Automated mapping of phenotype space with single-cell data

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm

(2015) Eli R Zunder et al.   Nature Protocols

An interactive reference framework for modeling a dynamic immune system

(2015) M. H. Spitzer et al.   SCIENCE

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

SWIFT-scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, Part 2: Biological evaluation

(2014) Tim R. Mosmann et al.   CYTOMETRY PART A

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

Critical assessment of automated flow cytometry data analysis techniques

(2013) Nima Aghaeepour et al.   NATURE METHODS

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

(2012) Y. Ge et al.   BIOINFORMATICS

Ly6C supports preferential homing of central memory CD8+ T cells into lymph nodes

(2011) Arno Hänninen et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

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

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

A weighted k-nearest neighbor density estimate for geometric inference

(2011) Gérard Biau et al.   Electronic Journal of Statistics

Data reduction for spectral clustering to analyze high throughput flow cytometry data

(2010) Habil Zare et al.   BMC BIOINFORMATICS

Rapid cell population identification in flow cytometry data

(2010) Nima Aghaeepour et al.   CYTOMETRY PART A

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

Plasma cells negatively regulate the follicular helper T cell program

(2010) Nadége Pelletier et al.   NATURE IMMUNOLOGY

Mice deficient in stem cell antigen‐1 (Sca1, Ly‐6A/E) develop normal primary and memory CD4+and CD8+T‐cell responses to virus infection

(2009) Jason K. Whitmire et al.   EUROPEAN JOURNAL OF IMMUNOLOGY