Waddington's epigenetic landscape is an abstract metaphor frequently used to represent the
relationship between gene activity and cell fates during development. Over the past few …

Myeloid cells are a major cellular compartment of the immune system comprising
monocytes, dendritic cells, tissue macrophages, and granulocytes. Models of cellular …

We present SCENIC, a computational method for simultaneous gene regulatory network
reconstruction and cell-state identification from single-cell RNA-seq data (http://scenic …

While single-cell gene expression experiments present new challenges for data processing,
the cell-to-cell variability observed also reveals statistical relationships that can be used by …

Motivation The analysis of RNA-Seq data from individual differentiating cells enables us to
reconstruct the differentiation process and the degree of differentiation (in pseudo-time) of …

Background A fundamental fact in biology states that genes do not operate in isolation, and
yet, methods that infer regulatory networks for single cell gene expression data have been …

Background Single-cell RNA sequencing (scRNA-seq) plays a pivotal role in our
understanding of cellular heterogeneity. Current analytical workflows are driven by …

Single-cell techniques are advancing rapidly and are yielding unprecedented insight into
cellular heterogeneity. Map** the gene regulatory networks (GRNs) underlying cell states …

Understanding cellular heterogeneity is the holy grail of biology and medicine. Cells
harboring identical genomes show a wide variety of behaviors in multicellular organisms …

The ability to quantify differentiation potential of single cells is a task of critical importance.
Here we demonstrate, using over 7,000 single-cell RNA-Seq profiles, that differentiation …