{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T19:17:30Z","timestamp":1776194250573,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T00:00:00Z","timestamp":1768176000000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Science and Engineering Research Council of Canada","doi-asserted-by":"crossref","award":["#04589-2020"],"award-info":[{"award-number":["#04589-2020"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100008459","name":"University of Calgary","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008459","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Molecular mimicry is used by pathogens to evade the host immune system and manipulate other host cellular processes. It is often mediated by short motifs in non-homologous proteins, whose detection challenges the sensitivity and specificity of existing bioinformatics tools.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present mimicDetector, a k-mer-based pipeline for identifying protein-level molecular mimicry between pathogens and their hosts. Applied to 17 globally important pathogens, mimicDetector identified a broad and biologically plausible set of mimicry candidates, including helminth proteins mimicking components of the human complement system and a Leishmania infantum mimic of Reticulon-4, a regulator of immune cell recruitment.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>mimicDetector is freely available at https:\/\/github.com\/kayleerich\/mimicDetector\/, implemented in Python and Snakemake, and compatible with Unix-based systems.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag012","type":"journal-article","created":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T12:38:55Z","timestamp":1768048735000},"source":"Crossref","is-referenced-by-count":0,"title":["mimicDetector: a pipeline for protein motif mimicry detection in host-pathogen interactions"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0316-0507","authenticated-orcid":false,"given":"Kaylee D","family":"Rich","sequence":"first","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary , Calgary, Alberta, T2N 4Z6,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9516-212X","authenticated-orcid":false,"given":"James D","family":"Wasmuth","sequence":"additional","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary , Calgary, Alberta, T2N 4Z6,","place":["Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,1,12]]},"reference":[{"key":"2026041414264656500_btag012-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2026041414264656500_btag012-B2","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1094\/MPMI-11-20-0332-R","article-title":"A novel In silico method for molecular mimicry detection finds a formin with the potential to manipulate the maize cell cytoskeleton","volume":"34","author":"Armijos-Jaramillo","year":"2021","journal-title":"Mol Plant Microbe Interact"},{"key":"2026041414264656500_btag012-B3","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2026041414264656500_btag012-B4","doi-asserted-by":"crossref","first-page":"534","DOI":"10.3390\/pathogens12040534","article-title":"Toll-like receptor-9 (TLR-9) signaling is crucial for inducing protective immunity following immunization with genetically modified live attenuated leishmania parasites","volume":"12","author":"Bhattacharya","year":"2023","journal-title":"Pathogens"},{"key":"2026041414264656500_btag012-B5","doi-asserted-by":"crossref","first-page":"e202104005","DOI":"10.1083\/jcb.202104005","article-title":"Lipid droplets and the host\u2013pathogen dynamic: FATal attraction?","volume":"220","author":"Bosch","year":"2021","journal-title":"J Cell Biol"},{"key":"2026041414264656500_btag012-B6","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"2026041414264656500_btag012-B7","doi-asserted-by":"crossref","first-page":"5488","DOI":"10.1038\/ncomms6488","article-title":"Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity","volume":"5","author":"Buck","year":"2014","journal-title":"Nat Commun"},{"key":"2026041414264656500_btag012-B8","doi-asserted-by":"crossref","first-page":"620144","DOI":"10.3389\/fimmu.2021.620144","article-title":"Unraveling the role of immune checkpoints in leishmaniasis","volume":"12","author":"De Freitas","year":"2021","journal-title":"Front Immunol"},{"key":"2026041414264656500_btag012-B9","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1093\/glycob\/cwp140","article-title":"Glycan gimmickry by parasitic helminths: a strategy for modulating the host immune response?","volume":"20","author":"van Die","year":"2010","journal-title":"Glycobiology"},{"key":"2026041414264656500_btag012-B10","doi-asserted-by":"crossref","first-page":"453","DOI":"10.4161\/viru.25180","article-title":"Prediction of molecular mimicry candidates in human pathogenic bacteria","volume":"4","author":"Doxey","year":"2013","journal-title":"Virulence"},{"key":"2026041414264656500_btag012-B11","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches. Pearson WR (ed.)","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"2026041414264656500_btag012-B12","doi-asserted-by":"crossref","first-page":"e967","DOI":"10.1371\/journal.pone.0000967","article-title":"SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins","volume":"2","author":"Edwards","year":"2007","journal-title":"PLoS One"},{"key":"2026041414264656500_btag012-B13","doi-asserted-by":"crossref","first-page":"105760","DOI":"10.1016\/j.micpath.2022.105760","article-title":"Prediction of molecular mimicry between proteins from Trypanosoma sp. and human antigens associated with systemic lupus erythematosus","volume":"172","author":"Emiliani","year":"2022","journal-title":"Microb Pathog"},{"key":"2026041414264656500_btag012-B14","doi-asserted-by":"crossref","first-page":"1101390","DOI":"10.3389\/fimmu.2023.1101390","article-title":"The many faces of parasite calreticulin","volume":"14","author":"Esperante","year":"2023","journal-title":"Front Immunol"},{"key":"2026041414264656500_btag012-B15","doi-asserted-by":"crossref","first-page":"e0006012","DOI":"10.1371\/journal.pntd.0006012","article-title":"Composition of the Schistosoma mansoni worm secretome: identification of immune modulatory Cyclophilin A","volume":"11","author":"Floudas","year":"2017","journal-title":"PLoS Negl Trop Dis"},{"key":"2026041414264656500_btag012-B16","doi-asserted-by":"crossref","first-page":"e1000071","DOI":"10.1371\/journal.pcbi.1000071","article-title":"Discovering sequence motifs with arbitrary insertions and deletions. Stormo G (ed.)","volume":"4","author":"Frith","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"2026041414264656500_btag012-B17","doi-asserted-by":"crossref","first-page":"106615","DOI":"10.1016\/j.actatropica.2022.106615","article-title":"A secreted MIF homologue from Trichinella spiralis binds to and interacts with host monocytes","volume":"234","author":"Huang","year":"2022","journal-title":"Acta Trop"},{"key":"2026041414264656500_btag012-B18","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1021\/pr700600n","article-title":"Assigning significance to peptides identified by tandem mass spectrometry using decoy databases","volume":"7","author":"K\u00e4ll","year":"2008","journal-title":"J Proteome Res"},{"key":"2026041414264656500_btag012-B19","doi-asserted-by":"crossref","first-page":"5426","DOI":"10.4049\/jimmunol.1402006","article-title":"Endoplasmic protein Nogo-B (RTN4-B) interacts with GRAMD4 and regulates TLR9-mediated innate immune responses","volume":"194","author":"Kimura","year":"2015","journal-title":"J Immunol"},{"key":"2026041414264656500_btag012-B20","doi-asserted-by":"crossref","first-page":"W342","DOI":"10.1093\/nar\/gki369","article-title":"POPSCOMP: an automated interaction analysis of biomolecular complexes","volume":"33","author":"Kleinjung","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2026041414264656500_btag012-B21","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s12953-021-00179-7","article-title":"Comparison of false-discovery rates of various decoy databases","volume":"19","author":"Lee","year":"2021","journal-title":"Proteome Sci"},{"key":"2026041414264656500_btag012-B22","author":"Li","year":"2018"},{"key":"2026041414264656500_btag012-B23","doi-asserted-by":"crossref","first-page":"e17546","DOI":"10.1371\/journal.pone.0017546","article-title":"Genome-Wide identification of molecular mimicry candidates in parasites. El-Sayed N (ed.)","volume":"6","author":"Ludin","year":"2011","journal-title":"PLoS ONE"},{"key":"2026041414264656500_btag012-B24","doi-asserted-by":"crossref","first-page":"9403","DOI":"10.1038\/s41467-024-53658-8","article-title":"Molecular mimicry as a mechanism of viral immune evasion and autoimmunity","volume":"15","author":"Maguire","year":"2024","journal-title":"Nat Commun"},{"key":"2026041414264656500_btag012-B25","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/s12859-018-2290-3","article-title":"TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases","volume":"19","author":"Medlar","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2026041414264656500_btag012-B26","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.jmb.2011.10.025","article-title":"Prediction of short linear protein binding regions","volume":"415","author":"Mooney","year":"2012","journal-title":"J Mol Biol"},{"key":"2026041414264656500_btag012-B27","doi-asserted-by":"publisher","first-page":"1162697","DOI":"10.3389\/fpara.2023.1162697","article-title":"Proteome-wide comparison of tertiary protein structures reveals molecular mimicry in plasmodium-human interactions","volume":"2","author":"Muthye","year":"2023","journal-title":"Front Parasitol"},{"key":"2026041414264656500_btag012-B28","doi-asserted-by":"crossref","first-page":"2284","DOI":"10.1093\/bioinformatics\/btv155","article-title":"QSLiMFinder: improved short linear motif prediction using specific query protein data","volume":"31","author":"Palopoli","year":"2015","journal-title":"Bioinformatics"},{"key":"2026041414264656500_btag012-B29","doi-asserted-by":"crossref","first-page":"5955","DOI":"10.1128\/IAI.66.12.5955-5963.1998","article-title":"Filarial nematode parasites secrete a homologue of the human cytokine macrophage migration inhibitory factor","volume":"66","author":"Pastrana","year":"1998","journal-title":"Infect Immun"},{"key":"2026041414264656500_btag012-B30","doi-asserted-by":"crossref","first-page":"3.5.1","DOI":"10.1002\/0471250953.bi0305s43","article-title":"Selecting the right Similarity-Scoring matrix","volume":"43","author":"Pearson","year":"2013","journal-title":"Curr Protoc Bioinf"},{"key":"2026041414264656500_btag012-B31","doi-asserted-by":"crossref","first-page":"e16339","DOI":"10.7717\/peerj.16339","article-title":"Identification of potential molecular mimicry in pathogen-host interactions","volume":"11","author":"Rich","year":"2023","journal-title":"PeerJ"},{"key":"2026041414264656500_btag012-B32","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1016\/j.tibs.2020.03.003","article-title":"Mimicry of short linear motifs by bacterial pathogens: a drugging opportunity","volume":"45","author":"S\u00e1mano-S\u00e1nchez","year":"2020","journal-title":"Trends Biochem Sci"},{"key":"2026041414264656500_btag012-B33","doi-asserted-by":"crossref","first-page":"794627","DOI":"10.3389\/fimmu.2021.794627","article-title":"Modulation of host immune response during Leishmania infantum natural infection: a Whole-Transcriptome analysis of the popliteal lymph nodes in dogs","volume":"12","author":"Sanz","year":"2021","journal-title":"Front Immunol"},{"key":"2026041414264656500_btag012-B34","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/0022-2836(87)90478-5","article-title":"A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons","volume":"197","author":"Waterman","year":"1987","journal-title":"J Mol Biol"},{"key":"2026041414264656500_btag012-B35","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/S0076-6879(96)66035-2","article-title":"Analysis of compositionally biased regions in sequence databases","volume":"266","author":"Wootton","year":"1996","journal-title":"Methods Enzymol"},{"key":"2026041414264656500_btag012-B36","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1021\/acsinfecdis.0c00565","article-title":"Immunization with Brugia malayi calreticulin protein generates robust antiparasitic immunity and offers protection during experimental lymphatic filariasis","volume":"7","author":"Yadav","year":"2021","journal-title":"ACS Infect Dis"},{"key":"2026041414264656500_btag012-B37","doi-asserted-by":"crossref","first-page":"5879","DOI":"10.1038\/s41467-023-41636-5","article-title":"Structure guided mimicry of an essential P. falciparum receptor-ligand complex enhances cross neutralizing antibodies","volume":"14","author":"Yanik","year":"2023","journal-title":"Nat Commun"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag012\/66379113\/btag012.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/2\/btag012\/66379113\/btag012.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/2\/btag012\/66379113\/btag012.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T18:26:58Z","timestamp":1776191218000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag012\/8423033"}},"subtitle":[],"editor":[{"given":"Jianlin","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,1,3]]},"references-count":37,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,1,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag012","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,2]]},"published":{"date-parts":[[2026,1,3]]},"article-number":"btag012"}}