Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research.

Single-cell RNA sequencing (scRNA-seq) revolutionized our understanding of disease biology. The promise it presents to also transform translational research requires highly standardized and robust software workflows. Here, we present the toolkit , which streamlines scRNA-seq analyses and their use to deconvolute bulk RNA-seq data according to current best practices.

Multiple rereads of single proteins at single-amino acid resolution using nanopores.

A proteomics tool capable of identifying single proteins would be important for cell biology research and applications. Here, we demonstrate a nanopore-based single-molecule peptide reader sensitive to single–amino acid substitutions within individual peptides. A DNA-peptide conjugate was pulled through the biological nanopore MspA by the DNA helicase Hel308.

Ready-to-use nanopore platform for the detection of any DNA/RNA oligo at attomole range using an Osmium tagged complementary probe.

Nanopores can serve as single molecule sensors. We exploited the MinION, a portable nanopore device from Oxford Nanopore Technologies, and repurposed it to detect any DNA/RNA oligo (target) in a complex mixture by conducting voltage-driven ion-channel measurements. The detection and quantitation of the target is enabled by the use of a unique complementary probe.

Locating patterns in Nanopore currents using time-warped signal representation of consensus nucleotides for demultiplexing and motif detection.

Nanopore-based approaches for the sequencing of DNA and RNA molecules are promising technologies with potential applications in clinical genomics. These approaches have generated large numbers of time series objects over the years, however, it remains a challenge to accurately decipher the underlying nucleotide sequence corresponding to a given signal. By using a combination of consensus signal averaging and stream monitoring of variable-length motifs, we outline an online pattern matching framework that can efficiently locate consensus sequences in real world Nanopore datasets.

Identification of New Regulators of the Oocyte-to-Embryo Transition in .

At the oocyte-to-embryo transition the highly differentiated oocyte arrested in meiosis becomes a totipotent embryo capable of embryogenesis. Oocyte maturation (release of the prophase I primary arrest) and egg activation (release from the secondary meiotic arrest and the trigger for the oocyte-to-embryo transition) serve as prerequisites for this transition, both events being controlled posttranscriptionally. Recently, we obtained a comprehensive list of proteins whose levels are developmentally regulated during these events via a high-throughput quantitative proteomic analysis of oocyte maturation and egg activation.