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5050134236"],"corresponding_institution_ids":["https://openalex.org/I58956616"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.9152,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.86604325,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"33","issue":"7","first_page":"1031","last_page":"1039"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9502999782562256,"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":0.9502999782562256,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.01119999960064888,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.00930000003427267,"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/context","display_name":"Context (archaeology)","score":0.6828703880310059},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.6325654983520508},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6080066561698914},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5346162915229797},{"id":"https://openalex.org/keywords/phenome","display_name":"Phenome","score":0.5092278718948364},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.4991140365600586},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.46458297967910767},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4612610936164856},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42924946546554565},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.42228570580482483},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4169856011867523},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35502684116363525},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3102007508277893},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.30482563376426697},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23111611604690552},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.17937621474266052}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6828703880310059},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.6325654983520508},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6080066561698914},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5346162915229797},{"id":"https://openalex.org/C7952369","wikidata":"https://www.wikidata.org/wiki/Q844116","display_name":"Phenome","level":4,"score":0.5092278718948364},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.4991140365600586},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.46458297967910767},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4612610936164856},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42924946546554565},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42228570580482483},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4169856011867523},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35502684116363525},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3102007508277893},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.30482563376426697},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23111611604690552},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.17937621474266052},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"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":"D000978","descriptor_name":"Antiparkinson Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000978","descriptor_name":"Antiparkinson Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000978","descriptor_name":"Antiparkinson Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010300","descriptor_name":"Parkinson Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010300","descriptor_name":"Parkinson Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010300","descriptor_name":"Parkinson Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw737","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw737","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/1031/25149859/btw737.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28062449","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28062449","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5860178","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860178","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw737","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw737","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/1031/25149859/btw737.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G3113449353","display_name":null,"funder_award_id":"DP2 HD084068","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"}],"funders":[{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1010479107","https://openalex.org/W1916919897","https://openalex.org/W1925517254","https://openalex.org/W1973880717","https://openalex.org/W1989590412","https://openalex.org/W2003738638","https://openalex.org/W2005132321","https://openalex.org/W2010187764","https://openalex.org/W2015286781","https://openalex.org/W2019707847","https://openalex.org/W2023575634","https://openalex.org/W2031740174","https://openalex.org/W2038122249","https://openalex.org/W2041073071","https://openalex.org/W2062533676","https://openalex.org/W2068153368","https://openalex.org/W2083045667","https://openalex.org/W2094791588","https://openalex.org/W2097498614","https://openalex.org/W2098711168","https://openalex.org/W2100582962","https://openalex.org/W2103518727","https://openalex.org/W2104261859","https://openalex.org/W2105924489","https://openalex.org/W2106350754","https://openalex.org/W2107638877","https://openalex.org/W2111957326","https://openalex.org/W2112168026","https://openalex.org/W2113072832","https://openalex.org/W2125972858","https://openalex.org/W2127006085","https://openalex.org/W2127607093","https://openalex.org/W2129585918","https://openalex.org/W2133313261","https://openalex.org/W2134886133","https://openalex.org/W2136410628","https://openalex.org/W2137546662","https://openalex.org/W2143282831","https://openalex.org/W2149023901","https://openalex.org/W2152276356","https://openalex.org/W2154654747","https://openalex.org/W2154896031","https://openalex.org/W2156991891","https://openalex.org/W2157360228","https://openalex.org/W2159413587","https://openalex.org/W2159583324","https://openalex.org/W2166860552","https://openalex.org/W2170282111","https://openalex.org/W2193474433","https://openalex.org/W2342000326","https://openalex.org/W2412446857","https://openalex.org/W2555846310","https://openalex.org/W6626352918","https://openalex.org/W6656364270"],"related_works":["https://openalex.org/W3009438210","https://openalex.org/W3010444534","https://openalex.org/W3037132967","https://openalex.org/W2011472225","https://openalex.org/W2767338541","https://openalex.org/W3000057026","https://openalex.org/W3048565508","https://openalex.org/W3157580922","https://openalex.org/W3163984363","https://openalex.org/W2947302526"],"abstract_inverted_index":{"Motivation:":[0],"Disease":[1],"phenotype":[2,18,139],"networks":[3,19,53,99],"play":[4],"an":[5],"important":[6],"role":[7],"in":[8,74],"computational":[9],"approaches":[10],"to":[11,47,161,220,245],"identifying":[12],"new":[13,45],"disease-gene":[14],"associations.":[15],"Current":[16],"disease":[17,22,49,62,120,132,138,208,249],"often":[20],"model":[21,48],"relationships":[23],"based":[24],"on":[25,33],"pairwise":[26],"similarities,":[27],"therefore":[28],"ignore":[29],"the":[30,67,71,97,110,136,150,155,170,179,185,193,214,248],"specific":[31],"context":[32],"how":[34],"two":[35,91,98],"diseases":[36,84],"are":[37,217],"connected.":[38],"In":[39,141,201,241],"this":[40],"study,":[41],"we":[42,89,129,203],"propose":[43],"a":[44,57,113,123,142,225],"strategy":[46],"associations":[50],"using":[51,93,122,135,209],"context-sensitive":[52],"(CSNs).":[54],"We":[55,78,108,223],"developed":[56],"CSN-based":[58,151],"phenome-driven":[59],"approach":[60,152,172,187,195],"for":[61,147,164,184,206,230,258],"genetics":[63,250],"prediction,":[64],"and":[65,103,118,211,232,255,263],"investigated":[66],"translational":[68],"potential":[69,259],"of":[70],"predicted":[72,119,204],"genes":[73,121,167,205,216],"drug":[75,227,260],"discovery.":[76],"Results:":[77],"constructed":[79,90],"CSNs":[80,92,111,243],"by":[81,239],"directly":[82],"connecting":[83],"with":[85,112,169,236,253],"associated":[86],"phenotypes.":[87],"Here,":[88],"different":[94],"data":[95],"sources;":[96],"contain":[100],"26":[101],"790":[102],"13":[104],"822":[105],"nodes":[106],"respectively.":[107],"integrated":[109],"genetic":[114],"functional":[115],"relationship":[116],"network":[117],"network-based":[124],"ranking":[125],"algorithm.":[126],"For":[127],"comparison,":[128],"built":[130],"Similarity-Based":[131],"Networks":[133],"(SBN)":[134],"same":[137],"data.":[140],"de":[143],"novo":[144],"cross":[145],"validation":[146],"3324":[148],"diseases,":[149],"significantly":[153,190,246],"increased":[154],"average":[156],"rank":[157],"from":[158],"top":[159,162],"12.6":[160],"8.8%":[163],"all":[165],"tested":[166],"comparing":[168,252],"SBN-based":[171],"(":[173],"p