OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

High-throughput flow cytometry data normalization for clinical trials

(2014) Greg Finak et al.   CYTOMETRY PART A

Safety and Comparative Immunogenicity of an HIV-1 DNA Vaccine in Combination with Plasmid Interleukin 12 and Impact of Intramuscular Electroporation for Delivery

(2013) Spyros A. Kalams et al.   JOURNAL OF INFECTIOUS DISEASES

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Critical assessment of automated flow cytometry data analysis techniques

(2013) Nima Aghaeepour et al.   NATURE METHODS

Application of user-guided automated cytometric data analysis to large-scale immunoprofiling of invariant natural killer T cells

(2013) X. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Overview of clinical flow cytometry data analysis: recent advances and future challenges

(2013) Carlos E. Pedreira et al.   TRENDS IN BIOTECHNOLOGY

Flow Cytometry Bioinformatics

(2013) Kieran O'Neill et al.   PLoS Computational Biology

Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples

(2013) Andrew Cron et al.   PLoS Computational Biology

B Cells With High Side Scatter Parameter by Flow Cytometry Correlate With Inferior Survival in Diffuse Large B-Cell Lymphoma

(2012) Ali Bashashati et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data

(2012) M. D. Linderman et al.   BIOINFORMATICS

Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays*

(2012) Nima Aghaeepour et al.   BIOINFORMATICS

flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding

(2012) Y. Ge et al.   BIOINFORMATICS

QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data

(2012) Greg Finak et al.   BMC BIOINFORMATICS

Single-cell mass cytometry adapted to measurements of the cell cycle

(2012) Gregory K. Behbehani et al.   CYTOMETRY PART A

Cell-Surface Proteomics Identifies Lineage-Specific Markers of Embryo-Derived Stem Cells

(2012) Peter J. Rugg-Gunn et al.   DEVELOPMENTAL CELL

Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8+ T Cell Phenotypes

(2012) Evan W. Newell et al.   IMMUNITY

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

Negative feedback confers mutational robustness in yeast transcription factor regulation

(2012) C. M. Denby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptation to a new environment allows cooperators to purge cheaters stochastically

(2012) A. J. Waite et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli

(2012) Selwyn Quan et al.   PLoS Genetics

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Adaptive informatics for multifactorial and high-content biological data

(2011) Bjorn L Millard et al.   NATURE METHODS

Parallel pathways in RAF-induced senescence and conditions for its reversion

(2011) M Jeanblanc et al.   ONCOGENE

Symmetry, asymmetry, and kinetics of silencing establishment in Saccharomyces cerevisiae revealed by single-cell optical assays

(2011) E. A. Osborne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flow Cytometry, Amped Up

(2011) C. Benoist et al.   SCIENCE

Development and optimization of a process for automated recovery of single cells identified by microengraving

(2010) Jae Hyeok Choi et al.   BIOTECHNOLOGY PROGRESS

Validation of Laboratory-Developed Molecular Assays for Infectious Diseases

(2010) E. M. Burd   CLINICAL MICROBIOLOGY REVIEWS

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

(2010) Yu Qian et al.   CYTOMETRY PART B-CLINICAL CYTOMETRY

Highly multiparametric analysis by mass cytometry

(2010) Olga Ornatsky et al.   JOURNAL OF IMMUNOLOGICAL METHODS

flowClust: a Bioconductor package for automated gating of flow cytometry data

(2009) Kenneth Lo et al.   BMC BIOINFORMATICS

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

Automated high-dimensional flow cytometric data analysis

(2009) S. Pyne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using flowViz to visualize flow cytometry data

(2008) D. Sarkar et al.   BIOINFORMATICS

Flow cytometer with mass spectrometer detection for massively multiplexed single-cell biomarker assay

(2008) Scott D. Tanner et al.   PURE AND APPLIED CHEMISTRY