Recent single-cell analysis technologies offer an unprecedented opportunity to elucidate
developmental pathways. Here we present Wishbone, an algorithm for positioning single …

Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage
differentiation trajectories, along with the characterization of cellular heterogeneity and state …

Single-cell RNA-sequencing offers unprecedented resolution of the continuum of state
transition during cell differentiation and development. However, tools for constructing multi …

We present single-cell clustering using bifurcation analysis (SCUBA), a novel computational
method for extracting lineage relationships from single-cell gene expression data and …

Single-cell RNA sequencing studies of differentiating systems have raised fundamental
questions regarding the discrete versus continuous nature of both differentiation and cell …

Single-cell RNA sequencing and high-dimensional cytometry can be used to generate
detailed trajectories of dynamic biological processes such as differentiation or development …

The temporal order of differentiating cells is intrinsically encoded in their single-cell
expression profiles. We describe an efficient way to robustly estimate this order according to …

Tissue regeneration is an orchestrated progression of cells from an immature state to a
mature one, conventionally represented as distinctive cell subsets. A continuum of …

Accurate identification of cell subsets in complex populations is key to discovering novelty in
multidimensional single-cell experiments. We present X-shift (http://web. stanford. edu …

A revolution in cellular measurement technology is under way: For the first time, we have the
ability to monitor global gene regulation in thousands of individual cells in a single …