{"id":"https://openalex.org/W2004444147","doi":"https://doi.org/10.1109/iccabs.2012.6182674","title":"Workshop: Bioinformatics methods for reconstruction of Infectious Bronchitis Virus quasispecies from next generation sequencing data","display_name":"Workshop: Bioinformatics methods for reconstruction of Infectious Bronchitis Virus quasispecies from next generation sequencing data","publication_year":2012,"publication_date":"2012-02-01","ids":{"openalex":"https://openalex.org/W2004444147","doi":"https://doi.org/10.1109/iccabs.2012.6182674","mag":"2004444147"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2012.6182674","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2012.6182674","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)","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/A5015873205","display_name":"Rachel J. O\u2019Neill","orcid":"https://orcid.org/0000-0002-1525-6821"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rachel O'Neill","raw_affiliation_strings":["Molecular and Cellular Biology Department, University of Connecticut, Storrs, CT, USA","Molecular and Cellular Biology Dept., University of Connecticut, Storrs, 06269 USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Molecular and Cellular Biology Department, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Molecular and Cellular Biology Dept., University of Connecticut, Storrs, 06269 USA#TAB#","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014788373","display_name":"Ion M\u0103ndoiu","orcid":"https://orcid.org/0000-0002-4818-0237"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ion Mandoiu","raw_affiliation_strings":["Computer Science & Engineering Department, University of Connecticut, Storrs, CT, USA","Computer Science and Engineering Department, University of Connecticut, Storrs, 06269, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science & Engineering Department, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Computer Science and Engineering Department, University of Connecticut, Storrs, 06269, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103690909","display_name":"Mazhar I. Khan","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mazhar I. Khan","raw_affiliation_strings":["Pathobiolgy Department, University of Connecticut, Storrs, CT, USA","Pathobiolgy Dept., University of Connecticut, Storrs, 06269 USA"],"affiliations":[{"raw_affiliation_string":"Pathobiolgy Department, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Pathobiolgy Dept., University of Connecticut, Storrs, 06269 USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054593951","display_name":"Craig Obergfell","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Craig Obergfell","raw_affiliation_strings":["Molecular and Cellular Biology Department, University of Connecticut, Storrs, CT, USA","Molecular and Cellular Biology Dept., University of Connecticut, Storrs, 06269 USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Molecular and Cellular Biology Department, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Molecular and Cellular Biology Dept., University of Connecticut, Storrs, 06269 USA#TAB#","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100357116","display_name":"Hongjun Wang","orcid":"https://orcid.org/0000-0002-9702-3000"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongjun Wang","raw_affiliation_strings":["Pathobiolgy Department, University of Connecticut, Storrs, CT, USA","Pathobiolgy Dept., University of Connecticut, Storrs, 06269 USA"],"affiliations":[{"raw_affiliation_string":"Pathobiolgy Department, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Pathobiolgy Dept., University of Connecticut, Storrs, 06269 USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035902390","display_name":"Andrew Bligh","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Bligh","raw_affiliation_strings":["Biomedical Engineering Program, University of Connecticut, Storrs, CT, USA","Biomedical Engineering Program, University of Connecticut, Storrs, 06269 USA"],"affiliations":[{"raw_affiliation_string":"Biomedical Engineering Program, University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Biomedical Engineering Program, University of Connecticut, Storrs, 06269 USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059280286","display_name":"Bassam Tork","orcid":null},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bassam Tork","raw_affiliation_strings":["Computer Science Department, Georgia State University, Atlanta, GA, USA","Computer Science Department, Georgia State University, Atlanta, 30303 USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Georgia State University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Computer Science Department, Georgia State University, Atlanta, 30303 USA","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029082038","display_name":"Nicholas Mancuso","orcid":"https://orcid.org/0000-0002-9352-5927"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Mancuso","raw_affiliation_strings":["Computer Science Department, Georgia State University, Atlanta, GA, USA","Computer Science Department, Georgia State University, Atlanta, 30303 USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Georgia State University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Computer Science Department, Georgia State University, Atlanta, 30303 USA","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072751459","display_name":"Alex Zelikovsky","orcid":"https://orcid.org/0000-0003-4424-4691"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Zelikovsky","raw_affiliation_strings":["Computer Science Department, Georgia State University, Atlanta, GA, USA","Computer Science Department, Georgia State University, Atlanta, 30303 USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, Georgia State University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Computer Science Department, Georgia State University, Atlanta, 30303 USA","institution_ids":["https://openalex.org/I181565077"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5015873205"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":null,"apc_paid":null,"fwci":0.4536,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.64360557,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11495","display_name":"Animal Virus Infections Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1103","display_name":"Animal Science and Zoology"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11495","display_name":"Animal Virus Infections Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1103","display_name":"Animal Science and Zoology"},"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9976000189781189,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9962999820709229,"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/viral-quasispecies","display_name":"Viral quasispecies","score":0.9712808132171631},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5304792523384094},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5159750580787659},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4876607656478882},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4816633462905884},{"id":"https://openalex.org/keywords/sanger-sequencing","display_name":"Sanger sequencing","score":0.44697675108909607},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.3675260841846466},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3375436067581177},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09417787194252014}],"concepts":[{"id":"https://openalex.org/C14500911","wikidata":"https://www.wikidata.org/wiki/Q3413375","display_name":"Viral quasispecies","level":4,"score":0.9712808132171631},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5304792523384094},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5159750580787659},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4876607656478882},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4816633462905884},{"id":"https://openalex.org/C76818968","wikidata":"https://www.wikidata.org/wiki/Q181940","display_name":"Sanger sequencing","level":4,"score":0.44697675108909607},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3675260841846466},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3375436067581177},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09417787194252014}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2012.6182674","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2012.6182674","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2160464112","https://openalex.org/W3089955370","https://openalex.org/W2412948090","https://openalex.org/W2805859037","https://openalex.org/W2403609377","https://openalex.org/W2041048994","https://openalex.org/W2472738690","https://openalex.org/W4313342334","https://openalex.org/W4225751448","https://openalex.org/W4313584754"],"abstract_inverted_index":{"Viral":[0],"infections":[1],"cause":[2],"a":[3,22,124,173],"significant":[4],"burden":[5],"on":[6,108,121],"animal":[7,42],"health,":[8],"reducing":[9],"yields":[10],"and":[11,50,58,111,117,165,200,207,227],"increasing":[12],"production":[13],"costs":[14],"due":[15,101],"to":[16,52,102,112,143],"expensive":[17],"control":[18,26],"programs.":[19],"Vaccination":[20],"is":[21,31,99,181],"vital":[23],"part":[24],"of":[25,37,63,69,88,96,106,162,176,213,221],"programs;":[27],"however,":[28],"its":[29],"effectiveness":[30],"reduced":[32],"by":[33],"the":[34,103,113,169,182],"quick":[35],"evolution":[36,49],"escape":[38],"viral":[39,89,185],"quasispecies":[40,48,90,198],"in":[41,184],"hosts.":[43],"Existing":[44],"techniques":[45],"for":[46,77,129,150,160,196],"studying":[47],"response":[51],"vaccines":[53],"have":[54,138,192],"severely":[55],"limited":[56],"sensitivity":[57],"often":[59],"require":[60],"prior":[61],"knowledge":[62],"sequence":[64],"polymorphisms.":[65],"By":[66],"generating":[67],"millions":[68],"short":[70,114],"reads":[71,131,216],"per":[72],"run,":[73],"with":[74,236],"no":[75],"need":[76],"culture":[78],"or":[79,137],"cloning,":[80],"next-generation":[81],"sequencing":[82,215],"(NGS)":[83],"technologies":[84],"enable":[85],"comprehensive":[86],"identification":[87],"infecting":[91],"an":[92],"animal.":[93],"However,":[94],"analysis":[95,212],"NGS":[97,144,156,209],"data":[98,107,157],"challenging":[100],"huge":[104],"amount":[105],"one":[109],"hand,":[110],"read":[115],"lengths":[116],"high":[118],"error":[119],"rates":[120],"another.":[122],"As":[123],"consequence,":[125],"many":[126],"tools":[127],"developed":[128,148,193],"Sanger":[130],"do":[132],"not":[133],"work":[134,166],"at":[135,231],"all":[136],"impractical":[139],"runtimes":[140],"when":[141,168],"applied":[142],"data.":[145,210],"Even":[146],"newly":[147],"algorithms":[149],"de":[151],"novo":[152],"genome":[153],"assembly":[154],"from":[155,204,218],"are":[158],"tuned":[159],"reconstruction":[161],"haploid":[163],"genomes,":[164],"poorly":[167],"sequenced":[170],"sample":[171],"contains":[172],"large":[174],"number":[175],"closely":[177],"related":[178],"sequences,":[179],"as":[180],"case":[183],"quasispecies.":[186],"To":[187],"address":[188],"these":[189],"shortcomings":[190],"we":[191],"computational":[194],"methods":[195],"reconstructing":[197],"sequences":[199],"estimate":[201],"their":[202],"frequencies":[203],"both":[205],"shotgun":[206],"amplicon":[208],"Preliminary":[211],"454":[214],"generated":[217],"synthetic":[219],"pools":[220],"Infectious":[222],"Bronchitis":[223],"Virus":[224],"(IBV)":[225],"clones":[226],"field":[228],"isolates":[229],"collected":[230],"various":[232],"intervals":[233],"after":[234],"vaccination":[235],"attenuated":[237],"live":[238],"IBV":[239],"vaccine":[240],"will":[241],"be":[242],"presented.":[243]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}