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U S A"},{"key":"10.1016\/j.celrep.2022.110341_bib77","doi-asserted-by":"crossref","first-page":"D362","DOI":"10.1093\/nar\/gkw937","article-title":"The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible","volume":"45","author":"Szklarczyk","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2022.110341_bib78","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1101\/gr.772403","article-title":"PANTHER: a library of protein families and subfamilies indexed by function","volume":"13","author":"Thomas","year":"2003","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2022.110341_bib79","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1016\/j.it.2020.04.001","article-title":"Improving vaccine-induced immunity: can baseline predict outcome?","volume":"41","author":"Tsang","year":"2020","journal-title":"Trends Immunol."},{"key":"10.1016\/j.celrep.2022.110341_bib80","doi-asserted-by":"crossref","first-page":"eaax9198","DOI":"10.1126\/science.aax9198","article-title":"A genome-wide transcriptomic analysis of protein-coding genes in human blood cells","volume":"366","author":"Uhlen","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.celrep.2022.110341_bib81","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1016\/j.molcel.2011.08.018","article-title":"Molecular mechanisms of long noncoding RNAs","volume":"43","author":"Wang","year":"2011","journal-title":"Mol. 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