Visualizing structure and transitions in high-dimensional biological data

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

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

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

On the diffusion geometry of graph laplacians and applications

(2018) Xiuyuan Cheng et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture

(2016) Emily M. Darrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry

(2015) Eli R. Zunder et al.   Cell Stem Cell

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Getting Things in Order: An Introduction to theRPackageseriation

(2015) Michael Hahsler et al.   Journal of Statistical Software

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

(2014) Sean C. Bendall et al.   CELL

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Conditional density-based analysis of T cell signaling in single-cell data

(2014) S. Krishnaswamy et al.   SCIENCE

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

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

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Coarse-grained localized diffusion

(2012) Guy Wolf et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

Hierarchical data organization, clustering and denoising via localized diffusion folders

(2011) Gil David et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

A visualization metric for dimensionality reduction

(2011) Flora S. Tsai   EXPERT SYSTEMS WITH APPLICATIONS

Quality Metrics in High-Dimensional Data Visualization: An Overview and Systematization

(2011) E. Bertini et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Shannon and von Neumann entropy of random networks with heterogeneous expected degree

(2011) Kartik Anand et al.   PHYSICAL REVIEW E

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

(2011) S. C. Bendall et al.   SCIENCE

Assembling Neural Crest Regulatory Circuits into a Gene Regulatory Network

(2010) Paola Betancur et al.   Annual Review of Cell and Developmental Biology

On Local Intrinsic Dimension Estimation and Its Applications

(2009) K.M. Carter et al.   IEEE TRANSACTIONS ON SIGNAL PROCESSING

Local Multidimensional Scaling for Nonlinear Dimension Reduction, Graph Drawing, and Proximity Analysis

(2009) Lisha Chen et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE