{"id":"https://openalex.org/W2129007011","doi":"https://doi.org/10.1093/bioinformatics/btv320","title":"tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation","display_name":"tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation","publication_year":2015,"publication_date":"2015-05-21","ids":{"openalex":"https://openalex.org/W2129007011","doi":"https://doi.org/10.1093/bioinformatics/btv320","mag":"2129007011","pmid":"https://pubmed.ncbi.nlm.nih.gov/26002884"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv320","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv320","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3054/49035278/bioinformatics_31_18_3054.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3054/49035278/bioinformatics_31_18_3054.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041398783","display_name":"Antoine Chambaz","orcid":"https://orcid.org/0000-0002-5592-6471"},"institutions":[{"id":"https://openalex.org/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]},{"id":"https://openalex.org/I4210097372","display_name":"\u00c9cole Nationale Sup\u00e9rieure d\u2019Informatique pour l\u2019Industrie et l\u2019Entreprise","ror":"https://ror.org/00tx98v53","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210097372"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210155549","display_name":"Laboratoire de Math\u00e9matiques","ror":"https://ror.org/05sd5r855","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I198244214","https://openalex.org/I4210141950","https://openalex.org/I4210155549"]},{"id":"https://openalex.org/I4387153769","display_name":"Laboratoire de Math\u00e9matiques et Mod\u00e9lisation d'\u00c9vry","ror":"https://ror.org/03jca6281","country_code":null,"type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210097372","https://openalex.org/I4387153769","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Antoine Chambaz","raw_affiliation_strings":["1 Modal\u2019X, Universit\u00e9 Paris Ouest Nanterre, Nanterre, France and 2Laboratoire de Math\u00e9matiques et Mod\u00e9lisation d\u2019\u00c9vry, Universit\u00e9 d\u2019\u00c9vry val d\u2019Essonne, UMR CNRS 8071, ENSIIE, USC INRA, \u00c9vry, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Modal\u2019X, Universit\u00e9 Paris Ouest Nanterre, Nanterre, France and 2Laboratoire de Math\u00e9matiques et Mod\u00e9lisation d\u2019\u00c9vry, Universit\u00e9 d\u2019\u00c9vry val d\u2019Essonne, UMR CNRS 8071, ENSIIE, USC INRA, \u00c9vry, France","institution_ids":["https://openalex.org/I88467170","https://openalex.org/I4210155549","https://openalex.org/I4210097372","https://openalex.org/I1294671590","https://openalex.org/I4387153769"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071356919","display_name":"Pierre Neuvial","orcid":"https://orcid.org/0000-0003-3584-9998"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210097372","display_name":"\u00c9cole Nationale Sup\u00e9rieure d\u2019Informatique pour l\u2019Industrie et l\u2019Entreprise","ror":"https://ror.org/00tx98v53","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210097372"]},{"id":"https://openalex.org/I4210155549","display_name":"Laboratoire de Math\u00e9matiques","ror":"https://ror.org/05sd5r855","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I198244214","https://openalex.org/I4210141950","https://openalex.org/I4210155549"]},{"id":"https://openalex.org/I4387153769","display_name":"Laboratoire de Math\u00e9matiques et Mod\u00e9lisation d'\u00c9vry","ror":"https://ror.org/03jca6281","country_code":null,"type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210097372","https://openalex.org/I4387153769","https://openalex.org/I88467170"]},{"id":"https://openalex.org/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre Neuvial","raw_affiliation_strings":["1 Modal\u2019X, Universit\u00e9 Paris Ouest Nanterre, Nanterre, France and 2Laboratoire de Math\u00e9matiques et Mod\u00e9lisation d\u2019\u00c9vry, Universit\u00e9 d\u2019\u00c9vry val d\u2019Essonne, UMR CNRS 8071, ENSIIE, USC INRA, \u00c9vry, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Modal\u2019X, Universit\u00e9 Paris Ouest Nanterre, Nanterre, France and 2Laboratoire de Math\u00e9matiques et Mod\u00e9lisation d\u2019\u00c9vry, Universit\u00e9 d\u2019\u00c9vry val d\u2019Essonne, UMR CNRS 8071, ENSIIE, USC INRA, \u00c9vry, France","institution_ids":["https://openalex.org/I88467170","https://openalex.org/I4210155549","https://openalex.org/I4210097372","https://openalex.org/I1294671590","https://openalex.org/I4387153769"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041398783"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210097372","https://openalex.org/I4210155549","https://openalex.org/I4387153769","https://openalex.org/I88467170"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7546,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.7220446,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"31","issue":"18","first_page":"3054","last_page":"3056"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9990000128746033,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9990000128746033,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9973999857902527,"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/T11928","display_name":"Genetic Syndromes and Imprinting","score":0.9972000122070312,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.7789326906204224},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5333589911460876},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5277486443519592},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5102078914642334},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49539363384246826},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4850877821445465},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.4123961329460144},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.41103145480155945},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3946797847747803},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.37168991565704346}],"concepts":[{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.7789326906204224},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5333589911460876},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5277486443519592},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5102078914642334},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49539363384246826},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4850877821445465},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.4123961329460144},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.41103145480155945},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3946797847747803},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.37168991565704346}],"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":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv320","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv320","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3054/49035278/bioinformatics_31_18_3054.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26002884","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26002884","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-01113680v1","is_oa":true,"landing_page_url":"https://hal.science/hal-01113680","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2015, 31 (18), pp.3054-6. &#x27E8;10.1093/bioinformatics/btv320&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/18/3054","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/18/3054","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv320","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv320","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/18/3054/49035278/bioinformatics_31_18_3054.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6299999952316284}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2129007011.pdf","grobid_xml":"https://content.openalex.org/works/W2129007011.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1525651898","https://openalex.org/W1981053870","https://openalex.org/W2006559366","https://openalex.org/W2022450888","https://openalex.org/W2061908600","https://openalex.org/W2076310052","https://openalex.org/W2096283457","https://openalex.org/W2100438487","https://openalex.org/W2154361640","https://openalex.org/W4248240383"],"related_works":["https://openalex.org/W2513883126","https://openalex.org/W3118014344","https://openalex.org/W2160911017","https://openalex.org/W2387464095","https://openalex.org/W2507940864","https://openalex.org/W1526237818","https://openalex.org/W4281746656","https://openalex.org/W2005336569","https://openalex.org/W2106650442","https://openalex.org/W3166677598"],"abstract_inverted_index":{"UNLABELLED:":[0],"We":[1,15],"describe":[2],"the":[3,6,22],"implementation":[4],"of":[5,25],"method":[7],"introduced":[8],"by":[9],"Chambaz":[10],"et":[11],"al.":[12],"in":[13,42],"2012.":[14],"also":[16],"demonstrate":[17],"its":[18],"genome-wide":[19],"application":[20],"to":[21],"integrative":[23],"search":[24],"new":[26],"regions":[27],"with":[28],"strong":[29],"association":[30],"between":[31],"DNA":[32,40],"copy":[33],"number":[34],"and":[35],"gene":[36],"expression":[37],"accounting":[38],"for":[39],"methylation":[41],"breast":[43],"cancers.":[44],"AVAILABILITY":[45],"AND":[46],"IMPLEMENTATION:":[47],"An":[48],"open-source":[49],"R":[50],"package":[51],"tmle.npvi":[52],"is":[53],"available":[54],"from":[55],"CRAN":[56],"(http://cran.r-project.org/).":[57],"CONTACT:":[58],"pierre.neuvial@genopole.cnrs.fr.":[59]},"counts_by_year":[{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":2}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}
