{"id":"https://openalex.org/W4379768536","doi":"https://doi.org/10.1186/s12859-023-05340-x","title":"Rescuing biologically relevant consensus regions across replicated samples","display_name":"Rescuing biologically relevant consensus regions across replicated samples","publication_year":2023,"publication_date":"2023-06-07","ids":{"openalex":"https://openalex.org/W4379768536","doi":"https://doi.org/10.1186/s12859-023-05340-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/37286963"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05340-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05340-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05340-x","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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05340-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087600054","display_name":"Vahid Jalili","orcid":"https://orcid.org/0000-0003-4986-2157"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vahid Jalili","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA, USA. jvahid@broadinstitute.org","Broad Institute of MIT and Harvard, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA. jvahid@broadinstitute.org","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065603929","display_name":"Marzia A. Cremona","orcid":"https://orcid.org/0000-0001-8899-7316"},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Marzia A. Cremona","raw_affiliation_strings":["CHU de Qu\u00e9bec - Universit\u00e9 Laval Research Center, Quebec, Canada. marzia.cremona@fsa.ulaval.ca","Department of Operations and Decision Systems, Universit\u00e9 Laval, Quebec, Canada. marzia.cremona@fsa.ulaval.ca","Department of Operations and Decision Systems, Universit\u00e9 Laval, Quebec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CHU de Qu\u00e9bec - Universit\u00e9 Laval Research Center, Quebec, Canada. marzia.cremona@fsa.ulaval.ca","institution_ids":["https://openalex.org/I43406934"]},{"raw_affiliation_string":"Department of Operations and Decision Systems, Universit\u00e9 Laval, Quebec, Canada. marzia.cremona@fsa.ulaval.ca","institution_ids":["https://openalex.org/I43406934"]},{"raw_affiliation_string":"Department of Operations and Decision Systems, Universit\u00e9 Laval, Quebec, Canada","institution_ids":["https://openalex.org/I43406934"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053517115","display_name":"Fernando Palluzzi","orcid":"https://orcid.org/0000-0003-0861-5512"},"institutions":[{"id":"https://openalex.org/I25217355","display_name":"University of Pavia","ror":"https://ror.org/00s6t1f81","country_code":"IT","type":"education","lineage":["https://openalex.org/I25217355"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Fernando Palluzzi","raw_affiliation_strings":["Department of Brain and Behavioral Sciences, Universit\u00e0 di Pavia, Pavia, Italy. fernando.palluzzi@policlinicogemelli.it","Department of Brain and Behavioral Sciences, Universit\u00e0 di Pavia, Pavia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Brain and Behavioral Sciences, Universit\u00e0 di Pavia, Pavia, Italy. fernando.palluzzi@policlinicogemelli.it","institution_ids":["https://openalex.org/I25217355"]},{"raw_affiliation_string":"Department of Brain and Behavioral Sciences, Universit\u00e0 di Pavia, Pavia, Italy","institution_ids":["https://openalex.org/I25217355"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053517115","https://openalex.org/A5065603929","https://openalex.org/A5087600054"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I25217355","https://openalex.org/I43406934"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.4606,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.57815854,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"24","issue":"1","first_page":"240","last_page":"240"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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/T10604","display_name":"RNA Research and Splicing","score":0.9987000226974487,"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":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6119226813316345},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.5755749344825745},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5357896685600281},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.5241782069206238},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4690219461917877},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37389546632766724},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3655785620212555},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19057244062423706},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14639443159103394}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6119226813316345},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.5755749344825745},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5357896685600281},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.5241782069206238},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4690219461917877},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37389546632766724},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3655785620212555},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19057244062423706},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14639443159103394},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05340-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05340-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05340-x","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:37286963","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37286963","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10246347","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10246347","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10246347/pdf/12859_2023_Article_5340.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,"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":"pmh:oai:doaj.org/article:db72d14d4072451c809dd9c79b36c411","is_oa":true,"landing_page_url":"https://doaj.org/article/db72d14d4072451c809dd9c79b36c411","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 24, Iss 1, Pp 1-16 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05340-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05340-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05340-x","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310137","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4379768536.pdf","grobid_xml":"https://content.openalex.org/works/W4379768536.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1873501834","https://openalex.org/W1950350291","https://openalex.org/W1966921801","https://openalex.org/W1970344715","https://openalex.org/W1984001597","https://openalex.org/W2001554877","https://openalex.org/W2009274826","https://openalex.org/W2015324225","https://openalex.org/W2016202595","https://openalex.org/W2044164623","https://openalex.org/W2070050178","https://openalex.org/W2080748115","https://openalex.org/W2081942683","https://openalex.org/W2084160423","https://openalex.org/W2098023402","https://openalex.org/W2099199578","https://openalex.org/W2104836314","https://openalex.org/W2110256992","https://openalex.org/W2118258530","https://openalex.org/W2125248983","https://openalex.org/W2128016314","https://openalex.org/W2128710484","https://openalex.org/W2131994815","https://openalex.org/W2144784334","https://openalex.org/W2146760472","https://openalex.org/W2157009395","https://openalex.org/W2157952888","https://openalex.org/W2158226173","https://openalex.org/W2163845664","https://openalex.org/W2167967077","https://openalex.org/W2170200272","https://openalex.org/W2171808845","https://openalex.org/W2192926654","https://openalex.org/W2231865019","https://openalex.org/W2261235911","https://openalex.org/W2278293665","https://openalex.org/W2293206103","https://openalex.org/W2305228807","https://openalex.org/W2310768041","https://openalex.org/W2344560359","https://openalex.org/W2385696187","https://openalex.org/W2486498812","https://openalex.org/W2520401971","https://openalex.org/W2620550305","https://openalex.org/W2740450751","https://openalex.org/W2754863086","https://openalex.org/W2762515171","https://openalex.org/W2767826728","https://openalex.org/W2768013244","https://openalex.org/W2884101170","https://openalex.org/W2888828946","https://openalex.org/W2908459030","https://openalex.org/W2909969480","https://openalex.org/W2951572348","https://openalex.org/W2966369432","https://openalex.org/W2972608565","https://openalex.org/W3000668959","https://openalex.org/W3012091681","https://openalex.org/W3083663781","https://openalex.org/W3091701318","https://openalex.org/W3104066961","https://openalex.org/W3145969289","https://openalex.org/W3152493975","https://openalex.org/W6792612449"],"related_works":["https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W2140163842","https://openalex.org/W3156537409","https://openalex.org/W2747931568","https://openalex.org/W2921090651","https://openalex.org/W2133055377","https://openalex.org/W2287365612"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein-DNA":[1],"binding":[2,11,37,43,113],"sites":[3,44,114],"of":[4,22,111,126],"ChIP-seq":[5],"experiments":[6],"are":[7,140],"identified":[8],"where":[9],"the":[10,23,53,108,116,127,133,137],"affinity":[12],"is":[13,25,147],"significant":[14],"based":[15],"on":[16,98],"a":[17,26,58,62,72,150],"given":[18],"threshold.":[19],"The":[20],"choice":[21],"threshold":[24,54],"trade-off":[27],"between":[28],"conservative":[29],"region":[30],"identification":[31],"and":[32,66,92,94,115,132,153],"discarding":[33],"weak,":[34],"but":[35],"true":[36],"sites.":[38],"RESULTS:":[39],"We":[40,84,106],"rescue":[41],"weak":[42,112],"using":[45],"MSPC,":[46],"which":[47],"efficiently":[48],"exploits":[49],"replicates":[50],"to":[51,56,70,135],"lower":[52],"required":[55],"identify":[57],"site":[59],"while":[60],"keeping":[61],"low":[63],"false-positive":[64],"rate,":[65],"we":[67],"compare":[68],"it":[69],"IDR,":[71],"widely":[73],"used":[74],"post-processing":[75],"method":[76],"for":[77],"identifying":[78],"highly":[79],"reproducible":[80],"peaks":[81],"across":[82],"replicates.":[83],"observe":[85],"several":[86],"master":[87],"transcription":[88],"regulators":[89],"(e.g.,":[90],"SP1":[91],"GATA3)":[93],"HDAC2-GATA1":[95],"regulatory":[96],"networks":[97],"rescued":[99,121],"regions":[100],"in":[101],"K562":[102],"cell":[103],"line.":[104],"CONCLUSIONS:":[105],"argue":[107],"biological":[109],"relevance":[110],"information":[117],"they":[118],"add":[119],"when":[120],"by":[122],"MSPC.":[123],"An":[124],"implementation":[125],"proposed":[128],"extended":[129],"MSPC":[130,146],"methodology":[131],"scripts":[134],"reproduce":[136],"performed":[138],"analysis":[139],"freely":[141],"available":[142,157],"at":[143],"https://genometric.github.io/MSPC/":[144],";":[145],"distributed":[148],"as":[149],"command-line":[151],"application":[152],"an":[154],"R":[155],"package":[156],"from":[158],"Bioconductor":[159],"(":[160],"https://doi.org/doi:10.18129/B9.bioc.rmspc":[161],").":[162]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2023-06-09T00:00:00"}
