Reversed graph embedding resolves complex single-cell trajectories

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

(2016) Andre Olsson et al.   NATURE

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

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

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

From Understanding the Development Landscape of the Canonical Fate-Switch Pair to Constructing a Dynamic Landscape for Two-Step Neural Differentiation

(2012) Xiaojie Qiu et al.   PLoS One