{"id":"https://openalex.org/W2040507896","doi":"https://doi.org/10.1093/bib/bbu016","title":"Methodological aspects of whole-genome bisulfite sequencing analysis","display_name":"Methodological aspects of whole-genome bisulfite sequencing analysis","publication_year":2014,"publication_date":"2014-05-27","ids":{"openalex":"https://openalex.org/W2040507896","doi":"https://doi.org/10.1093/bib/bbu016","mag":"2040507896","pmid":"https://pubmed.ncbi.nlm.nih.gov/24867940"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbu016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu016","pdf_url":"https://academic.oup.com/bib/article-pdf/16/3/369/671323/bbu016.pdf","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":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/16/3/369/671323/bbu016.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006500923","display_name":"Swarnaseetha Adusumalli","orcid":"https://orcid.org/0000-0003-0704-9061"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"S. Adusumalli","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052316032","display_name":"Mohamed Feroz Mohd Omar","orcid":"https://orcid.org/0009-0007-6763-1623"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. F. Mohd Omar","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052071706","display_name":"Richie Soong","orcid":"https://orcid.org/0000-0002-0152-1225"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. Soong","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5057599356","display_name":"Touati Benoukraf","orcid":"https://orcid.org/0000-0002-4789-8028"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"T. Benoukraf","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5006500923"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.2705,"has_fulltext":false,"cited_by_count":101,"citation_normalized_percentile":{"value":0.92643455,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"16","issue":"3","first_page":"369","last_page":"379"},"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":0.9983000159263611,"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/T13157","display_name":"Cancer-related gene regulation","score":0.9943000078201294,"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/dna-methylation","display_name":"DNA methylation","score":0.6819551587104797},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6444154977798462},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.6435610055923462},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.5234750509262085},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5171698927879333},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5109383463859558},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.48275989294052124},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47509539127349854},{"id":"https://openalex.org/keywords/cpg-site","display_name":"CpG site","score":0.46224522590637207},{"id":"https://openalex.org/keywords/bisulfite","display_name":"Bisulfite","score":0.4401080310344696},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42435795068740845},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28986066579818726},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.24802476167678833},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2048388421535492},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.11932492256164551},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.06170767545700073}],"concepts":[{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6819551587104797},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6444154977798462},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.6435610055923462},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5234750509262085},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5171698927879333},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5109383463859558},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.48275989294052124},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47509539127349854},{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.46224522590637207},{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.4401080310344696},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42435795068740845},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28986066579818726},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.24802476167678833},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2048388421535492},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.11932492256164551},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.06170767545700073}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":"Q000235","qualifier_name":"genetics","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":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbu016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu016","pdf_url":"https://academic.oup.com/bib/article-pdf/16/3/369/671323/bbu016.pdf","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:24867940","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24867940","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}],"best_oa_location":{"id":"doi:10.1093/bib/bbu016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu016","pdf_url":"https://academic.oup.com/bib/article-pdf/16/3/369/671323/bbu016.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2040507896.pdf","grobid_xml":"https://content.openalex.org/works/W2040507896.grobid-xml"},"referenced_works_count":104,"referenced_works":["https://openalex.org/W299332718","https://openalex.org/W1578830280","https://openalex.org/W1963590871","https://openalex.org/W1965598953","https://openalex.org/W1965970372","https://openalex.org/W1967735720","https://openalex.org/W1968458420","https://openalex.org/W1969327940","https://openalex.org/W1970095805","https://openalex.org/W1976695083","https://openalex.org/W1977371925","https://openalex.org/W1977922553","https://openalex.org/W1979576560","https://openalex.org/W1979892065","https://openalex.org/W1980184764","https://openalex.org/W1984130135","https://openalex.org/W1986849101","https://openalex.org/W1987545661","https://openalex.org/W1989568035","https://openalex.org/W1990021188","https://openalex.org/W1990937720","https://openalex.org/W1993502678","https://openalex.org/W1993848554","https://openalex.org/W1996543077","https://openalex.org/W1997824331","https://openalex.org/W2000491011","https://openalex.org/W2004729058","https://openalex.org/W2009904451","https://openalex.org/W2012703624","https://openalex.org/W2014852291","https://openalex.org/W2019229253","https://openalex.org/W2026116032","https://openalex.org/W2026343134","https://openalex.org/W2038722690","https://openalex.org/W2043472013","https://openalex.org/W2046615642","https://openalex.org/W2049907774","https://openalex.org/W2051273886","https://openalex.org/W2051465150","https://openalex.org/W2059735902","https://openalex.org/W2065751798","https://openalex.org/W2067130606","https://openalex.org/W2067151470","https://openalex.org/W2071154937","https://openalex.org/W2072488631","https://openalex.org/W2073105380","https://openalex.org/W2073587729","https://openalex.org/W2074746593","https://openalex.org/W2077213730","https://openalex.org/W2077562677","https://openalex.org/W2079891060","https://openalex.org/W2080324830","https://openalex.org/W2096441981","https://openalex.org/W2097205777","https://openalex.org/W2097821349","https://openalex.org/W2100744931","https://openalex.org/W2103441770","https://openalex.org/W2104570606","https://openalex.org/W2106446870","https://openalex.org/W2106889224","https://openalex.org/W2107337799","https://openalex.org/W2108234281","https://openalex.org/W2108664872","https://openalex.org/W2112113834","https://openalex.org/W2113588666","https://openalex.org/W2115701239","https://openalex.org/W2116120463","https://openalex.org/W2117131162","https://openalex.org/W2117608012","https://openalex.org/W2121016876","https://openalex.org/W2121475945","https://openalex.org/W2123174009","https://openalex.org/W2123750815","https://openalex.org/W2124729932","https://openalex.org/W2124985265","https://openalex.org/W2125162551","https://openalex.org/W2125269686","https://openalex.org/W2128059998","https://openalex.org/W2128793361","https://openalex.org/W2129246334","https://openalex.org/W2131271579","https://openalex.org/W2131374955","https://openalex.org/W2133229506","https://openalex.org/W2134075494","https://openalex.org/W2134315169","https://openalex.org/W2137130968","https://openalex.org/W2139760555","https://openalex.org/W2141820415","https://openalex.org/W2149502295","https://openalex.org/W2149784730","https://openalex.org/W2150194502","https://openalex.org/W2152451432","https://openalex.org/W2152642144","https://openalex.org/W2152710395","https://openalex.org/W2153896122","https://openalex.org/W2154731166","https://openalex.org/W2158804744","https://openalex.org/W2164214190","https://openalex.org/W2164732672","https://openalex.org/W2170356111","https://openalex.org/W2170546016","https://openalex.org/W2172087672","https://openalex.org/W2916083703","https://openalex.org/W2916251779"],"related_works":["https://openalex.org/W2805216920","https://openalex.org/W2619376220","https://openalex.org/W2064302386","https://openalex.org/W2134949149","https://openalex.org/W2035236309","https://openalex.org/W2895945844","https://openalex.org/W2033196363","https://openalex.org/W1964177829","https://openalex.org/W2075918583","https://openalex.org/W2039097638"],"abstract_inverted_index":{"The":[0],"combination":[1],"of":[2,13,47,51,81,105,114],"DNA":[3,15],"bisulfite":[4,71],"treatment":[5],"with":[6],"high-throughput":[7],"sequencing":[8,72,88],"technologies":[9,24,116],"has":[10],"enabled":[11],"investigation":[12],"genome-wide":[14],"methylation":[16,93,95],"beyond":[17],"CpG":[18,21],"sites":[19],"and":[20,38,45,57,103,117],"islands.":[22],"These":[23],"have":[25],"opened":[26],"new":[27],"avenues":[28],"to":[29,63,119],"understand":[30],"the":[31,42,82,112],"interplay":[32],"between":[33],"epigenetic":[34],"events,":[35],"chromatin":[36],"plasticity":[37],"gene":[39],"regulation.":[40],"However,":[41],"processing,":[43],"managing":[44],"mining":[46],"this":[48],"huge":[49],"volume":[50],"data":[52,101],"require":[53],"specialized":[54],"computational":[55],"tools":[56],"statistical":[58],"methods":[59],"that":[60],"are":[61],"yet":[62],"be":[64],"standardized.":[65],"Here,":[66],"we":[67,110],"describe":[68],"a":[69],"complete":[70],"analysis":[73,84],"workflow,":[74],"including":[75],"recently":[76],"developed":[77],"programs,":[78],"highlighting":[79],"each":[80],"crucial":[83],"steps":[85],"required,":[86],"i.e.":[87],"quality":[89],"control,":[90],"reads":[91],"alignment,":[92],"scoring,":[94],"heterogeneity":[96],"assessment,":[97],"genomic":[98],"features":[99],"annotation,":[100],"visualization":[102],"determination":[104],"differentially":[106],"methylated":[107],"cytosines.":[108],"Moreover,":[109],"discuss":[111],"limitations":[113],"these":[115],"considerations":[118],"perform":[120],"suitable":[121],"analyses.":[122]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":7}],"updated_date":"2026-03-17T09:09:15.849793","created_date":"2025-10-10T00:00:00"}