Article

SPEAR: Predicting Gene Expression from Single-Cell Chromatin Accessibility

2026-04-14

Abstract excerpt

Single-cell multiome assays enable direct measurement of chromatin accessibility and gene expression within the same cell. Still, most experimental designs remain constrained to two (and, less commonly, three) modalities per cell. This limitation motivates computational models that can predict unmeasured layers and, simultaneously, help dissect how cis-regulatory accessibility relates to transcription at gene reso...

Topics

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

Identifiers and source

Literature Corpus work: 3cf3abab-5aff-5419-a09a-1b605eb25e3c
DOI: 10.64898/2026.04.13.717809

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

SPEAR: Predicting Gene Expression from Single-Cell Chromatin AccessibilityDOI 10.64898/2026.04.13.717809Read

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networksSemantic proximity Read

UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibilitySemantic proximity Read

Single-cell multiome regression models identify functional and disease-associated enhancers and enable chromatin potential analysisSemantic proximity Read

EpiAgent: Foundation Model for Single-Cell EpigenomicsSemantic proximity Read

REnformer, a single-cell ATAC-seq predicting model to investigate open chromatin sitesSemantic proximity Read

XChrom: a cross-cell chromatin accessibility prediction model integrating genomic sequence and cellular contextSemantic proximity Read

Programming human cell type-specific gene expression via an atlas of AI-designed enhancersSemantic proximity Read

EpiAgent: Foundation model for single-cell epigenomic dataSemantic proximity Read

Regulatory Logic in Larger Single-Cell Foundation Models: A Sparse Autoencoder Comparison of scFoundation and GeneformerSemantic proximity Read

Regulatory Logic in Larger Single-Cell Foundation Models: A Sparse Autoencoder Comparison of scFoundation and GeneformerSemantic proximity Read

SCOPE: Localizing fate-decision states and their regulatory drivers in single-cell differentiationSemantic proximity Read

AENetMoX: Fast and Precise scRNA-seq Gene Regulatory Network Inference Through Multi-Modal Feature Integration in Brain OrganoidsSemantic proximity Read