{"id":"https://openalex.org/W3197777084","doi":"https://doi.org/10.1371/journal.pcbi.1009323","title":"A Bayesian model based computational analysis of the relationship between bisulfite accessible single-stranded DNA in chromatin and somatic hypermutation of immunoglobulin genes","display_name":"A Bayesian model based computational analysis of the relationship between bisulfite accessible single-stranded DNA in chromatin and somatic hypermutation of immunoglobulin genes","publication_year":2021,"publication_date":"2021-09-07","ids":{"openalex":"https://openalex.org/W3197777084","doi":"https://doi.org/10.1371/journal.pcbi.1009323","mag":"3197777084","pmid":"https://pubmed.ncbi.nlm.nih.gov/34491985"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009323","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009323","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009323&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009323&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041963813","display_name":"Guojun Yu","orcid":"https://orcid.org/0000-0003-2126-1827"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guojun Yu","raw_affiliation_strings":["Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039197849","display_name":"Yingru Wu","orcid":"https://orcid.org/0000-0002-3714-6447"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yingru Wu","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103961364","display_name":"Zhi Duan","orcid":null},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhi Duan","raw_affiliation_strings":["Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103003161","display_name":"Catherine Tang","orcid":"https://orcid.org/0000-0002-6293-2300"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Catherine Tang","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090567392","display_name":"Haipeng Xing","orcid":"https://orcid.org/0000-0003-2048-2353"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Haipeng Xing","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024371287","display_name":"Matthew D. Scharff","orcid":"https://orcid.org/0000-0003-0368-2433"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthew D. Scharff","raw_affiliation_strings":["Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019082613","display_name":"Thomas MacCarthy","orcid":"https://orcid.org/0000-0003-0025-9285"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thomas MacCarthy","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America","institution_ids":["https://openalex.org/I59553526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5019082613","https://openalex.org/A5024371287","https://openalex.org/A5090567392"],"corresponding_institution_ids":["https://openalex.org/I129975664","https://openalex.org/I59553526"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.4879,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.62350783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"17","issue":"9","first_page":"e1009323","last_page":"e1009323"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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":0.9975000023841858,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9965000152587891,"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/somatic-hypermutation","display_name":"Somatic hypermutation","score":0.7606732249259949},{"id":"https://openalex.org/keywords/bisulfite","display_name":"Bisulfite","score":0.6872287392616272},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5961704850196838},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5589755177497864},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5284179449081421},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.49910712242126465},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4840390086174011},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.47336336970329285},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.43356966972351074},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4205712378025055},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.4182446002960205},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.31236058473587036},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.22334378957748413},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.11385974287986755},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11049464344978333},{"id":"https://openalex.org/keywords/b-cell","display_name":"B cell","score":0.09485360980033875}],"concepts":[{"id":"https://openalex.org/C128526571","wikidata":"https://www.wikidata.org/wiki/Q619302","display_name":"Somatic hypermutation","level":4,"score":0.7606732249259949},{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.6872287392616272},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5961704850196838},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5589755177497864},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5284179449081421},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.49910712242126465},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4840390086174011},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.47336336970329285},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.43356966972351074},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4205712378025055},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.4182446002960205},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.31236058473587036},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.22334378957748413},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.11385974287986755},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11049464344978333},{"id":"https://openalex.org/C2778453870","wikidata":"https://www.wikidata.org/wiki/Q188930","display_name":"B cell","level":3,"score":0.09485360980033875}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004277","descriptor_name":"DNA, Single-Stranded","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004277","descriptor_name":"DNA, Single-Stranded","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004277","descriptor_name":"DNA, Single-Stranded","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004277","descriptor_name":"DNA, Single-Stranded","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005803","descriptor_name":"Genes, Immunoglobulin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005803","descriptor_name":"Genes, Immunoglobulin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005803","descriptor_name":"Genes, Immunoglobulin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005803","descriptor_name":"Genes, Immunoglobulin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054856","descriptor_name":"G-Quadruplexes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1009323","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009323","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009323&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:34491985","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34491985","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:25eefab5715547d3ad7ca2a44510f15a","is_oa":true,"landing_page_url":"https://doaj.org/article/25eefab5715547d3ad7ca2a44510f15a","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 17, Iss 9, p e1009323 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7352862","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8462741","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8462741","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8462741","pdf_url":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009323","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009323","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009323&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1699633969","display_name":null,"funder_award_id":"1R01AI132507-01A1","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5110453925","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320307136","funder_display_name":"American Association of Immunologists"}],"funders":[{"id":"https://openalex.org/F4320307136","display_name":"American Association of Immunologists","ror":"https://ror.org/04q9fhm49"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3197777084.pdf","grobid_xml":"https://content.openalex.org/works/W3197777084.grobid-xml"},"referenced_works_count":77,"referenced_works":["https://openalex.org/W101836494","https://openalex.org/W1450574606","https://openalex.org/W1515917266","https://openalex.org/W1802312377","https://openalex.org/W1963778872","https://openalex.org/W1968263601","https://openalex.org/W1968773604","https://openalex.org/W1979468302","https://openalex.org/W1981239551","https://openalex.org/W1983368955","https://openalex.org/W1985264665","https://openalex.org/W2002272439","https://openalex.org/W2011730338","https://openalex.org/W2015039578","https://openalex.org/W2031300940","https://openalex.org/W2034011874","https://openalex.org/W2036806870","https://openalex.org/W2040352723","https://openalex.org/W2042639249","https://openalex.org/W2046009254","https://openalex.org/W2050935005","https://openalex.org/W2058506354","https://openalex.org/W2059557296","https://openalex.org/W2062169797","https://openalex.org/W2071949631","https://openalex.org/W2077264333","https://openalex.org/W2084902847","https://openalex.org/W2098739051","https://openalex.org/W2112302692","https://openalex.org/W2113392525","https://openalex.org/W2125132050","https://openalex.org/W2133174470","https://openalex.org/W2133348586","https://openalex.org/W2147784564","https://openalex.org/W2151558930","https://openalex.org/W2151831732","https://openalex.org/W2164821987","https://openalex.org/W2165107875","https://openalex.org/W2165608602","https://openalex.org/W2166573244","https://openalex.org/W2167694553","https://openalex.org/W2169107624","https://openalex.org/W2238713843","https://openalex.org/W2275847773","https://openalex.org/W2290989326","https://openalex.org/W2295956658","https://openalex.org/W2312449754","https://openalex.org/W2323009818","https://openalex.org/W2327094479","https://openalex.org/W2394692813","https://openalex.org/W2410416567","https://openalex.org/W2492693765","https://openalex.org/W2561038494","https://openalex.org/W2562080254","https://openalex.org/W2741939580","https://openalex.org/W2744826395","https://openalex.org/W2755280714","https://openalex.org/W2766679495","https://openalex.org/W2795358647","https://openalex.org/W2800239491","https://openalex.org/W2800472595","https://openalex.org/W2866292647","https://openalex.org/W2910384850","https://openalex.org/W2978627376","https://openalex.org/W3017349264","https://openalex.org/W3017893346","https://openalex.org/W3021143157","https://openalex.org/W3045355398","https://openalex.org/W3091879274","https://openalex.org/W3093969500","https://openalex.org/W3098481821","https://openalex.org/W3155785778","https://openalex.org/W3212216148","https://openalex.org/W4231057646","https://openalex.org/W4249085322","https://openalex.org/W6672079833","https://openalex.org/W6775280952"],"related_works":["https://openalex.org/W1969673184","https://openalex.org/W3132115146","https://openalex.org/W2947266077","https://openalex.org/W2619166255","https://openalex.org/W1539994441","https://openalex.org/W2472738690","https://openalex.org/W3011303654","https://openalex.org/W2359210733","https://openalex.org/W1970342753","https://openalex.org/W2174242874"],"abstract_inverted_index":{"The":[0,22],"B":[1,68,137],"cells":[2],"in":[3,36,62,129,152,184,196,248,273],"our":[4,144],"body":[5],"generate":[6],"protective":[7],"antibodies":[8],"by":[9,26,75],"introducing":[10],"somatic":[11],"hypermutations":[12],"(SHM)":[13],"into":[14],"the":[15,63,106,126,130,134,168,190,197,212,224,274],"variable":[16],"region":[17],"of":[18,66,79,91,133,155,161,171,219,223,233],"immunoglobulin":[19],"genes":[20],"(IgVs).":[21],"mutations":[23],"are":[24,60,97,229],"generated":[25,41],"activation":[27],"induced":[28],"deaminase":[29],"(AID)":[30],"that":[31,59,189,255],"converts":[32],"cytosine":[33],"to":[34,48,55,99,124,243,269],"uracil":[35],"single":[37,245],"stranded":[38,246],"DNA":[39,182,247],"(ssDNA)":[40],"during":[42],"transcription.":[43],"Attempts":[44],"have":[45,72],"been":[46,73],"made":[47],"correlate":[49],"SHM":[50,220,261],"with":[51,109,193],"ssDNA":[52,127,215],"using":[53,76],"bisulfite":[54,213],"chemically":[56],"convert":[57],"cytosines":[58],"accessible":[61,81,214],"intact":[64],"chromatin":[65,249],"mutating":[67],"cells.":[69],"These":[70],"studies":[71,272],"complicated":[74],"different":[77],"definitions":[78],"\"bisulfite":[80],"regions\"":[82],"(BARs).":[83],"Recently,":[84],"deep-sequencing":[85,107],"has":[86],"provided":[87],"much":[88],"larger":[89],"datasets":[90],"such":[92],"regions":[93,128],"but":[94,221],"computational":[95],"methods":[96],"needed":[98],"enable":[100],"this":[101,162,165,185],"analysis.":[102],"Here":[103],"we":[104,148,238],"leveraged":[105],"approach":[108],"unique":[110],"molecular":[111],"identifiers":[112],"and":[113,143,158,187,216,262],"developed":[114,239],"a":[115,207,234,240,251],"novel":[116,241],"Hidden":[117],"Markov":[118],"Model":[119],"based":[120],"Bayesian":[121,146],"Segmentation":[122],"algorithm":[123],"characterize":[125],"IGHV4-34":[131],"gene":[132,186],"human":[135],"Ramos":[136],"cell":[138],"line.":[139],"Combining":[140],"hierarchical":[141],"clustering":[142],"new":[145,166],"model,":[147],"identified":[149,179],"recurrent":[150],"BARs":[151,172,191],"certain":[153],"subregions":[154],"both":[156],"top":[157],"bottom":[159],"strands":[160],"gene.":[163],"Using":[164,200],"system,":[167],"average":[169],"size":[170],"is":[173,205],"about":[174],"15":[175,231],"bp.":[176],"We":[177],"also":[178],"potential":[180,257],"G-quadruplex":[181,194],"structures":[183,195],"found":[188],"co-locate":[192],"opposite":[198],"strand.":[199],"various":[201],"correlation":[202],"analyses,":[203],"there":[204],"not":[206],"direct":[208],"site-to-site":[209],"relationship":[210],"between":[211],"all":[217],"sites":[218,228],"most":[222],"highly":[225],"AID":[226],"mutated":[227],"within":[230],"bp":[232],"BAR.":[235],"In":[236],"summary,":[237],"platform":[242,265],"study":[244],"at":[250],"base":[252],"pair":[253],"resolution":[254],"reveals":[256],"relationships":[258],"among":[259],"BARs,":[260],"G-quadruplexes.":[263],"This":[264],"could":[266],"be":[267],"applied":[268],"genome":[270],"wide":[271],"future.":[275]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}