{"id":"https://openalex.org/W2293972456","doi":"https://doi.org/10.1109/embc.2015.7319885","title":"Non-linear Bayesian framework to determine the transcriptional effects of cancer-associated genomic aberrations","display_name":"Non-linear Bayesian framework to determine the transcriptional effects of cancer-associated genomic aberrations","publication_year":2015,"publication_date":"2015-08-01","ids":{"openalex":"https://openalex.org/W2293972456","doi":"https://doi.org/10.1109/embc.2015.7319885","mag":"2293972456","pmid":"https://pubmed.ncbi.nlm.nih.gov/26737785"},"language":"en","primary_location":{"id":"doi:10.1109/embc.2015.7319885","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2015.7319885","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011987346","display_name":"Abolfazl Razi","orcid":"https://orcid.org/0000-0002-3330-6132"},"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":"Abolfazl Razi","raw_affiliation_strings":["Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053205624","display_name":"Nilanjana Banerjee","orcid":"https://orcid.org/0000-0001-8022-8598"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nilanjana Banerjee","raw_affiliation_strings":["Philips Research North America, Briarcliff Manor, NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Philips Research North America, Briarcliff Manor, NY","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017119312","display_name":"Nevenka Dimitrova","orcid":"https://orcid.org/0000-0003-4091-9233"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nevenka Dimitrova","raw_affiliation_strings":["Philips Research North America, Briarcliff Manor, NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Philips Research North America, Briarcliff Manor, NY","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005628876","display_name":"Vinay Varadan","orcid":"https://orcid.org/0000-0003-1520-1967"},"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":"Vinay Varadan","raw_affiliation_strings":["Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"33","issue":null,"first_page":"6514","last_page":"6518"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9995999932289124,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9958000183105469,"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/epigenetics","display_name":"Epigenetics","score":0.7204610109329224},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6838380098342896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6389954090118408},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6294801235198975},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4789170026779175},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4518992602825165},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.43951383233070374},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.43645384907722473},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.42357420921325684},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4225981831550598},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.374845027923584},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.31012383103370667},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.150641530752182}],"concepts":[{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.7204610109329224},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6838380098342896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6389954090118408},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6294801235198975},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4789170026779175},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4518992602825165},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.43951383233070374},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.43645384907722473},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.42357420921325684},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4225981831550598},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.374845027923584},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.31012383103370667},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.150641530752182}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/embc.2015.7319885","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2015.7319885","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:26737785","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26737785","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null},{"id":"pmh:oai:europepmc.org:4194730","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5341149","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.6000000238418579,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1866525876","display_name":null,"funder_award_id":"P50 CA150964","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G563423719","display_name":null,"funder_award_id":"R25 CA094186","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1978230112","https://openalex.org/W1982652137","https://openalex.org/W2009501477","https://openalex.org/W2097360283","https://openalex.org/W2100714130","https://openalex.org/W2110687686","https://openalex.org/W2127611185","https://openalex.org/W2130410032","https://openalex.org/W2150757282","https://openalex.org/W4294541781"],"related_works":["https://openalex.org/W2130939068","https://openalex.org/W3163717165","https://openalex.org/W2114466827","https://openalex.org/W249159571","https://openalex.org/W2791736663","https://openalex.org/W2010571965","https://openalex.org/W2806770614","https://openalex.org/W2129949791","https://openalex.org/W30633243","https://openalex.org/W2131550814"],"abstract_inverted_index":{"While":[0],"the":[1,19,23,54,60,148,156,181],"tumorigenic":[2],"effects":[3],"of":[4,22,26,56,131,152,184],"specific":[5],"recurrent":[6,27],"mutations":[7,28],"in":[8,45,144,155],"known":[9,17],"cancer":[10,46,162],"driver-genes":[11],"is":[12,16],"well-characterized,":[13],"not":[14],"much":[15],"about":[18],"functional":[20,38],"relevance":[21],"vast":[24],"majority":[25,55],"observed":[29],"across":[30,76],"cancers.":[31],"Prior":[32],"studies":[33],"have":[34],"attempted":[35],"to":[36,102,113,122,146],"identify":[37],"genomic":[39,92],"aberrations":[40],"by":[41,190],"integrating":[42],"multi-omics":[43,163],"measurements":[44],"samples":[47],"with":[48,180],"community-curated":[49],"biological":[50,62,105],"pathway":[51,66],"networks.":[52],"However,":[53],"these":[57,104],"approaches":[58],"overlook":[59],"following":[61],"considerations:":[63],"i)":[64],"signaling":[65],"networks":[67],"are":[68],"highly":[69],"tissue-specific":[70,115],"and":[71,91,121,134],"their":[72],"regulatory":[73,80,135,150,157],"interactions":[74],"differ":[75],"tissue":[77],"types;":[78],"ii)":[79],"factors":[81],"exhibit":[82,94],"heterogeneous":[83],"influence":[84,117],"on":[85,97],"downstream":[86],"gene":[87,98,186],"transcription;":[88],"iii)":[89],"epigenetic":[90,133],"alterations":[93],"nonlinear":[95],"impact":[96,151],"transcription.":[99],"In":[100],"order":[101,145],"accommodate":[103],"effects,":[106],"we":[107,166],"propose":[108],"a":[109,124,129,139,160],"hybrid":[110],"Bayesian":[111],"method":[112,171],"learn":[114],"pairwise":[116],"models":[118],"amongst":[119],"genes":[120],"predict":[123],"gene's":[125],"expression":[126],"level":[127],"as":[128],"nonlinear-function":[130],"its":[132],"influences.":[136],"We":[137],"employ":[138],"novel":[140],"tree-based":[141],"depth-penalization":[142],"mechanism":[143],"capture":[147],"higher":[149],"closer":[153],"neighbors":[154],"network.":[158],"Using":[159],"breast":[161],"dataset":[164],"(N=1190),":[165],"show":[167],"that":[168],"our":[169],"proposed":[170],"has":[172],"superior":[173],"prediction":[174],"power":[175],"over":[176],"optimization-based":[177],"regression":[178],"models,":[179],"additional":[182],"advantage":[183],"revealing":[185],"deregulations":[187],"potentially":[188],"driven":[189],"somatic":[191],"mutations.":[192]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
