Article

Three Classes of Confound in Gene-Regulatory-Network Inference: A Systematic Audit and Open-Source Diagnostic Toolkit

2026-03-26

Abstract excerpt

<title>Abstract</title> <p> <bold>Background</bold> : Inferred gene regulatory networks (GRNs) from single-cell RNA-seq are used to prioritize transcription-factor–target hypotheses, yet edge rankings can be inflated by confounds that are rarely audited systematically. Individual confound classes—technical batch effects, genomic proximity co-expression, and degree-distribution artifacts—have been studied in iso...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: aab2bf7d-0e4a-5418-9c2d-a1ddae8a257b
DOI: 10.21203/rs.3.rs-8997629/v1

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Three Classes of Confound in Gene-Regulatory-Network Inference: A Systematic Audit and Open-Source Diagnostic ToolkitDOI 10.21203/rs.3.rs-8997629/v1Read

Aggregation of <i>recount3</i> RNA-seq data improves inference of consensus and tissue-specific gene co-expression networksSemantic proximity Read

Benchmarking precision matrix estimation methods for differential co-expression network analysisSemantic proximity Read

X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation ModelsSemantic proximity Read

BoYueGRN: Zero-shot causal discovery of directed gene regulatory networks from single-cell transcriptomes via amortized inference over synthetic structural causal modelsSemantic proximity Read

Efficient Inference of Direct Gene--Gene Associations via High-Dimensional Precision Matrix with Rigorous FDR ControlSemantic proximity Read

geneRNIB: a living benchmark for gene regulatory network inferenceSemantic proximity Read

AlphaGenome deletion responses complement supervised enhancer–gene relation prediction in primary human astrocytesSemantic proximity Read

Uncertainty-Aware Gene Rankings Reveal Key Players in Coexpression NetworksSemantic proximity Read

Dozer: Debiased personalized gene co-expression networks for population-scale scRNA-seq dataSemantic proximity Read

Inhibitory Knowledge Flow from E-Communities of Practice Stabilizes Causal Gene Circuit Architectures in Single-Cell Foundation ModelsSemantic proximity Read

Exon inclusion signatures enable accurate estimation of splicing factor activitySemantic proximity Read

Sparse autoencoders reveal organized biological knowledge but minimal regulatory logic in single-cell foundation models: a comparative atlas of Geneformer and scGPTSemantic proximity Read