Here we list some papers that can provide context for addressing the proposed challenges

Benchmarking integration pipelines

Harmony

• Fast, sensitive and accurate integration of single-cell data with Harmony

LIGER

• Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

MOFA+

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

Current Benchmarking Papers

• Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data

• Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data

• Benchmarking atlas-level data integration in single-cell genomics