{"id":"https://openalex.org/W2004963628","doi":"https://doi.org/10.1371/journal.pcbi.0040025","title":"Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al.","display_name":"Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al.","publication_year":2008,"publication_date":"2008-01-22","ids":{"openalex":"https://openalex.org/W2004963628","doi":"https://doi.org/10.1371/journal.pcbi.0040025","mag":"2004963628","pmid":"https://pubmed.ncbi.nlm.nih.gov/18463692"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0040025","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0040025","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040025&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"letter","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040025&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028344545","display_name":"David C. Nickle","orcid":"https://orcid.org/0000-0002-8672-6261"},"institutions":[{"id":"https://openalex.org/I4210123531","display_name":"Merck (Japan)","ror":"https://ror.org/0292awh62","country_code":"JP","type":"company","lineage":["https://openalex.org/I164928964","https://openalex.org/I4210123531"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"David C Nickle","raw_affiliation_strings":["Merck"],"affiliations":[{"raw_affiliation_string":"Merck","institution_ids":["https://openalex.org/I4210123531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108373424","display_name":"Neboj\u0161a Joji\u0107","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nebojsa Jojic","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016386034","display_name":"David Heckerman","orcid":"https://orcid.org/0000-0002-4274-6084"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"David Heckerman","raw_affiliation_strings":["Microsoft , USA "],"affiliations":[{"raw_affiliation_string":"Microsoft , USA ","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005113963","display_name":"Vladimir Jojic","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vladimir Jojic","raw_affiliation_strings":["Stanford University"],"affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030613945","display_name":"Darko Kirovski","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Darko Kirovski","raw_affiliation_strings":["Microsoft , USA "],"affiliations":[{"raw_affiliation_string":"Microsoft , USA ","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067755958","display_name":"Morgane Rolland","orcid":"https://orcid.org/0000-0003-3650-8490"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Morgane Rolland","raw_affiliation_strings":["University of Washington"],"affiliations":[{"raw_affiliation_string":"University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011410563","display_name":"Sergei L. Kosakovsky Pond","orcid":"https://orcid.org/0000-0003-4817-4029"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergei Kosakovsky Pond","raw_affiliation_strings":["University of California at San Diego"],"affiliations":[{"raw_affiliation_string":"University of California at San Diego","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028336562","display_name":"James I. Mullins","orcid":"https://orcid.org/0000-0002-4461-8158"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James I Mullins","raw_affiliation_strings":["University of Washington"],"affiliations":[{"raw_affiliation_string":"University of Washington","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5028344545"],"corresponding_institution_ids":["https://openalex.org/I4210123531"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.5075,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.58817134,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"4","issue":"1","first_page":"e25","last_page":"e25"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998999834060669,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9994000196456909,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/immunogen","display_name":"Immunogen","score":0.6100556254386902},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4494721591472626},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3916756510734558},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.38342756032943726},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3039650321006775},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07876428961753845}],"concepts":[{"id":"https://openalex.org/C2779909307","wikidata":"https://www.wikidata.org/wiki/Q1660181","display_name":"Immunogen","level":4,"score":0.6100556254386902},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4494721591472626},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3916756510734558},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.38342756032943726},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3039650321006775},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07876428961753845},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.0},{"id":"https://openalex.org/C542903549","wikidata":"https://www.wikidata.org/wiki/Q422248","display_name":"Monoclonal antibody","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000940","descriptor_name":"Antigenic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000940","descriptor_name":"Antigenic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000940","descriptor_name":"Antigenic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016915","descriptor_name":"AIDS Vaccines","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016915","descriptor_name":"AIDS Vaccines","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016915","descriptor_name":"AIDS Vaccines","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016915","descriptor_name":"AIDS Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D016915","descriptor_name":"AIDS Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D016915","descriptor_name":"AIDS Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018604","descriptor_name":"Epitope Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.0040025","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0040025","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040025&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:18463692","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18463692","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:0040025","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0040025","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:ba7907e2cb4a498a819cf56055175440","is_oa":true,"landing_page_url":"https://doaj.org/article/ba7907e2cb4a498a819cf56055175440","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 4, Iss 1, p e25 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2217581","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2217581","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:scholarshare.temple.edu:20.500.12613/5612","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.12613/5612","pdf_url":null,"source":{"id":"https://openalex.org/S4306402624","display_name":"TUScholarShare (Temple University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I84392919","host_organization_name":"Temple University","host_organization_lineage":["https://openalex.org/I84392919"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Letter"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0040025","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0040025","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040025&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.6499999761581421}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2004963628.pdf","grobid_xml":"https://content.openalex.org/works/W2004963628.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W206843697","https://openalex.org/W1977837530","https://openalex.org/W1992391009","https://openalex.org/W2015125044","https://openalex.org/W2017809447","https://openalex.org/W2059613424","https://openalex.org/W2072334833","https://openalex.org/W2089825402","https://openalex.org/W2093658347","https://openalex.org/W2102398565","https://openalex.org/W2105323221","https://openalex.org/W2109822798","https://openalex.org/W2137680370"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2607424097","https://openalex.org/W2393764744","https://openalex.org/W2606230654","https://openalex.org/W2319480705"],"abstract_inverted_index":{"In":[0],"our":[1,31,466,473,511],"paper":[2,467],"\u201cCoping":[3],"with":[4,77,90,136,185,206,221,335,364,706,780],"Viral":[5],"Diversity":[6],"in":[7,71,88,233,242,246,435,468,494,510,552,565,572,647,662],"HIV":[8,456],"Vaccine":[9],"Design\u201d":[10],"[1],":[11,122,237],"we":[12,191,719],"presented":[13,661],"several":[14],"approaches":[15,32,209,476],"to":[16,41,102,118,145,182,202,329,350,403,414,420,477,502,507,594,611,677,688,694,771,778],"incorporate":[17],"viral":[18,133,138,150,732,782],"variability":[19,712,725],"within":[20],"vaccine":[21,695],"immunogens,":[22],"including":[23],"judicious":[24,750],"choice":[25],"of":[26,30,56,64,81,132,149,196,219,260,269,277,295,305,332,359,385,408,418,450,460,465,485,489,540,554,568,575,597,650,668,710,728],"natural":[27],"strains.":[28],"Most":[29],"included":[33],"at":[34,167,308],"least":[35],"one":[36,264],"collinear":[37,184],"gene":[38,134,535],"length":[39],"corresponding":[40],"the":[42,62,65,78,141,157,174,186,217,254,275,287,313,318,322,330,341,348,397,406,416,427,436,463,483,495,521,537,541,560,566,573,576,595,648,651,682,707,729,760,764],"Center-of-Tree":[43],"(COT)":[44],"sequence,":[45],"which":[46,238,767],"has":[47,713],"near-optimal":[48],"peptide":[49,82,86,378],"coverage":[50,80,87,104,164,204,218,276,294,325,331],"for":[51,67,263,343,429,454,559],"a":[52,57,74,194,267,278,345,352,527,532,598,748],"single":[53,353],"gene.":[54,188,543],"Inclusion":[55],"COT":[58],"sequence":[59],"and":[60,169,244,253,368,370,413,424,536,564,607,645,660,671],"optimizing":[61],"rest":[63],"immunogen":[66,349,478,696],"coverage,":[68],"as":[69,190,493,508,716,718],"suggested":[70],"[2],":[72],"yielded":[73],"construct":[75,279,528],"(COT+)":[76],"greatest":[79],"diversity,":[83],"minimally":[84],"sacrificing":[85],"comparison":[89],"unconstrained":[91],"diversity":[92],"optimization.":[93],"Fischer":[94,123,439],"et":[95,120,124,235,289,440,513],"al.":[96,121,125,236,290,441,514],"[3]":[97],"introduced":[98],"mosaics\u2014a":[99],"different":[100,618],"approach":[101,144,259,399,693,751],"increasing":[103],"while":[105],"maintaining":[106,129],"collinearity":[107,131,283,337],"using":[108,286],"an":[109,486,679,753],"optimization":[110,197,227,258,300],"algorithm":[111,316],"based":[112,155],"on":[113,156,248,266,347,411,475,482,520],"simulated":[114],"recombination.\r\n\r\nIn":[115],"their":[116,386],"response":[117,437],"Nickle":[119,234],"[4]":[126],"suggest":[127],"that":[128,159,176,304,340,374,442,589,622,655,742],"full":[130,187],"sequences":[135,379,644],"native":[137,652],"proteins":[139,733],"is":[140,301,326,356,685,768],"only":[142,548],"tractable":[143],"producing":[146],"immunogens":[147],"inclusive":[148],"variability.":[151],"This":[152],"claim":[153],"was":[154],"observation":[158],"mosaics":[160,220,387],"had":[161],"slightly":[162],"higher":[163],"than":[165,303,481,752],"COT+":[166,222,296,324,375,398,448,498,765],"3\u00d7":[168],"4\u00d7":[170],"strain":[171,355],"lengths,":[172],"despite":[173,665],"fact":[175],"all":[177],"mosaic":[178,319,496],"components":[179],"are":[180,591,608,639,734],"constrained":[181],"be":[183,200,240,401,421,444,452,500,549,557,628,658,741,747],"However,":[189,382,544,580],"pointed":[192],"out,":[193],"variety":[195],"algorithms":[198],"can":[199,239,400,499,547,627,657],"used":[201],"perform":[203],"optimization,":[205],"computationally":[207],"intensive":[208,672],"typically":[210],"yielding":[211],"better":[212],"results.":[213],"Figure":[214],"1":[215],"compares":[216],"constructs":[223,333],"produced":[224,390],"by":[225,298,380,438,526,530,641,763],"two":[226],"algorithms\u2014the":[228],"simple":[229,314],"greedy":[230,315],"extension":[231],"described":[232],"implemented":[241],"hours":[243],"run":[245,262],"seconds":[247],"any":[249,282],"modern":[250],"personal":[251],"computer,":[252],"more":[255,749],"complex":[256],"combinatiorial":[257],"[5]":[261,291],"day":[265],"cluster":[268],"300":[270],"PCs.":[271],"We":[272,586],"also":[273,372,515],"include":[274,351],"optimized":[280,323,334,453,501],"without":[281],"constraints,":[284,338],"derived":[285],"Kirovski":[288],"algorithm.":[292],"The":[293],"created":[297],"combinatorial":[299],"greater":[302],"mosaics,":[306],"especially":[307],"larger":[309],"lengths":[310],"where":[311],"even":[312],"surpasses":[317],"coverage.":[320],"Furthermore,":[321,396],"almost":[327],"identical":[328],"no":[336],"indicating":[339],"price":[342],"imposing":[344],"constraint":[346],"virus-like":[354],"small.\r\n\r\n\r\n\r\nFigure":[357],"1\r\n\r\nComparison":[358],"Peptide":[360],"Coverage":[361],"Scores":[362],"Achievable":[363],"Different":[365],"Immunogen":[366],"Formats":[367],"Algorithms\r\n\r\n\r\n\r\nFischer":[369],"colleagues":[371],"argued":[373],"creates":[376],"unnatural":[377,393,409],"concatenation.":[381],"similar":[383],"concatenation":[384],"would":[388,556],"have":[389,605,620],"about":[391],"18":[392],"9-mer":[394],"peptides.":[395],"tuned":[402],"both":[404],"penalize":[405],"introduction":[407],"peptides":[410],"concatenation,":[412],"define":[415],"number":[417],"segments":[419],"separately":[422],"expressed,":[423],"thus":[425],"reduce":[426],"requirement":[428],"concatenation.\r\n\r\nSeveral":[430],"additional":[431],"inferences":[432],"were":[433,583],"made":[434],"should":[443],"commented":[445],"upon.":[446],"First,":[447],"may,":[449],"course,":[451],"arbitrary":[455],"clades":[457],"or":[458,726],"combinations":[459],"clades,":[461],"but":[462],"publication":[464],"PLoS":[469],"Computational":[470],"Biology":[471],"reflects":[472],"focus":[474],"design":[479,697],"rather":[480],"production":[484],"exhaustive":[487],"series":[488],"constructs.":[490],"Also,":[491],"just":[492],"approach,":[497,766],"exclude":[503],"rare":[504],"variants":[505],"(referred":[506],"smoothing":[509],"paper).\r\n\r\nFischer":[512],"discussed":[516],"disappointing":[517],"unpublished":[518],"findings":[519],"immunogenicity":[522],"induced":[523],"against":[524,631],"Nef":[525,542,562],"obtained":[529],"fusing":[531],"full-length":[533,561,731,772,781],"Gag":[534],"central":[538],"portion":[539],"these":[545,581],"results":[546],"fairly":[550],"assessed":[551],"light":[553],"what":[555],"expected":[558],"protein,":[563,653],"case":[567],"cellular":[569],"immune":[570],"responses,":[571],"context":[574,649],"same":[577,708],"MHC":[578],"specificities.":[579],"controls":[582],"not":[584,646,721,769],"provided.":[585],"certainly":[587],"agree":[588],"there":[590],"substantial":[592],"challenges":[593],"establishment":[596],"multivalent":[599],"CD8":[600],"response,":[601],"yet":[602,673],"multiple":[603],"strategies":[604],"been":[606],"being":[609],"devised":[610],"overcome":[612],"this":[613],"important":[614],"problem.":[615],"For":[616],"example,":[617],"groups":[619],"shown":[621],"CD8+":[623,632],"T":[624,633],"cell":[625,634],"responses":[626],"successfully":[629],"elicited":[630],"epitope":[635,755],"strings":[636],"when":[637],"they":[638,656],"separated":[640],"short":[642],"linker":[643],"implying":[654],"processed":[659],"vivo":[663],"[6\u201311].\r\n\r\nFinally,":[664],"25":[666],"years":[667],"AIDS":[669,680],"research":[670],"uniformly":[674],"failed":[675],"efforts":[676],"develop":[678],"vaccine,":[681],"scientific":[683],"community":[684],"poorly":[686],"positioned":[687],"determine":[689],"which,":[690],"if":[691],"any,":[692],"will":[698],"prove":[699,776],"successful.":[700],"Thus,":[701],"arguing":[702],"over":[703],"methodologies":[704],"developed":[705],"goal":[709],"incorporating":[711],"little":[714],"significance":[715],"long":[717],"do":[720],"know":[722],"whether":[723],"maximizing":[724],"inclusion":[727],"entire":[730],"valid":[735],"strategies.":[736],"It":[737],"may":[738,774],"very":[739],"well":[740,775],"removing":[743],"certain":[744],"epitopes":[745],"could":[746],"overall":[754],"maximization":[756],"strategy":[757],"[12].":[758],"Indeed,":[759],"flexibility":[761],"afforded":[762],"limited":[770],"proteins,":[773],"superior":[777],"immunization":[779],"protein":[783],"immunogens.":[784]},"counts_by_year":[{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
