{"id":"https://openalex.org/W4412526151","doi":"https://doi.org/10.1186/s12859-025-06182-5","title":"Aryana-bs: context-aware alignment of bisulfite-sequencing reads","display_name":"Aryana-bs: context-aware alignment of bisulfite-sequencing reads","publication_year":2025,"publication_date":"2025-07-21","ids":{"openalex":"https://openalex.org/W4412526151","doi":"https://doi.org/10.1186/s12859-025-06182-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/40691759"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06182-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06182-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06182-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06182-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004115318","display_name":"Hassan Nikaein","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hassan Nikaein","raw_affiliation_strings":["Department of Computer Engineering, Sharif University of Technology, Tehran, Iran. nikaein@ce.sharif.edu"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Sharif University of Technology, Tehran, Iran. nikaein@ce.sharif.edu","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084845496","display_name":"Ali Sharifi\u2010Zarchi","orcid":"https://orcid.org/0000-0002-0087-7596"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ali Sharifi-Zarchi","raw_affiliation_strings":["Department of Computer Engineering, Sharif University of Technology, Tehran, Iran. sharifi@sharif.edu"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Sharif University of Technology, Tehran, Iran. sharifi@sharif.edu","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056999946","display_name":"Afsoon Afzal","orcid":"https://orcid.org/0000-0003-1942-6573"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Afsoon Afzal","raw_affiliation_strings":["School of Computer Science, Carnegie Mellon University, Pittsburgh, USA"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Carnegie Mellon University, Pittsburgh, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093773426","display_name":"Saeedeh Ezzati","orcid":null},"institutions":[{"id":"https://openalex.org/I133529467","display_name":"Sharif University of Technology","ror":"https://ror.org/024c2fq17","country_code":"IR","type":"education","lineage":["https://openalex.org/I133529467"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Saeedeh Ezzati","raw_affiliation_strings":["Department of Computer Engineering, Sharif University of Technology, Tehran, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Sharif University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I133529467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003222941","display_name":"Farzane Rasti","orcid":null},"institutions":[{"id":"https://openalex.org/I133529467","display_name":"Sharif University of Technology","ror":"https://ror.org/024c2fq17","country_code":"IR","type":"education","lineage":["https://openalex.org/I133529467"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Farzane Rasti","raw_affiliation_strings":["Department of Computer Engineering, Sharif University of Technology, Tehran, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Sharif University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I133529467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090254834","display_name":"Hamidreza Chitsaz","orcid":null},"institutions":[{"id":"https://openalex.org/I4210094699","display_name":"Shenzhen Sixth People's Hospital","ror":"https://ror.org/00qftst12","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210094699"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hamidreza Chitsaz","raw_affiliation_strings":["AutoX technologies, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"AutoX technologies, Shenzhen, China","institution_ids":["https://openalex.org/I4210094699"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009043073","display_name":"Govindarajan Kunde\u2010Ramamoorthy","orcid":null},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Govindarajan Kunde-Ramamoorthy","raw_affiliation_strings":["The Jackson Laboratory, Bar Harbor, USA"],"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, USA","institution_ids":["https://openalex.org/I4210115256"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5004115318"],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.16167925,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"188","last_page":"188"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9983999729156494,"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":0.9983999729156494,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9979000091552734,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6897614598274231},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6104369163513184},{"id":"https://openalex.org/keywords/bisulfite","display_name":"Bisulfite","score":0.5615543723106384},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5482483506202698},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49030163884162903},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4142165184020996},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37429675459861755},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36961615085601807},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32153427600860596},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.29589390754699707},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2949329614639282},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15442705154418945}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6897614598274231},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6104369163513184},{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.5615543723106384},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5482483506202698},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49030163884162903},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4142165184020996},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37429675459861755},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36961615085601807},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32153427600860596},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.29589390754699707},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2949329614639282},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15442705154418945},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","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":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06182-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06182-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06182-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40691759","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40691759","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:3290ac53e2f14317a44e68f52bd6b2b6","is_oa":true,"landing_page_url":"https://doaj.org/article/3290ac53e2f14317a44e68f52bd6b2b6","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-19 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11093438","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12281798","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06182-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06182-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06182-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC 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/W4412526151.pdf","grobid_xml":"https://content.openalex.org/works/W4412526151.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1913581775","https://openalex.org/W1963590871","https://openalex.org/W1973530293","https://openalex.org/W2000491011","https://openalex.org/W2009346579","https://openalex.org/W2027108048","https://openalex.org/W2030181113","https://openalex.org/W2032700279","https://openalex.org/W2050077513","https://openalex.org/W2072464606","https://openalex.org/W2075823962","https://openalex.org/W2101259235","https://openalex.org/W2101668231","https://openalex.org/W2103441770","https://openalex.org/W2106340111","https://openalex.org/W2110119545","https://openalex.org/W2115314035","https://openalex.org/W2126698259","https://openalex.org/W2127192982","https://openalex.org/W2131374955","https://openalex.org/W2145064637","https://openalex.org/W2152656267","https://openalex.org/W2154929782","https://openalex.org/W2170551349","https://openalex.org/W2231664225","https://openalex.org/W2618782736","https://openalex.org/W2804369390","https://openalex.org/W2830752343","https://openalex.org/W2968658941","https://openalex.org/W3009733381","https://openalex.org/W3091154116","https://openalex.org/W3159459467","https://openalex.org/W3160819488","https://openalex.org/W3186165141","https://openalex.org/W4221136004","https://openalex.org/W4225543469","https://openalex.org/W4293565812","https://openalex.org/W4318149614","https://openalex.org/W6612939751"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2054484492","https://openalex.org/W2905022623","https://openalex.org/W1990950482","https://openalex.org/W2811448415","https://openalex.org/W2619376220","https://openalex.org/W3008042233","https://openalex.org/W2953262169","https://openalex.org/W2887849541","https://openalex.org/W1871059078"],"abstract_inverted_index":{"ARYANA-BS":[0],"significantly":[1],"improves":[2],"alignment":[3,37],"accuracy":[4],"for":[5,44,66],"bisulfite":[6],"sequencing":[7],"data":[8],"by":[9],"effectively":[10],"integrating":[11],"DNA":[12,49],"methylation-specific":[13],"alterations":[14],"and":[15,28,36,47,69],"genomic":[16,34],"context.":[17],"It":[18],"outperforms":[19],"existing":[20],"methods,":[21],"such":[22],"as":[23],"BSMAP,":[24],"bwa-meth,":[25],"Bismark,":[26],"BSBolt,":[27],"abismal,":[29],"particularly":[30],"in":[31,72],"robustness":[32],"against":[33],"biases":[35],"of":[38],"longer,":[39],"higher-error":[40],"reads,":[41],"demonstrating":[42],"suitability":[43],"cancer":[45],"research":[46],"cell-free":[48],"studies.":[50],"While":[51],"the":[52],"Expectation-Maximization":[53],"(EM)":[54],"algorithm":[55],"provides":[56],"only":[57],"modest":[58],"initial":[59],"improvements,":[60],"it":[61],"establishes":[62],"a":[63],"valuable":[64],"framework":[65],"future":[67],"refinement":[68],"potential":[70],"enhancements":[71],"sensitive":[73],"applications.":[74]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
