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Gene regulatory network inference in the era of single-cell multi-omics

Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis

Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Decoding gene regulation in the mouse embryo using single-cell multi-omics

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution

Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness

Computational principles and challenges in single-cell data integration

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

Multi-omics profiling of mouse gastrulation at single-cell resolution