{"id":"https://openalex.org/W4411170804","doi":"https://doi.org/10.1093/bioinformatics/btaf335","title":"Sequence analysis and decoding with extra low-quality reads for DNA data storage","display_name":"Sequence analysis and decoding with extra low-quality reads for DNA data storage","publication_year":2025,"publication_date":"2025-06-01","ids":{"openalex":"https://openalex.org/W4411170804","doi":"https://doi.org/10.1093/bioinformatics/btaf335","pmid":"https://pubmed.ncbi.nlm.nih.gov/40493760"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf335","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf335/63464588/btaf335.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf335/63464588/btaf335.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jiyeon Park","orcid":"https://orcid.org/0000-0002-7146-334X"},"institutions":[{"id":"https://openalex.org/I111277659","display_name":"Chonnam National University","ror":"https://ror.org/05kzjxq56","country_code":"KR","type":"education","lineage":["https://openalex.org/I111277659"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jiyeon Park","raw_affiliation_strings":["Department of Intelligent Electronics and Computer Engineering, Chonnam National University , Gwangju 61186,","Department of Intelligent Electronics and Computer Engineering, Chonnam National University, Gwangju 61186, South Korea"],"raw_orcid":"https://orcid.org/0000-0002-7146-334X","affiliations":[{"raw_affiliation_string":"Department of Intelligent Electronics and Computer Engineering, Chonnam National University , Gwangju 61186,","institution_ids":["https://openalex.org/I111277659"]},{"raw_affiliation_string":"Department of Intelligent Electronics and Computer Engineering, Chonnam National University, Gwangju 61186, South Korea","institution_ids":["https://openalex.org/I111277659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078669022","display_name":"Ha Hyeon Jeon","orcid":null},"institutions":[{"id":"https://openalex.org/I123900574","display_name":"Pohang University of Science and Technology","ror":"https://ror.org/04xysgw12","country_code":"KR","type":"education","lineage":["https://openalex.org/I123900574"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Ha Hyeon Jeon","raw_affiliation_strings":["Department of Chemical Engineering, POSTECH , Pohang 37673,","Department of Chemical Engineering, POSTECH, Pohang 37673, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, POSTECH , Pohang 37673,","institution_ids":["https://openalex.org/I123900574"]},{"raw_affiliation_string":"Department of Chemical Engineering, POSTECH, Pohang 37673, South Korea","institution_ids":["https://openalex.org/I123900574"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101660981","display_name":"Jeong Wook Lee","orcid":"https://orcid.org/0000-0003-0705-0177"},"institutions":[{"id":"https://openalex.org/I123900574","display_name":"Pohang University of Science and Technology","ror":"https://ror.org/04xysgw12","country_code":"KR","type":"education","lineage":["https://openalex.org/I123900574"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jeong Wook Lee","raw_affiliation_strings":["Department of Chemical Engineering, POSTECH , Pohang 37673,","Department of Chemical Engineering, POSTECH, Pohang 37673, South Korea"],"raw_orcid":"https://orcid.org/0000-0003-0705-0177","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, POSTECH , Pohang 37673,","institution_ids":["https://openalex.org/I123900574"]},{"raw_affiliation_string":"Department of Chemical Engineering, POSTECH, Pohang 37673, South Korea","institution_ids":["https://openalex.org/I123900574"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032601178","display_name":"Hosung Park","orcid":"https://orcid.org/0000-0001-7854-7792"},"institutions":[{"id":"https://openalex.org/I111277659","display_name":"Chonnam National University","ror":"https://ror.org/05kzjxq56","country_code":"KR","type":"education","lineage":["https://openalex.org/I111277659"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Hosung Park","raw_affiliation_strings":["Department of Intelligent Electronics and Computer Engineering, Chonnam National University , Gwangju 61186,","Department of Intelligent Electronics and Computer Engineering, Chonnam National University, Gwangju 61186, South Korea"],"raw_orcid":"https://orcid.org/0000-0001-7854-7792","affiliations":[{"raw_affiliation_string":"Department of Intelligent Electronics and Computer Engineering, Chonnam National University , Gwangju 61186,","institution_ids":["https://openalex.org/I111277659"]},{"raw_affiliation_string":"Department of Intelligent Electronics and Computer Engineering, Chonnam National University, Gwangju 61186, South Korea","institution_ids":["https://openalex.org/I111277659"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5032601178"],"corresponding_institution_ids":["https://openalex.org/I111277659"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.818,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.70352685,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"41","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9876999855041504,"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/T12029","display_name":"DNA and Biological Computing","score":0.9876999855041504,"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":0.005400000140070915,"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/T11269","display_name":"Algorithms and Data Compression","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6815742254257202},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6398975849151611},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.6336814761161804},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4271775782108307},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37585097551345825},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.21573710441589355},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20448660850524902},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1991432011127472}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6815742254257202},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6398975849151611},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.6336814761161804},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4271775782108307},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37585097551345825},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.21573710441589355},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20448660850524902},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1991432011127472},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf335","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf335/63464588/btaf335.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40493760","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40493760","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:10996721","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12187058","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf335","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf335/63464588/btaf335.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G339979444","display_name":null,"funder_award_id":"RS-2022-00156287","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G4700831490","display_name":null,"funder_award_id":"2022-","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G6818685394","display_name":null,"funder_award_id":"IITP-2025-RS-2022-00156287","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G7555702357","display_name":null,"funder_award_id":"RS-2022-00156287","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G8947095435","display_name":null,"funder_award_id":"2025-RS-2022-00156287","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"},{"id":"https://openalex.org/F4320335489","display_name":"Institute for Information and Communications Technology Promotion","ror":"https://ror.org/01g0hqq23"},{"id":"https://openalex.org/F4320337407","display_name":"Division of Human Resource Development","ror":"https://ror.org/03mamvh39"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411170804.pdf","grobid_xml":"https://content.openalex.org/works/W4411170804.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W2025383314","https://openalex.org/W2114487425","https://openalex.org/W2116699248","https://openalex.org/W2128711701","https://openalex.org/W2144940978","https://openalex.org/W2471091339","https://openalex.org/W2592122940","https://openalex.org/W2615068531","https://openalex.org/W2625597035","https://openalex.org/W2788257106","https://openalex.org/W2936307398","https://openalex.org/W2951912016","https://openalex.org/W2962809499","https://openalex.org/W2972936807","https://openalex.org/W3015526058","https://openalex.org/W3042993760","https://openalex.org/W3118614175","https://openalex.org/W3135906068","https://openalex.org/W3159176552","https://openalex.org/W3210767789","https://openalex.org/W4226284345","https://openalex.org/W4285181352","https://openalex.org/W4309191898","https://openalex.org/W4319333566","https://openalex.org/W4386456660","https://openalex.org/W4392878834","https://openalex.org/W4394711581","https://openalex.org/W4395110885","https://openalex.org/W4402259332","https://openalex.org/W4404294295","https://openalex.org/W4405180118","https://openalex.org/W6636915900"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"MOTIVATION:":[0],"Error":[1],"detection/correction":[2,68],"codes":[3],"play":[4],"an":[5],"important":[6],"role":[7],"to":[8,60,78,125,144],"reduce":[9],"writing":[10,149],"and/or":[11],"reading":[12,136],"costs":[13],"in":[14,83],"DNA":[15,51],"data":[16,52],"storage.":[17],"Sequence":[18],"analysis":[19,62],"algorithms":[20],"also":[21],"make":[22],"a":[23,107,115],"crucial":[24],"effect":[25],"on":[26,119,140],"error":[27,38,67,98,123],"correction":[28,39],"but":[29],"have":[30],"been":[31],"executed":[32],"independently":[33],"from":[34],"the":[35,64,73,80,89,92,128,135,148],"decoding":[36,102],"of":[37,66,91],"codes.":[40,69],"In":[41],"conventional":[42],"sequence":[43,61,108],"analysis,":[44],"low-quality":[45,54,74,94],"reads":[46,55,75,95,113],"are":[47],"usually":[48],"discarded.":[49],"For":[50],"storage,":[53],"can":[56],"be":[57],"constructively":[58],"used":[59],"with":[63,103],"assistance":[65],"RESULTS:":[70],"We":[71,87,105],"obtained":[72],"which":[76],"failed":[77],"pass":[79],"chastity":[81],"filter":[82],"Illumina":[84],"NGS":[85],"sequencing.":[86],"confirmed":[88],"effectiveness":[90],"extra":[93,129],"by":[96,138],"providing":[97],"statistics":[99],"and":[100,114,122,142],"performing":[101],"them.":[104],"proposed":[106,132],"clustering":[109],"algorithm":[110,117],"for":[111],"various-length":[112],"consensus":[116],"based":[118],"probabilistic":[120],"majority":[121],"detection":[124],"efficiently":[126],"exploit":[127],"reads.":[130],"The":[131],"methods":[133],"reduced":[134],"cost":[137],"6.83%":[139],"average":[141],"up":[143],"19.67%":[145],"while":[146],"maintaining":[147],"cost.":[150],"AVAILABILITY":[151],"AND":[152],"IMPLEMENTATION:":[153],"https://github.com/PParkJy/SAD-DNAstorage":[154],"(10.5281/zenodo.15571858).":[155]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
