{"id":"https://openalex.org/W3158604732","doi":"https://doi.org/10.1186/s13040-021-00262-x","title":"A maximum flow-based network approach for identification of stable noncoding biomarkers associated with the multigenic neurological condition, autism","display_name":"A maximum flow-based network approach for identification of stable noncoding biomarkers associated with the multigenic neurological condition, autism","publication_year":2021,"publication_date":"2021-05-03","ids":{"openalex":"https://openalex.org/W3158604732","doi":"https://doi.org/10.1186/s13040-021-00262-x","mag":"3158604732","pmid":"https://pubmed.ncbi.nlm.nih.gov/33941233"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-021-00262-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-021-00262-x","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-021-00262-x","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/s13040-021-00262-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012771499","display_name":"Maya Varma","orcid":"https://orcid.org/0000-0003-0693-7753"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Maya Varma","raw_affiliation_strings":["Department of Computer Science, Stanford University, Stanford, CA, USA"],"raw_orcid":"https://orcid.org/0000-0003-0693-7753","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073093951","display_name":"Kelley Paskov","orcid":"https://orcid.org/0000-0002-5252-1401"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kelley M. Paskov","raw_affiliation_strings":["Department of Biomedical Data Science, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059970218","display_name":"Brianna Chrisman","orcid":"https://orcid.org/0000-0002-7157-607X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brianna S. Chrisman","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089070900","display_name":"Min Sun","orcid":"https://orcid.org/0000-0003-1049-1854"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Min Woo Sun","raw_affiliation_strings":["Department of Biomedical Data Science, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007058506","display_name":"Jae-Yoon Jung","orcid":"https://orcid.org/0000-0001-7948-9803"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jae-Yoon Jung","raw_affiliation_strings":["Department of Biomedical Data Science, Stanford University, Stanford, CA, USA","Department of Pediatrics, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Pediatrics, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029670549","display_name":"Nate Stockham","orcid":"https://orcid.org/0000-0002-0752-6801"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nate T. Stockham","raw_affiliation_strings":["Department of Neuroscience, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037490912","display_name":"Peter Washington","orcid":"https://orcid.org/0000-0003-3276-4411"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Y. Washington","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027872863","display_name":"Dennis P. Wall","orcid":"https://orcid.org/0000-0002-7889-9146"},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dennis P. Wall","raw_affiliation_strings":["Department of Biomedical Data Science, Stanford University, Stanford, CA, USA. dpwall@stanford.edu","Department of Pediatrics, Stanford University, Stanford, CA, USA. dpwall@stanford.edu","Department of Biomedical Data Science, Stanford University, Stanford, CA, USA","Department of Pediatrics, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University, Stanford, CA, USA. dpwall@stanford.edu","institution_ids":["https://openalex.org/I97018004","https://openalex.org/I4210137306"]},{"raw_affiliation_string":"Department of Pediatrics, Stanford University, Stanford, CA, USA. dpwall@stanford.edu","institution_ids":["https://openalex.org/I97018004","https://openalex.org/I4210137306"]},{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Pediatrics, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5012771499"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04484812,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"14","issue":"1","first_page":"28","last_page":"28"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.7114999890327454,"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":0.7114999890327454,"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":0.21549999713897705,"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":0.01889999955892563,"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":0.6534716486930847},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.520576536655426},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5088639259338379},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.49045392870903015},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.48046988248825073},{"id":"https://openalex.org/keywords/logistic-regression","display_name":"Logistic regression","score":0.4595780074596405},{"id":"https://openalex.org/keywords/autism","display_name":"Autism","score":0.4182703495025635},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3377007842063904},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3217034339904785},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20984545350074768},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.11096891760826111}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6534716486930847},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.520576536655426},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5088639259338379},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.49045392870903015},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.48046988248825073},{"id":"https://openalex.org/C151956035","wikidata":"https://www.wikidata.org/wiki/Q1132755","display_name":"Logistic regression","level":2,"score":0.4595780074596405},{"id":"https://openalex.org/C205778803","wikidata":"https://www.wikidata.org/wiki/Q38404","display_name":"Autism","level":2,"score":0.4182703495025635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3377007842063904},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3217034339904785},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20984545350074768},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.11096891760826111},{"id":"https://openalex.org/C118552586","wikidata":"https://www.wikidata.org/wiki/Q7867","display_name":"Psychiatry","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-021-00262-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-021-00262-x","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-021-00262-x","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:33941233","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33941233","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:8091705","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8091705","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:b32dee4bb5c24f978d9c6303ebb00245","is_oa":true,"landing_page_url":"https://doaj.org/article/b32dee4bb5c24f978d9c6303ebb00245","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 14, Iss 1, Pp 1-15 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13040-021-00262-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-021-00262-x","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-021-00262-x","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309331","display_name":"Hartwell Foundation","ror":"https://ror.org/038cgyc59"},{"id":"https://openalex.org/F4320333063","display_name":"Stanford Bio-X","ror":"https://ror.org/00f54p054"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3158604732.pdf","grobid_xml":"https://content.openalex.org/works/W3158604732.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1437423","https://openalex.org/W124018459","https://openalex.org/W1540386974","https://openalex.org/W1546348152","https://openalex.org/W1964866242","https://openalex.org/W1971376634","https://openalex.org/W2002531683","https://openalex.org/W2003933468","https://openalex.org/W2038894244","https://openalex.org/W2078178396","https://openalex.org/W2088489316","https://openalex.org/W2101234009","https://openalex.org/W2128016314","https://openalex.org/W2130077241","https://openalex.org/W2146481951","https://openalex.org/W2154501376","https://openalex.org/W2156332695","https://openalex.org/W2162162988","https://openalex.org/W2165250079","https://openalex.org/W2167898988","https://openalex.org/W2169795969","https://openalex.org/W2293825098","https://openalex.org/W2333980451","https://openalex.org/W2410375143","https://openalex.org/W2476100783","https://openalex.org/W2488220022","https://openalex.org/W2499542379","https://openalex.org/W2605675484","https://openalex.org/W2615562152","https://openalex.org/W2728946616","https://openalex.org/W2758479384","https://openalex.org/W2793070660","https://openalex.org/W2799448805","https://openalex.org/W2902775069","https://openalex.org/W2903177761","https://openalex.org/W2921790220","https://openalex.org/W2922844241","https://openalex.org/W2955612236","https://openalex.org/W2959289532","https://openalex.org/W2959750635","https://openalex.org/W2962941624","https://openalex.org/W2963160524","https://openalex.org/W2969167159","https://openalex.org/W2969932277","https://openalex.org/W2992152394","https://openalex.org/W3023126556","https://openalex.org/W4213060883","https://openalex.org/W4231913388","https://openalex.org/W4236182060","https://openalex.org/W6675354045","https://openalex.org/W6767264000"],"related_works":["https://openalex.org/W4280602684","https://openalex.org/W4310092953","https://openalex.org/W2227393071","https://openalex.org/W4402326599","https://openalex.org/W1995350144","https://openalex.org/W2082102603","https://openalex.org/W2166141227","https://openalex.org/W3133980636","https://openalex.org/W4378085486","https://openalex.org/W4366602711"],"abstract_inverted_index":{"BACKGROUND:":[0],"Machine":[1],"learning":[2,154],"approaches":[3],"for":[4,149,171],"predicting":[5],"disease":[6],"risk":[7],"from":[8,80],"high-dimensional":[9],"whole":[10],"genome":[11],"sequence":[12],"(WGS)":[13],"data":[14],"often":[15],"result":[16],"in":[17,76,98],"unstable":[18],"models":[19,155],"that":[20,156],"can":[21,157],"be":[22,134],"difficult":[23],"to":[24,54,87,117,126,133],"interpret,":[25],"limiting":[26],"the":[27,48,77,93,107,138,142,150,165],"identification":[28],"of":[29,32,50,58,100,110,152],"putative":[30],"sets":[31,57,109],"biomarkers.":[33],"Here,":[34],"we":[35,91,131],"design":[36],"and":[37,104],"validate":[38],"a":[39,113],"graph-based":[40],"methodology":[41],"based":[42],"on":[43],"maximum":[44,121],"flow,":[45],"which":[46,130],"leverages":[47],"presence":[49],"linkage":[51],"disequilibrium":[52],"(LD)":[53],"identify":[55,127,158],"stable":[56,136],"variants":[59,94],"associated":[60],"with":[61],"complex":[62,172],"multigenic":[63],"disorders.":[64,174],"RESULTS:":[65],"-regularized":[66],"model":[67,89],"exhibits":[68],"high":[69],"predictive":[70,159],"accuracy":[71],"yet":[72],"demonstrates":[73],"great":[74],"variability":[75],"features":[78,111,139],"selected":[79],"over":[81],"230,000":[82],"possible":[83],"variants.":[84,160],"In":[85],"order":[86],"improve":[88],"stability,":[90],"extract":[92],"assigned":[95],"non-zero":[96],"weights":[97],"each":[99],"5":[101],"cross-validation":[102],"folds":[103],"then":[105],"assemble":[106],"five":[108],"into":[112],"flow":[114,122],"network":[115],"subject":[116],"LD":[118],"constraints.":[119],"The":[120],"formulation":[123],"allowed":[124],"us":[125],"55":[128],"variants,":[129],"show":[132],"more":[135],"than":[137],"identified":[140],"by":[141],"original":[143],"classifier.":[144],"CONCLUSION:":[145],"Our":[146,161],"method":[147],"allows":[148],"creation":[151],"machine":[153],"results":[162],"help":[163],"pave":[164],"way":[166],"towards":[167],"biomarker-based":[168],"diagnosis":[169],"methods":[170],"genetic":[173]},"counts_by_year":[],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
