Chemical reprogramming offers an unprecedented opportunity to control somatic cell fate
and generate desired cell types including pluripotent stem cells for applications in …

The multistep process of in vivo reprogramming, mediated by the transcription factors (TFs)
Oct4, Sox2, Klf4, and c-Myc (OSKM), holds great promise for the development of …

We describe a workflow for preprocessing of single-cell RNA-sequencing data that balances
efficiency and accuracy. Our workflow is based on the kallisto and bustools programs, and is …

Dimensionality reduction is often used to visualize complex expression profiling data. Here,
we use the Uniform Manifold Approximation and Projection (UMAP) method on published …

Transposable elements (TEs) make up a majority of a typical eukaryote's genome, and
contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are …

Cell fate transitions are accompanied by global transcriptional, epigenetic and topological
changes driven by transcription factors, as is exemplified by reprogramming somatic cells to …

Partial pluripotent reprogramming can reverse features of aging in mammalian cells, but the
impact on somatic identity and the necessity of individual reprogramming factors remain …

Langerhans cells (LCs) play a pivotal role in skin homeostasis, and the heterogeneity of LCs
has long been considered. In this study, we have identified two steady-state (LC1 and LC2) …

Coordinated changes of cellular plasticity and identity are critical for pluripotent
reprogramming and oncogenic transformation. However, the sequences of events that …

Abstract Analysis of single-cell RNA-seq data begins with pre-processing of sequencing
reads to generate count matrices. We investigate algorithm choices for the challenges of pre …