As the field of single-cell transcriptomics matures, research is shifting focus from
phenomenological descriptions of cellular phenotypes to a mechanistic understanding of the …

Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present
sciCSR (pronounced 'scissor', single-cell inference of class-switch recombination), a …

Abstract Deep Generative Models (DGMs) are becoming instrumental for inferring
probability distributions inherent to complex processes, such as most questions in …

Gene expression dynamics provide directional information for trajectory inference from
single-cell RNA sequencing data. Traditional approaches compute RNA velocity using strict …

RNA velocity is a powerful paradigm that exploits the temporal information contained in
spliced and unspliced RNA counts to infer transcriptional dynamics. Existing velocity models …

Single-cell RNA Velocity has dramatically advanced our ability to model cellular
differentiation and cell fate decisions. However, current preprocessing choices and model …

Typical differential single-nucleus gene expression (snRNA-seq) analyses in Alzheimer's
disease (AD) provide fixed snapshots of cellular alterations, making the accurate detection …

Across a range of biological processes, cells undergo coordinated changes in gene
expression, resulting in transcriptome dynamics that unfold within a low-dimensional …

RNA velocity estimation is a potentially powerful tool to reveal the directionality of
transcriptional changes in single-cell RNA-sequencing data, but it lacks accuracy, absent …

The snapshot nature of single-cell transcriptomics presents a challenge for studying the
dynamics of cell fate decisions. Metabolic labeling and splicing can provide temporal …