{"id":"https://openalex.org/W3100939371","doi":"https://doi.org/10.1109/niles50944.2020.9257881","title":"Insilico Codon Bias Correction for Transgenic Biological Protein Sequences for Vaccine Production","display_name":"Insilico Codon Bias Correction for Transgenic Biological Protein Sequences for Vaccine Production","publication_year":2020,"publication_date":"2020-10-24","ids":{"openalex":"https://openalex.org/W3100939371","doi":"https://doi.org/10.1109/niles50944.2020.9257881","mag":"3100939371"},"language":"en","primary_location":{"id":"doi:10.1109/niles50944.2020.9257881","is_oa":false,"landing_page_url":"https://doi.org/10.1109/niles50944.2020.9257881","pdf_url":null,"source":{"id":"https://openalex.org/S4306498600","display_name":"2020 2nd Novel Intelligent and Leading Emerging Sciences Conference (NILES)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 2nd Novel Intelligent and Leading Emerging Sciences Conference (NILES)","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/A5033589829","display_name":"Mohamed Abuelanin","orcid":"https://orcid.org/0000-0002-3419-4785"},"institutions":[{"id":"https://openalex.org/I57629906","display_name":"Nile University","ror":"https://ror.org/03cg7cp61","country_code":"EG","type":"education","lineage":["https://openalex.org/I57629906"]}],"countries":["EG"],"is_corresponding":true,"raw_author_name":"Mohamed Abuelanin","raw_affiliation_strings":["Center for Informatics Science (CIS), Nile University, Giza, Egypt"],"affiliations":[{"raw_affiliation_string":"Center for Informatics Science (CIS), Nile University, Giza, Egypt","institution_ids":["https://openalex.org/I57629906"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068690978","display_name":"Mohamed Fares","orcid":"https://orcid.org/0000-0003-3600-3716"},"institutions":[{"id":"https://openalex.org/I57629906","display_name":"Nile University","ror":"https://ror.org/03cg7cp61","country_code":"EG","type":"education","lineage":["https://openalex.org/I57629906"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Mohamed Fares","raw_affiliation_strings":["Center for Informatics Science (CIS), Nile University, Giza, Egypt"],"affiliations":[{"raw_affiliation_string":"Center for Informatics Science (CIS), Nile University, Giza, Egypt","institution_ids":["https://openalex.org/I57629906"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069484090","display_name":"Mohamed El-Hadidi","orcid":"https://orcid.org/0000-0002-3593-8061"},"institutions":[{"id":"https://openalex.org/I57629906","display_name":"Nile University","ror":"https://ror.org/03cg7cp61","country_code":"EG","type":"education","lineage":["https://openalex.org/I57629906"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Mohamed El-Hadidi","raw_affiliation_strings":["Center for Informatics Science (CIS), Nile University, Giza, Egypt"],"affiliations":[{"raw_affiliation_string":"Center for Informatics Science (CIS), Nile University, Giza, Egypt","institution_ids":["https://openalex.org/I57629906"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5033589829"],"corresponding_institution_ids":["https://openalex.org/I57629906"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.23396226,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"158","issue":null,"first_page":"465","last_page":"468"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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/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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.9269630908966064},{"id":"https://openalex.org/keywords/genetic-code","display_name":"Genetic code","score":0.6878331899642944},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.605536162853241},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5062936544418335},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49614033102989197},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.4821705222129822},{"id":"https://openalex.org/keywords/gc-content","display_name":"GC-content","score":0.4777854382991791},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.46407440304756165},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.4604623317718506},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2155017852783203}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.9269630908966064},{"id":"https://openalex.org/C10853874","wikidata":"https://www.wikidata.org/wiki/Q180618","display_name":"Genetic code","level":3,"score":0.6878331899642944},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.605536162853241},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5062936544418335},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49614033102989197},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.4821705222129822},{"id":"https://openalex.org/C42251679","wikidata":"https://www.wikidata.org/wiki/Q933491","display_name":"GC-content","level":4,"score":0.4777854382991791},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.46407440304756165},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.4604623317718506},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2155017852783203}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/niles50944.2020.9257881","is_oa":false,"landing_page_url":"https://doi.org/10.1109/niles50944.2020.9257881","pdf_url":null,"source":{"id":"https://openalex.org/S4306498600","display_name":"2020 2nd Novel Intelligent and Leading Emerging Sciences Conference (NILES)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 2nd Novel Intelligent and Leading Emerging Sciences Conference (NILES)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.550000011920929,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1539868719","https://openalex.org/W1692054786","https://openalex.org/W1966778471","https://openalex.org/W1987984230","https://openalex.org/W2050888933","https://openalex.org/W2064050626","https://openalex.org/W2070163065","https://openalex.org/W2078755055","https://openalex.org/W2094148055","https://openalex.org/W2099435024","https://openalex.org/W2155765704"],"related_works":["https://openalex.org/W2346776410","https://openalex.org/W1988590400","https://openalex.org/W2175799720","https://openalex.org/W2383580825","https://openalex.org/W2220941019","https://openalex.org/W2373572162","https://openalex.org/W2391050383","https://openalex.org/W2371354124","https://openalex.org/W4220674955","https://openalex.org/W2113191934"],"abstract_inverted_index":{"Codon":[0],"optimization":[1],"is":[2,182],"primarily":[3],"used":[4],"in":[5,12,30,61,101,197],"enhancing":[6],"the":[7,13,26,34,41,44,53,65,77,85,122,134,140,144,153,162,167,189],"levels":[8,60],"of":[9,43,71,79],"protein":[10,58,137,163],"expression":[11,59,78,164,196],"host":[14,35,54,80,145,199],"species.":[15,32],"Each":[16],"species":[17],"has":[18],"its":[19],"own":[20],"codon":[21,72,81,99,124],"usage":[22,36,100,125,191],"bias,":[23],"which":[24,181],"represents":[25],"codons":[27,115,120],"abundance":[28],"frequency":[29,73,119],"that":[31,47],"Using":[33],"profile":[37],"contributes":[38],"to":[39,75,111,160,184],"personalize":[40],"synthesis":[42],"DNA":[45,168],"vaccines":[46],"can":[48],"achieve":[49],"highly":[50],"active":[51],"vectors":[52],"cells.":[55,200],"For":[56],"optimizing":[57,98,152],"a":[62,108],"particular":[63],"host,":[64],"genetic":[66],"code":[67],"sequence":[68,142,186],"needs":[69],"correction":[70],"bias":[74,126],"match":[76],"landscape":[82],"rather":[83],"than":[84,188],"donating":[86],"organism":[87],"profile.":[88],"In":[89],"this":[90],"work,":[91],"we":[92],"have":[93],"applied":[94],"two":[95],"approaches":[96],"for":[97,194],"protein-coding":[102],"sequences.":[103],"The":[104,128],"first":[105],"approach":[106,130],"adopts":[107],"substitution-based":[109],"method":[110,171],"replace":[112],"less":[113],"frequent":[114],"with":[116,175],"differentially":[117],"higher":[118,176],"at":[121],"specific":[123],"tables.":[127],"second":[129],"finds":[131],"and":[132,143],"replaces":[133],"maximal":[135],"exact":[136],"matches":[138],"between":[139],"unoptimized":[141],"proteome.":[146],"We":[147],"evaluated":[148],"our":[149],"work":[150],"by":[151,179],"Avian":[154],"Influenza":[155],"H1N1":[156],"virus's":[157],"HA":[158],"gene":[159],"maximize":[161],"before":[165],"synthesizing":[166],"vaccine.":[169],"Our":[170],"produced":[172],"optimized":[173],"sequences":[174],"GC":[177],"content":[178],"17%,":[180],"similar":[183],"eukaryotic":[185],"profiles":[187],"viral":[190],"profiles,":[192],"allowing":[193],"better":[195],"avian":[198]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
