Pieter Mestdagh

This study shows that altering the MYC/MAX ratio in Drosophila eye progenitors changes cell fate by rewiring HOX gene expression and reprogramming progenitor identity.

The paper shows that many reported RNA-chromatin interactions are technical artifacts caused by DNA off-targeting, not true biological interactions.

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 identifies lncRNAs that coordinately regulate both transcription and post-transcriptional processing of their targets, showing tight coupling between lncRNA and target abundance, with implications for cancer gene regulation.

This study attempts to replicate the claimed sensitivity of NISDA but fails to achieve detectable signals except at very high concentrations.

The paper identifies NESPR, an adrenergic-specific lncRNA, as a regulator of neuroblastoma cell identity that prevents cell death by attenuating stress.

This study identifies sources of skeletal muscle fiber heterogeneity beyond myosin heavy chains using transcriptomic and proteomic data from human muscle fibers.

This study investigates the role of MAPT-AS1 in regulating Tau expression in human neurons and finds no evidence supporting its function as described in Simone et al.

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.

The paper evaluates deconvolution methods for bulk RNA-Seq using scnRNA-Seq data, identifies biases, and introduces SQUID, a method that outperforms others in predicting cell mixtures and identifying cancer subclones.

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.

This paper introduces a 3'-end capture sequencing method for targeted gene expression profiling, achieving 100-fold enrichment of target genes with shallow sequencing.

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 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.

The paper introduces a non-parametric specificity score to identify tissue-specific genes from unbalanced datasets and applies it to GTEx data.

This study benchmarks deconvolution methods for bulk transcriptomics data, showing reference marker selection and normalization impact performance, with single-cell methods performing comparably to bulk methods.

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 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.