{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T04:34:17Z","timestamp":1777955657358,"version":"3.51.4"},"reference-count":50,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,7,15]],"date-time":"2021-07-15T00:00:00Z","timestamp":1626307200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI123070"],"award-info":[{"award-number":["AI123070"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003074","name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","doi-asserted-by":"publisher","award":["PICT-2013-1193"],"award-info":[{"award-number":["PICT-2013-1193"]}],"id":[{"id":"10.13039\/501100003074","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003074","name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","doi-asserted-by":"publisher","award":["PICT-2017-0175"],"award-info":[{"award-number":["PICT-2017-0175"]}],"id":[{"id":"10.13039\/501100003074","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>\n                    Availability of highly parallelized immunoassays has renewed interest in the discovery of serology biomarkers for infectious diseases. Protein and peptide microarrays now provide a rapid, high-throughput platform for immunological testing and validation of potential antigens and B-cell epitopes. However, there is still a need for tools to prioritize and select relevant probes when designing these arrays. In this work we describe a computational method called APRANK (Antigenic Protein and Peptide Ranker) which integrates multiple molecular features to prioritize potentially antigenic proteins and peptides in a given pathogen proteome. These features include subcellular localization, presence of repetitive motifs, natively disordered regions, secondary structure, transmembrane spans and predicted interaction with the immune system. We trained and tested this method with a number of bacteria and protozoa causing human diseases:\n                    <jats:italic>Borrelia burgdorferi<\/jats:italic>\n                    (Lyme disease),\n                    <jats:italic>Brucella melitensis<\/jats:italic>\n                    (Brucellosis),\n                    <jats:italic>Coxiella burnetii<\/jats:italic>\n                    (Q fever),\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    (Gastroenteritis),\n                    <jats:italic>Francisella tularensis<\/jats:italic>\n                    (Tularemia),\n                    <jats:italic>Leishmania braziliensis<\/jats:italic>\n                    (Leishmaniasis),\n                    <jats:italic>Leptospira interrogans<\/jats:italic>\n                    (Leptospirosis),\n                    <jats:italic>Mycobacterium leprae<\/jats:italic>\n                    (Leprae),\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    (Tuberculosis),\n                    <jats:italic>Plasmodium falciparum<\/jats:italic>\n                    (Malaria),\n                    <jats:italic>Porphyromonas gingivalis<\/jats:italic>\n                    (Periodontal disease),\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    (Bacteremia),\n                    <jats:italic>Streptococcus pyogenes<\/jats:italic>\n                    (Group A Streptococcal infections),\n                    <jats:italic>Toxoplasma gondii<\/jats:italic>\n                    (Toxoplasmosis) and\n                    <jats:italic>Trypanosoma cruzi<\/jats:italic>\n                    (Chagas Disease). We have evaluated this integrative method using non-parametric ROC-curves and made an unbiased validation using\n                    <jats:italic>Onchocerca volvulus<\/jats:italic>\n                    as an independent data set. We found that APRANK is successful in predicting antigenicity for all pathogen species tested, facilitating the production of antigen-enriched protein subsets. We make APRANK available to facilitate the identification of novel diagnostic antigens in infectious diseases.\n                  <\/jats:p>","DOI":"10.3389\/fimmu.2021.702552","type":"journal-article","created":{"date-parts":[[2021,7,15]],"date-time":"2021-07-15T10:30:03Z","timestamp":1626345003000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":11,"title":["APRANK: Computational Prioritization of Antigenic Proteins and Peptides From Complete Pathogen Proteomes"],"prefix":"10.3389","volume":"12","author":[{"given":"Alejandro D.","family":"Ricci","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mauricio","family":"Brunner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Diego","family":"Ramoa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Santiago J.","family":"Carmona","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Morten","family":"Nielsen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fern\u00e1n","family":"Ag\u00fcero","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2021,7,15]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1016\/j.idc.2011.06.002","article-title":"Drugs and Diagnostic Innovations to Improve Global Health","volume":"25","author":"Peeling","year":"2011","journal-title":"Infect Dis Clinics North Am"},{"key":"B2","article-title":"Principles of Diagnosis","volume-title":"Medical Microbiology","author":"Washington","year":"1996"},{"key":"B3","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/B978-012374410-4.00585-9","article-title":"Diagnostic Techniques: Serological and Molecular Approaches","author":"Vainionp\u00e4\u00e4","year":"2008","journal-title":"Encycl Virol"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1038\/nbt723","article-title":"Individually Addressable Parallel Peptide Synthesis on Microchips","volume":"20","author":"Pellois","year":"2002","journal-title":"Nat Biotechnol"},{"key":"B5","doi-asserted-by":"crossref","DOI":"10.1002\/0471140864.ps2701s72","article-title":"Overview of Protein Microarrays","volume-title":"Current Protocols in Protein Science Chapter 27","author":"Sutandy","year":"2013"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1016\/j.pt.2020.12.002","article-title":"Serological Approaches for Trypanosoma Cruzi Strain Typing","volume":"37","author":"Balouz","year":"2021","journal-title":"Trends Parasitol"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M112.020800","article-title":"High-Resolution Mapping of Linear Antibody Epitopes Using Ultrahigh-Density Peptide Microarrays","volume":"11","author":"Buus","year":"2012","journal-title":"Mol Cell Proteomics"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M114.045906","article-title":"Towards High-Throughput Immunomics for Infectious Diseases: Use of Next-Generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants","volume":"14","author":"Carmona","year":"2015","journal-title":"Mol Cell Proteomics"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0005986","article-title":"High-Resolution Profiling of Linear B-Cell Epitopes From Mucin-Associated Surface Proteins (MASPs) of Trypanosoma Cruzi During Human Infections","volume":"11","author":"Durante","year":"2017","journal-title":"PloS Negl Trop Dis"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0005972","article-title":"Next-Generation ELISA Diagnostic Assay for Chagas Disease Based on the Combination of Short Peptidic Epitopes","volume":"11","author":"Mucci","year":"2017","journal-title":"PloS Negl Trop Dis"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0050748","article-title":"Diagnostic Peptide Discovery: Prioritization of Pathogen Diagnostic Markers Using Multiple Features","volume":"7","author":"Carmona","year":"2012","journal-title":"PloS One"},{"key":"B12","doi-asserted-by":"publisher","first-page":"57","DOI":"10.4269\/ajtmh.17-0437","article-title":"Protein-Specific Features Associated With Variability in Human Antibody Responses to Plasmodium Falciparum Malaria Antigens","volume":"98","author":"Liu","year":"2018","journal-title":"Am J Trop Med Hyg"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1002\/cbdv.201100360","article-title":"Predicting Antigenicity of Proteins in a Bacterial Proteome; 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