{"id":"https://openalex.org/W2006046315","doi":"https://doi.org/10.1109/bibmw.2011.6112365","title":"QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads","display_name":"QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads","publication_year":2011,"publication_date":"2011-11-01","ids":{"openalex":"https://openalex.org/W2006046315","doi":"https://doi.org/10.1109/bibmw.2011.6112365","mag":"2006046315"},"language":"en","primary_location":{"id":"doi:10.1109/bibmw.2011.6112365","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2011.6112365","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","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/A5103078881","display_name":"Austin Huang","orcid":"https://orcid.org/0000-0003-1349-4030"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Austin Huang","raw_affiliation_strings":["Division of Infectious Disease, Brown University, Providence, RI, USA","Division of Infectious Disease"],"affiliations":[{"raw_affiliation_string":"Division of Infectious Disease, Brown University, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Division of Infectious Disease","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005395265","display_name":"Rami Kantor","orcid":"https://orcid.org/0000-0003-3659-1108"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rami Kantor","raw_affiliation_strings":["Division of Infectious Disease, Brown University, Providence, RI, USA","Division of Infectious Disease"],"affiliations":[{"raw_affiliation_string":"Division of Infectious Disease, Brown University, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Division of Infectious Disease","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055307587","display_name":"Allison DeLong","orcid":"https://orcid.org/0000-0001-8660-8073"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Allison DeLong","raw_affiliation_strings":["Center for Statistical Sciences, Brown University, Providence, RI, USA","Center for Statistical Sciences"],"affiliations":[{"raw_affiliation_string":"Center for Statistical Sciences, Brown University, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Center for Statistical Sciences","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045213284","display_name":"Leeann Schreier","orcid":null},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leeann Schreier","raw_affiliation_strings":["Division of Infectious Disease, Brown University, Providence, RI, USA","Division of Infectious Disease"],"affiliations":[{"raw_affiliation_string":"Division of Infectious Disease, Brown University, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Division of Infectious Disease","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108392816","display_name":"Sorin Istrail","orcid":null},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sorin Istrail","raw_affiliation_strings":["Department of Computer Science, Brown University, Providence, RI, USA","Department of Computer Science, Brown University, Providence RI, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brown University, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Department of Computer Science, Brown University, Providence RI, USA#TAB#","institution_ids":["https://openalex.org/I27804330"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5103078881"],"corresponding_institution_ids":["https://openalex.org/I27804330"],"apc_list":null,"apc_paid":null,"fwci":0.912,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.72451788,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"15","issue":null,"first_page":"130","last_page":"136"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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":0.9990000128746033,"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/T10112","display_name":"HIV Research and Treatment","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.982200026512146,"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":0.9777923822402954},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.6758314371109009},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.5840107798576355},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5059005618095398},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4856501817703247},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4741729497909546},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4595443606376648},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42176929116249084},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4145027995109558},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30406731367111206},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.21190840005874634},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15083396434783936},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13394862413406372}],"concepts":[{"id":"https://openalex.org/C14500911","wikidata":"https://www.wikidata.org/wiki/Q3413375","display_name":"Viral quasispecies","level":4,"score":0.9777923822402954},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.6758314371109009},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.5840107798576355},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5059005618095398},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4856501817703247},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4741729497909546},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4595443606376648},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42176929116249084},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4145027995109558},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30406731367111206},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.21190840005874634},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15083396434783936},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13394862413406372}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibmw.2011.6112365","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2011.6112365","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7300000190734863,"display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W345637930","https://openalex.org/W1487612538","https://openalex.org/W1531813767","https://openalex.org/W1597035440","https://openalex.org/W1598647205","https://openalex.org/W1972561423","https://openalex.org/W1978073898","https://openalex.org/W1992442812","https://openalex.org/W1993210385","https://openalex.org/W2008088525","https://openalex.org/W2009803466","https://openalex.org/W2011039300","https://openalex.org/W2011630381","https://openalex.org/W2012069101","https://openalex.org/W2016974511","https://openalex.org/W2022910024","https://openalex.org/W2024585092","https://openalex.org/W2026721694","https://openalex.org/W2036192699","https://openalex.org/W2037809979","https://openalex.org/W2041469490","https://openalex.org/W2043714862","https://openalex.org/W2047927409","https://openalex.org/W2048818637","https://openalex.org/W2057578063","https://openalex.org/W2060128897","https://openalex.org/W2067391188","https://openalex.org/W2080921667","https://openalex.org/W2087464200","https://openalex.org/W2087839385","https://openalex.org/W2097847166","https://openalex.org/W2104564525","https://openalex.org/W2109046728","https://openalex.org/W2111283804","https://openalex.org/W2116007667","https://openalex.org/W2116387239","https://openalex.org/W2116614415","https://openalex.org/W2117681036","https://openalex.org/W2121942252","https://openalex.org/W2129326667","https://openalex.org/W2133758885","https://openalex.org/W2134007392","https://openalex.org/W2136651963","https://openalex.org/W2140849404","https://openalex.org/W2148399664","https://openalex.org/W2150215096","https://openalex.org/W2151017710","https://openalex.org/W2152241467","https://openalex.org/W2152365654","https://openalex.org/W2160969485","https://openalex.org/W2163326395","https://openalex.org/W2163576465","https://openalex.org/W2164762627","https://openalex.org/W2170219825","https://openalex.org/W2170765088","https://openalex.org/W2411895135","https://openalex.org/W2416360749","https://openalex.org/W2476848496","https://openalex.org/W2917119881","https://openalex.org/W4297914773","https://openalex.org/W6630897105","https://openalex.org/W6714975745","https://openalex.org/W6716504786"],"related_works":["https://openalex.org/W2370565492","https://openalex.org/W2016766059","https://openalex.org/W2029741357","https://openalex.org/W2144907742","https://openalex.org/W1748700469","https://openalex.org/W2009366069","https://openalex.org/W2620872782","https://openalex.org/W2086431635","https://openalex.org/W2412948090","https://openalex.org/W2472738690"],"abstract_inverted_index":{"Next":[0],"generation":[1,37],"sequencing":[2,38,70,189],"technologies":[3],"have":[4],"been":[5,85],"successfully":[6,178],"applied":[7,43],"to":[8,13,74,79,91,114,125,140,161,181],"HIV-infected":[9],"patients":[10],"in":[11,44,60,87],"order":[12],"obtain":[14],"the":[15,28,55,93,117,120,152,172,175],"mutational":[16],"spectrum":[17],"of":[18,31,52,57,97,107,119,133,151,174],"heterogeneous":[19],"viral":[20],"populations":[21],"within":[22],"individuals,":[23],"known":[24],"as":[25,167],"quasispecies.":[26],"However,":[27],"metage-nomics":[29],"problem":[30],"quasispecies":[32,127,134,145],"sequence":[33,121],"reconstruction":[34],"from":[35],"next":[36],"reads":[39,165],"is":[40],"not-yet":[41],"widely":[42],"current":[45],"practice":[46],"and":[47,111],"remains":[48],"an":[49,143],"emerging":[50],"area":[51],"research.":[53],"Furthermore,":[54],"majority":[56],"research":[58],"methodology":[59],"HIV":[61],"has":[62,84],"focused":[63],"on":[64,184],"454":[65,80],"sequencing,":[66],"while":[67],"many":[68],"next-generation":[69],"platforms":[71],"are":[72],"limited":[73],"shorter":[75],"read":[76,94,109,112],"lengths":[77],"relative":[78],"sequencing.":[81,169],"Little":[82],"work":[83],"done":[86],"determining":[88],"how":[89],"best":[90],"address":[92],"length":[95],"limitations":[96],"other":[98],"platforms.":[99],"The":[100],"approach":[101],"described":[102],"here":[103],"incorporates":[104],"graph":[105],"representations":[106],"both":[108],"differences":[110],"overlap":[113],"conservatively":[115],"determine":[116],"regions":[118,132],"with":[122,163],"sufficient":[123],"variability":[124],"separate":[126],"sequences.":[128],"Within":[129],"these":[130],"tractable":[131],"inference,":[135],"we":[136],"use":[137],"constraint":[138],"programming":[139],"solve":[141],"for":[142],"optimal":[144],"subsequence":[146],"determination":[147],"via":[148],"vertex":[149],"coloring":[150],"conflict":[153],"graph,":[154],"a":[155],"representation":[156],"which":[157],"also":[158],"lends":[159],"itself":[160],"data":[162],"non-contiguous":[164],"such":[166],"paired-end":[168],"We":[170],"demonstrate":[171],"utility":[173],"method":[176],"by":[177],"applying":[179],"it":[180],"simulations":[182],"based":[183],"actual":[185],"intra-patient":[186],"clonal":[187],"HIV-1":[188],"data.":[190]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
