{"id":"https://openalex.org/W3015526058","doi":"https://doi.org/10.1109/icassp40776.2020.9053441","title":"Overcoming High Nanopore Basecaller Error Rates for DNA Storage via Basecaller-Decoder Integration and Convolutional Codes","display_name":"Overcoming High Nanopore Basecaller Error Rates for DNA Storage via Basecaller-Decoder Integration and Convolutional Codes","publication_year":2020,"publication_date":"2020-04-09","ids":{"openalex":"https://openalex.org/W3015526058","doi":"https://doi.org/10.1109/icassp40776.2020.9053441","mag":"3015526058"},"language":"en","primary_location":{"id":"doi:10.1109/icassp40776.2020.9053441","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icassp40776.2020.9053441","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086012490","display_name":"Shubham Chandak","orcid":"https://orcid.org/0000-0002-1130-9762"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shubham Chandak","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023778508","display_name":"Joachim Neu","orcid":"https://orcid.org/0000-0002-9777-6168"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joachim Neu","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045177980","display_name":"Kedar Tatwawadi","orcid":"https://orcid.org/0000-0003-3677-4174"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kedar Tatwawadi","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065018530","display_name":"Jay Mardia","orcid":"https://orcid.org/0000-0002-1538-9202"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jay Mardia","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043566220","display_name":"Billy T. Lau","orcid":"https://orcid.org/0000-0002-8934-3370"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Billy Lau","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041479083","display_name":"Matthew Kubit","orcid":"https://orcid.org/0000-0001-8997-5290"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Kubit","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008139466","display_name":"Reyna Hulett","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Reyna Hulett","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103482188","display_name":"Peter B. Griffin","orcid":"https://orcid.org/0000-0003-0966-800X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Griffin","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022963784","display_name":"Mary Wootters","orcid":"https://orcid.org/0000-0002-2345-2531"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary Wootters","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043344688","display_name":"Tsachy Weissman","orcid":"https://orcid.org/0009-0008-1099-691X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tsachy Weissman","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057314465","display_name":"Hanlee P. Ji","orcid":"https://orcid.org/0000-0003-3772-3424"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanlee Ji","raw_affiliation_strings":["Stanford University,Stanford,CA,USA","Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Stanford,CA,USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5086012490"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":null,"apc_paid":null,"fwci":2.5916,"has_fulltext":false,"cited_by_count":50,"citation_normalized_percentile":{"value":0.90525814,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"8822","last_page":"8826"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9980000257492065,"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"}},{"id":"https://openalex.org/T12162","display_name":"Cellular Automata and Applications","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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":0.7682439088821411},{"id":"https://openalex.org/keywords/convolutional-code","display_name":"Convolutional code","score":0.6698962450027466},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.5945025086402893},{"id":"https://openalex.org/keywords/error-detection-and-correction","display_name":"Error detection and correction","score":0.5749189853668213},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5662645101547241},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.44358372688293457},{"id":"https://openalex.org/keywords/viterbi-decoder","display_name":"Viterbi decoder","score":0.425098717212677},{"id":"https://openalex.org/keywords/computer-data-storage","display_name":"Computer data storage","score":0.41137734055519104},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.3410820960998535},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3358609974384308},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.33495643734931946},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.32724449038505554},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.17977535724639893},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.17571303248405457},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.09996810555458069},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09290528297424316},{"id":"https://openalex.org/keywords/wireless","display_name":"Wireless","score":0.08928689360618591}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7682439088821411},{"id":"https://openalex.org/C157899210","wikidata":"https://www.wikidata.org/wiki/Q1395022","display_name":"Convolutional code","level":3,"score":0.6698962450027466},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.5945025086402893},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.5749189853668213},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5662645101547241},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.44358372688293457},{"id":"https://openalex.org/C117379686","wikidata":"https://www.wikidata.org/wiki/Q6996459","display_name":"Viterbi decoder","level":3,"score":0.425098717212677},{"id":"https://openalex.org/C194739806","wikidata":"https://www.wikidata.org/wiki/Q66221","display_name":"Computer data storage","level":2,"score":0.41137734055519104},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.3410820960998535},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3358609974384308},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.33495643734931946},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.32724449038505554},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.17977535724639893},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.17571303248405457},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.09996810555458069},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09290528297424316},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.08928689360618591},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/icassp40776.2020.9053441","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icassp40776.2020.9053441","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.8799999952316284}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1946587648","https://openalex.org/W1977467261","https://openalex.org/W2025383314","https://openalex.org/W2063573129","https://openalex.org/W2105597036","https://openalex.org/W2114487425","https://openalex.org/W2122683098","https://openalex.org/W2142384583","https://openalex.org/W2148575324","https://openalex.org/W2149072083","https://openalex.org/W2162980030","https://openalex.org/W2296600582","https://openalex.org/W2471091339","https://openalex.org/W2528151179","https://openalex.org/W2550586733","https://openalex.org/W2592122940","https://openalex.org/W2615068531","https://openalex.org/W2788257106","https://openalex.org/W2791982652","https://openalex.org/W2883511460","https://openalex.org/W2947129118","https://openalex.org/W2949279762","https://openalex.org/W2950609999","https://openalex.org/W2950993016","https://openalex.org/W2951269465","https://openalex.org/W2951989222","https://openalex.org/W2955617048","https://openalex.org/W2962809499","https://openalex.org/W2964325683","https://openalex.org/W2972726870","https://openalex.org/W2972936807","https://openalex.org/W2976482814","https://openalex.org/W2993276217","https://openalex.org/W4229922087","https://openalex.org/W6666485203","https://openalex.org/W6728127629"],"related_works":["https://openalex.org/W2373717821","https://openalex.org/W2093256002","https://openalex.org/W2101868111","https://openalex.org/W1498678092","https://openalex.org/W2347424896","https://openalex.org/W2587681282","https://openalex.org/W2078980669","https://openalex.org/W2365203640","https://openalex.org/W2360399606","https://openalex.org/W2548538278"],"abstract_inverted_index":{"As":[0],"magnetization":[1],"and":[2,31,53,83,153],"semiconductor":[3],"based":[4,127],"storage":[5,22,28,60],"technologies":[6],"approach":[7,94],"their":[8,26],"limits,":[9],"bio-molecules,":[10],"such":[11],"as":[12,17,46,48],"DNA,":[13],"have":[14],"been":[15],"identified":[16],"promising":[18],"media":[19],"for":[20,58,133],"future":[21],"systems,":[23],"due":[24],"to":[25,63,117],"high":[27,65,87,98],"density":[29],"(petabytes/gram)":[30],"long-term":[32],"durability":[33],"(thousands":[34],"of":[35],"years).":[36],"Furthermore,":[37],"nanopore":[38,72],"DNA":[39,59],"sequencing":[40,43],"enables":[41],"high-throughput":[42],"using":[44],"devices":[45],"small":[47],"a":[49,92,106],"USB":[50],"thumb":[51],"drive":[52],"thus":[54,84],"is":[55,156],"ideally":[56],"suited":[57],"applications.":[61],"Due":[62],"the":[64,97,112,115,119,124,144],"insertion/deletion":[66],"error":[67,99,108,134],"rates":[68,100],"associated":[69],"with":[70,111],"base-called":[71],"reads,":[73],"current":[74],"approaches":[75],"rely":[76],"heavily":[77],"on":[78],"consensus":[79],"among":[80],"multiple":[81],"reads":[82],"incur":[85],"very":[86],"reading":[88,141],"costs.":[89],"We":[90],"propose":[91],"novel":[93],"which":[95],"overcomes":[96],"in":[101,123],"basecalled":[102],"sequences":[103],"by":[104],"integrating":[105],"Viterbi":[107],"correction":[109],"decoder":[110,116],"basecaller,":[113],"enabling":[114],"exploit":[118],"soft":[120],"information":[121],"available":[122,157],"deep":[125],"learning":[126],"basecaller":[128],"pipeline.":[129],"Using":[130],"convolutional":[131],"codes":[132],"correction,":[135],"we":[136],"experimentally":[137],"observed":[138],"3x":[139],"lower":[140],"costs":[142],"than":[143],"state-of-the-art":[145],"techniques":[146],"at":[147,158],"comparable":[148],"writing":[149],"costs.The":[150],"code,":[151],"data":[152],"Supplementary":[154],"Material":[155],"https://github.com/shubhamchandak94/nanopore_dna_storage.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":2}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
