Koen Van den Berge

CD8 T cells with classical and NK-like cytotoxic gene expression programs mediate control of HBV replication and functional cure

The paper identifies two distinct CD8 T cell gene expression programs in HBV infection that correlate with viral control and functional cure.

transfactor: Transcription factor activity estimation via probabilistic gene expression deconvolution

This paper introduces a statistical model to estimate transcription factor activity from gene expression data by leveraging gene regulatory networks, improving interpretation of biological differences.

Assessing differential cell composition in single-cell studies using voomCLR

This paper introduces voomCLR, a method to assess differential cell composition in single-cell studies by accounting for bias uncertainty and mean-variance structure.

Differential detection workflows for multi-sample single-cell RNA-seq data

The paper develops a workflow for differential detection analysis in single-cell RNA-seq data and shows it provides complementary information to differential expression analysis.

Strategies for addressing pseudoreplication in multi-patient scRNA-seq data

This paper evaluates strategies to address pseudoreplication in multi-patient scRNA-seq data, finding that Poisson GEEs and pseudobulk approaches outperform single-cell methods.

Improving replicability in single-cell RNA-Seq cell type discovery with Dune

Dune improves replicability of cell type discovery in scRNA-Seq by optimizing the trade-off between cluster resolution and cross-dataset consistency.

A guide to trajectory inference and RNA velocity

This paper explains trajectory inference and RNA velocity methods for analyzing single-cell RNA-seq data to study cellular dynamics.

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

The paper benchmarks ATAC-seq normalization methods and shows that GC-content effects must be accounted for to improve downstream analysis accuracy.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

satuRn: Scalable Analysis of differential Transcript Usage for bulk and single-cell RNA-sequencing applications

satuRn analyzes differential transcript usage in bulk and single-cell RNA-seq data, offering scalability and accurate false discovery rate control.

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression.

The paper introduces a method to infer and compare cell trajectories across multiple conditions, detecting differences in progression, population structure, and gene expression.

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta

The paper identifies genes responding to sex-inducing pheromones in the diatom Seminavis robusta and links them to sexual reproduction processes.

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

The paper identifies non-neuronal cell types in the olfactory system expressing SARS-CoV-2 entry genes, suggesting indirect mechanisms for COVID-19-associated anosmia.

Trajectory-based differential expression analysis for single-cell sequencing data

The paper introduces a generalized additive model framework for trajectory-based differential expression analysis in single-cell RNA-seq data, enabling flexible inference of within and between lineage gene expression differences.

Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications

The paper introduces a weighting strategy using a zero-inflated negative binomial model to improve bulk RNA-seq tools for single-cell RNA-seq data with zero inflation.

A general and powerful stage-wise testing procedure for differential expression and differential transcript usage

The paper introduces a stage-wise testing procedure for differential expression and transcript usage that provides gene-level FDR control while maintaining transcript-level resolution.

zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications

zingeR improves differential expression analysis in scRNA-seq by using a zero-inflated negative binomial model to address zero-inflation, matching performance of dedicated scRNA-seq tools.