{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T13:32:35Z","timestamp":1783690355521,"version":"3.55.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013799","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T00:00:00Z","timestamp":1766361600000}}],"reference-count":117,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T00:00:00Z","timestamp":1765756800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_UU_00040\/01"],"award-info":[{"award-number":["MC_UU_00040\/01"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_UU_00040\/05"],"award-info":[{"award-number":["MC_UU_00040\/05"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/Y010078\/1"],"award-info":[{"award-number":["MR\/Y010078\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["WT107881"],"award-info":[{"award-number":["WT107881"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["214298\/Z\/18\/Z"],"award-info":[{"award-number":["214298\/Z\/18\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Todd-Bird Junior Research Fellowship"},{"name":"EU Horizon 2020 programme INFRAIA project EPIC-XS","award":["project 823839"],"award-info":[{"award-number":["project 823839"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    The subcellular localisation of proteins is a key determinant of their function. High-throughput analyses of these localisations can be performed using mass spectrometry-based spatial proteomics, which enables us to examine the localisation and relocalisation of proteins. Furthermore, complementary data sources can provide additional sources of functional or localisation information. Examples include protein annotations and other high-throughput \u2018omic assays. Integrating these modalities can provide new insights as well as additional confidence in results, but existing approaches for integrative analyses of spatial proteomics datasets, such as concatenation-based methods and transfer learning approaches like KNN-TL, are limited in the types of data they can integrate and do not quantify uncertainty in their predictions. Here we propose a semi-supervised Bayesian approach (wherein model parameters are inferred from\n                    <jats:italic>both<\/jats:italic>\n                    labeled marker proteins and unlabeled data while quantifying prediction uncertainty) to integrate spatial proteomics datasets with other data sources, to improve the inference of protein sub-cellular localisation. We demonstrate our approach outperforms other transfer-learning methods and has greater flexibility in the data it can model - including categorical annotations (e.g., Gene Ontology terms), continuous measurements (e.g., protein abundance), and temporal profiles (e.g., time-series expression data). To demonstrate the flexibility of our approach, we apply our method to integrate spatial proteomics data generated for the parasite\n                    <jats:italic>Toxoplasma gondii<\/jats:italic>\n                    with time-series gene expression data generated over its cell cycle. Our findings suggest that proteins linked to invasion organelles are associated with expression programs that peak at the end of the first cell-cycle. Furthermore, this integrative analysis divides the dense granule proteins into heterogeneous populations suggestive of potentially different functions. Our method is disseminated via the\n                    <jats:monospace>mdir<\/jats:monospace>\n                    R package available on the lead author\u2019s Github.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1013799","type":"journal-article","created":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T18:40:32Z","timestamp":1765824032000},"page":"e1013799","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Semi-supervised Bayesian integration of multiple spatial proteomics datasets"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2294-8869","authenticated-orcid":true,"given":"Stephen","family":"Coleman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Breckels","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ross F.","family":"Waller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn S.","family":"Lilley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris","family":"Wallace","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver M.","family":"Crook","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul D. 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Olkkonen","year":"2006","journal-title":"J Cell Sci."},{"issue":"1","key":"pcbi.1013799.ref004","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.cbpa.2008.02.011","article-title":"Protein misfolding and disease: from the test tube to the organism","volume":"12","author":"LM Luheshi","year":"2008","journal-title":"Curr Opin Chem Biol."},{"issue":"10","key":"pcbi.1013799.ref005","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1056\/NEJMra0910494","article-title":"Mendelian disorders of membrane trafficking","volume":"365","author":"MA De Matteis","year":"2011","journal-title":"N Engl J Med."},{"issue":"48","key":"pcbi.1013799.ref006","doi-asserted-by":"crossref","first-page":"19414","DOI":"10.1073\/pnas.1309720110","article-title":"Unexpected gain of function for the scaffolding protein plectin due to mislocalization in pancreatic cancer","volume":"110","author":"SJ Shin","year":"2013","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"2","key":"pcbi.1013799.ref007","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/s41588-017-0020-9","article-title":"Subcellular localization of MC4R with ADCY3 at neuronal primary cilia underlies a common pathway for genetic predisposition to obesity","volume":"50","author":"JE Siljee","year":"2018","journal-title":"Nat Genet."},{"key":"pcbi.1013799.ref008","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.cbpa.2018.09.021","article-title":"Location is everything: protein translocations as a viral infection strategy","volume":"48","author":"KC Cook","year":"2019","journal-title":"Curr Opin Chem Biol."},{"key":"pcbi.1013799.ref009","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.16950","article-title":"Global, quantitative and dynamic mapping of protein subcellular localization","volume":"5","author":"DN Itzhak","year":"2016","journal-title":"Elife."},{"issue":"1","key":"pcbi.1013799.ref010","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/s41467-018-08191-w","article-title":"Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics","volume":"10","author":"A Geladaki","year":"2019","journal-title":"Nat Commun."},{"issue":"11","key":"pcbi.1013799.ref011","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1074\/mcp.T400009-MCP200","article-title":"Localization of organelle proteins by isotope tagging (LOPIT)","volume":"3","author":"TPJ Dunkley","year":"2004","journal-title":"Mol Cell Proteomics."},{"key":"pcbi.1013799.ref012","doi-asserted-by":"crossref","first-page":"8992","DOI":"10.1038\/ncomms9992","article-title":"A draft map of the mouse pluripotent stem cell spatial proteome","volume":"7","author":"A Christoforou","year":"2016","journal-title":"Nat Commun."},{"issue":"1","key":"pcbi.1013799.ref013","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.cell.2006.03.022","article-title":"A mammalian organelle map by protein correlation profiling","volume":"125","author":"LJ Foster","year":"2006","journal-title":"Cell."},{"issue":"1","key":"pcbi.1013799.ref014","article-title":"SubCellBarCode: proteome-wide mapping of protein localization and relocalization","volume":"73","author":"LM Orre","year":"2019","journal-title":"Mol Cell."},{"issue":"1","key":"pcbi.1013799.ref015","doi-asserted-by":"crossref","first-page":"5987","DOI":"10.1038\/s41467-020-19840-4","article-title":"Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers","volume":"11","author":"JJH Shin","year":"2020","journal-title":"Nat Commun."},{"issue":"17","key":"pcbi.1013799.ref016","doi-asserted-by":"crossref","first-page":"6518","DOI":"10.1073\/pnas.0506958103","article-title":"Mapping the Arabidopsis organelle proteome","volume":"103","author":"TPJ Dunkley","year":"2006","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"6","key":"pcbi.1013799.ref017","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1038\/nprot.2017.026","article-title":"Using hyperLOPIT to perform high-resolution mapping of the spatial proteome","volume":"12","author":"CM Mulvey","year":"2017","journal-title":"Nat Protoc."},{"issue":"8","key":"pcbi.1013799.ref018","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1021\/ac0262560","article-title":"Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS\/MS","volume":"75","author":"A Thompson","year":"2003","journal-title":"Anal Chem."},{"issue":"1030","key":"pcbi.1013799.ref019","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1098\/rspb.1969.0039","article-title":"The peroxisome: a new cytoplasmic organelle","volume":"173","year":"1969","journal-title":"Proc R Soc Lond B."},{"key":"pcbi.1013799.ref020","doi-asserted-by":"crossref","DOI":"10.1083\/jcb.91.3.293s","article-title":"A short history of tissue fractionation","volume":"91","author":"C De Duve","year":"1981","journal-title":"J Cell Biol."},{"issue":"6","key":"pcbi.1013799.ref021","doi-asserted-by":"crossref","first-page":"2667","DOI":"10.1021\/pr800866n","article-title":"Mapping organelle proteins and protein complexes in Drosophila melanogaster","volume":"8","author":"DJL Tan","year":"2009","journal-title":"J Proteome Res."},{"key":"pcbi.1013799.ref022","unstructured":"Jiang Y, Rex DAB, Schuster D, Neely BA, Rosano GL, Volkmar N. Comprehensive overview of bottom-up proteomics using mass spectrometry. 2023."},{"issue":"11","key":"pcbi.1013799.ref023","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1006516","article-title":"A Bayesian mixture modelling approach for spatial proteomics","volume":"14","author":"OM Crook","year":"2018","journal-title":"PLoS Comput Biol."},{"issue":"4","key":"pcbi.1013799.ref024","doi-asserted-by":"crossref","DOI":"10.1214\/22-AOAS1603","article-title":"Semi-supervised non-parametric Bayesian modelling of spatial proteomics","volume":"16","author":"OM Crook","year":"2022","journal-title":"Ann Appl Stat."},{"issue":"1","key":"pcbi.1013799.ref025","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1021\/pr9008332","article-title":"Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes","volume":"9","author":"AT Qattan","year":"2010","journal-title":"J Proteome Res."},{"issue":"3","key":"pcbi.1013799.ref026","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1212\/WNL.0b013e3182605801","article-title":"Novel late-onset Alzheimer disease loci variants associate with brain gene expression","volume":"79","author":"M Allen","year":"2012","journal-title":"Neurology."},{"issue":"38","key":"pcbi.1013799.ref027","doi-asserted-by":"crossref","first-page":"15307","DOI":"10.1073\/pnas.1201632109","article-title":"Role of genes linked to sporadic Alzheimer\u2019s disease risk in the production of \u03b2-amyloid peptides","volume":"109","author":"J Bali","year":"2012","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"2","key":"pcbi.1013799.ref028","doi-asserted-by":"crossref","DOI":"10.1016\/j.devcel.2018.09.017","article-title":"Organellar proteomics and phospho-proteomics reveal subcellular reorganization in diet-induced hepatic steatosis","volume":"47","author":"N Krahmer","year":"2018","journal-title":"Dev Cell."},{"issue":"7852","key":"pcbi.1013799.ref029","first-page":"93","article-title":"Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator","volume":"592","author":"L Allou","year":"2021","journal-title":"Nature."},{"issue":"2","key":"pcbi.1013799.ref030","doi-asserted-by":"crossref","first-page":"108981","DOI":"10.1016\/j.celrep.2021.108981","article-title":"Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene","volume":"35","author":"I Akerman","year":"2021","journal-title":"Cell Rep."},{"issue":"5","key":"pcbi.1013799.ref031","doi-asserted-by":"crossref","DOI":"10.1016\/j.chom.2020.09.011","article-title":"A comprehensive subcellular Atlas of the toxoplasma proteome via hyperLOPIT provides spatial context for protein functions","volume":"28","author":"K Barylyuk","year":"2020","journal-title":"Cell Host Microbe."},{"issue":"2","key":"pcbi.1013799.ref032","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1208\/s12248-012-9447-1","article-title":"Strategic applications of gene expression: from drug discovery\/development to bedside","volume":"15","author":"JPF Bai","year":"2013","journal-title":"AAPS J."},{"key":"pcbi.1013799.ref033","doi-asserted-by":"crossref","first-page":"38","DOI":"10.3389\/fcell.2014.00038","article-title":"Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks","volume":"2","author":"F Emmert-Streib","year":"2014","journal-title":"Front Cell Dev Biol."},{"issue":"7418","key":"pcbi.1013799.ref034","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature11412","article-title":"Comprehensive molecular portraits of human breast tumours","volume":"490","year":"2012","journal-title":"Nature."},{"issue":"2","key":"pcbi.1013799.ref035","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1093\/bib\/bbw114","article-title":"Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences","volume":"19","author":"C Manzoni","year":"2018","journal-title":"Brief Bioinform."},{"issue":"1","key":"pcbi.1013799.ref036","first-page":"523","article-title":"Joint and Individual Variation Explained (JIVE) for integrated analysis of multiple data types","volume":"7","author":"EF Lock","year":"2013","journal-title":"Ann Appl Stat."},{"issue":"6","key":"pcbi.1013799.ref037","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20178124","article-title":"Multi-omics factor analysis-a framework for unsupervised integration of multi-omics data sets","volume":"14","author":"R Argelaguet","year":"2018","journal-title":"Mol Syst Biol."},{"issue":"20","key":"pcbi.1013799.ref038","doi-asserted-by":"crossref","first-page":"2610","DOI":"10.1093\/bioinformatics\/btt425","article-title":"Bayesian consensus clustering","volume":"29","author":"EF Lock","year":"2013","journal-title":"Bioinformatics."},{"issue":"10","key":"pcbi.1013799.ref039","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005781","article-title":"Clusternomics: integrative context-dependent clustering for heterogeneous datasets","volume":"13","author":"E Gabasova","year":"2017","journal-title":"PLoS Comput Biol."},{"issue":"24","key":"pcbi.1013799.ref040","doi-asserted-by":"crossref","first-page":"3290","DOI":"10.1093\/bioinformatics\/bts595","article-title":"Bayesian correlated clustering to integrate multiple datasets","volume":"28","author":"P Kirk","year":"2012","journal-title":"Bioinformatics."},{"issue":"5","key":"pcbi.1013799.ref041","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004920","article-title":"Learning from heterogeneous data sources: an application in spatial proteomics","volume":"12","author":"LM Breckels","year":"2016","journal-title":"PLoS Comput Biol."},{"key":"pcbi.1013799.ref042","doi-asserted-by":"crossref","DOI":"10.1201\/b16018","volume-title":"Bayesian data analysis","author":"A Gelman","year":"2013"},{"issue":"458","key":"pcbi.1013799.ref043","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1198\/016214502760047131","article-title":"Model-based clustering, discriminant analysis, and density estimation","volume":"97","author":"C Fraley","year":"2002","journal-title":"Journal of the American Statistical Association."},{"issue":"10","key":"pcbi.1013799.ref044","doi-asserted-by":"crossref","first-page":"1300","DOI":"10.1093\/bioinformatics\/btp139","article-title":"Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data","volume":"25","author":"PDW Kirk","year":"2009","journal-title":"Bioinformatics."},{"issue":"1","key":"pcbi.1013799.ref045","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/1471-2105-12-180","article-title":"A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression","volume":"12","author":"AA Kalaitzis","year":"2011","journal-title":"BMC Bioinformatics."},{"key":"pcbi.1013799.ref046","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1186\/1471-2105-12-399","article-title":"Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements","volume":"12","author":"EJ Cooke","year":"2011","journal-title":"BMC Bioinformatics."},{"key":"pcbi.1013799.ref047","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1186\/1471-2105-14-252","article-title":"Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters","volume":"14","author":"J Hensman","year":"2013","journal-title":"BMC Bioinformatics."},{"key":"pcbi.1013799.ref048","unstructured":"Rouanet A, Johnson R, Strauss ME, Richardson S, Tom BD, White SR. Bayesian profile regression for clustering analysis involving a longitudinal response and explanatory variables. arXiv preprint 2021. https:\/\/arxiv.org\/abs\/2111.04518"},{"issue":"2","key":"pcbi.1013799.ref049","first-page":"370","article-title":"A rigorous statistical framework for spatio-temporal pollution prediction and estimation of its long-term impact on health","volume":"18","author":"D Lee","year":"2017","journal-title":"Biostatistics."},{"issue":"4","key":"pcbi.1013799.ref050","doi-asserted-by":"crossref","first-page":"1743","DOI":"10.1214\/20-AOAS1363","article-title":"Identifying main effects and interactions among exposures using gaussian processes","volume":"14","author":"F Ferrari","year":"2020","journal-title":"Ann Appl Stat."},{"key":"pcbi.1013799.ref051","first-page":"5311","article-title":"Bayesian Gaussian processes for identifying the deteriorating patient","volume":"2016","author":"GW Colopy","year":"2016","journal-title":"Annu Int Conf IEEE Eng Med Biol Soc."},{"issue":"1","key":"pcbi.1013799.ref052","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1186\/s12911-020-1069-4","article-title":"Sparse multi-output Gaussian processes for online medical time series prediction","volume":"20","author":"L-F Cheng","year":"2020","journal-title":"BMC Med Inform Decis Mak."},{"issue":"3","key":"pcbi.1013799.ref053","doi-asserted-by":"crossref","DOI":"10.1214\/009053607000000613","article-title":"Rates of contraction of posterior distributions based on Gaussian process priors","volume":"36","author":"AW van der Vaart","year":"2008","journal-title":"Ann Statist."},{"issue":"6","key":"pcbi.1013799.ref054","article-title":"Information rates of nonparametric Gaussian process methods","volume":"12","author":"A van der Vaart","year":"2011","journal-title":"Journal of Machine Learning Research."},{"issue":"4","key":"pcbi.1013799.ref055","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1137\/19M1284816","article-title":"Convergence of Gaussian process regression with estimated hyper-parameters and applications in Bayesian inverse problems","volume":"8","author":"AL Teckentrup","year":"2020","journal-title":"SIAM\/ASA J Uncertainty Quantification."},{"key":"pcbi.1013799.ref056","unstructured":"Stephenson WT, Ghosh S, Nguyen TD, Yurochkin M, Deshpande S, Broderick T. Measuring the robustness of Gaussian processes to kernel choice. In: Proceedings of the 25th International Conference on Artificial Intelligence and Statistics. 2022. p. 3308\u201331. https:\/\/proceedings.mlr.press\/v151\/stephenson22a.html"},{"key":"pcbi.1013799.ref057","volume-title":"Gaussian processes for machine learning","author":"CK Williams","year":"2006"},{"key":"pcbi.1013799.ref058","first-page":"1939","article-title":"A unifying view of sparse approximate Gaussian process regression","volume":"6","author":"J Quinonero-Candela","year":"2005","journal-title":"The Journal of Machine Learning Research."},{"issue":"1","key":"pcbi.1013799.ref059","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/biomet\/ass068","article-title":"Efficient Gaussian process regression for large datasets","volume":"100","author":"A Banerjee","year":"2013","journal-title":"Biometrika."},{"issue":"11","key":"pcbi.1013799.ref060","doi-asserted-by":"crossref","first-page":"4405","DOI":"10.1109\/TNNLS.2019.2957109","article-title":"When Gaussian process meets big data: a review of scalable GPs","volume":"31","author":"H Liu","year":"2020","journal-title":"IEEE Trans Neural Netw Learn Syst."},{"key":"pcbi.1013799.ref061","unstructured":"Zhang Y, Leithead WE, Leith DJ. Time-series Gaussian Process Regression Based on Toeplitz Computation of O(N2) Operations and O(N)-level Storage. In: Proceedings of the 44th IEEE Conference on Decision and Control; 2005. p. 3711\u20136."},{"issue":"4","key":"pcbi.1013799.ref062","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1021\/acs.jproteome.1c00859","article-title":"Challenges and opportunities for Bayesian statistics in proteomics","volume":"21","author":"OM Crook","year":"2022","journal-title":"J Proteome Res."},{"issue":"5","key":"pcbi.1013799.ref063","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1111\/j.1467-9868.2011.00781.x","article-title":"Asymptotic behaviour of the posterior distribution in overfitted mixture models","volume":"73","author":"J Rousseau","year":"2011","journal-title":"Journal of the Royal Statistical Society Series B: Statistical Methodology."},{"issue":"2","key":"pcbi.1013799.ref064","doi-asserted-by":"crossref","DOI":"10.1214\/aos\/1176342360","article-title":"A Bayesian analysis of some nonparametric problems","volume":"1","author":"TS Ferguson","year":"1973","journal-title":"Ann Statist."},{"issue":"6","key":"pcbi.1013799.ref065","doi-asserted-by":"crossref","DOI":"10.1214\/aos\/1176342871","article-title":"Mixtures of dirichlet processes with applications to Bayesian nonparametric problems","volume":"2","author":"CE Antoniak","year":"1974","journal-title":"Ann Statist."},{"key":"pcbi.1013799.ref066","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/B978-0-12-589320-6.50018-6","volume-title":"Recent advances in statistics","author":"TS Ferguson","year":"1983"},{"issue":"1","key":"pcbi.1013799.ref067","first-page":"351","article-title":"On a class of Bayesian nonparametric estimates: I. density estimates","volume":"12","author":"AY Lo","year":"1984","journal-title":"Ann Statist."},{"issue":"11","key":"pcbi.1013799.ref068","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1008288","article-title":"A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection","volume":"16","author":"OM Crook","year":"2020","journal-title":"PLoS Comput Biol."},{"issue":"247","key":"pcbi.1013799.ref069","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1080\/01621459.1949.10483310","article-title":"The Monte Carlo method","volume":"44","author":"N Metropolis","year":"1949","journal-title":"Journal of the American Statistical Association."},{"issue":"6","key":"pcbi.1013799.ref070","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1063\/1.1699114","article-title":"Equation of state calculations by fast computing machines","volume":"21","author":"N Metropolis","year":"1953","journal-title":"The Journal of Chemical Physics."},{"key":"pcbi.1013799.ref071","doi-asserted-by":"crossref","unstructured":"Hastings WK. Monte Carlo sampling methods using Markov chains and their applications. Biometrika. 1970; p. 14.","DOI":"10.2307\/2334940"},{"issue":"410","key":"pcbi.1013799.ref072","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1080\/01621459.1990.10476213","article-title":"Sampling-based approaches to calculating marginal densities","volume":"85","author":"AE Gelfand","year":"1990","journal-title":"Journal of the American Statistical Association."},{"key":"pcbi.1013799.ref073","doi-asserted-by":"crossref","unstructured":"Robert CP, Casella G. Monte Carlo statistical methods. vol. 2. Springer; 1999.","DOI":"10.1007\/978-1-4757-3071-5"},{"issue":"452","key":"pcbi.1013799.ref074","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1080\/01621459.2000.10474328","article-title":"Bayesian analysis: a look at today and thoughts of tomorrow","volume":"95","author":"JO Berger","year":"2000","journal-title":"Journal of the American Statistical Association."},{"key":"pcbi.1013799.ref075","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-4314-2","volume-title":"The Bayesian choice: a decision-theoretic motivation","author":"CP Robert","year":"1994"},{"key":"pcbi.1013799.ref076","volume-title":"The Theory That Would Not Die: How Bayes\u2019 Rule Cracked the Enigma Code, Hunted Down Russian Submarines, & Emerged Triumphant from Two Centuries of C","author":"SB McGrayne","year":"2011"},{"key":"pcbi.1013799.ref077","unstructured":"Dahl DB. An improved merge-split sampler for conjugate Dirichlet process mixture models. Technical Report. 2003."},{"issue":"1","key":"pcbi.1013799.ref078","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1198\/1061860043001","article-title":"A split-merge Markov chain Monte Carlo procedure for the Dirichlet process mixture model","volume":"13","author":"S Jain","year":"2004","journal-title":"Journal of Computational and Graphical Statistics."},{"issue":"28","key":"pcbi.1013799.ref079","article-title":"Particle Gibbs split-merge sampling for Bayesian inference in mixture models","volume":"18","author":"A Bouchard-Cote","year":"2017","journal-title":"Journal of Machine Learning Research."},{"issue":"1","key":"pcbi.1013799.ref080","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/biomet\/asz066","article-title":"The Hastings algorithm at fifty","volume":"107","author":"DB Dunson","year":"2019","journal-title":"Biometrika."},{"key":"pcbi.1013799.ref081","unstructured":"Lu Y, Lu J, Nolen J. Accelerating Langevin Sampling with Birth-Death. arXiv preprint 2019. https:\/\/arxiv.org\/abs\/1905.09863"},{"key":"pcbi.1013799.ref082","unstructured":"Syed S, Romaniello V, Campbell T, Bouchard-Cote A. Parallel tempering on optimized paths. In: Proceedings of the 38th International Conference on Machine Learning. 2021. p. 10033\u201342. https:\/\/proceedings.mlr.press\/v139\/syed21a.html"},{"issue":"2","key":"pcbi.1013799.ref083","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1111\/rssb.12464","article-title":"Non-reversible parallel tempering: a scalable highly parallel MCMC scheme","volume":"84","author":"S Syed","year":"2021","journal-title":"Journal of the Royal Statistical Society Series B: Statistical Methodology."},{"issue":"6","key":"pcbi.1013799.ref084","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1109\/TPAMI.1984.4767596","article-title":"Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images","volume":"6","author":"S Geman","year":"1984","journal-title":"IEEE Trans Pattern Anal Mach Intell."},{"issue":"1","key":"pcbi.1013799.ref085","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1186\/s12859-022-04830-8","article-title":"Consensus clustering for Bayesian mixture models","volume":"23","author":"S Coleman","year":"2022","journal-title":"BMC Bioinformatics."},{"issue":"2","key":"pcbi.1013799.ref086","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1214\/17-BA1073","article-title":"Bayesian cluster analysis: point estimation and credible balls (with discussion)","volume":"13","author":"S Wade","year":"2018","journal-title":"Bayesian Anal."},{"key":"pcbi.1013799.ref087","unstructured":"Chaumeny Y, Moris JvdM, Davison AC, Kirk PDW. Bayesian nonparametric mixture inconsistency for the number of components: how worried should we be in practice? arXiv preprint 2022. https:\/\/arxiv.org\/abs\/2207.14717"},{"issue":"2","key":"pcbi.1013799.ref088","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1214\/09-BA414","article-title":"Improved criteria for clustering based on the posterior similarity matrix","volume":"4","author":"A Fritsch","year":"2009","journal-title":"Bayesian Anal."},{"key":"pcbi.1013799.ref089","unstructured":"Dahl DB, Johnson DJ, Mueller P. Search algorithms and loss functions for Bayesian clustering. arXiv preprint 2021. https:\/\/arxiv.org\/abs\/2105.04451"},{"key":"pcbi.1013799.ref090","doi-asserted-by":"crossref","unstructured":"Wu P, Dietterich TG. Improving SVM accuracy by training on auxiliary data sources. In: Twenty-first international conference on Machine learning - ICML \u201904. 2004. p. 110. https:\/\/doi.org\/10.1145\/1015330.1015436","DOI":"10.1145\/1015330.1015436"},{"issue":"1","key":"pcbi.1013799.ref091","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/BF01908075","article-title":"Comparing partitions","volume":"2","author":"L Hubert","year":"1985","journal-title":"Journal of Classification."},{"key":"pcbi.1013799.ref092","unstructured":"Chandra NK, Canale A, Dunson DB. Escaping the curse of dimensionality in Bayesian model based clustering. arXiv preprint 2020. https:\/\/arxiv.org\/abs\/2006.02700"},{"issue":"2","key":"pcbi.1013799.ref093","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1021\/pr4008464","article-title":"Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue","volume":"13","author":"AJ Groen","year":"2014","journal-title":"J Proteome Res."},{"key":"pcbi.1013799.ref094","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.jprot.2013.02.019","article-title":"The effect of organelle discovery upon sub-cellular protein localisation","volume":"88","author":"LM Breckels","year":"2013","journal-title":"J Proteomics."},{"key":"pcbi.1013799.ref095","unstructured":"Gatto L, Crook O, Breckels L. pRolocdata: Data accompanying the pRoloc package. 2023. https:\/\/bioconductor.org\/packages\/pRolocdata"},{"issue":"4","key":"pcbi.1013799.ref096","article-title":"A portrait of the human organelle proteome in space and time during cytomegalovirus infection","volume":"3","author":"PM Jean Beltran","year":"2016","journal-title":"Cell Syst."},{"issue":"1","key":"pcbi.1013799.ref097","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1128\/MMBR.66.1.21-38.2002","article-title":"Cytoskeleton of apicomplexan parasites","volume":"66","author":"NS Morrissette","year":"2002","journal-title":"Microbiol Mol Biol Rev."},{"issue":"8","key":"pcbi.1013799.ref098","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1016\/j.ijpara.2005.03.011","article-title":"Dense granules: are they key organelles to help understand the parasitophorous vacuole of all apicomplexa parasites?","volume":"35","author":"C Mercier","year":"2005","journal-title":"Int J Parasitol."},{"issue":"2","key":"pcbi.1013799.ref099","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1017\/S0031182018001282","article-title":"A systematic review on modelling approaches for economic losses studies caused by parasites and their associated diseases in cattle","volume":"146","author":"M Rashid","year":"2019","journal-title":"Parasitology."},{"issue":"9888","key":"pcbi.1013799.ref100","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/S0140-6736(13)60844-2","article-title":"Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study","volume":"382","author":"KL Kotloff","year":"2013","journal-title":"Lancet."},{"issue":"12","key":"pcbi.1013799.ref101","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pmed.1001923","article-title":"World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010","volume":"12","author":"AH Havelaar","year":"2015","journal-title":"PLoS Med."},{"issue":"9","key":"pcbi.1013799.ref102","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1017\/S003118201800001X","article-title":"New and emerging uses of CRISPR\/Cas9 to genetically manipulate apicomplexan parasites","volume":"145","author":"M Di Cristina","year":"2018","journal-title":"Parasitology."},{"issue":"2","key":"pcbi.1013799.ref103","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/S0001-706X(01)00201-7","article-title":"Host cell invasion by the opportunistic pathogen Toxoplasma gondii","volume":"81","author":"VB Carruthers","year":"2002","journal-title":"Acta Trop."},{"issue":"2","key":"pcbi.1013799.ref104","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1111\/j.1600-0854.2007.00681.x","article-title":"Protein trafficking to apical organelles of malaria parasites - building an invasion machine","volume":"9","author":"LM Kats","year":"2008","journal-title":"Traffic."},{"key":"pcbi.1013799.ref105","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/B978-0-12-396481-6.00012-X","volume-title":"Toxoplasma gondii","author":"M Lebrun","year":"2014"},{"issue":"6","key":"pcbi.1013799.ref106","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1016\/j.cell.2007.10.049","article-title":"Subcellular discharge of a serine protease mediates release of invasive malaria parasites from host erythrocytes","volume":"131","author":"S Yeoh","year":"2007","journal-title":"Cell."},{"issue":"3","key":"pcbi.1013799.ref107","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1128\/CMR.00005-17","article-title":"Toxoplasma effectors targeting host signaling and transcription","volume":"30","author":"M-A Hakimi","year":"2017","journal-title":"Clin Microbiol Rev."},{"issue":"6","key":"pcbi.1013799.ref108","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1016\/S0092-8674(00)81071-5","article-title":"Toxoplasma invasion of mammalian cells is powered by the actin cytoskeleton of the parasite","volume":"84","author":"JM Dobrowolski","year":"1996","journal-title":"Cell."},{"issue":"5","key":"pcbi.1013799.ref109","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/S1360-1385(01)01921-5","article-title":"The apicoplast: a new member of the plastid family","volume":"6","author":"E Mar\u00e9chal","year":"2001","journal-title":"Trends Plant Sci."},{"issue":"8","key":"pcbi.1013799.ref110","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0012354","article-title":"Coordinated progression through two subtranscriptomes underlies the tachyzoite cycle of Toxoplasma gondii","volume":"5","author":"MS Behnke","year":"2010","journal-title":"PLoS One."},{"key":"pcbi.1013799.ref111","doi-asserted-by":"crossref","first-page":"38842","DOI":"10.1038\/srep38842","article-title":"A critical role for toxoplasma gondii vacuolar protein sorting VPS9 in secretory organelle biogenesis and host infection","volume":"6","author":"T Sakura","year":"2016","journal-title":"Sci Rep."},{"issue":"1","key":"pcbi.1013799.ref112","doi-asserted-by":"crossref","first-page":"7419","DOI":"10.1038\/s41467-024-51011-7","article-title":"Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver","volume":"15","author":"J Lou","year":"2024","journal-title":"Nat Commun."},{"issue":"1","key":"pcbi.1013799.ref113","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/s41467-020-20216-x","article-title":"TgAP2IX-5 is a key transcriptional regulator of the asexual cell cycle division in Toxoplasma gondii","volume":"12","author":"AS Khelifa","year":"2021","journal-title":"Nat Commun."},{"issue":"2","key":"pcbi.1013799.ref114","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/S0166-6851(98)00074-7","article-title":"A cell cycle model for the tachyzoite of Toxoplasma gondii using the Herpes simplex virus thymidine kinase","volume":"94","author":"JR Radke","year":"1998","journal-title":"Mol Biochem Parasitol."},{"issue":"22","key":"pcbi.1013799.ref115","doi-asserted-by":"crossref","first-page":"12164","DOI":"10.1073\/pnas.1921245117","article-title":"Ancient MAPK ERK7 is regulated by an unusual inhibitory scaffold required for Toxoplasma apical complex biogenesis","volume":"117","author":"PS Back","year":"2020","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"4","key":"pcbi.1013799.ref116","doi-asserted-by":"crossref","DOI":"10.1016\/j.chom.2023.03.001","article-title":"Cryptosporidium uses multiple distinct secretory organelles to interact with and modify its host cell","volume":"31","author":"A Gu\u00e9rin","year":"2023","journal-title":"Cell Host Microbe."},{"issue":"2","key":"pcbi.1013799.ref117","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.pt.2014.12.002","article-title":"Toxoplasma secretory granules: one population or more?","volume":"31","author":"C Mercier","year":"2015","journal-title":"Trends Parasitol."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1013799","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T00:00:00Z","timestamp":1766361600000}}],"container-title":["PLOS Computational 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