Human tissues comprise trillions of cells that populate a complex space of molecular
phenotypes and functions and that vary in abundance by 4–9 orders of magnitude. Relying …

High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene
expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing …

Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and
sorted cells to characterize transcriptomes,,,,,,,,,,, but applying this technology to single cells …

We developed a massive-scale RNA sequencing protocol, short quantitative random RNA
libraries or SQRL, to survey the complexity, dynamics and sequence content of …

We present STARsolo, a comprehensive turnkey solution for quantifying gene expression in
single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR. Using simulated data …

RNA-seq is an effective method for studying the transcriptome, but it can be difficult to apply
to scarce or degraded RNA from fixed clinical samples, rare cell populations or cadavers …

Motivation: Promoter analysis is an essential step on the way to identify regulatory networks.
A prerequisite for successful promoter analysis is the prediction of potential transcription …

Abstract We previously reported Paired-Tag, a combinatorial indexing-based method that
can simultaneously map histone modifications and gene expression at single-cell resolution …

A generic DNA microarray design applicable to any species would greatly benefit
comparative genomics. We have addressed the feasibility of such a design by leveraging …

Massively parallel reporter assays (MPRAs) enable nucleotide-resolution dissection of
transcriptional regulatory regions, such as enhancers, but only few regions at a time. Here …