arXiv subjects

Maaike van Gerwen

Publications and source records attributed to Maaike van Gerwen.

3 recordsLinked to original sources

arXiv2026

A Quasi-Regression Method for the Mediation Analysis of Zero-Inflated Single-Cell Data

Recent advances in single-cell technologies have advanced our understanding of gene regulation and cellular heterogeneity at single-cell resolution. Single-cell data contain both gene expression levels and the proportion of expressing cells, which makes them structurally different from bulk data. Currently, methodological work on causal mediation analysis for single-cell data remains limited and often requires specific distributional assumptions. To address this challenge, we present QuasiMed, a mediation framework specialized for single-cell data. Our proposed method comprises three steps, including (i) screening mediator candidates through penalized regression and marginal models (similar to sure independence screening), (ii) estimation of indirect effects through the average expression and the proportion of expressing cells, (iii) and hypothesis testing with multiplicity control. The key benefit of QuasiMed is that it specifies only the mean functions of the mediation models through a quasi-regression framework, thereby relaxing strict distributional assumptions. The method performance was evaluated through the real-data-inspired simulations, and demonstrated high power, false discovery rate control, and computational efficiency. Lastly, we applied QuasiMed to ROSMAP single-cell data to illustrate its potential to identify mediating causal pathways. R package is freely available on GitHub repository at https://github.com/sjahnn/QuasiMed.

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arXiv2025

A Statistical Framework for Co-Mediators of Zero-Inflated Single-Cell RNA-Seq Data

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity, enabling detailed molecular profiling at the individual cell level. However, integrating high-dimensional single-cell data into causal mediation analysis remains challenging due to zero inflation and complex mediator structures. We propose a novel mediation framework leveraging zero-inflated negative binomial models to characterize cell-level mediator distributions and beta regression for zero-inflation proportions. The model can identify expression level as well as expressed proportion that could mediate disease-leading causal pathway. Extensive simulation studies demonstrate improved power and controlled false discovery rates. We further illustrate the utility of this approach through application to ROSMAP single-cell transcriptomic data, uncovering biologically meaningful mediation effects that enhance understanding of disease mechanisms.

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arXiv2025

A Multi-Omics Framework for Survival Mediation Analysis of High-Dimensional Proteogenomic Data

Survival analysis plays a crucial role in understanding time-to-event (survival) outcomes such as disease progression. Despite recent advancements in causal mediation frameworks for survival analysis, existing methods are typically based on Cox regression and primarily focus on a single exposure or individual omics layers, often overlooking multi-omics interplay. This limitation hinders the full potential of integrated biological insights. In this paper, we propose SMAHP, a novel method for survival mediation analysis that simultaneously handles high-dimensional exposures and mediators, integrates multi-omics data, and offers a robust statistical framework for identifying causal pathways on survival outcomes. This is one of the first attempts to introduce the accelerated failure time (AFT) model within a multi-omics causal mediation framework for survival outcomes. Through simulations across multiple scenarios, we demonstrate that SMAHP achieves high statistical power, while effectively controlling false discovery rate (FDR), compared with two other approaches. We further apply SMAHP to the largest head-and-neck carcinoma proteogenomic data, detecting a gene mediated by a protein that influences survival time.

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