{"id":"https://openalex.org/W3217549876","doi":"https://doi.org/10.1109/itw48936.2021.9611362","title":"Sequence Reconstruction Under Stutter Noise in Enzymatic DNA Synthesis","display_name":"Sequence Reconstruction Under Stutter Noise in Enzymatic DNA Synthesis","publication_year":2021,"publication_date":"2021-10-17","ids":{"openalex":"https://openalex.org/W3217549876","doi":"https://doi.org/10.1109/itw48936.2021.9611362","mag":"3217549876"},"language":"en","primary_location":{"id":"doi:10.1109/itw48936.2021.9611362","is_oa":false,"landing_page_url":"https://doi.org/10.1109/itw48936.2021.9611362","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE Information Theory Workshop (ITW)","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/A5057100523","display_name":"Roy Shafir","orcid":null},"institutions":[{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Roy Shafir","raw_affiliation_strings":["Taub Faculty of Computer Science, Technion, Haifa, Israel"],"affiliations":[{"raw_affiliation_string":"Taub Faculty of Computer Science, Technion, Haifa, Israel","institution_ids":["https://openalex.org/I174306211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035584245","display_name":"Omer Sabary","orcid":"https://orcid.org/0000-0001-6099-4113"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Omer Sabary","raw_affiliation_strings":["Electrical and Computer Engineering Department, UCSD, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Department, UCSD, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042951994","display_name":"Leon Anavy","orcid":"https://orcid.org/0000-0002-6681-7377"},"institutions":[{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]},{"id":"https://openalex.org/I138898306","display_name":"Reichman University","ror":"https://ror.org/01px5cv07","country_code":"IL","type":"education","lineage":["https://openalex.org/I138898306"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Leon Anavy","raw_affiliation_strings":["School of Computer Science, Herzliya IDC, Herzliya, Israel","Taub Faculty of Computer Science, Technion, Haifa, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Herzliya IDC, Herzliya, Israel","institution_ids":["https://openalex.org/I138898306"]},{"raw_affiliation_string":"Taub Faculty of Computer Science, Technion, Haifa, Israel","institution_ids":["https://openalex.org/I174306211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021586372","display_name":"Eitan Yaakobi","orcid":"https://orcid.org/0000-0002-9851-5234"},"institutions":[{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Eitan Yaakobi","raw_affiliation_strings":["Taub Faculty of Computer Science, Technion, Haifa, Israel"],"affiliations":[{"raw_affiliation_string":"Taub Faculty of Computer Science, Technion, Haifa, Israel","institution_ids":["https://openalex.org/I174306211"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002511176","display_name":"Zohar Yakhini","orcid":"https://orcid.org/0000-0002-0420-5412"},"institutions":[{"id":"https://openalex.org/I138898306","display_name":"Reichman University","ror":"https://ror.org/01px5cv07","country_code":"IL","type":"education","lineage":["https://openalex.org/I138898306"]},{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Zohar Yakhini","raw_affiliation_strings":["School of Computer Science, Herzliya IDC, Herzliya, Israel","Taub Faculty of Computer Science, Technion, Haifa, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Herzliya IDC, Herzliya, Israel","institution_ids":["https://openalex.org/I138898306"]},{"raw_affiliation_string":"Taub Faculty of Computer Science, Technion, Haifa, Israel","institution_ids":["https://openalex.org/I174306211"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5057100523"],"corresponding_institution_ids":["https://openalex.org/I174306211"],"apc_list":null,"apc_paid":null,"fwci":0.5631,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.65088419,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9973999857902527,"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":0.9934999942779541,"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":0.667278528213501},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6581279039382935},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5589837431907654},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.475725919008255},{"id":"https://openalex.org/keywords/word-error-rate","display_name":"Word error rate","score":0.45519885420799255},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.4308759272098541},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21794632077217102},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13845881819725037},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11687928438186646}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.667278528213501},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6581279039382935},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5589837431907654},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.475725919008255},{"id":"https://openalex.org/C40969351","wikidata":"https://www.wikidata.org/wiki/Q3516228","display_name":"Word error rate","level":2,"score":0.45519885420799255},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4308759272098541},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21794632077217102},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13845881819725037},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11687928438186646},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/itw48936.2021.9611362","is_oa":false,"landing_page_url":"https://doi.org/10.1109/itw48936.2021.9611362","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE Information Theory Workshop (ITW)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.6399999856948853}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1969151232","https://openalex.org/W2025177415","https://openalex.org/W2025383314","https://openalex.org/W2063573129","https://openalex.org/W2096408325","https://openalex.org/W2101549738","https://openalex.org/W2110009858","https://openalex.org/W2114487425","https://openalex.org/W2154119782","https://openalex.org/W2162980030","https://openalex.org/W2170484108","https://openalex.org/W2177790274","https://openalex.org/W2471091339","https://openalex.org/W2570365641","https://openalex.org/W2592122940","https://openalex.org/W2788257106","https://openalex.org/W2793140590","https://openalex.org/W2808129035","https://openalex.org/W2947129118","https://openalex.org/W2951269465","https://openalex.org/W2963134372","https://openalex.org/W2963712885","https://openalex.org/W2972936807","https://openalex.org/W2976050422","https://openalex.org/W2992522882","https://openalex.org/W3080129822","https://openalex.org/W3085477517","https://openalex.org/W3105489941","https://openalex.org/W3106529392","https://openalex.org/W3164788607","https://openalex.org/W3217549876","https://openalex.org/W4299366542","https://openalex.org/W6656576250","https://openalex.org/W6666485203","https://openalex.org/W6747734592","https://openalex.org/W6783381151","https://openalex.org/W6784230070"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2317200988","https://openalex.org/W2052122378","https://openalex.org/W2544423928","https://openalex.org/W2053286651","https://openalex.org/W2770593030","https://openalex.org/W2181743346","https://openalex.org/W2187401768","https://openalex.org/W2181413294"],"abstract_inverted_index":{"Synthetic":[0],"DNA":[1,23,35],"is":[2,42,113],"an":[3],"attractive":[4],"alternative":[5],"for":[6,37,103,163],"data":[7,38],"storage":[8],"media":[9],"due":[10],"to":[11,28,150,194],"its":[12],"high":[13,166],"information":[14,111],"density,":[15],"low":[16],"energy":[17],"usage,":[18],"and":[19,94,100,158],"exceptional":[20],"robustness.":[21],"Enzymatic":[22],"synthesis":[24,32,155],"was":[25],"recently":[26],"introduced":[27],"allow":[29],"cost":[30],"effective":[31],"of":[33,72,80,141,172,191],"longer":[34],"molecules":[36],"storage.":[39],"This":[40],"method":[41],"characterized":[43],"by":[44,127],"stutter":[45,117],"errors":[46],"which":[47,112],"are":[48,131],"sticky":[49],"insertions":[50],"so":[51],"that":[52,107],"every":[53],"base":[54],"in":[55,134,183],"the":[56,70,74,85,110,116,136,142,152,159,170,178,184,189,196],"designed":[57],"sequence":[58,76],"may":[59],"be":[60,148],"synthesized":[61],"more":[62],"than":[63],"once.":[64],"In":[65,168],"this":[66],"work,":[67],"we":[68],"study":[69],"problem":[71],"reconstructing":[73],"original":[75],"from":[77,84],"a":[78,139],"set":[79],"noisy":[81],"reads":[82],"originating":[83],"stuttering":[86],"enzymatic":[87],"synthesis.":[88],"We":[89,119,130,186],"present":[90],"different":[91,105],"reconstruction":[92,164,173],"algorithms":[93],"analyze":[95,188],"their":[96],"expected":[97],"success":[98],"probability":[99,171],"error":[101,197],"rate":[102],"three":[104],"scenarios":[106],"depend":[108],"on":[109],"known":[114],"about":[115],"errors.":[118],"evaluate":[120,151],"algorithmic":[121],"performance":[122,137],"analytically":[123],"as":[124,126,138,181],"well":[125],"using":[128],"simulations.":[129],"especially":[132],"interested":[133],"characterizing":[135],"function":[140],"read":[143],"depth.":[144],"Our":[145],"findings":[146],"can":[147],"used":[149],"trade-offs":[153],"between":[154],"quality":[156],"indicators":[157],"sequencing":[160,179],"depth":[161],"required":[162],"with":[165,177],"probability.":[167],"principle,":[169],"failure":[174],"exponentially":[175],"decays":[176],"depth,":[180],"demonstrated":[182],"study.":[185],"also":[187],"use":[190],"error-correcting":[192],"codes":[193],"improve":[195],"performance.":[198]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
