{"id":"https://openalex.org/W4416734717","doi":"https://doi.org/10.1093/bioinformatics/btaf612","title":"DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing","display_name":"DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4416734717","doi":"https://doi.org/10.1093/bioinformatics/btaf612","pmid":"https://pubmed.ncbi.nlm.nih.gov/41288610"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf612","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf612","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btaf612","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103911327","display_name":"Liu Shu","orcid":"https://orcid.org/0009-0005-6119-4368"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Liyuan Shu","raw_affiliation_strings":["Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054624380","display_name":"Deyu Zhuang","orcid":"https://orcid.org/0009-0000-3326-5708"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Deyu Zhuang","raw_affiliation_strings":["Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101699121","display_name":"Jiao Tang","orcid":"https://orcid.org/0009-0007-1567-324X"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiao Tang","raw_affiliation_strings":["Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001492966","display_name":"Junyong Zhao","orcid":"https://orcid.org/0000-0002-1319-2211"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junyong Zhao","raw_affiliation_strings":["Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107808148","display_name":"Wei Shao","orcid":"https://orcid.org/0000-0002-8554-7245"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Shao","raw_affiliation_strings":["Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010394567","display_name":"Xiaoyu Guan","orcid":"https://orcid.org/0000-0003-3985-3900"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyu Guan","raw_affiliation_strings":["Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114155452","display_name":"Daoqiang Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Daoqiang Zhang","raw_affiliation_strings":["Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","institution_ids":["https://openalex.org/I9842412"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5103911327"],"corresponding_institution_ids":["https://openalex.org/I9842412"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.34964175,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.6621999740600586,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.6621999740600586,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.26809999346733093,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.007499999832361937,"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/barcode","display_name":"Barcode","score":0.8944000005722046},{"id":"https://openalex.org/keywords/multiplexing","display_name":"Multiplexing","score":0.6261000037193298},{"id":"https://openalex.org/keywords/convolution","display_name":"Convolution (computer science)","score":0.5730000138282776},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.49160000681877136},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.48890000581741333},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.4528999924659729}],"concepts":[{"id":"https://openalex.org/C2776841711","wikidata":"https://www.wikidata.org/wiki/Q856","display_name":"Barcode","level":2,"score":0.8944000005722046},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7764999866485596},{"id":"https://openalex.org/C19275194","wikidata":"https://www.wikidata.org/wiki/Q222903","display_name":"Multiplexing","level":2,"score":0.6261000037193298},{"id":"https://openalex.org/C45347329","wikidata":"https://www.wikidata.org/wiki/Q5166604","display_name":"Convolution (computer science)","level":3,"score":0.5730000138282776},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.49160000681877136},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.48890000581741333},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.4528999924659729},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41040000319480896},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4052000045776367},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3896999955177307},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.37290000915527344},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3192000091075897},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.30959999561309814},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.26759999990463257},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.258899986743927}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaf612","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf612","pdf_url":null,"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:41288610","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41288610","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf612","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf612","pdf_url":null,"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/G2320048606","display_name":null,"funder_award_id":"2023YFF1204803","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7869937607","display_name":null,"funder_award_id":"62136004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8386303559","display_name":null,"funder_award_id":"62276130","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W2170747616","https://openalex.org/W2346680365","https://openalex.org/W2792451020","https://openalex.org/W2797840564","https://openalex.org/W2807773783","https://openalex.org/W2881827384","https://openalex.org/W2883511460","https://openalex.org/W2950891420","https://openalex.org/W2950993016","https://openalex.org/W2963470893","https://openalex.org/W2965823869","https://openalex.org/W3138967848","https://openalex.org/W3152667468","https://openalex.org/W3160881677","https://openalex.org/W4242377930","https://openalex.org/W4308772822","https://openalex.org/W4311788922"],"related_works":[],"abstract_inverted_index":{"The":[0],"code":[1],"and":[2],"datasets":[3],"are":[4],"publicly":[5],"available":[6],"on":[7],"https://github.com/LiyuanShu116/Demuxtrans.":[8]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-11-27T00:00:00"}