{"id":"https://openalex.org/W2051427941","doi":"https://doi.org/10.1186/1752-0509-6-s3-s8","title":"A vertex similarity-based framework to discover and rank orphan disease-related genes","display_name":"A vertex similarity-based framework to discover and rank orphan disease-related genes","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W2051427941","doi":"https://doi.org/10.1186/1752-0509-6-s3-s8","mag":"2051427941","pmid":"https://pubmed.ncbi.nlm.nih.gov/23281592"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-s3-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s3-s8","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S3-S8","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S3-S8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102000316","display_name":"Cheng Zhu","orcid":"https://orcid.org/0000-0003-3632-6435"},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cheng Zhu","raw_affiliation_strings":["Department of Computer Science, University of Cincinnati, Cincinnati, Ohio 45229, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Cincinnati, Cincinnati, Ohio 45229, USA","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073107326","display_name":"Akash Kushwaha","orcid":null},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Akash Kushwaha","raw_affiliation_strings":["Department of Computer Science, University of Cincinnati, Cincinnati, Ohio, 45229, USA","[Department of Computer Science, University of Cincinnati, Cincinnati, USA]"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Cincinnati, Cincinnati, Ohio, 45229, USA","institution_ids":["https://openalex.org/I63135867"]},{"raw_affiliation_string":"[Department of Computer Science, University of Cincinnati, Cincinnati, USA]","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110098262","display_name":"Kenneth A. Berman","orcid":null},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kenneth Berman","raw_affiliation_strings":["Department of Computer Science, University of Cincinnati, Cincinnati, Ohio, 45229, USA","[Department of Computer Science, University of Cincinnati, Cincinnati, USA]"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Cincinnati, Cincinnati, Ohio, 45229, USA","institution_ids":["https://openalex.org/I63135867"]},{"raw_affiliation_string":"[Department of Computer Science, University of Cincinnati, Cincinnati, USA]","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061689835","display_name":"Anil G. Jegga","orcid":"https://orcid.org/0000-0002-4881-7752"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]},{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anil G Jegga","raw_affiliation_strings":["Department of Computer Science, University of Cincinnati, Cincinnati, Ohio, 45229, USA","Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, 45229, USA","Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA","Division of Biomedical Informatics, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, USA","Department of Pediatrics, University of Cincinnati, Cincinnati, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Cincinnati, Cincinnati, Ohio, 45229, USA","institution_ids":["https://openalex.org/I63135867"]},{"raw_affiliation_string":"Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, 45229, USA","institution_ids":["https://openalex.org/I63135867"]},{"raw_affiliation_string":"Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA","institution_ids":["https://openalex.org/I1285204247"]},{"raw_affiliation_string":"Division of Biomedical Informatics, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, USA","institution_ids":["https://openalex.org/I1285204247"]},{"raw_affiliation_string":"Department of Pediatrics, University of Cincinnati, Cincinnati, USA","institution_ids":["https://openalex.org/I63135867"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102000316"],"corresponding_institution_ids":["https://openalex.org/I63135867"],"apc_list":null,"apc_paid":null,"fwci":1.2078,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.7781202,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"6","issue":"S3","first_page":"S8","last_page":"S8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9973000288009644,"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":0.9837999939918518,"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/candidate-gene","display_name":"Candidate gene","score":0.702028751373291},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5879345536231995},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.5285595655441284},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45385465025901794},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4444458484649658},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38620129227638245},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.384573757648468},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32281821966171265},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3050008714199066},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.25393402576446533}],"concepts":[{"id":"https://openalex.org/C69991583","wikidata":"https://www.wikidata.org/wiki/Q1423575","display_name":"Candidate gene","level":3,"score":0.702028751373291},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5879345536231995},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5285595655441284},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45385465025901794},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4444458484649658},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38620129227638245},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.384573757648468},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32281821966171265},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3050008714199066},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.25393402576446533},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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":"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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-6-s3-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s3-s8","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S3-S8","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:23281592","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23281592","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 systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:fcd6f4a7357a40bebbb527984fc11a78","is_oa":true,"landing_page_url":"https://doaj.org/article/fcd6f4a7357a40bebbb527984fc11a78","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 6, Iss Suppl 3, p S8 (2012)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3524320","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3524320","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-s3-s8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s3-s8","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S3-S8","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309575","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2051427941.pdf","grobid_xml":"https://content.openalex.org/works/W2051427941.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W80748578","https://openalex.org/W105330602","https://openalex.org/W1502421007","https://openalex.org/W1598494905","https://openalex.org/W1605637875","https://openalex.org/W1868578820","https://openalex.org/W1929627202","https://openalex.org/W1981858341","https://openalex.org/W1983965561","https://openalex.org/W1985479322","https://openalex.org/W1989058582","https://openalex.org/W1991517256","https://openalex.org/W1994127362","https://openalex.org/W1994803330","https://openalex.org/W2006249044","https://openalex.org/W2008840655","https://openalex.org/W2016133673","https://openalex.org/W2035595951","https://openalex.org/W2037705937","https://openalex.org/W2038122249","https://openalex.org/W2058539819","https://openalex.org/W2059546403","https://openalex.org/W2063389953","https://openalex.org/W2066536638","https://openalex.org/W2075155461","https://openalex.org/W2083045667","https://openalex.org/W2097498614","https://openalex.org/W2099656145","https://openalex.org/W2100463963","https://openalex.org/W2101181377","https://openalex.org/W2102281458","https://openalex.org/W2102427034","https://openalex.org/W2104261859","https://openalex.org/W2105187843","https://openalex.org/W2105813018","https://openalex.org/W2107580398","https://openalex.org/W2108181223","https://openalex.org/W2109555487","https://openalex.org/W2119220491","https://openalex.org/W2120051475","https://openalex.org/W2122207295","https://openalex.org/W2124649657","https://openalex.org/W2125118217","https://openalex.org/W2128245545","https://openalex.org/W2130453712","https://openalex.org/W2131397321","https://openalex.org/W2132056568","https://openalex.org/W2135586354","https://openalex.org/W2138020005","https://openalex.org/W2138621811","https://openalex.org/W2145001205","https://openalex.org/W2147714160","https://openalex.org/W2148606196","https://openalex.org/W2152653671","https://openalex.org/W2156750171","https://openalex.org/W2160273867","https://openalex.org/W2170461266","https://openalex.org/W2410525650","https://openalex.org/W4247545505"],"related_works":["https://openalex.org/W4206918580","https://openalex.org/W4280529353","https://openalex.org/W2062935816","https://openalex.org/W2112289353","https://openalex.org/W2139462925","https://openalex.org/W2188500270","https://openalex.org/W2303858293","https://openalex.org/W2517462780","https://openalex.org/W2915512527","https://openalex.org/W2065112873"],"abstract_inverted_index":{"We":[0],"demonstrate":[1],"that":[2],"VS-based":[3],"parameter-free":[4],"ranking":[5],"approach":[6],"can":[7,17],"be":[8],"successfully":[9],"used":[10],"for":[11,22,33,45],"disease":[12,24],"candidate":[13,23,31],"gene":[14,25],"prioritization":[15],"and":[16],"complement":[18],"other":[19],"network-based":[20],"methods":[21],"ranking.":[26],"Importantly,":[27],"our":[28],"VS-ranked":[29],"top":[30],"genes":[32],"the":[34,37],"ODs":[35],"match":[36],"known":[38],"literature,":[39],"suggesting":[40],"several":[41],"novel":[42],"causal":[43],"relationships":[44],"further":[46],"investigation.":[47]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
