{"id":"https://openalex.org/W2139518905","doi":"https://doi.org/10.1109/ipdps.2010.5470397","title":"Parallel de novo assembly of large genomes from high-throughput short reads","display_name":"Parallel de novo assembly of large genomes from high-throughput short reads","publication_year":2010,"publication_date":"2010-01-01","ids":{"openalex":"https://openalex.org/W2139518905","doi":"https://doi.org/10.1109/ipdps.2010.5470397","mag":"2139518905"},"language":"en","primary_location":{"id":"doi:10.1109/ipdps.2010.5470397","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2010.5470397","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Symposium on Parallel &amp; Distributed Processing (IPDPS)","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/A5100809047","display_name":"Benjamin Jackson","orcid":"https://orcid.org/0009-0003-9129-4568"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"B. G. Jackson","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","Department of Electrical and Computer Engineering"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023441763","display_name":"M. Regennitter","orcid":null},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Regennitter","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","Department of Electrical and Computer Engineering"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083812342","display_name":"Xiao Yang","orcid":"https://orcid.org/0000-0002-5429-9162"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"X. Yang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","Department of Electrical and Computer Engineering"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008968750","display_name":"Patrick S. Schnable","orcid":"https://orcid.org/0000-0001-9169-5204"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. S. Schnable","raw_affiliation_strings":["Department of Agronomy, Iowa State University, Ames, IA, USA","Department of Agronomy , Iowa State University , Ames, IA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Agronomy, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Department of Agronomy , Iowa State University , Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074347913","display_name":"Srinivas Aluru","orcid":"https://orcid.org/0000-0003-4279-469X"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Aluru","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","Department of Electrical and Computer Engineering"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100809047"],"corresponding_institution_ids":["https://openalex.org/I173911158"],"apc_list":null,"apc_paid":null,"fwci":2.9078,"has_fulltext":false,"cited_by_count":46,"citation_normalized_percentile":{"value":0.91341866,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"437","issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9909999966621399,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9825000166893005,"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/computer-science","display_name":"Computer science","score":0.7215171456336975},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5624616742134094},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5540211200714111},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5499722957611084},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.537925660610199},{"id":"https://openalex.org/keywords/automatic-summarization","display_name":"Automatic summarization","score":0.48783305287361145},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.44949010014533997},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.35032719373703003},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2591404914855957},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14437097311019897},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13432982563972473},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1296405792236328},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12534227967262268}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7215171456336975},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5624616742134094},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5540211200714111},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5499722957611084},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.537925660610199},{"id":"https://openalex.org/C170858558","wikidata":"https://www.wikidata.org/wiki/Q1394144","display_name":"Automatic summarization","level":2,"score":0.48783305287361145},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.44949010014533997},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.35032719373703003},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2591404914855957},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14437097311019897},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13432982563972473},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1296405792236328},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12534227967262268},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"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":1,"locations":[{"id":"doi:10.1109/ipdps.2010.5470397","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2010.5470397","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Symposium on Parallel &amp; Distributed Processing (IPDPS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","score":0.4699999988079071,"display_name":"Responsible consumption and production"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320311090","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78"},{"id":"https://openalex.org/F4320333867","display_name":"Plant Sciences Institute, Iowa State University","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1498892184","https://openalex.org/W1507265336","https://openalex.org/W1539571741","https://openalex.org/W1572970249","https://openalex.org/W1966822396","https://openalex.org/W2022910024","https://openalex.org/W2023911006","https://openalex.org/W2037859624","https://openalex.org/W2085204501","https://openalex.org/W2112120145","https://openalex.org/W2119585128","https://openalex.org/W2127651281","https://openalex.org/W2128114769","https://openalex.org/W2142749416","https://openalex.org/W2151017710","https://openalex.org/W2155011418","https://openalex.org/W2156104322","https://openalex.org/W2160969485","https://openalex.org/W2171475724","https://openalex.org/W4243977291","https://openalex.org/W6677917386"],"related_works":["https://openalex.org/W2366403280","https://openalex.org/W1495108544","https://openalex.org/W2091301346","https://openalex.org/W3148229873","https://openalex.org/W4389760904","https://openalex.org/W2150160875","https://openalex.org/W4242223894","https://openalex.org/W4306886878","https://openalex.org/W1517524280","https://openalex.org/W4323520239"],"abstract_inverted_index":{"The":[0],"advent":[1],"of":[2,28,62,80,135,165,193],"high-throughput":[3],"short":[4,32,85,111],"read":[5,33,86,127,137,142,167],"technology":[6,24],"is":[7,36,42,99,116],"revolutionizing":[8],"life":[9],"sciences":[10],"by":[11,122],"providing":[12],"an":[13,37],"inexpensive":[14],"way":[15],"to":[16,52,59,91,110,180],"sequence":[17],"genomes":[18,56,93,204],"at":[19],"high":[20,95],"coverage.":[21,96],"Exploiting":[22],"this":[23,72],"requires":[25],"the":[26,76,102,114,176,186],"development":[27,79],"a":[29,81,119,133,191],"de":[30,83],"novo":[31,84],"assembler,":[34],"which":[35],"important":[38],"open":[39],"problem":[40],"that":[41,88],"garnering":[43],"significant":[44],"research":[45],"effort.":[46],"Current":[47],"methods":[48],"are":[49,57,108],"largely":[50],"limited":[51],"microbial":[53],"organisms,":[54],"whose":[55],"two":[58],"three":[60],"orders":[61],"magnitude":[63],"smaller":[64],"than":[65],"complex":[66],"mammalian":[67],"and":[68,78,113,139,159,161,198,205],"plant":[69],"genomes.":[70],"In":[71],"paper,":[73],"we":[74,174],"present":[75,145,190,206],"design":[77],"parallel":[82,146],"assembler":[87],"can":[89,131],"scale":[90],"large":[92,182],"with":[94],"Our":[97,129],"approach":[98],"based":[100,156],"on":[101,196,209],"string":[103,149,152],"graph":[104,150,153,155,170,178],"formulation.":[105],"Input":[106],"reads":[107],"mapped":[109],"paths,":[112],"genome":[115],"reconstructed":[117],"as":[118],"superpath":[120],"anchored":[121],"distance":[123],"constraints":[124],"inferred":[125],"from":[126,185,201],"pairs.":[128],"method":[130],"handle":[132],"mixture":[134],"multiple":[136,140,202],"sizes":[138],"paired":[141,166],"distances.":[143],"We":[144,189],"algorithms":[147],"for":[148],"construction,":[151],"compaction,":[154],"error":[157],"detection":[158],"removal,":[160],"computing":[162],"aggregate":[163],"summarization":[164],"links":[168],"across":[169],"edges.":[171],"Using":[172],"this,":[173],"navigate":[175],"final":[177],"structure":[179],"reproduce":[181],"contiguous":[183],"sequences":[184],"underlying":[187],"genome.":[188],"validation":[192],"our":[194],"framework":[195],"experimental":[197],"simulated":[199],"data":[200],"known":[203],"scaling":[207],"results":[208],"IBM":[210],"Blue":[211],"Gene/L.":[212]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
