{"id":"https://openalex.org/W4360595708","doi":"https://doi.org/10.15302/j-qb-022-0309","title":"Modeling the relationship between gene expression and mutational signature","display_name":"Modeling the relationship between gene expression and mutational signature","publication_year":2023,"publication_date":"2023-03-01","ids":{"openalex":"https://openalex.org/W4360595708","doi":"https://doi.org/10.15302/j-qb-022-0309","pmid":"https://pubmed.ncbi.nlm.nih.gov/37032811","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/10078980"},"language":"en","primary_location":{"id":"doi:10.15302/j-qb-022-0309","doi":"https://doi.org/10.15302/j-qb-022-0309","is_oa":true,"landing_page_url":"https://doi.org/10.15302/j-qb-022-0309","pdf_url":"https://journal.hep.com.cn/qb/EN/PDF/10.15302/J-QB-022-0309","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","poland-70","russia-white-list-1"],"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":"Quantitative Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://journal.hep.com.cn/qb/EN/PDF/10.15302/J-QB-022-0309","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089549770","display_name":"Limin Jiang","orcid":"https://orcid.org/0000-0002-4320-3698","observed_orcids":["https://orcid.org/0000-0002-4320-3698"]},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]},{"id":"https://openalex.org/I4390039284","display_name":"UNM Comprehensive Cancer Center","ror":"https://ror.org/05kx2e072","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I169521973","https://openalex.org/I4390039284"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Limin Jiang","raw_affiliation_strings":["Department of Internal Medicine Comprehensive Cancer Center University of New Mexico Albuquerque Albuquerque NM 87109 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine Comprehensive Cancer Center University of New Mexico Albuquerque Albuquerque NM 87109 USA","institution_ids":["https://openalex.org/I169521973","https://openalex.org/I4390039284"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024895838","display_name":"Hui Yu","orcid":"https://orcid.org/0000-0002-4491-8855","observed_orcids":["https://orcid.org/0000-0002-4491-8855"]},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]},{"id":"https://openalex.org/I4390039284","display_name":"UNM Comprehensive Cancer Center","ror":"https://ror.org/05kx2e072","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I169521973","https://openalex.org/I4390039284"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hui Yu","raw_affiliation_strings":["Department of Internal Medicine Comprehensive Cancer Center University of New Mexico Albuquerque Albuquerque NM 87109 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine Comprehensive Cancer Center University of New Mexico Albuquerque Albuquerque NM 87109 USA","institution_ids":["https://openalex.org/I169521973","https://openalex.org/I4390039284"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056796466","display_name":"Yan Ping Guo","orcid":"https://orcid.org/0000-0001-5252-3960","observed_orcids":["https://orcid.org/0000-0001-5252-3960"]},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]},{"id":"https://openalex.org/I4390039284","display_name":"UNM Comprehensive Cancer Center","ror":"https://ror.org/05kx2e072","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I169521973","https://openalex.org/I4390039284"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yan Guo","raw_affiliation_strings":["Department of Internal Medicine Comprehensive Cancer Center University of New Mexico Albuquerque Albuquerque NM 87109 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine Comprehensive Cancer Center University of New Mexico Albuquerque Albuquerque NM 87109 USA","institution_ids":["https://openalex.org/I169521973","https://openalex.org/I4390039284"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5056796466"],"corresponding_institution_ids":["https://openalex.org/I169521973","https://openalex.org/I4390039284"],"apc_list":{"value":0,"currency":"USD","value_usd":0},"apc_paid":null,"fwci":0.2535,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.43735579,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"11","issue":"1","first_page":"31","last_page":"43"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9351000189781189,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9351000189781189,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.03680000081658363,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0024999999441206455,"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/mutational-signatures","display_name":"mutational signatures","score":0.9980000257492065},{"id":"https://openalex.org/keywords/gene-expression","display_name":"gene expression","score":0.9300000071525574},{"id":"https://openalex.org/keywords/somatic-mutations","display_name":"somatic mutations","score":0.9919999837875366},{"id":"https://openalex.org/keywords/cancer-genomics","display_name":"cancer genomics","score":0.6169999837875366},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-seq","score":0.7099999785423279},{"id":"https://openalex.org/keywords/lung-cancer","display_name":"lung cancer","score":0.75},{"id":"https://openalex.org/keywords/smoking-status","display_name":"smoking status","score":0.8389999866485596},{"id":"https://openalex.org/keywords/protein-coding-genes","display_name":"protein-coding genes","score":0.7369999885559082},{"id":"https://openalex.org/keywords/gene-expression-models","display_name":"gene expression models","score":0.3529999852180481},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"carcinogenesis","score":0.8370000123977661}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.7040772438049316},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6321898698806763},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6162775158882141},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5782486200332642},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5655092000961304},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.5504574775695801},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.4583337903022766},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4482000768184662},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.4295782446861267},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4096372723579407},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.12484744191169739},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.15302/j-qb-022-0309","doi":"https://doi.org/10.15302/j-qb-022-0309","is_oa":true,"landing_page_url":"https://doi.org/10.15302/j-qb-022-0309","pdf_url":"https://journal.hep.com.cn/qb/EN/PDF/10.15302/J-QB-022-0309","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","poland-70","russia-white-list-1"],"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":"Quantitative Biology","raw_type":"journal-article"},{"id":"pmid:37032811","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37032811","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,"listed_in":[],"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":"Quantitative biology (Beijing, China)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10078980","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10078980","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10078980/pdf/nihms-1878532.pdf","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,"listed_in":[],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Quant Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:a1549c61e4b143dfa9f89c09f0c2e641","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/a1549c61e4b143dfa9f89c09f0c2e641","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Quantitative Biology, Vol 11, Iss 1, Pp 31-43 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.15302/j-qb-022-0309","doi":"https://doi.org/10.15302/j-qb-022-0309","is_oa":true,"landing_page_url":"https://doi.org/10.15302/j-qb-022-0309","pdf_url":"https://journal.hep.com.cn/qb/EN/PDF/10.15302/J-QB-022-0309","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","poland-70","russia-white-list-1"],"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":"Quantitative Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8048999905586243}],"study_designs":[],"awards":[{"id":"https://openalex.org/G9000873017","display_name":"University of New Mexico Cancer Center Support Grant","funder_award_id":"P30CA118100","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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4360595708.pdf","grobid_xml":"https://content.openalex.org/works/W4360595708.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1987313243","https://openalex.org/W2008255210","https://openalex.org/W2032424314","https://openalex.org/W2035222601","https://openalex.org/W2120010359","https://openalex.org/W2152061559","https://openalex.org/W2173818354","https://openalex.org/W2176435849","https://openalex.org/W2275935873","https://openalex.org/W2342628598","https://openalex.org/W2345503748","https://openalex.org/W2531004925","https://openalex.org/W2547187744","https://openalex.org/W2596164112","https://openalex.org/W2749641460","https://openalex.org/W2765243483","https://openalex.org/W2766220272","https://openalex.org/W2784208206","https://openalex.org/W2796207838","https://openalex.org/W2799563655","https://openalex.org/W2800002600","https://openalex.org/W2888205332","https://openalex.org/W2892065844","https://openalex.org/W2901416251","https://openalex.org/W2919337517","https://openalex.org/W2938255062","https://openalex.org/W2939332654","https://openalex.org/W2970967145","https://openalex.org/W2980190143","https://openalex.org/W2980681023","https://openalex.org/W2999626196","https://openalex.org/W3007509781"],"related_works":["https://openalex.org/W4401954722","https://openalex.org/W2947192149","https://openalex.org/W4297347997","https://openalex.org/W2343285674","https://openalex.org/W2957367608","https://openalex.org/W2953163445","https://openalex.org/W7101029574","https://openalex.org/W2951272706","https://openalex.org/W4280533574","https://openalex.org/W6947633211"],"abstract_inverted_index":{"Background:":[0],"Mutational":[1],"signatures":[2,57],"computed":[3],"from":[4],"somatic":[5,27,135],"mutations,":[6],"allow":[7],"an":[8],"in-depth":[9],"understanding":[10],"of":[11,80],"tumorigenesis":[12],"and":[13,29,44,64,86,119,134,145],"may":[14],"illuminate":[15],"early":[16],"prevention":[17],"strategies.":[18],"Many":[19],"studies":[20],"have":[21],"shown":[22],"the":[23,67,122,129,140],"regulation":[24],"effects":[25],"between":[26,41,131,142],"mutation":[28],"gene":[30,45,100,132,143],"expression":[31,101,133,144],"dysregulation.":[32],"Methods:":[33],"We":[34,47],"hypothesized":[35],"that":[36,128],"there":[37],"are":[38],"potential":[39],"associations":[40,130,141],"mutational":[42,56,146],"signature":[43],"expression.":[46],"capitalized":[48],"upon":[49],"RNA-seq":[50],"data":[51],"to":[52],"model":[53],"49":[54],"established":[55],"in":[58,74],"33":[59],"cancer":[60,105],"types.":[61],"Both":[62],"accuracy":[63,118],"area":[65,120],"under":[66,121],"curve":[68],"were":[69,92],"used":[70,109],"as":[71],"performance":[72],"measures":[73],"five-fold":[75],"cross-validation.":[76],"Results:":[77],"A":[78],"total":[79],"475":[81],"models":[82,88],"using":[83,89],"unconstrained":[84],"genes,":[85],"112":[87],"protein-coding":[90],"genes":[91],"selected":[93],"for":[94,110,116],"future":[95],"inference":[96],"purposes.":[97],"An":[98],"independent":[99],"dataset":[102],"on":[103],"lung":[104],"smoking":[106],"status":[107],"was":[108],"validation":[111],"which":[112],"achieved":[113],"over":[114],"80%":[115],"both":[117],"curve.":[123],"Conclusion:":[124],"These":[125],"results":[126],"demonstrate":[127],"mutations":[136],"can":[137],"translate":[138],"into":[139],"signatures.":[147]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-10-29T09:56:32.521200","created_date":"2023-03-24T00:00:00"}
