{"id":"https://openalex.org/W4206362576","doi":"https://doi.org/10.1109/access.2022.3144113","title":"Graph Theoretical Strategies in De Novo Assembly","display_name":"Graph Theoretical Strategies in De Novo Assembly","publication_year":2022,"publication_date":"2022-01-01","ids":{"openalex":"https://openalex.org/W4206362576","doi":"https://doi.org/10.1109/access.2022.3144113"},"language":"en","primary_location":{"id":"doi:10.1109/access.2022.3144113","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3144113","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09684373.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09684373.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083215622","display_name":"Kimia Behizadi","orcid":null},"institutions":[{"id":"https://openalex.org/I1516879","display_name":"Tarbiat Modares University","ror":"https://ror.org/03mwgfy56","country_code":"IR","type":"education","lineage":["https://openalex.org/I1516879"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Kimia Behizadi","raw_affiliation_strings":["Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran","institution_ids":["https://openalex.org/I1516879"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002182178","display_name":"Nafiseh Jafarzadeh","orcid":"https://orcid.org/0000-0002-1816-2994"},"institutions":[{"id":"https://openalex.org/I1516879","display_name":"Tarbiat Modares University","ror":"https://ror.org/03mwgfy56","country_code":"IR","type":"education","lineage":["https://openalex.org/I1516879"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Nafiseh Jafarzadeh","raw_affiliation_strings":["Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran","institution_ids":["https://openalex.org/I1516879"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059777426","display_name":"Ali Iranmanesh","orcid":"https://orcid.org/0000-0003-2639-9454"},"institutions":[{"id":"https://openalex.org/I1516879","display_name":"Tarbiat Modares University","ror":"https://ror.org/03mwgfy56","country_code":"IR","type":"education","lineage":["https://openalex.org/I1516879"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Ali Iranmanesh","raw_affiliation_strings":["Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran","institution_ids":["https://openalex.org/I1516879"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5083215622"],"corresponding_institution_ids":["https://openalex.org/I1516879"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.3126,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.52731635,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"10","issue":null,"first_page":"9328","last_page":"9339"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9944999814033508,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9811000227928162,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.7611314058303833},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5796095728874207},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5565492510795593},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.51735919713974},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5167633295059204},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3876149654388428},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3362046480178833},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25528040528297424},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.236045241355896}],"concepts":[{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.7611314058303833},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5796095728874207},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5565492510795593},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.51735919713974},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5167633295059204},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3876149654388428},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3362046480178833},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25528040528297424},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.236045241355896},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2022.3144113","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3144113","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09684373.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:735be4de815d434ab5c6683180c3ff77","is_oa":true,"landing_page_url":"https://doaj.org/article/735be4de815d434ab5c6683180c3ff77","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 10, Pp 9328-9339 (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2022.3144113","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3144113","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09684373.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5517081548","display_name":null,"funder_award_id":"IG-39706","funder_id":"https://openalex.org/F4320324984","funder_display_name":"Tarbiat Modares University"}],"funders":[{"id":"https://openalex.org/F4320324984","display_name":"Tarbiat Modares University","ror":"https://ror.org/03mwgfy56"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4206362576.pdf","grobid_xml":"https://content.openalex.org/works/W4206362576.grobid-xml"},"referenced_works_count":87,"referenced_works":["https://openalex.org/W194848955","https://openalex.org/W344138311","https://openalex.org/W1493192698","https://openalex.org/W1598134722","https://openalex.org/W1635391495","https://openalex.org/W1966822396","https://openalex.org/W1980606681","https://openalex.org/W1983403167","https://openalex.org/W1984236772","https://openalex.org/W1992595091","https://openalex.org/W2003979986","https://openalex.org/W2009119978","https://openalex.org/W2010361633","https://openalex.org/W2022910024","https://openalex.org/W2022986961","https://openalex.org/W2023911006","https://openalex.org/W2048124712","https://openalex.org/W2057253402","https://openalex.org/W2074332603","https://openalex.org/W2087064593","https://openalex.org/W2096634299","https://openalex.org/W2099809434","https://openalex.org/W2105191441","https://openalex.org/W2105656684","https://openalex.org/W2105708056","https://openalex.org/W2115501618","https://openalex.org/W2120902911","https://openalex.org/W2121911035","https://openalex.org/W2128114769","https://openalex.org/W2129933858","https://openalex.org/W2130530163","https://openalex.org/W2131813051","https://openalex.org/W2132069633","https://openalex.org/W2133531097","https://openalex.org/W2136651963","https://openalex.org/W2138071529","https://openalex.org/W2138270253","https://openalex.org/W2141408763","https://openalex.org/W2141920662","https://openalex.org/W2142749416","https://openalex.org/W2151017710","https://openalex.org/W2156104322","https://openalex.org/W2156660460","https://openalex.org/W2157624015","https://openalex.org/W2160969485","https://openalex.org/W2161048357","https://openalex.org/W2161488606","https://openalex.org/W2161546116","https://openalex.org/W2163830511","https://openalex.org/W2179507357","https://openalex.org/W2180318265","https://openalex.org/W2194172909","https://openalex.org/W2397469828","https://openalex.org/W2538143681","https://openalex.org/W2562683361","https://openalex.org/W2589379462","https://openalex.org/W2784936077","https://openalex.org/W2788228074","https://openalex.org/W2789843538","https://openalex.org/W2883210274","https://openalex.org/W2894808609","https://openalex.org/W2895878640","https://openalex.org/W2938605561","https://openalex.org/W2948487375","https://openalex.org/W2950354111","https://openalex.org/W2952167528","https://openalex.org/W2952379095","https://openalex.org/W2953147862","https://openalex.org/W2980672119","https://openalex.org/W2981265504","https://openalex.org/W2992976869","https://openalex.org/W3017034896","https://openalex.org/W3022783334","https://openalex.org/W3042933198","https://openalex.org/W3045408080","https://openalex.org/W3047598142","https://openalex.org/W3049406222","https://openalex.org/W3091506611","https://openalex.org/W3099661149","https://openalex.org/W3110957961","https://openalex.org/W3120530641","https://openalex.org/W3128198169","https://openalex.org/W3134382222","https://openalex.org/W3164465449","https://openalex.org/W3200242814","https://openalex.org/W6679663036","https://openalex.org/W6683504902"],"related_works":["https://openalex.org/W2086525401","https://openalex.org/W2006735166","https://openalex.org/W2794386548","https://openalex.org/W4381279187","https://openalex.org/W1992950355","https://openalex.org/W2013063066","https://openalex.org/W2890379969","https://openalex.org/W1841715584","https://openalex.org/W2766401759","https://openalex.org/W3134563641"],"abstract_inverted_index":{"De":[0],"novo":[1,23,58,98],"genome":[2,7,41,59,96],"assemblers":[3,99],"assume":[4],"the":[5,53,65,91,104],"reference":[6],"is":[8],"unavailable,":[9],"incomplete,":[10],"highly":[11],"fragmented,":[12],"or":[13],"significantly":[14],"altered":[15],"as":[16],"in":[17,78,86],"cancer":[18],"tissues.":[19],"Algorithms":[20],"for":[21],"de":[22,57,97],"assembly":[24,60],"have":[25,48,63],"been":[26],"developed":[27],"to":[28,73,80,103],"deal":[29],"with":[30],"and":[31,75,82,94,110],"assemble":[32],"a":[33],"large":[34],"number":[35],"of":[36,52,56,67,107,113],"short":[37],"sequence":[38],"reads":[39],"from":[40],"sequencing.":[42],"In":[43,89],"this":[44],"review":[45],"paper,":[46],"we":[47],"provided":[49],"an":[50],"overview":[51],"graph-theoretical":[54],"side":[55],"algorithms.":[61],"We":[62],"investigated":[64],"construction":[66],"fourteen":[68],"graph":[69,114],"data":[70,115],"structures":[71],"related":[72],"OLC-based":[74],"DBG-based":[76],"algorithms":[77],"order":[79],"compare":[81],"discuss":[83],"their":[84],"application":[85],"different":[87],"assemblers.":[88],"addition,":[90],"most":[92],"significant":[93],"recent":[95],"are":[100],"classified":[101],"according":[102],"extensive":[105],"variety":[106],"original,":[108],"generalized,":[109],"specialized":[111],"versions":[112],"structures.":[116]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
