{"id":"https://openalex.org/W2055577791","doi":"https://doi.org/10.1109/bibmw.2012.6470223","title":"An efficient overlap graph coarsening approach for modeling short reads","display_name":"An efficient overlap graph coarsening approach for modeling short reads","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W2055577791","doi":"https://doi.org/10.1109/bibmw.2012.6470223","mag":"2055577791"},"language":"en","primary_location":{"id":"doi:10.1109/bibmw.2012.6470223","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2012.6470223","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","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/A5036842977","display_name":"Julia Warnke-Sommer","orcid":"https://orcid.org/0000-0003-2263-8972"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Julia Warnke","raw_affiliation_strings":["College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA","College of Information Science and Technology, University of Nebraska at Omaha, Omaha, Nebraska 68182#TAB#"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA","institution_ids":["https://openalex.org/I122266389"]},{"raw_affiliation_string":"College of Information Science and Technology, University of Nebraska at Omaha, Omaha, Nebraska 68182#TAB#","institution_ids":["https://openalex.org/I122266389"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047703641","display_name":"Hesham Ali","orcid":"https://orcid.org/0000-0001-6675-7987"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hesham H. Ali","raw_affiliation_strings":["College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA","College of Information Science and Technology, University of Nebraska at Omaha, Omaha, Nebraska 68182#TAB#"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA","institution_ids":["https://openalex.org/I122266389"]},{"raw_affiliation_string":"College of Information Science and Technology, University of Nebraska at Omaha, Omaha, Nebraska 68182#TAB#","institution_ids":["https://openalex.org/I122266389"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5036842977"],"corresponding_institution_ids":["https://openalex.org/I122266389"],"apc_list":null,"apc_paid":null,"fwci":0.2627,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.57104888,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":null,"first_page":"704","last_page":"711"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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":0.9986000061035156,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9854999780654907,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9818000197410583,"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/graph-traversal","display_name":"Graph traversal","score":0.7943383455276489},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7130709886550903},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5000796318054199},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.4691696763038635},{"id":"https://openalex.org/keywords/tree-traversal","display_name":"Tree traversal","score":0.4630224108695984},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4522819519042969},{"id":"https://openalex.org/keywords/granularity","display_name":"Granularity","score":0.4288952946662903},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.323356956243515},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3219621777534485},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.1623115837574005}],"concepts":[{"id":"https://openalex.org/C96333769","wikidata":"https://www.wikidata.org/wiki/Q907955","display_name":"Graph traversal","level":3,"score":0.7943383455276489},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7130709886550903},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5000796318054199},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.4691696763038635},{"id":"https://openalex.org/C140745168","wikidata":"https://www.wikidata.org/wiki/Q1210082","display_name":"Tree traversal","level":2,"score":0.4630224108695984},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4522819519042969},{"id":"https://openalex.org/C177774035","wikidata":"https://www.wikidata.org/wiki/Q1246948","display_name":"Granularity","level":2,"score":0.4288952946662903},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.323356956243515},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3219621777534485},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.1623115837574005},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibmw.2012.6470223","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2012.6470223","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W17958277","https://openalex.org/W1972924519","https://openalex.org/W1978393037","https://openalex.org/W1983169073","https://openalex.org/W2000905326","https://openalex.org/W2040827479","https://openalex.org/W2046137036","https://openalex.org/W2047927409","https://openalex.org/W2048818637","https://openalex.org/W2070232376","https://openalex.org/W2074231493","https://openalex.org/W2104564525","https://openalex.org/W2109848222","https://openalex.org/W2111217142","https://openalex.org/W2113135059","https://openalex.org/W2116041602","https://openalex.org/W2134061682","https://openalex.org/W2149616469","https://openalex.org/W2163326395","https://openalex.org/W2164762627","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2200188075","https://openalex.org/W4252596799","https://openalex.org/W4254594467","https://openalex.org/W4230405657","https://openalex.org/W2552915643","https://openalex.org/W3213135344","https://openalex.org/W170547082","https://openalex.org/W3183956626","https://openalex.org/W2136735429","https://openalex.org/W244044452"],"abstract_inverted_index":{"Next":[0],"generation":[1],"sequencing":[2,17],"has":[3],"quickly":[4],"emerged":[5],"as":[6],"the":[7,46,51,57,62,79,155,181,196,202,208],"most":[8,52],"exciting":[9],"yet":[10],"challenging":[11],"computational":[12],"problem":[13],"in":[14,34],"Bioinformatics.":[15],"Current":[16],"technologies":[18],"are":[19,72,91],"capable":[20],"of":[21,25,30,78,146,151,176,195,205],"producing":[22],"several":[23,28],"hundreds":[24],"thousands":[26],"to":[27,60,93,136,153,191],"millions":[29],"short":[31],"sequence":[32,82],"reads":[33,48,64,71,86,97,115],"a":[35,75,133,144,162,169,193],"single":[36,134],"run.":[37],"However,":[38],"current":[39],"methods":[40,130],"for":[41,50,113,167,201],"managing,":[42],"storing,":[43],"and":[44,55,66,95,116,128],"processing":[45],"produced":[47,63,73],"remain":[49],"part":[53],"simple":[54],"lack":[56],"complexity":[58],"needed":[59],"model":[61,137],"efficiently":[65],"assemble":[67],"them":[68],"correctly.":[69],"These":[70],"at":[74,173],"high":[76],"coverage":[77],"original":[80],"target":[81],"such":[83],"that":[84,131,199],"many":[85],"overlap.":[87],"The":[88],"overlap":[89,109,118,139,158,197],"relationships":[90],"used":[92],"align":[94],"merge":[96],"into":[98],"contiguous":[99],"sequences":[100],"called":[101],"contigs.":[102],"In":[103],"this":[104],"paper,":[105],"we":[106,142],"present":[107,161],"an":[108],"graph":[110,135,164,183,188,198,209],"coarsening":[111,165,184],"scheme":[112,185],"modeling":[114],"their":[117],"relationships.":[119,140,159],"Our":[120],"approach":[121],"is":[122],"different":[123,149],"from":[124],"previous":[125],"read":[126,138,157],"analysis":[127],"assembly":[129],"use":[132,143,180],"Instead,":[141],"series":[145],"graphs":[147],"with":[148,187],"granularities":[150],"information":[152],"represent":[154],"complex":[156],"We":[160,178],"new":[163],"algorithm":[166],"clustering":[168],"simulated":[170],"metagenomics":[171],"dataset":[172],"various":[174],"levels":[175],"granularity.":[177],"also":[179],"proposed":[182],"along":[186],"traversal":[189],"algorithms":[190],"find":[192],"labeling":[194],"allows":[200],"efficient":[203],"organization":[204],"nodes":[206],"within":[207],"data":[210],"structure.":[211]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}