{"id":"https://openalex.org/W4313813664","doi":"https://doi.org/10.1093/bib/bbac617","title":"Comparative epigenome analysis using Infinium DNA methylation BeadChips","display_name":"Comparative epigenome analysis using Infinium DNA methylation BeadChips","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4313813664","doi":"https://doi.org/10.1093/bib/bbac617","pmid":"https://pubmed.ncbi.nlm.nih.gov/36617464"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac617","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac617","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10147478/pdf/bbac617.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051377484","display_name":"Wubin Ding","orcid":"https://orcid.org/0000-0002-5355-7561"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wubin Ding","raw_affiliation_strings":["Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , PA, 19104 , USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , PA, 19104 , USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087083224","display_name":"Diljeet Kaur","orcid":null},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Diljeet Kaur","raw_affiliation_strings":["Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , PA, 19104 , USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , PA, 19104 , USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000192581","display_name":"Steve Horvath","orcid":"https://orcid.org/0000-0002-4110-3589"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]},{"id":"https://openalex.org/I4387153853","display_name":"Altos Labs","ror":"https://ror.org/05467hx49","country_code":null,"type":"company","lineage":["https://openalex.org/I4387153853"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steve Horvath","raw_affiliation_strings":["Altos Labs , San Diego, CA , USA","Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles , Los Angeles, CA, 90095 , USA"],"affiliations":[{"raw_affiliation_string":"Altos Labs , San Diego, CA , USA","institution_ids":["https://openalex.org/I4387153853"]},{"raw_affiliation_string":"Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles , Los Angeles, CA, 90095 , USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010106597","display_name":"Wanding Zhou","orcid":"https://orcid.org/0000-0001-9126-1932"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wanding Zhou","raw_affiliation_strings":["Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , PA, 19104 , USA","Department of Pathology and Laboratory Medicine, University of Pennsylvania , Philadelphia, PA, 19104 , USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , PA, 19104 , USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, University of Pennsylvania , Philadelphia, PA, 19104 , USA","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5010106597"],"corresponding_institution_ids":["https://openalex.org/I1335321130","https://openalex.org/I79576946"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":7.5019,"has_fulltext":true,"cited_by_count":49,"citation_normalized_percentile":{"value":0.97817868,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"24","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":1.0,"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":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9911999702453613,"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/epigenome","display_name":"Epigenome","score":0.833472490310669},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.6944963335990906},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4706360995769501},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40591344237327576},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24363964796066284},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23929104208946228},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11958584189414978}],"concepts":[{"id":"https://openalex.org/C117717151","wikidata":"https://www.wikidata.org/wiki/Q3589155","display_name":"Epigenome","level":5,"score":0.833472490310669},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6944963335990906},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4706360995769501},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40591344237327576},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24363964796066284},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23929104208946228},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11958584189414978},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000081122","descriptor_name":"Epigenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081122","descriptor_name":"Epigenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081122","descriptor_name":"Epigenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbac617","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac617","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36617464","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36617464","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10147478","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10147478","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10147478/pdf/bbac617.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:10147478","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10147478","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10147478/pdf/bbac617.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.550000011920929}],"awards":[{"id":"https://openalex.org/G4359693134","display_name":null,"funder_award_id":"NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7343992758","display_name":null,"funder_award_id":"R35GM146978","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7994062141","display_name":null,"funder_award_id":"R35GM146978","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309099","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4313813664.pdf"},"referenced_works_count":79,"referenced_works":["https://openalex.org/W1778749218","https://openalex.org/W1804818244","https://openalex.org/W1821330255","https://openalex.org/W1963802469","https://openalex.org/W1967064280","https://openalex.org/W1969670934","https://openalex.org/W1970608287","https://openalex.org/W1971225285","https://openalex.org/W1975528145","https://openalex.org/W1983275320","https://openalex.org/W1986167448","https://openalex.org/W1991543373","https://openalex.org/W1995223692","https://openalex.org/W2004078197","https://openalex.org/W2004511530","https://openalex.org/W2005501593","https://openalex.org/W2010227476","https://openalex.org/W2017502278","https://openalex.org/W2018363492","https://openalex.org/W2020066516","https://openalex.org/W2022873912","https://openalex.org/W2024848067","https://openalex.org/W2042087070","https://openalex.org/W2051406511","https://openalex.org/W2052072017","https://openalex.org/W2055142831","https://openalex.org/W2081182312","https://openalex.org/W2082073317","https://openalex.org/W2084203180","https://openalex.org/W2091037845","https://openalex.org/W2095727856","https://openalex.org/W2095903180","https://openalex.org/W2101491950","https://openalex.org/W2102619694","https://openalex.org/W2110679814","https://openalex.org/W2112296601","https://openalex.org/W2121678464","https://openalex.org/W2127431419","https://openalex.org/W2128969076","https://openalex.org/W2129915465","https://openalex.org/W2142721632","https://openalex.org/W2143135390","https://openalex.org/W2162906882","https://openalex.org/W2418839526","https://openalex.org/W2537310520","https://openalex.org/W2752687869","https://openalex.org/W2759600539","https://openalex.org/W2769117443","https://openalex.org/W2887474968","https://openalex.org/W2898598946","https://openalex.org/W2898601376","https://openalex.org/W2922281162","https://openalex.org/W2950817352","https://openalex.org/W2953103743","https://openalex.org/W2954492537","https://openalex.org/W2968658941","https://openalex.org/W3010649284","https://openalex.org/W3046171324","https://openalex.org/W3048090444","https://openalex.org/W3084107046","https://openalex.org/W3087569053","https://openalex.org/W3121787444","https://openalex.org/W3133455019","https://openalex.org/W3135897081","https://openalex.org/W3164688358","https://openalex.org/W3171783357","https://openalex.org/W3203959602","https://openalex.org/W3212334377","https://openalex.org/W4200282598","https://openalex.org/W4200473888","https://openalex.org/W4221117299","https://openalex.org/W4242156021","https://openalex.org/W4280519025","https://openalex.org/W4285097559","https://openalex.org/W4297674379","https://openalex.org/W6716897525","https://openalex.org/W6728994268","https://openalex.org/W6753979321","https://openalex.org/W6775039167"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W3004038459","https://openalex.org/W2172945310","https://openalex.org/W2787062849","https://openalex.org/W4388200994","https://openalex.org/W2005986419","https://openalex.org/W2165266865","https://openalex.org/W2035252963"],"abstract_inverted_index":{"The":[0],"arrival":[1],"of":[2,19,78,106,124,131],"the":[3,17,20,104,107,136],"Infinium":[4],"DNA":[5,42,145],"methylation":[6,43,128,146],"BeadChips":[7],"for":[8,26,149],"mice":[9,54],"and":[10,37,51,72,81,86,93,114,140],"other":[11],"nonhuman":[12],"mammalian":[13],"species":[14,67,80,159],"has":[15],"outpaced":[16],"development":[18],"informatics":[21,35],"that":[22,88],"supports":[23],"their":[24],"use":[25],"epigenetics":[27],"study":[28],"in":[29,110],"model":[30],"organisms.":[31],"Here,":[32],"we":[33,60,102],"present":[34],"infrastructure":[36],"methods":[38,153],"to":[39,135,157],"allow":[40],"easy":[41],"analysis":[44,64,148],"on":[45],"multiple":[46],"species,":[47],"including":[48],"domesticated":[49],"animals":[50],"inbred":[52,83,125],"laboratory":[53],"(in":[55],"SeSAMe":[56],"version":[57],"1.16.0+).":[58],"First,":[59],"developed":[61],"a":[62,122],"data-driven":[63],"pipeline":[65],"covering":[66],"inference,":[68],"genome-specific":[69,89],"data":[70],"preprocessing":[71,90],"regression":[73],"modeling.":[74],"We":[75,120],"targeted":[76],"genomes":[77],"310":[79],"37":[82],"mouse":[84,126],"strains":[85],"showed":[87],"prevents":[91],"artifacts":[92],"yields":[94],"more":[95],"accurate":[96],"measurements":[97],"than":[98],"generic":[99],"pipelines.":[100],"Second,":[101],"uncovered":[103],"dynamics":[105],"epigenome":[108,155],"evolution":[109],"different":[111],"genomic":[112],"territories":[113],"tissue":[115],"types":[116],"through":[117],"comparative":[118],"analysis.":[119],"identified":[121],"catalog":[123],"strain-specific":[127],"differences,":[129],"some":[130],"which":[132],"are":[133],"linked":[134],"strains'":[137],"immune,":[138],"metabolic":[139],"neurological":[141],"phenotypes.":[142],"By":[143],"streamlining":[144],"array":[147],"undesigned":[150],"genomes,":[151],"our":[152],"extend":[154],"research":[156],"broad":[158],"contexts.":[160]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":6}],"updated_date":"2026-04-04T08:04:53.788161","created_date":"2025-10-10T00:00:00"}
