{"id":"https://openalex.org/W2024844089","doi":"https://doi.org/10.1093/bib/bbs066","title":"A guide to in silico vaccine discovery for eukaryotic pathogens","display_name":"A guide to in silico vaccine discovery for eukaryotic pathogens","publication_year":2012,"publication_date":"2012-10-24","ids":{"openalex":"https://openalex.org/W2024844089","doi":"https://doi.org/10.1093/bib/bbs066","mag":"2024844089","pmid":"https://pubmed.ncbi.nlm.nih.gov/23097412"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbs066","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbs066","pdf_url":"https://academic.oup.com/bib/article-pdf/14/6/753/471345/bbs066.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/14/6/753/471345/bbs066.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045984899","display_name":"Stephen J. Goodswen","orcid":"https://orcid.org/0000-0001-6184-3157"},"institutions":[{"id":"https://openalex.org/I114017466","display_name":"University of Technology Sydney","ror":"https://ror.org/03f0f6041","country_code":"AU","type":"education","lineage":["https://openalex.org/I114017466"]},{"id":"https://openalex.org/I4210146488","display_name":"Institute of Molecular Medicine","ror":"https://ror.org/04eb14s37","country_code":"IN","type":"facility","lineage":["https://openalex.org/I4210146488"]}],"countries":["AU","IN"],"is_corresponding":false,"raw_author_name":"S. J. Goodswen","raw_affiliation_strings":["School of Medical and Molecular Sciences, Ithree Institute, University of Technology Sydney. Tel.: +61 2 9514 4161; John.Ellis@uts.edu.au ","School of Medical and Molecular Sciences, Ithree Institute, University of Technology Sydney. Tel.: +61 2 9514 4161;  "],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medical and Molecular Sciences, Ithree Institute, University of Technology Sydney. Tel.: +61 2 9514 4161; John.Ellis@uts.edu.au ","institution_ids":["https://openalex.org/I4210146488"]},{"raw_affiliation_string":"School of Medical and Molecular Sciences, Ithree Institute, University of Technology Sydney. Tel.: +61 2 9514 4161;  ","institution_ids":["https://openalex.org/I114017466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052377220","display_name":"Paul Kennedy","orcid":"https://orcid.org/0000-0001-7837-3171"},"institutions":[{"id":"https://openalex.org/I4210105785","display_name":"Intelligent Systems Research (United States)","ror":"https://ror.org/01reevc91","country_code":"US","type":"company","lineage":["https://openalex.org/I4210105785"]},{"id":"https://openalex.org/I4210160728","display_name":"St. Johns Hospital","ror":"https://ror.org/05d50hn21","country_code":"IE","type":"healthcare","lineage":["https://openalex.org/I4210160728"]}],"countries":["IE","US"],"is_corresponding":false,"raw_author_name":"P. J. Kennedy","raw_affiliation_strings":["Paul Kennedy obtained his PhD in Computing Science at the University of Technology, Sydney, in 1999 where he currently directs the Knowledge Infrastructure Laboratory in the Centre for Quantum Computation and Intelligent Systems. His interests involve data mining of biomedical data, particularly visualization and classification of childhood cancer patients using their systems biology","John.Ellis@uts.edu.au "],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul Kennedy obtained his PhD in Computing Science at the University of Technology, Sydney, in 1999 where he currently directs the Knowledge Infrastructure Laboratory in the Centre for Quantum Computation and Intelligent Systems. His interests involve data mining of biomedical data, particularly visualization and classification of childhood cancer patients using their systems biology","institution_ids":["https://openalex.org/I4210105785"]},{"raw_affiliation_string":"John.Ellis@uts.edu.au ","institution_ids":["https://openalex.org/I4210160728"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007566988","display_name":"John Ellis","orcid":"https://orcid.org/0000-0001-7328-4831"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. T. Ellis","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.2092,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.77596795,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"14","issue":"6","first_page":"753","last_page":"774"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","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/T12576","display_name":"vaccines and immunoinformatics approaches","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/T11688","display_name":"Microbial infections and disease research","score":0.9968000054359436,"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"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9959999918937683,"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/reverse-vaccinology","display_name":"Reverse vaccinology","score":0.979037880897522},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7946171164512634},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.633267879486084},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.594531238079071},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5512491464614868},{"id":"https://openalex.org/keywords/human-pathogen","display_name":"Human pathogen","score":0.41496044397354126},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.32116615772247314},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18594026565551758},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16327977180480957}],"concepts":[{"id":"https://openalex.org/C2781152039","wikidata":"https://www.wikidata.org/wiki/Q7318278","display_name":"Reverse vaccinology","level":4,"score":0.979037880897522},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7946171164512634},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.633267879486084},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.594531238079071},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5512491464614868},{"id":"https://openalex.org/C24527192","wikidata":"https://www.wikidata.org/wiki/Q17149729","display_name":"Human pathogen","level":3,"score":0.41496044397354126},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32116615772247314},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18594026565551758},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16327977180480957},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbs066","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbs066","pdf_url":"https://academic.oup.com/bib/article-pdf/14/6/753/471345/bbs066.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23097412","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23097412","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:digital.library.adelaide.edu.au:2440/96539","is_oa":false,"landing_page_url":"http://hdl.handle.net/2440/96539","pdf_url":null,"source":{"id":"https://openalex.org/S4306401835","display_name":"Adelaide Research & Scholarship (AR&S) (University of Adelaide)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5681781","host_organization_name":"The University of Adelaide","host_organization_lineage":["https://openalex.org/I5681781"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://dx.doi.org/10.1093/bib/bbs066","raw_type":"Journal article"},{"id":"pmh:oai:opus.lib.uts.edu.au:10453/28021","is_oa":false,"landing_page_url":"http://hdl.handle.net/10453/28021","pdf_url":null,"source":{"id":"https://openalex.org/S4306401357","display_name":"UTS ePRESS (University of Technology Sydney)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114017466","host_organization_name":"University of Technology Sydney","host_organization_lineage":["https://openalex.org/I114017466"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbs066","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbs066","pdf_url":"https://academic.oup.com/bib/article-pdf/14/6/753/471345/bbs066.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":133,"referenced_works":["https://openalex.org/W1484347389","https://openalex.org/W1495465671","https://openalex.org/W1509052503","https://openalex.org/W1511730061","https://openalex.org/W1526839960","https://openalex.org/W1536580680","https://openalex.org/W1542067597","https://openalex.org/W1573784907","https://openalex.org/W1576514183","https://openalex.org/W1606770439","https://openalex.org/W1864675704","https://openalex.org/W1968361401","https://openalex.org/W1969250533","https://openalex.org/W1976804192","https://openalex.org/W1981106544","https://openalex.org/W1984624697","https://openalex.org/W1985471440","https://openalex.org/W1986733193","https://openalex.org/W1989401029","https://openalex.org/W1989654677","https://openalex.org/W1990334093","https://openalex.org/W1991036680","https://openalex.org/W1991461541","https://openalex.org/W1993568862","https://openalex.org/W1993772622","https://openalex.org/W2001707651","https://openalex.org/W2003501191","https://openalex.org/W2003647795","https://openalex.org/W2004216886","https://openalex.org/W2014495976","https://openalex.org/W2017321063","https://openalex.org/W2019369558","https://openalex.org/W2019711015","https://openalex.org/W2020577720","https://openalex.org/W2021901733","https://openalex.org/W2023975285","https://openalex.org/W2024899437","https://openalex.org/W2025617121","https://openalex.org/W2025692710","https://openalex.org/W2028339001","https://openalex.org/W2034164729","https://openalex.org/W2034911186","https://openalex.org/W2035014358","https://openalex.org/W2041073668","https://openalex.org/W2042415836","https://openalex.org/W2042990958","https://openalex.org/W2046391188","https://openalex.org/W2054017637","https://openalex.org/W2056538898","https://openalex.org/W2056681132","https://openalex.org/W2062345582","https://openalex.org/W2066609648","https://openalex.org/W2068353613","https://openalex.org/W2070510621","https://openalex.org/W2071755065","https://openalex.org/W2072091429","https://openalex.org/W2073958510","https://openalex.org/W2074503585","https://openalex.org/W2079843249","https://openalex.org/W2087077137","https://openalex.org/W2087202599","https://openalex.org/W2089047063","https://openalex.org/W2090228310","https://openalex.org/W2094619873","https://openalex.org/W2096730786","https://openalex.org/W2097090163","https://openalex.org/W2098859487","https://openalex.org/W2099500226","https://openalex.org/W2099770099","https://openalex.org/W2100350770","https://openalex.org/W2103074382","https://openalex.org/W2104244040","https://openalex.org/W2106082576","https://openalex.org/W2106150646","https://openalex.org/W2106678197","https://openalex.org/W2110574412","https://openalex.org/W2111119053","https://openalex.org/W2113000643","https://openalex.org/W2114443453","https://openalex.org/W2118300412","https://openalex.org/W2118970397","https://openalex.org/W2119452210","https://openalex.org/W2120399005","https://openalex.org/W2120663978","https://openalex.org/W2121840477","https://openalex.org/W2122992512","https://openalex.org/W2125732073","https://openalex.org/W2128433194","https://openalex.org/W2129612249","https://openalex.org/W2130354820","https://openalex.org/W2131074700","https://openalex.org/W2131185306","https://openalex.org/W2131581981","https://openalex.org/W2134213012","https://openalex.org/W2134968830","https://openalex.org/W2136145671","https://openalex.org/W2141816565","https://openalex.org/W2141847640","https://openalex.org/W2142352021","https://openalex.org/W2142831360","https://openalex.org/W2143931068","https://openalex.org/W2144244209","https://openalex.org/W2144528434","https://openalex.org/W2148420646","https://openalex.org/W2149238618","https://openalex.org/W2149350146","https://openalex.org/W2149984099","https://openalex.org/W2152118986","https://openalex.org/W2152458080","https://openalex.org/W2152770371","https://openalex.org/W2154058033","https://openalex.org/W2154267586","https://openalex.org/W2156790306","https://openalex.org/W2156976607","https://openalex.org/W2158173168","https://openalex.org/W2158781610","https://openalex.org/W2159833474","https://openalex.org/W2160053034","https://openalex.org/W2161396601","https://openalex.org/W2161448051","https://openalex.org/W2161746138","https://openalex.org/W2164154943","https://openalex.org/W2166187656","https://openalex.org/W2168688111","https://openalex.org/W2169661568","https://openalex.org/W2170496993","https://openalex.org/W2171091522","https://openalex.org/W2172218870","https://openalex.org/W2181987174","https://openalex.org/W2902218972","https://openalex.org/W4230246035","https://openalex.org/W4235859326","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2003194288","https://openalex.org/W2513589746","https://openalex.org/W2213189664","https://openalex.org/W2153919606","https://openalex.org/W2113024639","https://openalex.org/W2062254828","https://openalex.org/W4237480606","https://openalex.org/W2936968863","https://openalex.org/W4378672831","https://openalex.org/W1971792277"],"abstract_inverted_index":{"In":[0],"this":[1],"article,":[2],"a":[3,13,54,125,132,154],"framework":[4],"for":[5,20],"an":[6],"in":[7,45],"silico":[8],"pipeline":[9,63],"is":[10,64,73,114,164],"presented":[11],"as":[12,24],"guide":[14],"to":[15,42,88,115,157],"high-throughput":[16],"vaccine":[17],"candidate":[18],"discovery":[19,90],"eukaryotic":[21,101,112],"pathogens,":[22,113],"such":[23],"helminths":[25],"and":[26,33,40,47,59,72,122,151],"protozoa.":[27],"Eukaryotic":[28],"pathogens":[29,52,96],"are":[30,81,137,146,152],"mostly":[31],"parasitic":[32,51],"cause":[34],"some":[35],"of":[36,69,85,91,106,120,128,141,153],"the":[37,67,89,107,142,149,168,172],"most":[38],"damaging":[39],"difficult":[41],"treat":[43],"diseases":[44],"humans":[46],"livestock.":[48],"Consequently,":[49],"these":[50],"have":[53],"significant":[55],"impact":[56],"on":[57,66,111,131],"economy":[58],"human":[60],"health.":[61],"The":[62,103],"based":[65,130],"principle":[68],"reverse":[70,86],"vaccinology":[71,87],"constructed":[74],"from":[75,171],"freely":[76],"available":[77],"bioinformatics":[78],"programs.":[79],"There":[80],"several":[82],"successful":[83],"applications":[84],"subunit":[92],"vaccines":[93],"against":[94,100],"prokaryotic":[95],"but":[97],"not":[98],"yet":[99,165],"pathogens.":[102],"overriding":[104],"aim":[105],"pipeline,":[108],"which":[109],"focuses":[110],"generate":[116],"through":[117],"computational":[118],"processes":[119],"elimination":[121],"evidence":[123],"gathering":[124],"ranked":[126],"list":[127,173],"proteins":[129,136,170],"scoring":[133],"system.":[134],"These":[135],"either":[138],"surface":[139],"components":[140],"target":[143],"pathogen":[144,150],"or":[145],"secreted":[147],"by":[148],"type":[155],"known":[156],"be":[158],"antigenic.":[159],"No":[160],"perfect":[161],"predictive":[162],"method":[163],"available;":[166],"therefore,":[167],"highest-scoring":[169],"require":[174],"laboratory":[175],"validation.":[176]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
