Jo Vandesompele

The paper shows that different RNase R enzymes from the same supplier can produce inconsistent results in circRNA validation, emphasizing the need for consistent verification with linear controls.

The paper introduces the Digital PCR Data Essentials Standard (DDES) to standardize data structure for dPCR, improving interoperability and reproducibility across platforms and applications.

This paper introduces FibeRtypeR, a tool to estimate muscle fiber type proportions from bulk transcriptomics and proteomics data using single-fiber reference profiles.

The paper introduces PCR-ValiPal, a web tool for standardized dPCR assay validation, and evaluates its performance across four platforms for BPV quantification.

This study identifies intact messenger RNA in human blood plasma and urine using long-read sequencing, showing differences and shared transcripts between biofluids and their macromolecular compartments.

HTSplotter automates data processing, analysis, and visualization for in vitro perturbation screens, supporting multiple experimental types and time-course data.

This paper introduces three new statistical methods for variance estimation in digital PCR experiments, showing they provide more accurate results than classical binomial methods.

The paper benchmarks 16 circRNA detection tools across three human cell types, finding large differences in sensitivity but consistent precision, and recommends tool combinations for improved detection.

The paper introduces a method to block abundant RNA transcripts during library preparation, improving transcriptome coverage and complexity by reducing competition from highly abundant RNAs.

The paper evaluates three DNA sample tracking tools in a whole exome sequencing workflow, finding the pxlence kit most reliable and cost-effective.

The paper introduces a custom lncRNA capture sequencing approach to improve detection sensitivity of lncRNAs in various human sample types.

The paper evaluates RNA purification kits and blood collection tubes for exRNA quality, finding that preservation tubes and purification methods significantly affect RNA stability, sensitivity, and reproducibility.

The paper creates a comprehensive atlas of RNA transcriptomes across 20 human biofluids, revealing significant differences in RNA concentration and composition, and validates potential biomarkers in disease cohorts.

This study benchmarks single cell RNA-seq technologies to assess their ability to detect transcriptional changes in NGP neuroblastoma cells after nutlin-3 treatment, finding heterogeneity in response not captured by bulk RNA-seq.

This study evaluates how blood collection tubes and time delay affect cfDNA methylation, finding robust results across tubes but recommending EDTA tubes processed within 24 hours.

The paper evaluates SILVER-Seq data for DNA contamination and finds low exonic and splice read fractions, suggesting contamination issues in the technology.

This study demonstrates that reduced representation bisulfite sequencing of cell-free DNA can accurately classify pediatric solid tumors with high sensitivity.

The paper introduces a semi-parametric probabilistic index model for differential expression testing in scRNA-seq, showing it effectively controls false discovery rate and identifies biologically meaningful DE.

SPsimSeq simulates bulk and single-cell RNA-seq data by estimating the empirical distribution of real data, allowing for various experimental scenarios and library preparation protocols.

The paper evaluates the SMARTer Stranded Total RNA-Seq method's performance in quantifying total RNA from various human biofluids and extracellular vesicles, finding it accurate, precise, and capable of detecting thousands of genes.

The paper presents a comprehensive human transcriptome atlas with single-nucleotide resolution, identifying thousands of novel RNA species and regulatory interactions.

The paper presents a comprehensive dataset of TLX1 positive ALL-SIL lymphoblasts and primary T-ALL leukemias using polyA[+] and total RNA sequencing, ATAC sequencing, and ChIP sequencing, validated for quality and biological relevance.

The paper introduces a novel single cell strand-specific total RNA sequencing method that overcomes limitations of existing techniques and detects more genes, including non-polyadenylated ones.

The paper identifies focal copy number alterations in lncRNAs across cancer cell lines, suggesting potential oncogenic or tumor suppressive roles.

The paper evaluates DE tools for RNA-seq data, finding poor performance for lncRNAs and highlighting the need for more samples to achieve acceptable sensitivity.

The paper introduces Zipper plot, a tool to visualize transcriptional activity around TSSs using RNA-seq and other genomic data.