{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T15:12:52Z","timestamp":1777129972542,"version":"3.51.4"},"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2014,8,28]],"date-time":"2014-08-28T00:00:00Z","timestamp":1409184000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003806","type":"journal-article","created":{"date-parts":[[2014,8,28]],"date-time":"2014-08-28T17:54:56Z","timestamp":1409248496000},"page":"e1003806","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":206,"title":["OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis"],"prefix":"10.1371","volume":"10","author":[{"given":"Greg","family":"Finak","sequence":"first","affiliation":[]},{"given":"Jacob","family":"Frelinger","sequence":"additional","affiliation":[]},{"given":"Wenxin","family":"Jiang","sequence":"additional","affiliation":[]},{"given":"Evan W.","family":"Newell","sequence":"additional","affiliation":[]},{"given":"John","family":"Ramey","sequence":"additional","affiliation":[]},{"given":"Mark M.","family":"Davis","sequence":"additional","affiliation":[]},{"given":"Spyros A.","family":"Kalams","sequence":"additional","affiliation":[]},{"given":"Stephen C.","family":"De Rosa","sequence":"additional","affiliation":[]},{"given":"Raphael","family":"Gottardo","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,8,28]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1126\/science.1206351","article-title":"Immunology. Flow cytometry, amped up","volume":"332","author":"C Benoist","year":"2011","journal-title":"Science"},{"issue":"7","key":"ref2","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/j.tibtech.2013.04.008","article-title":"Overview of clinical flow cytometry data analysis: recent advances and future challenges","volume":"31","author":"CE Pedreira","year":"2013","journal-title":"Trends Biotechnol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1002\/btpr.374","article-title":"Development and optimization of a process for automated recovery of single cells identified by microengraving","volume":"26","author":"JH Choi","journal-title":"Biotechnol Prog"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jim.2010.07.002","article-title":"Highly multiparametric analysis by mass cytometry","volume":"361","author":"O Ornatsky","year":"2010","journal-title":"J Immunol Methods"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"2627","DOI":"10.1351\/pac200880122627","article-title":"Flow cytometer with mass spectrometer detection for massively multiplexed single-cell biomarker assay","volume":"80","author":"SD Tanner","year":"2008","journal-title":"Pure Appl Chem"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"iv","DOI":"10.1038\/nmeth.f.259","article-title":"Fluidigm Dynamic Arrays provide a platform for single-cell gene expression analysis","volume":"6","author":"M Pieprzyk","year":"2009","journal-title":"Nat Methods"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1471-2172-6-13","article-title":"Standardization of cytokine flow cytometry assays","volume":"6","author":"HT Maecker","year":"2005","journal-title":"BMC Immunol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nri3229","article-title":"Standardizing immunophenotyping for the Human Immunology Project","volume":"12","author":"HT Maecker","year":"2012","journal-title":"Nat Rev Immunol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"8519","DOI":"10.1073\/pnas.0903028106","article-title":"Automated high-dimensional flow cytometric data analysis","volume":"106","author":"S Pyne","year":"2009","journal-title":"Proc Natl Acad Sci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"247646","DOI":"10.1155\/2009\/247646","article-title":"Merging mixture components for cell population identification in flow cytometry","volume":"2009","author":"G Finak","year":"2009","journal-title":"Adv Bioinformatics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1093\/bioinformatics\/bts300","article-title":"flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding","volume":"8","author":"Y Ge","year":"2012","journal-title":"Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/nmeth0513-445e","article-title":"Critical assessment of automated flow cytometry data analysis techniques","volume":"10","author":"N Aghaeepour","year":"2013","journal-title":"Nat Methods"},{"key":"ref13","first-page":"509","article-title":"SWIFT: Scalable weighted iterative sampling for flow cytometry clustering","author":"I Naim","year":"2010","journal-title":"Proc IEEE Intl Conf Acoust Speech Sig Proc"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"S69","DOI":"10.1002\/cyto.b.20554","article-title":"Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data","volume":"78","author":"Y Qian","year":"2010","journal-title":"Cytom Part B Clin Cytom"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1287\/isre.11.4.342.11872","article-title":"Determinants of Perceived Ease of Use: Integrating Control, Intrinsic Motivation, and Emotion into the Technology Acceptance Model","volume":"11","author":"V Venkatesh","year":"2000","journal-title":"Inf Syst Res"},{"issue":"10","key":"ref16","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1038\/nbt.1991","article-title":"Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE","volume":"29","author":"P Qiu","year":"2011","journal-title":"Nat Biotechnol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/nbt.2594","article-title":"viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia","volume":"31","author":"ED Amir","year":"2013","journal-title":"Nat Biotechnol"},{"key":"ref18","first-page":"Unit10.17","article-title":"Web-based analysis and publication of flow cytometry experiments","volume":"Chapter 10","author":"N Kotecha","year":"2010","journal-title":"Curr Protoc Cytom"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"19030","DOI":"10.1073\/pnas.1318322110","article-title":"Application of user-guided automated cytometric data analysis to large-scale immunoprofiling of invariant natural killer T cells","volume":"110","author":"X Hu","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e1003130","DOI":"10.1371\/journal.pcbi.1003130","article-title":"Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples","volume":"9","author":"A Cron","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e1003365","DOI":"10.1371\/journal.pcbi.1003365","article-title":"Flow Cytometry Bioinformatics","volume":"9","author":"K O'Neill","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1128\/CMR.00074-09","article-title":"Validation of laboratory-developed molecular assays for infectious diseases","volume":"23","author":"EM Burd","year":"2010","journal-title":"Clin Microbiol Rev"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1186\/1471-2105-10-106","article-title":"flowCore: a Bioconductor package for high throughput flow cytometry","volume":"10","author":"F Hahne","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1093\/bioinformatics\/btn021","article-title":"Using flowViz to visualize flow cytometry data","volume":"24","author":"D Sarkar","year":"2008","journal-title":"Bioinformatics"},{"key":"ref25","unstructured":"Hahne F, Gopalakrishnan N, Khodabakhshi AH, Wong C-J, Lee K (2009) flowStats: Statistical methods for the analysis of flow cytometry data."},{"key":"ref26","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1186\/1471-2105-13-252","article-title":"QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data","volume":"13","author":"G Finak","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1109\/38.56302","article-title":"NetCDF: an interface for scientific data access","volume":"10","author":"R Rew","year":"1990","journal-title":"Comput Graph Appl IEEE"},{"key":"ref28","first-page":"1","article-title":"Mixture models for single-cell assays with applications to vaccine studies","author":"G Finak","year":"2013","journal-title":"Biostatistics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1002\/cyto.a.22433","article-title":"High-throughput flow cytometry data normalization for clinical trials","volume":"85","author":"G Finak","year":"2013","journal-title":"Cytometry A"},{"issue":"1","key":"ref30","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.immuni.2012.01.002","article-title":"Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8+ T Cell Phenotypes","volume":"36","author":"EW Newell","year":"2012","journal-title":"Immunity"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1186\/1471-2105-10-145","article-title":"flowClust: a Bioconductor package for automated gating of flow cytometry data","volume":"10","author":"K Lo","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1093\/infdis\/jit236","article-title":"Safety and Comparative Immunogenicity of an HIV-1 DNA Vaccine in Combination with Plasmid Interleukin 12 and Impact of Intramuscular Electroporation for Delivery","volume":"208","author":"SA Kalams","year":"2013","journal-title":"J Infect Dis"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.jim.2007.03.002","article-title":"Optimization and validation of an 8-color intracellular cytokine staining (ICS) assay to quantify antigen-specific T cells induced by vaccination","volume":"323","author":"H Horton","year":"2007","journal-title":"J Immunol Methods"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"255","DOI":"10.2307\/2532051","article-title":"A concordance correlation coefficient to evaluate reproducibility","volume":"45","author":"LI Lin","year":"1989","journal-title":"Biometrics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S0140-6736(86)90837-8","article-title":"Statistical methods for assessing agreement between two methods of clinical measurement","volume":"1(8476)","author":"JM Bland","year":"1986","journal-title":"Lancet"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/nmeth.1600","article-title":"Adaptive informatics for multifactorial and high-content biological data","volume":"8","author":"BL Millard","year":"2011","journal-title":"Nat Methods"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1007\/978-1-4419-5913-3_77","article-title":"Standardizing the next generation of bioinformatics software development with BioHDF (HDF5)","volume":"680","author":"CE Mason","year":"2010","journal-title":"Adv Exp Med Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1145\/1966895.1966900","article-title":"An overview of the HDF5 technology suite and its applications","author":"M Folk","year":"2011","journal-title":"Proc EDBTICDT 2011 Work Array Databases"},{"key":"ref39","unstructured":"Fletez-Brant K (n.d.) flowClean: flowClean."},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/bts082","article-title":"Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays","volume":"28","author":"N Aghaeepour","year":"2012","journal-title":"Bioinformatics"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1309\/AJCPGR8BG4JDVOWR","article-title":"B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma","volume":"137","author":"A Bashashati","year":"2012","journal-title":"Am J Clin Pathol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1002\/cyto.a.22075","article-title":"Single-cell mass cytometry adapted to measurements of the cell cycle","volume":"81","author":"GK Behbehani","year":"2012","journal-title":"Cytometry A"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1038\/nbt.2317","article-title":"Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators","volume":"30","author":"B Bodenmiller","year":"2012","journal-title":"Nat Biotechnol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"3874","DOI":"10.1073\/pnas.1116360109","article-title":"Negative feedback confers mutational robustness in yeast transcription factor regulation","volume":"109","author":"CM Denby","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"3072","DOI":"10.1038\/onc.2011.481","article-title":"Parallel pathways in RAF-induced senescence and conditions for its reversion","volume":"31","author":"M Jeanblanc","year":"2012","journal-title":"Oncogene"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"2400","DOI":"10.1093\/bioinformatics\/bts425","article-title":"CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data","volume":"28","author":"MD Linderman","year":"2012","journal-title":"Bioinformatics"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1073\/pnas.1018742108","article-title":"Symmetry, asymmetry, and kinetics of silencing establishment in Saccharomyces cerevisiae revealed by single-cell optical assays","volume":"108","author":"EA Osborne","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"e1002444","DOI":"10.1371\/journal.pgen.1002444","article-title":"Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli","volume":"8","author":"S Quan","year":"2012","journal-title":"PLoS Genet"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1016\/j.devcel.2012.01.005","article-title":"Cell-surface proteomics identifies lineage-specific markers of embryo-derived stem cells","volume":"22","author":"PJ Rugg-Gunn","year":"2012","journal-title":"Dev Cell"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"19079","DOI":"10.1073\/pnas.1210190109","article-title":"Adaptation to a new environment allows cooperators to purge cheaters stochastically","volume":"109","author":"AJ Waite","year":"2012","journal-title":"Proc Natl Acad Sci U S A"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003806","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T20:26:23Z","timestamp":1588969583000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003806"}},"subtitle":[],"editor":[{"given":"Andreas","family":"Prlic","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,8,28]]},"references-count":50,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2014,8,28]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003806","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,8,28]]}}}