Katleen De Preter

This study benchmarks artificial cfDNA generated by fragmentation methods against native cfDNA, finding enzymatic methods better replicate native characteristics.

This study benchmarks DNA methylation deconvolution methods for tumoral fraction estimation in cfDNA, finding CelFiE most accurate and introducing DecoNFlow as a comprehensive pipeline.

The paper introduces cf-RRBS, a method for methylation profiling of fragmented plasma DNA, enabling cost-effective and accurate non-invasive lung cancer subtyping.

This study evaluates single-sample network inference methods for cancer subtyping using bulk RNA-seq data from cancer cell lines.

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 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.

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

Unsupervised trajectory inference by SCORPIUS outperformed Wanderlust, Monocle and Waterfall across ten scRNA-seq datasets and predicted falling protein synthesis during dendritic cell development, validated in vivo.

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