{"id":"https://openalex.org/W3104459592","doi":"https://doi.org/10.1145/3632176","title":"Genome Assembly, from Practice to Theory: Safe, Complete and <i>Linear-Time</i>","display_name":"Genome Assembly, from Practice to Theory: Safe, Complete and <i>Linear-Time</i>","publication_year":2023,"publication_date":"2023-11-08","ids":{"openalex":"https://openalex.org/W3104459592","doi":"https://doi.org/10.1145/3632176","mag":"3104459592"},"language":"en","primary_location":{"id":"doi:10.1145/3632176","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3632176","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3632176","source":{"id":"https://openalex.org/S137348503","display_name":"ACM Transactions on Algorithms","issn_l":"1549-6325","issn":["1549-6325","1549-6333"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Algorithms","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3632176","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007584366","display_name":"Massimo Cairo","orcid":"https://orcid.org/0000-0001-7247-756X"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Massimo Cairo","raw_affiliation_strings":["Department of Computer Science, University of Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0001-7247-756X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061874157","display_name":"Rom\u00e9o Rizzi","orcid":"https://orcid.org/0000-0002-2387-0952"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Romeo Rizzi","raw_affiliation_strings":["Department of Computer Science, University of Verona, Italy"],"raw_orcid":"https://orcid.org/0000-0002-2387-0952","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063897224","display_name":"Alexandru I. Tomescu","orcid":"https://orcid.org/0000-0002-5747-8350"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Alexandru I. Tomescu","raw_affiliation_strings":["Department of Computer Science, University of Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0002-5747-8350","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008708532","display_name":"Elia C. Zirondelli","orcid":"https://orcid.org/0000-0001-5302-0580"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Elia C. Zirondelli","raw_affiliation_strings":["Department of Mathematics, University of Trento, Italy and Department of Computer Science, University of Verona, Italy"],"raw_orcid":"https://orcid.org/0000-0001-5302-0580","affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Trento, Italy and Department of Computer Science, University of Verona, Italy","institution_ids":["https://openalex.org/I119439378","https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1853,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.43437428,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"20","issue":"1","first_page":"1","last_page":"26"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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":0.9990000128746033,"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":0.9968000054359436,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9846000075340271,"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/substring","display_name":"Substring","score":0.708158016204834},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.542717695236206},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.507143497467041},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47017401456832886},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.46089333295822144},{"id":"https://openalex.org/keywords/quadratic-equation","display_name":"Quadratic equation","score":0.43721821904182434},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.40847906470298767},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39967092871665955},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.3745920658111572},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33180469274520874},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.26287877559661865}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.708158016204834},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.542717695236206},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.507143497467041},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47017401456832886},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.46089333295822144},{"id":"https://openalex.org/C129844170","wikidata":"https://www.wikidata.org/wiki/Q41299","display_name":"Quadratic equation","level":2,"score":0.43721821904182434},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.40847906470298767},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39967092871665955},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.3745920658111572},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33180469274520874},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.26287877559661865},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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:10.1145/3632176","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3632176","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3632176","source":{"id":"https://openalex.org/S137348503","display_name":"ACM Transactions on Algorithms","issn_l":"1549-6325","issn":["1549-6325","1549-6333"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Algorithms","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1145/3632176","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3632176","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3632176","source":{"id":"https://openalex.org/S137348503","display_name":"ACM Transactions on Algorithms","issn_l":"1549-6325","issn":["1549-6325","1549-6333"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Algorithms","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G434337789","display_name":null,"funder_award_id":"HORIZON2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6224492464","display_name":null,"funder_award_id":"851093","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7457209830","display_name":null,"funder_award_id":"322595, 328877","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3104459592.pdf","grobid_xml":"https://content.openalex.org/works/W3104459592.grobid-xml"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W27418195","https://openalex.org/W88386512","https://openalex.org/W156230010","https://openalex.org/W184202005","https://openalex.org/W653088692","https://openalex.org/W1493192698","https://openalex.org/W1539571741","https://openalex.org/W1544644664","https://openalex.org/W1583878779","https://openalex.org/W1584400721","https://openalex.org/W1599141268","https://openalex.org/W1850079471","https://openalex.org/W1883762821","https://openalex.org/W1967528843","https://openalex.org/W1970858544","https://openalex.org/W1984236772","https://openalex.org/W1988110322","https://openalex.org/W2009570821","https://openalex.org/W2033292629","https://openalex.org/W2035596374","https://openalex.org/W2055043387","https://openalex.org/W2055693471","https://openalex.org/W2061687898","https://openalex.org/W2078331392","https://openalex.org/W2090526848","https://openalex.org/W2103441770","https://openalex.org/W2104677379","https://openalex.org/W2105067980","https://openalex.org/W2113416388","https://openalex.org/W2113679889","https://openalex.org/W2113852734","https://openalex.org/W2120349185","https://openalex.org/W2136651963","https://openalex.org/W2151674273","https://openalex.org/W2156104322","https://openalex.org/W2158322625","https://openalex.org/W2162402470","https://openalex.org/W2165847428","https://openalex.org/W2170551349","https://openalex.org/W2174237477","https://openalex.org/W2207058206","https://openalex.org/W2241126083","https://openalex.org/W2241574292","https://openalex.org/W2406547600","https://openalex.org/W2410251856","https://openalex.org/W2515489235","https://openalex.org/W2532755849","https://openalex.org/W2535388830","https://openalex.org/W2569880348","https://openalex.org/W2765521106","https://openalex.org/W2777505017","https://openalex.org/W2792957821","https://openalex.org/W2962686126","https://openalex.org/W2962692351","https://openalex.org/W2963251468","https://openalex.org/W2963299914","https://openalex.org/W2963892102","https://openalex.org/W2964091527","https://openalex.org/W2964236121","https://openalex.org/W2965565043","https://openalex.org/W2966735921","https://openalex.org/W2992976869","https://openalex.org/W3003217347","https://openalex.org/W3108387212","https://openalex.org/W3167621737","https://openalex.org/W4234397737","https://openalex.org/W4239574223","https://openalex.org/W4245668478","https://openalex.org/W4247746673","https://openalex.org/W4287588955","https://openalex.org/W4288077753","https://openalex.org/W6638338329"],"related_works":["https://openalex.org/W1583922594","https://openalex.org/W2998448420","https://openalex.org/W1974038726","https://openalex.org/W1953626159","https://openalex.org/W1598224733","https://openalex.org/W4304731099","https://openalex.org/W4280502676","https://openalex.org/W2000769876","https://openalex.org/W2120581723","https://openalex.org/W2519362558"],"abstract_inverted_index":{"Genome":[0],"assembly":[1,75,97,131,154,335],"asks":[2],"to":[3,87,164,203,319,330],"reconstruct":[4],"an":[5,74,130],"unknown":[6],"string":[7],"from":[8,36,46,328],"many":[9],"shorter":[10],"substrings":[11],"of":[12,19,42,104,129,183,208,220,222,237,240,256,258,279,290,311,324],"it.":[13],"Even":[14,156],"though":[15,157],"it":[16,25,120,175],"is":[17,26,232],"one":[18,93],"the":[20,47,105,126,148,179,218,235,246,250,309,322,340],"key":[21,344],"problems":[22],"in":[23,73,110,313],"Bioinformatics,":[24],"generally":[27],"lacking":[28],"major":[29],"theoretical":[30,300],"advances.":[31],"Its":[32],"hardness":[33],"stems":[34],"both":[35],"practical":[37,304,331],"issues":[38],"(size":[39],"and":[40,45,134,151,214,332],"errors":[41],"real":[43],"data),":[44],"fact":[48],"that":[49,248],"problem":[50],"formulations":[51],"inherently":[52],"admit":[53],"multiple":[54],"solutions.":[55,117],"Given":[56],"these,":[57],"at":[58,321],"their":[59],"core,":[60],"most":[61],"state-of-the-art":[62],"assemblers":[63],"are":[64,85,124,253],"based":[65,233],"on":[66,234,293],"finding":[67,160,184],"non-branching":[68],"paths":[69,79],"(":[70,143,242],"unitigs":[71,108,185,312],")":[72,244],"graph.":[76,132],"While":[77],"such":[78,140],"constitute":[80],"only":[81],"partial":[82,116],"assemblies,":[83],"they":[84],"likely":[86],"be":[88,187,320],"correct.":[89],"More":[90],"precisely,":[91],"if":[92],"defines":[94],"a":[95,100,198,209,238,259,298,325],"genome":[96,153,305,334],"solution":[98],"as":[99,337],"closed":[101],"arc-covering":[102],"walk":[103],"graph,":[106],"then":[107],"appear":[109],"all":[111,125,139,205,249,271,280],"solutions,":[112],"being":[113],"thus":[114,146],"safe":[115,127,141,150],"Until":[118],"recently,":[119],"was":[121,161],"open":[122,177],"what":[123],"walks":[128,142,241],"Tomescu":[133],"Medvedev":[135],"(RECOMB":[136],"2016)":[137],"characterized":[138],"omnitigs":[144,207,252],"),":[145],"giving":[147],"first":[149],"complete":[152,333],"algorithm.":[155],"maximal":[158,206,228,272,281],"omnitig":[159,229],"later":[162],"improved":[163],"quadratic":[165],"time":[166],"by":[167,196,303],"Cairo":[168],"et":[169],"al.":[170],"(ACM":[171],"Trans.":[172],"Algorithms":[173],"2019),":[174],"remained":[176],"whether":[178],"crucial":[180],"linear-time":[181,267],"feature":[182],"can":[186],"attained":[188],"with":[189,211,224,245,308],"omnitigs.":[190,273],"We":[191,315],"answer":[192],"this":[193],"question":[194,301],"affirmatively,":[195],"describing":[197],"surprising":[199],"O(m)":[200,277,287],"-time":[201,288],"algorithm":[202,269],"identify":[204],"graph":[210],"n":[212],"nodes":[213],"m":[215],"arcs,":[216],"notwithstanding":[217],"existence":[219],"families":[221],"graphs":[223],"\u0398":[225],"(mn)":[226],"total":[227],"size.":[230],"This":[231,261],"discovery":[236],"family":[239],"macrotigs":[243],"property":[247],"non-trivial":[251],"univocal":[254],"extensions":[255],"subwalks":[257],"macrotig.":[260],"has":[262,338],"two":[263],"consequences:":[264],"(1)":[265],"A":[266,275],"output-sensitive":[268],"enumerating":[270],"(2)":[274],"compact":[276],"representation":[278],"omnitigs,":[282],"which":[283],"allows,":[284],"e.g.,":[285],"for":[286,342],"computation":[289],"various":[291],"statistics":[292],"them.":[294],"Our":[295],"results":[296,318],"close":[297],"long-standing":[299],"inspired":[302],"assemblers,":[306],"originating":[307],"use":[310],"1995.":[314],"envision":[316],"our":[317],"core":[323],"reverse":[326],"transfer":[327],"theory":[329],"programs,":[336],"been":[339],"case":[341],"other":[343],"Bioinformatics":[345],"problems.":[346]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-04T08:18:43.703281","created_date":"2025-10-10T00:00:00"}
