FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets

Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data

(2019) George C. Linderman et al.   NATURE METHODS

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Inferring population dynamics from single-cell RNA-sequencing time series data

(2019) David S. Fischer et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut

(2018) Charles A. Herring et al.   Cell Systems

Population snapshots predict early haematopoietic and erythroid hierarchies

(2018) Betsabeh Khoramian Tusi et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data

(2016) David DeTomaso et al.   BMC BIOINFORMATICS

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Computational methods for trajectory inference from single-cell transcriptomics

(2016) Robrecht Cannoodt et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Visualization and cellular hierarchy inference of single-cell data using SPADE

(2016) Benedict Anchang et al.   Nature Protocols

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline

(2016) Hao Chen et al.   PLoS Computational Biology

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

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

(2015) Jacob H. Levine et al.   CELL

Early reprogramming regulators identified by prospective isolation and mass cytometry

(2015) Ernesto Lujan et al.   NATURE

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

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

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

(2014) Mathieu Jacomy et al.   PLoS One

Knowledge discovery by accuracy maximization

(2014) S. Cacciatore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Normalization of mass cytometry data with bead standards

(2013) Rachel Finck et al.   CYTOMETRY PART A

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

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

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst

(2012) F. Buettner et al.   BIOINFORMATICS

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

Highly multiparametric analysis by mass cytometry

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

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

Anterior Definitive Endoderm from ESCs Reveals a Role for FGF Signaling

(2008) Gillian M. Morrison et al.   Cell Stem Cell

Wnt, Activin, and BMP Signaling Regulate Distinct Stages in the Developmental Pathway from Embryonic Stem Cells to Blood

(2008) M. Cristina Nostro et al.   Cell Stem Cell

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

What is principal component analysis?

(2008) Markus Ringnér   NATURE BIOTECHNOLOGY