{"id":"https://openalex.org/W2409976299","doi":"https://doi.org/10.1385/1-59259-182-5:029","title":"Methylation Analysis by Chemical DNA Sequencing","display_name":"Methylation Analysis by Chemical DNA Sequencing","publication_year":2003,"publication_date":"2003-11-14","ids":{"openalex":"https://openalex.org/W2409976299","doi":"https://doi.org/10.1385/1-59259-182-5:029","mag":"2409976299","pmid":"https://pubmed.ncbi.nlm.nih.gov/11951653"},"language":"en","primary_location":{"id":"doi:10.1385/1-59259-182-5:029","doi":"https://doi.org/10.1385/1-59259-182-5:029","is_oa":false,"landing_page_url":"https://doi.org/10.1385/1-59259-182-5:029","pdf_url":null,"source":{"id":"https://openalex.org/S4306463399","display_name":"Humana Press eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310315801","host_organization_name":"Humana Press","host_organization_lineage":["https://openalex.org/P4310315801","https://openalex.org/P4310319900"],"host_organization_lineage_names":["Humana Press","Springer Science+Business Media"],"type":"ebook platform"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"DNA Methylation Protocols","raw_type":"book-chapter"},"volume":{"id":"https://openalex.org/W606994887","display_name":"DNA Methylation Protocols"},"type":"book-chapter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023474946","display_name":"Piroska E. Szab\u00f3","orcid":"https://orcid.org/0000-0001-9314-7009","observed_orcids":["https://orcid.org/0000-0001-9314-7009"]},"institutions":[{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":"US","type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Piroska E. Szab\u00f3","raw_affiliation_strings":["Department of Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA","Department of Biology, Beckman Research Institute of the City of Hope, Duarte"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA","institution_ids":["https://openalex.org/I4387156432"]},{"raw_affiliation_string":"Department of Biology, Beckman Research Institute of the City of Hope, Duarte","institution_ids":["https://openalex.org/I4387156432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004292678","display_name":"Jeff R. Mann","orcid":"https://orcid.org/0000-0003-0028-8692","observed_orcids":["https://orcid.org/0000-0003-0028-8692"]},"institutions":[{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":"US","type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey R. Mann","raw_affiliation_strings":["Department of Biology, Beckman Research Institute of the City of Hope, Duarte"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Beckman Research Institute of the City of Hope, Duarte","institution_ids":["https://openalex.org/I4387156432"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048312997","display_name":"Gerd P. Pfeifer","orcid":"https://orcid.org/0000-0002-5080-9604","observed_orcids":["https://orcid.org/0000-0002-5080-9604"]},"institutions":[{"id":"https://openalex.org/I4387156432","display_name":"Beckman Research Institute","ror":"https://ror.org/05fazth07","country_code":"US","type":"facility","lineage":["https://openalex.org/I1301076528","https://openalex.org/I4387156432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gerd P. Pfeifer","raw_affiliation_strings":["Department of Biology, Beckman Research Institute of the City of Hope, Duarte"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Beckman Research Institute of the City of Hope, Duarte","institution_ids":["https://openalex.org/I4387156432"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4387156432"],"apc_list":null,"apc_paid":null,"fwci":0.4381,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.62597701,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"200","issue":null,"first_page":"029","last_page":"041"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9976000189781189,"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":0.9976000189781189,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.0003000000142492354,"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/T11928","display_name":"Genetic Syndromes and Imprinting","score":0.0003000000142492354,"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":0.9959999918937683},{"id":"https://openalex.org/keywords/5-methylcytosine","display_name":"5-methylcytosine","score":0.9729999899864197},{"id":"https://openalex.org/keywords/cpg-dinucleotides","display_name":"CpG","score":0.8109999895095825},{"id":"https://openalex.org/keywords/dna-methyltransferases","display_name":"DNA methyltransferases","score":0.9190000295639038},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"bisulfite sequencing","score":0.7919999957084656},{"id":"https://openalex.org/keywords/ligation-mediated-pcr","display_name":"ligation-mediated PCR","score":0.906000018119812},{"id":"https://openalex.org/keywords/single-copy-gene","display_name":"single-copy gene","score":0.5649999976158142},{"id":"https://openalex.org/keywords/mammalian-dna","display_name":"mammalian DNA","score":0.5540000200271606}],"concepts":[{"id":"https://openalex.org/C52182516","wikidata":"https://www.wikidata.org/wiki/Q17144128","display_name":"Sequencing by ligation","level":5,"score":0.8155412673950195},{"id":"https://openalex.org/C136953436","wikidata":"https://www.wikidata.org/wiki/Q6000286","display_name":"Illumina Methylation Assay","level":5,"score":0.6037849187850952},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6029733419418335},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5650976300239563},{"id":"https://openalex.org/C54887055","wikidata":"https://www.wikidata.org/wiki/Q5205758","display_name":"DNA nanoball sequencing","level":5,"score":0.564260721206665},{"id":"https://openalex.org/C156385826","wikidata":"https://www.wikidata.org/wiki/Q1341059","display_name":"Multiple displacement amplification","level":5,"score":0.5464909076690674},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.5076195001602173},{"id":"https://openalex.org/C17757408","wikidata":"https://www.wikidata.org/wiki/Q4135516","display_name":"genomic DNA","level":3,"score":0.47746801376342773},{"id":"https://openalex.org/C52001828","wikidata":"https://www.wikidata.org/wiki/Q2902493","display_name":"Primer dimer","level":5,"score":0.4755032956600189},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.4694732427597046},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4694646894931793},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.4600927233695984},{"id":"https://openalex.org/C114851143","wikidata":"https://www.wikidata.org/wiki/Q13080815","display_name":"Single molecule real time sequencing","level":5,"score":0.45555999875068665},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.43929439783096313},{"id":"https://openalex.org/C116114238","wikidata":"https://www.wikidata.org/wiki/Q6823960","display_name":"Methylated DNA immunoprecipitation","level":5,"score":0.4374639391899109},{"id":"https://openalex.org/C51064596","wikidata":"https://www.wikidata.org/wiki/Q7452482","display_name":"Sequencing by hybridization","level":5,"score":0.4333268404006958},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4140249490737915},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3661055862903595},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.34871336817741394},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2474597692489624},{"id":"https://openalex.org/C13575015","wikidata":"https://www.wikidata.org/wiki/Q1562492","display_name":"Genomic library","level":4,"score":0.24705737829208374},{"id":"https://openalex.org/C90583042","wikidata":"https://www.wikidata.org/wiki/Q1952456","display_name":"Multiplex polymerase chain reaction","level":4,"score":0.182131826877594},{"id":"https://openalex.org/C78063203","wikidata":"https://www.wikidata.org/wiki/Q3062596","display_name":"DNA extraction","level":4,"score":0.14874741435050964},{"id":"https://openalex.org/C70712619","wikidata":"https://www.wikidata.org/wiki/Q908889","display_name":"DNA sequencer","level":4,"score":0.11168050765991211},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.05291646718978882},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","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":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1385/1-59259-182-5:029","doi":"https://doi.org/10.1385/1-59259-182-5:029","is_oa":false,"landing_page_url":"https://doi.org/10.1385/1-59259-182-5:029","pdf_url":null,"source":{"id":"https://openalex.org/S4306463399","display_name":"Humana Press eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310315801","host_organization_name":"Humana Press","host_organization_lineage":["https://openalex.org/P4310315801","https://openalex.org/P4310319900"],"host_organization_lineage_names":["Humana Press","Springer Science+Business Media"],"type":"ebook platform"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"DNA Methylation Protocols","raw_type":"book-chapter"},{"id":"pmid:11951653","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11951653","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in molecular biology (Clifton, N.J.)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3455863546","display_name":null,"funder_award_id":"ES-06070","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W158760893","https://openalex.org/W1732253485","https://openalex.org/W1869138232","https://openalex.org/W1896727857","https://openalex.org/W1979273476","https://openalex.org/W1979909696","https://openalex.org/W2015232786","https://openalex.org/W2038531677","https://openalex.org/W2039067014","https://openalex.org/W2056103475","https://openalex.org/W2059520437","https://openalex.org/W2131286935","https://openalex.org/W2135157239","https://openalex.org/W2138100316","https://openalex.org/W2144515939","https://openalex.org/W2192716493","https://openalex.org/W2313812356","https://openalex.org/W2417538191"],"related_works":["https://openalex.org/W1986149419","https://openalex.org/W2015232786","https://openalex.org/W2791859752","https://openalex.org/W2107081820","https://openalex.org/W2097596363","https://openalex.org/W1979273476","https://openalex.org/W606994887","https://openalex.org/W2153745676","https://openalex.org/W2414691148","https://openalex.org/W4238166333"],"abstract_inverted_index":{"The":[0,31,48,201],"presence":[1],"of":[2,25,50,83,86,104,130,141,149,186],"5-methylcytosine":[3],"as":[4],"a":[5,76,157,168],"modified":[6],"base":[7],"in":[8,66,215],"DNA":[9,26,46,51,113,117,151,162,188,198,211],"was":[10,154],"discovered":[11],"many":[12],"decades":[13],"ago.":[14],"Surprisingly,":[15],"however,":[16],"and":[17,79,112],"despite":[18],"intense":[19],"research":[20],"efforts,":[21],"the":[22,35,84,94,139,146],"principal":[23],"function":[24],"methylation":[27,43,52,85,132,207],"is":[28,34,99,124,136,191,213],"still":[29],"unknown.":[30],"CpG":[32],"dinucleotide":[33],"predominant":[36],"if":[37],"not":[38],"exclusive":[39],"target":[40],"sequence":[41,170,199],"for":[42,81,128,181,206],"by":[44,89,107,156,209],"mammalian":[45,67,187],"methyltransferases.":[47],"analysis":[49,82,208],"at":[53,64],"single-nucleotide":[54],"resolution":[55],"(genomic":[56],"sequencing)":[57],"has":[58],"long":[59],"been":[60,72],"considered":[61],"technically":[62],"difficult,":[63],"least":[65],"cells.":[68],"Recently,":[69],"techniques":[70,91],"have":[71],"developed":[73],"that":[74,153],"give":[75],"sufficient":[77,194],"specificity":[78],"sensitivity":[80],"single-copy":[87],"genes":[88],"DNA-sequencing":[90],"(,).":[92],"Currently,":[93],"most":[95],"widely":[96],"used":[97,180,205],"method":[98,127],"based":[100,137],"on":[101,138,171],"bisulfite-induced":[102],"deamination":[103],"cytosines":[105],"followed":[106],"polymerase":[108],"chain":[109],"reaction":[110,159,166],"(PCR)":[111],"sequencing":[114,118,212],"().":[115,134],"Chemical":[116],"combined":[119],"with":[120],"ligation-mediated":[121],"PCR":[122,177],"(LM-PCR)":[123],"an":[125,142],"alternative":[126],"determination":[129],"genomic":[131],"patterns":[133],"LM-PCR":[135,203],"ligation":[140,165],"oligonucleotide":[143],"linker":[144],"onto":[145],"5\u2032":[147,173],"end":[148],"each":[150],"molecule":[152],"created":[155],"strand-cleavage":[158],"during":[160],"chemical":[161,210],"sequencing.":[163],"This":[164],"provides":[167],"common":[169],"all":[172],"ends":[174],"allowing":[175],"exponential":[176],"to":[178,195],"be":[179],"signal":[182],"amplification.":[183],"One":[184],"microgram":[185],"per":[189],"lane":[190],"more":[192],"than":[193],"obtain":[196],"good-quality":[197],"ladders.":[200],"general":[202],"procedure":[204],"outlined":[214],"Fig.":[216],"1":[217]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}