Olivier Thas

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

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

The paper addresses the winners curse in statistical estimation under dependence, proposing a density convolution method to improve empirical Bayes approaches and demonstrating its effectiveness through simulations and a real-world application.

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 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.

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.

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.

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

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