{"id":"https://openalex.org/W3194367446","doi":"https://doi.org/10.1186/s12859-021-04320-3","title":"CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes","display_name":"CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes","publication_year":2021,"publication_date":"2021-08-17","ids":{"openalex":"https://openalex.org/W3194367446","doi":"https://doi.org/10.1186/s12859-021-04320-3","mag":"3194367446","pmid":"https://pubmed.ncbi.nlm.nih.gov/34404353"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04320-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04320-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04320-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04320-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015552765","display_name":"L\u00e9lia Polit","orcid":"https://orcid.org/0000-0002-6349-2415"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210141964","display_name":"Institut Cochin","ror":"https://ror.org/051sk4035","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210096427","https://openalex.org/I4210141964"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"L\u00e9lia Polit","raw_affiliation_strings":["Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210141964","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004333630","display_name":"Gwenneg Kerdivel","orcid":"https://orcid.org/0000-0003-4381-623X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210141964","display_name":"Institut Cochin","ror":"https://ror.org/051sk4035","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210096427","https://openalex.org/I4210141964"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Gwenneg Kerdivel","raw_affiliation_strings":["Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210141964","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010181844","display_name":"Sebastian Gregoricchio","orcid":"https://orcid.org/0000-0001-9209-5403"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sebastian Gregoricchio","raw_affiliation_strings":["INSERM UMR1170, Equipe Labellis\u00e9e Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INSERM UMR1170, Equipe Labellis\u00e9e Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107747395","display_name":"Michela Esposito","orcid":null},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Michela Esposito","raw_affiliation_strings":["INSERM UMR1170, Equipe Labellis\u00e9e Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INSERM UMR1170, Equipe Labellis\u00e9e Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083480115","display_name":"Christel Guillouf","orcid":"https://orcid.org/0000-0001-7013-3149"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Christel Guillouf","raw_affiliation_strings":["INSERM UMR1170, Equipe Labellis\u00e9e Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INSERM UMR1170, Equipe Labellis\u00e9e Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I277688954"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074876525","display_name":"Valentina Boeva","orcid":"https://orcid.org/0000-0002-4382-7185"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210090941","display_name":"Institute for Biomedical Engineering","ror":"https://ror.org/00baskk38","country_code":"CH","type":"facility","lineage":["https://openalex.org/I202697423","https://openalex.org/I2799323385","https://openalex.org/I35440088","https://openalex.org/I4210090941"]},{"id":"https://openalex.org/I4210141964","display_name":"Institut Cochin","ror":"https://ror.org/051sk4035","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210096427","https://openalex.org/I4210141964"]}],"countries":["CH","FR"],"is_corresponding":true,"raw_author_name":"Valentina Boeva","raw_affiliation_strings":["Department of Computer Science, Institute for Machine Learning, ETH Zurich, 8092, Zurich, Switzerland. valentina.boeva@inf.ethz.ch","Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France. valentina.boeva@inf.ethz.ch","Swiss Institute for Bioinformatics (SIB), Z\u00fcrich, Switzerland. valentina.boeva@inf.ethz.ch","Department of Computer Science, Institute for Machine Learning, ETH Zurich, 8092, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-4382-7185","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Institute for Machine Learning, ETH Zurich, 8092, Zurich, Switzerland. valentina.boeva@inf.ethz.ch","institution_ids":["https://openalex.org/I35440088","https://openalex.org/I4210090941"]},{"raw_affiliation_string":"Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France. valentina.boeva@inf.ethz.ch","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I4210141964","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Swiss Institute for Bioinformatics (SIB), Z\u00fcrich, Switzerland. valentina.boeva@inf.ethz.ch","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Department of Computer Science, Institute for Machine Learning, ETH Zurich, 8092, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5074876525"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I35440088","https://openalex.org/I4210090941","https://openalex.org/I4210141964"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.8729,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.86313082,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"407","last_page":"407"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.7511000037193298,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.7511000037193298,"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":0.16220000386238098,"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":0.02449999935925007,"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/normalization","display_name":"Normalization (sociology)","score":0.9270113110542297},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5242350697517395},{"id":"https://openalex.org/keywords/chip","display_name":"Chip","score":0.49449798464775085},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4881806969642639},{"id":"https://openalex.org/keywords/database-normalization","display_name":"Database normalization","score":0.4550233781337738},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.43838363885879517},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3702654242515564},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3629932701587677},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3278336822986603},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31348586082458496},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29605844616889954},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2806444764137268},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2100575864315033}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.9270113110542297},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5242350697517395},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.49449798464775085},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4881806969642639},{"id":"https://openalex.org/C162984825","wikidata":"https://www.wikidata.org/wiki/Q339072","display_name":"Database normalization","level":3,"score":0.4550233781337738},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.43838363885879517},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3702654242515564},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3629932701587677},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3278336822986603},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31348586082458496},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29605844616889954},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2806444764137268},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2100575864315033},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1186/s12859-021-04320-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04320-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04320-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34404353","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34404353","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/501750","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/501750","pdf_url":"http://hdl.handle.net/20.500.11850/501750","source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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":"BMC Bioinformatics, 22 (1)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:HAL:hal-03410838v1","is_oa":true,"landing_page_url":"https://hal.science/hal-03410838","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":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:HAL:inserm-03330789v1","is_oa":true,"landing_page_url":"https://inserm.hal.science/inserm-03330789","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":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:c301d6c0cb1f4752a9b84cf9cae998d8","is_oa":true,"landing_page_url":"https://doaj.org/article/c301d6c0cb1f4752a9b84cf9cae998d8","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,"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":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-14 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8371782","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8371782","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"doi:10.3929/ethz-b-000501750","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000501750","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04320-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04320-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04320-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5099999904632568}],"awards":[{"id":"https://openalex.org/G1241245949","display_name":null,"funder_award_id":"ANR-11-IDEX-0005-02","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G2063112341","display_name":null,"funder_award_id":"INCA-DGOS-INSERM_12561","funder_id":"https://openalex.org/F4320323807","funder_display_name":"Institut National Du Cancer"},{"id":"https://openalex.org/G2092792612","display_name":null,"funder_award_id":"20141PLBIO06-1","funder_id":"https://openalex.org/F4320323807","funder_display_name":"Institut National Du Cancer"},{"id":"https://openalex.org/G2247820705","display_name":null,"funder_award_id":"RAC16002KSA","funder_id":"https://openalex.org/F4320322361","funder_display_name":"Fondation ARC pour la Recherche sur le Cancer"},{"id":"https://openalex.org/G3054294689","display_name":null,"funder_award_id":"11-IDEX-0005-02","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G3221280478","display_name":null,"funder_award_id":"ANR-11-LABX-0071","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G3232492675","display_name":null,"funder_award_id":"ANR-11-IDEX-0005-02","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"},{"id":"https://openalex.org/G4599119665","display_name":null,"funder_award_id":"R15093KS","funder_id":"https://openalex.org/F4320322361","funder_display_name":"Fondation ARC pour la Recherche sur le Cancer"},{"id":"https://openalex.org/G4774453313","display_name":null,"funder_award_id":"IDEX-0005","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4866930200","display_name":null,"funder_award_id":"ANR-11-IDEX","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8336719376","display_name":null,"funder_award_id":"ANR-11-IDEX-0005","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8756535577","display_name":null,"funder_award_id":"ARC-RAC16002KSA-R15093KS","funder_id":"https://openalex.org/F4320322361","funder_display_name":"Fondation ARC pour la Recherche sur le Cancer"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320320893","display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","ror":"https://ror.org/02vjkv261"},{"id":"https://openalex.org/F4320322361","display_name":"Fondation ARC pour la Recherche sur le Cancer","ror":"https://ror.org/0489qz649"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"},{"id":"https://openalex.org/F4320323807","display_name":"Institut National Du Cancer","ror":"https://ror.org/03m8vkq32"},{"id":"https://openalex.org/F4320325668","display_name":"Direction G\u00e9n\u00e9rale de l\u2019offre de Soins","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3194367446.pdf","grobid_xml":"https://content.openalex.org/works/W3194367446.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1617099866","https://openalex.org/W1967656072","https://openalex.org/W1982658542","https://openalex.org/W1992430937","https://openalex.org/W2015416439","https://openalex.org/W2039523995","https://openalex.org/W2091244202","https://openalex.org/W2096083625","https://openalex.org/W2108696643","https://openalex.org/W2120347928","https://openalex.org/W2127081697","https://openalex.org/W2162080206","https://openalex.org/W2163797186","https://openalex.org/W2170200272","https://openalex.org/W2171808845","https://openalex.org/W2201642794","https://openalex.org/W2341539131","https://openalex.org/W2568451064","https://openalex.org/W2738563754","https://openalex.org/W2767826728","https://openalex.org/W2889236955","https://openalex.org/W2979008768","https://openalex.org/W3017630629"],"related_works":["https://openalex.org/W4241705247","https://openalex.org/W2145362441","https://openalex.org/W2101622345","https://openalex.org/W2582603276","https://openalex.org/W3134304369","https://openalex.org/W4386281023","https://openalex.org/W4312138714","https://openalex.org/W2113286112","https://openalex.org/W2012771827","https://openalex.org/W2096302356"],"abstract_inverted_index":{"BACKGROUND:":[0],"Multiple":[1],"studies":[2],"rely":[3],"on":[4,17,62,118,122,190,203,251],"ChIP-seq":[5,32,74,95,127,149,205,230],"experiments":[6,237],"to":[7,41,80,147,165,182,215],"assess":[8,166],"the":[9,29,39,42,57,119,133,163,167,170,174,177,200],"effect":[10],"of":[11,31,45,59,73,136,157,169,176],"gene":[12,107],"modulation":[13],"and":[14,20,159,172,208],"drug":[15],"treatments":[16],"protein":[18],"binding":[19,33],"chromatin":[21,192],"structure.":[22],"However,":[23],"most":[24],"methods":[25],"commonly":[26,217],"used":[27,187,218],"for":[28,229],"normalization":[30,40,72,114,171,219,232],"intensity":[34],"signals":[35,68,96,128],"across":[36,53,97,143,233],"conditions,":[37],"e.g.,":[38],"same":[43],"number":[44,156],"reads,":[46],"either":[47],"assume":[48],"a":[49,87,155,226,246],"constant":[50,142],"signal-to-noise":[51],"ratio":[52],"conditions":[54,234],"or":[55,194],"base":[56],"estimates":[58],"correction":[60],"factors":[61],"genomic":[63],"regions":[64,135],"with":[65],"intrinsically":[66],"different":[67,98],"between":[69],"conditions.":[70],"Inaccurate":[71],"signal":[75,231],"may,":[76],"in":[77,126,132,213,245],"turn,":[78],"lead":[79],"erroneous":[81],"biological":[82],"conclusions.":[83],"RESULTS:":[84],"We":[85,198],"developed":[86],"new":[88,227],"R":[89,248],"package,":[90],"CHIPIN,":[91],"that":[92],"allows":[93],"normalizing":[94,148],"conditions/samples":[99],"when":[100,235],"spike-in":[101,236],"information":[102],"is":[103,116,243],"not":[104,239],"available,":[105],"but":[106],"expression":[108,139],"data":[109,206],"are":[110,141,238],"at":[111],"hand.":[112],"Our":[113],"technique":[115],"based":[117],"assumption":[120],"that,":[121],"average,":[123],"no":[124],"differences":[125],"should":[129],"be":[130,186],"observed":[131],"regulatory":[134],"genes":[137],"whose":[138],"levels":[140],"samples/conditions.":[144],"In":[145,180],"addition":[146,181],"signals,":[150],"CHIPIN":[151,184,201,223],"provides":[152,225],"as":[153],"output":[154],"graphs":[158],"calculates":[160],"statistics":[161],"allowing":[162],"user":[164],"efficiency":[168],"qualify":[173],"specificity":[175],"antibody":[178],"used.":[179],"ChIP-seq,":[183],"can":[185],"without":[188],"restriction":[189],"open":[191],"ATAC-seq":[193],"DNase":[195],"hypersensitivity":[196],"data.":[197],"validated":[199],"method":[202,224,242],"several":[204,216],"sets":[207],"documented":[209],"its":[210],"superior":[211],"performance":[212],"comparison":[214],"techniques.":[220],"CONCLUSIONS:":[221],"The":[222,241],"way":[228],"available.":[240],"implemented":[244],"user-friendly":[247],"package":[249],"available":[250],"GitHub:":[252],"https://github.com/BoevaLab/CHIPIN.":[253]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}