{"id":"https://openalex.org/W7112401914","doi":null,"title":"Recoding of Vesicular Stomatitis Virus genes by computer-aided design provides a live attenuated vaccine candidate","display_name":"Recoding of Vesicular Stomatitis Virus genes by computer-aided design provides a live attenuated vaccine candidate","publication_year":2015,"publication_date":"2015-12-01","ids":{"openalex":"https://openalex.org/W7112401914"},"language":"en","primary_location":{"id":"pmh:oai:commons.library.stonybrook.edu:stony-brook-theses-and-dissertations-collection-3446","doi":null,"is_oa":false,"landing_page_url":"https://commons.library.stonybrook.edu/stony-brook-theses-and-dissertations-collection/2447","pdf_url":null,"source":{"id":"https://openalex.org/S4377196674","display_name":"Academic Commons (Stony Brook University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I59553526","host_organization_name":"Stony Brook University","host_organization_lineage":["https://openalex.org/I59553526"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)","raw_type":"text"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Wang, Bingyin","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Wang, Bingyin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9032999873161316,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9032999873161316,"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/T11135","display_name":"Virology and Viral Diseases","score":0.05119999870657921,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.006200000178068876,"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/vesicular-stomatitis-virus","display_name":"vesicular stomatitis virus","score":0.9879999756813049},{"id":"https://openalex.org/keywords/codon-pair-bias","display_name":"codon pair bias","score":0.8629999756813049},{"id":"https://openalex.org/keywords/live-attenuated-vaccine","display_name":"live attenuated vaccine","score":0.9399999976158142},{"id":"https://openalex.org/keywords/l-gene","display_name":"L gene","score":0.6669999957084656},{"id":"https://openalex.org/keywords/g-gene","display_name":"G gene","score":0.9779999852180481},{"id":"https://openalex.org/keywords/synonymous-mutations","display_name":"synonymous mutations","score":0.9399999976158142},{"id":"https://openalex.org/keywords/virus-attenuation","display_name":"viral attenuation","score":0.46799999475479126},{"id":"https://openalex.org/keywords/neurovirulence","display_name":"neurovirulence","score":0.7549999952316284},{"id":"https://openalex.org/keywords/reverse-genetics","display_name":"reverse genetics","score":0.5580000281333923},{"id":"https://openalex.org/keywords/immunogenicity","display_name":"immunogenicity","score":0.6510000228881836},{"id":"https://openalex.org/keywords/negative-strand-rna-viruses","display_name":"negative-strand RNA viruses","score":0.7200000286102295},{"id":"https://openalex.org/keywords/protein-folding-kinetics","display_name":"protein folding kinetics","score":0.5289999842643738},{"id":"https://openalex.org/keywords/translation-elongation-rate","display_name":"translation elongation rate","score":0.8820000290870667},{"id":"https://openalex.org/keywords/mouse-model","display_name":"mouse model","score":0.43700000643730164},{"id":"https://openalex.org/keywords/recombinant-viruses","display_name":"recombinant virus","score":0.4659999907016754},{"id":"https://openalex.org/keywords/histopathology","display_name":"histopathology","score":0.5920000076293945},{"id":"https://openalex.org/keywords/morbidity-and-mortality","display_name":"morbidity and mortality","score":0.46299999952316284},{"id":"https://openalex.org/keywords/vaccine-immunogenicity","display_name":"vaccine immunogenicity","score":0.3330000042915344}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.7720999717712402},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7689999938011169},{"id":"https://openalex.org/C2779057330","wikidata":"https://www.wikidata.org/wiki/Q162762","display_name":"Vesicular stomatitis virus","level":3,"score":0.7310000061988831},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.7214999794960022},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6582000255584717},{"id":"https://openalex.org/C54602769","wikidata":"https://www.wikidata.org/wiki/Q1810913","display_name":"Attenuated vaccine","level":4,"score":0.5504999756813049},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5198000073432922},{"id":"https://openalex.org/C20580545","wikidata":"https://www.wikidata.org/wiki/Q28354","display_name":"Stop codon","level":3,"score":0.5169000029563904},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.5098000168800354},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.5020999908447266},{"id":"https://openalex.org/C138025448","wikidata":"https://www.wikidata.org/wiki/Q7662597","display_name":"Synonymous substitution","level":5,"score":0.44999998807907104},{"id":"https://openalex.org/C2779174946","wikidata":"https://www.wikidata.org/wiki/Q751911","display_name":"RNA virus","level":4,"score":0.41449999809265137},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4090000092983246},{"id":"https://openalex.org/C195491092","wikidata":"https://www.wikidata.org/wiki/Q2717121","display_name":"Silent mutation","level":5,"score":0.40560001134872437},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3930000066757202},{"id":"https://openalex.org/C176990463","wikidata":"https://www.wikidata.org/wiki/Q1854186","display_name":"Start codon","level":4,"score":0.38679999113082886},{"id":"https://openalex.org/C8769409","wikidata":"https://www.wikidata.org/wiki/Q2066554","display_name":"Viral evolution","level":4,"score":0.3172999918460846},{"id":"https://openalex.org/C2909090456","wikidata":"https://www.wikidata.org/wiki/Q162762","display_name":"Vesicular stomatitis Indiana virus","level":4,"score":0.31220000982284546},{"id":"https://openalex.org/C25365240","wikidata":"https://www.wikidata.org/wiki/Q1897151","display_name":"Reverse genetics","level":4,"score":0.2775000035762787},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.27469998598098755},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.26570001244544983},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.2635999917984009},{"id":"https://openalex.org/C98638677","wikidata":"https://www.wikidata.org/wiki/Q2067051","display_name":"Mutation rate","level":3,"score":0.2614000141620636},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.2556000053882599}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:commons.library.stonybrook.edu:stony-brook-theses-and-dissertations-collection-3446","doi":null,"is_oa":false,"landing_page_url":"https://commons.library.stonybrook.edu/stony-brook-theses-and-dissertations-collection/2447","pdf_url":null,"source":{"id":"https://openalex.org/S4377196674","display_name":"Academic Commons (Stony Brook University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I59553526","host_organization_name":"Stony Brook University","host_organization_lineage":["https://openalex.org/I59553526"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.4043000042438507}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2122618891","https://openalex.org/W2001674944","https://openalex.org/W2896563752","https://openalex.org/W3133493899","https://openalex.org/W6906695012","https://openalex.org/W4200119808","https://openalex.org/W2786771608","https://openalex.org/W3138823886","https://openalex.org/W2885255976","https://openalex.org/W2790985646"],"abstract_inverted_index":{"Codon":[0,436],"pair":[1,45,83,92,130,437,481,519,528,566],"bias":[2,84,93,438,520,529],"(CPB),":[3,439],"which":[4,245,333,418,440,681,769,854],"has":[5,298,441,734],"been":[6,300,442,736],"observed":[7,443],"in":[8,33,94,234,261,287,302,355,369,375,444,469,530,670,697,723,738,791,805,811],"all":[9,445],"organisms,":[10,446],"is":[11,47,391,447,483,827],"a":[12,144,156,165,212,229,249,283,376,392,406,411,422,448,580,592,601,648,665,685,719,812,828,842,847,858],"neglected":[13,449],"genomic":[14,450],"phenomenon":[15,451],"that":[16,26,384,452,462,820],"substantially":[17,453],"affects":[18,454],"gene":[19,152,172,310,320,351,455,588,608,746,756,787],"expression.":[20,456],"CPB":[21,457],"results":[22,404,458,840],"from":[23,248,459,684],"synonymous":[24,61,460,497],"codons":[25,461],"are":[27,75,463,511],"paired":[28,464],"more":[29,465],"or":[30,67,389,466,503,825],"less":[31,349,467,785],"frequently":[32,468],"ORFeomes":[34,470],"regardless":[35,471],"of":[36,41,60,90,97,106,128,139,158,168,220,232,239,336,345,427,472,477,496,526,533,542,564,575,594,604,656,668,675,772,781,863],"codon":[37,44,65,82,91,129,188,338,473,480,501,518,527,565,624,774],"bias.":[38,474],"The":[39,237,324,475,673,760],"effect":[40,476],"an":[42,121,478,557],"individual":[43,479],"change":[46,294,482,730],"usually":[48,484],"small,":[49,485],"but":[50,274,386,486,710,822],"when":[51,487],"amplified":[52,488],"by":[53,104,489,540],"large-scale":[54,490],"genome":[55,227,491,663],"recoding":[56,492],"(simultaneously":[57,493],"generating":[58,494],"hundreds":[59,335,495,771],"mutations":[62,163,316,498,599,752],"without":[63,499],"altering":[64,500],"usage":[66,502],"amino":[68,504],"acid":[69,505],"sequence),":[70,506],"strikingly":[71,507],"altered":[72,508],"biological":[73,509],"phenotypes":[74,510],"observed.":[76,512],"Although":[77,340,513,776],"the":[78,88,95,125,134,169,204,218,221,225,240,263,271,279,288,308,318,342,358,425,514,524,531,561,570,605,640,654,657,661,676,699,707,715,724,744,754,778,794,861],"molecular":[79,515],"mechanism":[80,516],"underlying":[81,517],"still":[85,521],"remains":[86,522],"enigmatic,":[87,523],"utility":[89,525],"development":[96,532],"live":[98,394,534,830],"attenuated":[99,395,535,831],"vaccines":[100,536],"was":[101,243,266,329,537,679,702,765],"recently":[102,538],"demonstrated":[103,539],"recodings":[105,541],"poliovirus":[107,543],"(a":[108,115,544,551],"positive-strand":[109,545],"RNA":[110,118,148,431,546,554,584,867],"virus)":[111,547],"and":[112,136,160,184,198,255,372,416,548,572,596,620,634,691,808,852],"influenza":[113,549],"virus":[114,142,242,265,281,328,346,360,550,578,678,701,717,764,782,796],"negative-strand":[116,552],"segmented":[117,553],"virus).":[119,555],"In":[120,401,556,837],"attempt":[122,558],"to":[123,176,409,559,612,845],"expand":[124,560],"attenuation":[126,233,426,562,669,862],"spectrum":[127,563],"bias,":[131,567],"I":[132,154,312,568,590,748],"recoded":[133,569],"L":[135,151,171,571,587,607],"G":[137,309,319,350,573,745,755,786],"genes":[138,574],"vesicular":[140,576],"stomatitis":[141,577],"(VSV),":[143,579],"non-segmented":[145,430,581,866],"negative":[146,582],"strand":[147,583],"virus.":[149,585],"For":[150,586],"recoding,":[153,311,589,747],"introduced":[155,313,591,749],"total":[157,593],"858":[159,595],"623":[161,597],"silent":[162,315,598,751],"into":[164,224,317,600,660,753],"5\u2019-terminal":[166],"segment":[167,603],"viral":[170,226,606,662],"(designated":[173,609],"as":[174,196,268,270,331,363,365,421,610,632,704,706,767,799,801,857],"L1),":[175,611],"create":[177,613],"sequences":[178,193,614,629],"containing":[179,203,615,639],"either":[180,616],"overrepresented":[181,617],"(sdmax":[182,618],"design)":[183,187,619,623],"underrepresented":[185,337,621,773],"(min":[186,622],"pairs,":[189,625],"respectively.":[190,200,626,636],"These":[191,627],"two":[192,628],"were":[194,353,630,789],"designated":[195,330,631,766],"L1sdmax":[197,222,241,264,633,658,677,700],"L1min,":[199,635],"Recombinant":[201,637],"VSV":[202,399,414,638,835,850],"L1min":[205,388,641,824],"sequence":[206,223,642,659],"could":[207,419,643,855],"not":[208,387,644,823],"be":[209,645],"recovered":[210,646],"via":[211,647],"well-established":[213,649],"reverse":[214,650],"genetics":[215,651],"system":[216,652],"whereas":[217,653],"introduction":[219,655],"conferred":[228,664],"modest":[230,666],"level":[231,667],"cell":[235,671],"culture.":[236,672],"phenotype":[238,674],"unexpected,":[244,680],"might":[246,682],"result":[247,683],"discoordination":[250,686],"between":[251,413,687,849],"translation":[252,688],"elongation":[253,689],"rate":[254,690],"protein":[256,692],"folding":[257,693],"kinetics.":[258,694],"More":[259,695],"strikingly,":[260,696],"mice":[262,698],"almost":[267,703],"immunogenic":[269,705],"parental":[272,367,708,803],"strain":[273,368,709,804],"highly":[275,711],"attenuated.":[276,712],"Despite":[277,713],"this,":[278,714],"recombinant":[280,327,716,763],"showed":[282,373,718,809],"temporarily":[284,720],"productive":[285,721],"replication":[286,722],"infected":[289,304,356,725,740,792],"tissues":[290,726],"while":[291,727],"neither":[292,728],"histopathological":[293,729],"nor":[295,731],"severe":[296,732],"morbidity":[297,733],"ever":[299,735],"found":[301,737],"L1sdmax-":[303,739],"animals.":[305,741],"As":[306,742],"for":[307,398,424,743,834,860],"323":[314,750],"open-":[321,757],"reading":[322,758],"frame.":[323,759],"newly":[325,761],"generated":[326,762],"Gmin,":[332,390,768,826],"contained":[334,770],"pairs.":[339,775],"during":[341,777],"early":[343,779],"stages":[344,780],"infection":[347,783],"significantly":[348,784],"products":[352,788],"produced":[354,790],"cells,":[357,793],"Gmin":[359,795],"replicated":[361,797],"just":[362,798],"well":[364,800],"its":[366,802],"tissue":[370,806],"culture":[371,807],"neurovirulence":[374,810],"mouse":[377,813],"model.":[378,814],"Taken":[379,815],"together,":[380,816],"my":[381,817],"research":[382,818],"suggests":[383,819],"L1sdmax,":[385,821],"promising":[393,829],"vaccine":[396,832],"candidate":[397,833],"infection.":[400,836],"addition,":[402,838],"these":[403,839],"demonstrate":[405,841],"novel":[407,843],"approach":[408,844],"attain":[410,846],"balance":[412,848],"virulence":[415,851],"immunogenicity,":[417,853],"serve":[420,856],"paradigm":[423,859],"other":[428,864],"negative-strand,":[429,865],"viruses":[432,868],"(NNS":[433,869],"viruses).":[434,870],"|":[435,871],"5\u00e2\u20ac\u2122-terminal":[602],"135":[872],"pages":[873]},"counts_by_year":[],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-12-10T00:00:00"}