{"id":"https://openalex.org/W2082900371","doi":"https://doi.org/10.1109/iccabs.2014.6863916","title":"How genome complexity can explain the hardness of aligning reads to genomes","display_name":"How genome complexity can explain the hardness of aligning reads to genomes","publication_year":2014,"publication_date":"2014-06-01","ids":{"openalex":"https://openalex.org/W2082900371","doi":"https://doi.org/10.1109/iccabs.2014.6863916","mag":"2082900371"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2014.6863916","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2014.6863916","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5019979430","display_name":"Vinhthuy Phan","orcid":"https://orcid.org/0000-0001-6108-1228"},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vinhthuy Phan","raw_affiliation_strings":["Department of Computer Science, the University of Memphis, Memphis, Tennessee","Department of Computer Science, the University of Memphis, Tennessee 38152, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, the University of Memphis, Memphis, Tennessee","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Department of Computer Science, the University of Memphis, Tennessee 38152, USA","institution_ids":["https://openalex.org/I94658018"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064788213","display_name":"Shanshan Gao","orcid":"https://orcid.org/0000-0003-3920-3713"},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shanshan Gao","raw_affiliation_strings":["Department of Computer Science, the University of Memphis, Memphis, Tennessee","Department of Computer Science, the University of Memphis, Tennessee 38152, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, the University of Memphis, Memphis, Tennessee","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Department of Computer Science, the University of Memphis, Tennessee 38152, USA","institution_ids":["https://openalex.org/I94658018"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021784087","display_name":"Quang Tran","orcid":"https://orcid.org/0000-0002-9263-0733"},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Quang Tran","raw_affiliation_strings":["Department of Computer Science, the University of Memphis, Memphis, Tennessee","Department of Computer Science, the University of Memphis, Tennessee 38152, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, the University of Memphis, Memphis, Tennessee","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Department of Computer Science, the University of Memphis, Tennessee 38152, USA","institution_ids":["https://openalex.org/I94658018"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043745628","display_name":"Nam S. Vo","orcid":"https://orcid.org/0000-0002-5454-9176"},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nam S. Vo","raw_affiliation_strings":["Department of Computer Science, the University of Memphis, Memphis, Tennessee","Department of Computer Science, the University of Memphis, Tennessee 38152, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, the University of Memphis, Memphis, Tennessee","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Department of Computer Science, the University of Memphis, Tennessee 38152, USA","institution_ids":["https://openalex.org/I94658018"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I94658018"],"apc_list":null,"apc_paid":null,"fwci":2.2026,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.88203215,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"2"},"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9965000152587891,"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"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9962999820709229,"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":0.8397771120071411},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6246893405914307},{"id":"https://openalex.org/keywords/intuition","display_name":"Intuition","score":0.5429745316505432},{"id":"https://openalex.org/keywords/computational-complexity-theory","display_name":"Computational complexity theory","score":0.42575469613075256},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4220830798149109},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.390155166387558},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3379482626914978},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2905253767967224},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22979167103767395},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15825194120407104}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8397771120071411},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6246893405914307},{"id":"https://openalex.org/C132010649","wikidata":"https://www.wikidata.org/wiki/Q189222","display_name":"Intuition","level":2,"score":0.5429745316505432},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.42575469613075256},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4220830798149109},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.390155166387558},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3379482626914978},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2905253767967224},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22979167103767395},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15825194120407104},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2014.6863916","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2014.6863916","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"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":13,"referenced_works":["https://openalex.org/W1649017551","https://openalex.org/W2078711260","https://openalex.org/W2098291606","https://openalex.org/W2103441770","https://openalex.org/W2128524432","https://openalex.org/W2129714591","https://openalex.org/W2139523073","https://openalex.org/W2139747296","https://openalex.org/W2139760555","https://openalex.org/W2140154634","https://openalex.org/W2170551349","https://openalex.org/W4247053599","https://openalex.org/W6636941577"],"related_works":["https://openalex.org/W2364252372","https://openalex.org/W4234066492","https://openalex.org/W1998063895","https://openalex.org/W1967044713","https://openalex.org/W2133470120","https://openalex.org/W2747625183","https://openalex.org/W1994286895","https://openalex.org/W2378393413","https://openalex.org/W2802922463","https://openalex.org/W2080622457"],"abstract_inverted_index":{"Although":[0],"it":[1],"is":[2],"known":[3],"that":[4,52],"aligning":[5,84],"short":[6],"reads":[7,87],"to":[8,27,42,88],"reference":[9],"genomes":[10,15],"becomes":[11],"harder":[12],"if":[13],"such":[14],"are":[16],"embedded":[17],"with":[18,67],"complex":[19],"repeat":[20],"structures,":[21],"there":[22],"has":[23],"been":[24],"little":[25],"effort":[26],"quantify":[28],"this":[29],"intuition.":[30],"We":[31],"investigated":[32],"several":[33],"measures":[34,64],"of":[35,47,56,61,70,78,81,86],"complexity,":[36,57],"employed":[37],"10":[38],"popular":[39],"short-read":[40,71],"aligners":[41],"align":[43],"a":[44,58],"large":[45],"number":[46],"diverse":[48],"genomes,":[49],"and":[50],"found":[51],"unlike":[53],"existing":[54],"notions":[55],"proposed":[59],"notion":[60],"length":[62],"sensitive":[63],"correlated":[65],"highly":[66],"the":[68,79],"hardness":[69,80],"alignment.":[72],"This":[73],"result":[74],"enables":[75],"speedy":[76],"estimation":[77],"alignment":[82],"without":[83],"millions":[85],"unknown":[89],"genomes.":[90]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2017,"cited_by_count":2}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
