{"id":"https://openalex.org/W4403205334","doi":"https://doi.org/10.1186/s13040-024-00392-y","title":"MDVarP: modifier\u2009~\u2009disease-causing variant pairs predictor","display_name":"MDVarP: modifier\u2009~\u2009disease-causing variant pairs predictor","publication_year":2024,"publication_date":"2024-10-08","ids":{"openalex":"https://openalex.org/W4403205334","doi":"https://doi.org/10.1186/s13040-024-00392-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/39379981"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-024-00392-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00392-y","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00392-y","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/s13040-024-00392-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101710314","display_name":"Hong Sun","orcid":"https://orcid.org/0000-0003-1306-7629"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210159420","display_name":"Shanghai Children's Hospital","ror":"https://ror.org/05pea1m70","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159420"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hong Sun","raw_affiliation_strings":["Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, School of Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China. shpolor@163.com","Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, School of Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, School of Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China. shpolor@163.com","institution_ids":[]},{"raw_affiliation_string":"Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, School of Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China","institution_ids":["https://openalex.org/I4210159420","https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070498614","display_name":"Yunqin Chen","orcid":"https://orcid.org/0000-0002-8619-0890"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yunqin Chen","raw_affiliation_strings":["Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, 200237, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, 200237, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014322418","display_name":"Liangxiao Ma","orcid":"https://orcid.org/0000-0002-9103-4913"},"institutions":[{"id":"https://openalex.org/I4210096013","display_name":"Shanghai Institute of Nutrition and Health","ror":"https://ror.org/00rytkh49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210096013"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liangxiao Ma","raw_affiliation_strings":["Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Science, Shanghai, 200031, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Science, Shanghai, 200031, China","institution_ids":["https://openalex.org/I4210096013"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101710314"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210159420"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19070078,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"39","last_page":"39"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.47679999470710754,"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"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.47679999470710754,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.4327999949455261,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.057999998331069946,"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/computer-science","display_name":"Computer science","score":0.5169934034347534},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.49530234932899475},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.21359464526176453},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.17249855399131775}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5169934034347534},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.49530234932899475},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.21359464526176453},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.17249855399131775}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-024-00392-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00392-y","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00392-y","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:39379981","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39379981","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:pubmedcentral.nih.gov:11460193","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11460193","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:e507bc43003e40afa889ca5ee8e6eb8c","is_oa":true,"landing_page_url":"https://doaj.org/article/e507bc43003e40afa889ca5ee8e6eb8c","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 17, Iss 1, Pp 1-14 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13040-024-00392-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00392-y","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00392-y","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4403205334.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1955518362","https://openalex.org/W1987585879","https://openalex.org/W1997476591","https://openalex.org/W2032315443","https://openalex.org/W2053817355","https://openalex.org/W2073818070","https://openalex.org/W2081872599","https://openalex.org/W2104549677","https://openalex.org/W2126015874","https://openalex.org/W2130410032","https://openalex.org/W2141307855","https://openalex.org/W2143602768","https://openalex.org/W2160995259","https://openalex.org/W2167852161","https://openalex.org/W2256016639","https://openalex.org/W2417483443","https://openalex.org/W2462242997","https://openalex.org/W2513408092","https://openalex.org/W2568523137","https://openalex.org/W2600260436","https://openalex.org/W2604078450","https://openalex.org/W2742614542","https://openalex.org/W2804994040","https://openalex.org/W2905452503","https://openalex.org/W2911964244","https://openalex.org/W2949598989","https://openalex.org/W2952988698","https://openalex.org/W2981452366","https://openalex.org/W2983166786","https://openalex.org/W2999215340","https://openalex.org/W3029661147","https://openalex.org/W3093053585","https://openalex.org/W3095583226","https://openalex.org/W3160629642","https://openalex.org/W3198868363","https://openalex.org/W4231311503","https://openalex.org/W4287218243","https://openalex.org/W4321371315","https://openalex.org/W4366605966","https://openalex.org/W4367600858","https://openalex.org/W4386530204","https://openalex.org/W4386861232"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W4402327032","https://openalex.org/W2382290278"],"abstract_inverted_index":{"BACKGROUND:":[0],"Modifiers":[1],"significantly":[2],"impact":[3],"disease":[4,16,142],"phenotypes":[5],"by":[6],"modulating":[7],"the":[8,97],"effects":[9],"of":[10,65,99,116],"disease-causing":[11,27,47,74,120],"variants,":[12],"resulting":[13],"in":[14,132,138],"varying":[15],"manifestations":[17],"among":[18],"individuals.":[19],"However,":[20],"identifying":[21],"genetic":[22,66,127],"interactions":[23,128],"between":[24],"modifier":[25,45,72,122],"and":[26,54,77,92,121,141],"variants":[28],"is":[29],"challenging.":[30],"RESULTS:":[31],"We":[32,68],"developed":[33],"MDVarP,":[34],"an":[35,59],"ensemble":[36],"model":[37],"comprising":[38],"1000":[39],"random":[40],"forest":[41],"predictors,":[42],"to":[43],"identify":[44],"~":[46,73],"variant":[48,75,106],"combinations.":[49],"MDVarP":[50,84,104],"achieves":[51],"high":[52],"accuracy":[53],"precision,":[55],"as":[56],"verified":[57],"using":[58],"independent":[60],"dataset":[61],"with":[62,109,135],"published":[63],"evidence":[64,80],"interactions.":[67],"identified":[69],"25":[70],"novel":[71],"combinations":[76],"obtained":[78],"supporting":[79],"for":[81],"these":[82],"associations.":[83],"outputs":[85],"a":[86,100],"class":[87],"label":[88],"(\"Associated-pair\"":[89],"or":[90],"\"Nonrelevant-pair\")":[91],"two":[93],"prediction":[94],"scores":[95],"indicating":[96],"probability":[98],"true":[101],"association.":[102],"CONCLUSIONS:":[103],"prioritizes":[105],"pairs":[107],"associated":[108],"phenotypic":[110,130],"modulations,":[111],"enabling":[112],"more":[113],"effective":[114],"mapping":[115],"functional":[117],"contributions":[118],"from":[119],"variants.":[123],"This":[124],"framework":[125],"interprets":[126],"underlying":[129],"variations":[131],"human":[133],"diseases,":[134],"potential":[136],"applications":[137],"personalized":[139],"medicine":[140],"prevention.":[143]},"counts_by_year":[],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}