{"id":"https://openalex.org/W2562867831","doi":"https://doi.org/10.1109/tmbmc.2016.2641440","title":"Fundamental Limits of Genome Assembly Under an Adversarial Erasure Model","display_name":"Fundamental Limits of Genome Assembly Under an Adversarial Erasure Model","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2562867831","doi":"https://doi.org/10.1109/tmbmc.2016.2641440","mag":"2562867831"},"language":"en","primary_location":{"id":"doi:10.1109/tmbmc.2016.2641440","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmbmc.2016.2641440","pdf_url":null,"source":{"id":"https://openalex.org/S2490853239","display_name":"IEEE Transactions on Molecular Biological and Multi-Scale Communications","issn_l":"2332-7804","issn":["2332-7804","2372-2061"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Molecular, Biological and Multi-Scale Communications","raw_type":"journal-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/A5046640187","display_name":"Ilan Shomorony","orcid":"https://orcid.org/0000-0001-5077-2269"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ilan Shomorony","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5077-2269","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059985425","display_name":"Thomas A. Courtade","orcid":"https://orcid.org/0000-0001-7106-7358"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas A. Courtade","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024072566","display_name":"David Tse","orcid":"https://orcid.org/0000-0003-1460-5900"},"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":"David Tse","raw_affiliation_strings":["Department of Electrical Engineering, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5046640187"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":null,"apc_paid":null,"fwci":0.523,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.72893923,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"2","issue":"2","first_page":"199","last_page":"208"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T12029","display_name":"DNA and Biological Computing","score":0.9890999794006348,"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":0.9879999756813049,"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/genome","display_name":"Genome","score":0.6182228326797485},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6093382239341736},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5221231579780579},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5103151202201843},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4297364354133606},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4093160331249237},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22430658340454102},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21251454949378967},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.145441472530365}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6182228326797485},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6093382239341736},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5221231579780579},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5103151202201843},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4297364354133606},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4093160331249237},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22430658340454102},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21251454949378967},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.145441472530365},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tmbmc.2016.2641440","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmbmc.2016.2641440","pdf_url":null,"source":{"id":"https://openalex.org/S2490853239","display_name":"IEEE Transactions on Molecular Biological and Multi-Scale Communications","issn_l":"2332-7804","issn":["2332-7804","2372-2061"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Molecular, Biological and Multi-Scale Communications","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1739869781","display_name":null,"funder_award_id":"CCF-0939370","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1579534339","https://openalex.org/W1598134722","https://openalex.org/W1954100204","https://openalex.org/W1982579644","https://openalex.org/W1983403167","https://openalex.org/W2017593339","https://openalex.org/W2021134019","https://openalex.org/W2043481183","https://openalex.org/W2072234624","https://openalex.org/W2075013491","https://openalex.org/W2088310213","https://openalex.org/W2115562934","https://openalex.org/W2120349185","https://openalex.org/W2121530737","https://openalex.org/W2122812051","https://openalex.org/W2133956160","https://openalex.org/W2136651963","https://openalex.org/W2157888653","https://openalex.org/W2160265768","https://openalex.org/W2160969485","https://openalex.org/W2162055898","https://openalex.org/W2165847428","https://openalex.org/W2466423648","https://openalex.org/W2509049257","https://openalex.org/W2515489235","https://openalex.org/W2953147862","https://openalex.org/W6719572431"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2053286651","https://openalex.org/W2181743346","https://openalex.org/W2187401768","https://openalex.org/W2181413294","https://openalex.org/W2086525401","https://openalex.org/W2052122378","https://openalex.org/W2544423928","https://openalex.org/W2006735166"],"abstract_inverted_index":{"In":[0,100,156],"contrast":[1],"to":[2,19,79,102,142,217],"second-generation":[3],"DNA":[4],"sequencing":[5],"technologies,":[6],"emerging":[7],"third-generation":[8],"technologies":[9],"are":[10,16,30,95,132],"capable":[11],"of":[12,27,35,42,54,59,83,115,148,186,203,237],"delivering":[13],"reads":[14,29],"that":[15,67,134,161,171,207],"long":[17,28,89],"enough":[18],"enable":[20],"perfect":[21,52,245],"genome":[22,73,124,154,188],"assembly.":[23],"Unfortunately,":[24],"the":[25,55,65,72,84,113,123,129,146,169,174,187,190,208,235,241],"benefits":[26],"accompanied":[31],"by":[32,64],"higher":[33],"rates":[34],"read":[36,93,130,151,238],"errors.":[37],"This":[38],"motivates":[39],"a":[40,109,120,143,162,226],"question":[41],"fundamental":[43],"import:":[44],"what":[45],"read-length":[46],"and":[47,75,92,98,107,128,152,214],"error-rate":[48],"combinations":[49],"allow":[50],"for":[51,71,189,231,244],"assembly":[53,246],"genome?":[56],"Formal":[57],"investigation":[58],"this":[60,116,157],"tradeoff":[61],"is":[62,126,166,212,247],"complicated":[63],"fact":[66],"tractable":[68],"probabilistic":[69],"models":[70],"sequence":[74,125],"error":[76,223],"process":[77],"fail":[78],"capture":[80],"key":[81],"features":[82],"problem:":[85],"real":[86,233],"genomes":[87],"contain":[88],"repetitive":[90],"patterns,":[91],"errors":[94,131,239],"often":[96],"bursty":[97],"sequence-dependent.":[99],"order":[101],"circumvent":[103],"these":[104],"modeling":[105],"barriers":[106],"take":[108],"first":[110],"step":[111],"toward":[112],"study":[114,218],"question,":[117],"we":[118,159,228],"consider":[119],"simple":[121],"setting:":[122],"arbitrary,":[127],"erasures":[133,149],"can":[135],"occur":[136],"at":[137],"adversarially":[138],"chosen":[139],"positions,":[140],"up":[141],"limit":[144],"in":[145,168],"number":[147],"per":[150,153],"position.":[155],"context,":[158],"show":[160,229],"natural":[163],"error-correction":[164,210],"scheme":[165],"optimal":[167],"sense":[170],"it":[172],"recovers":[173],"error-free":[175],"<inline-formula":[176,193],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[177,184,194],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">":[178,195],"<tex-math":[179,196],"notation=\"LaTeX\">${k}$":[180,197],"</tex-math></inline-formula>":[181,198],"-":[182],"<italic":[183],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">spectrum</i>":[185],"largest":[191],"possible":[192],".":[199],"The":[200],"worst-case":[201],"nature":[202],"our":[204],"analysis":[205],"ensures":[206],"proposed":[209],"method":[211],"robust":[213],"allows":[215],"us":[216],"its":[219],"performance":[220],"under":[221],"stochastic":[222],"models.":[224],"As":[225],"result,":[227],"that,":[230],"several":[232],"genomes,":[234],"impact":[236],"on":[240],"information-theoretic":[242],"requirements":[243],"relatively":[248],"mild.":[249]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
