Tommaso Mansi

Benchmarking single-cell foundation models for real-world RNA-seq data integration

This study benchmarks single-cell foundation models for data integration using real-world RNA-seq data and finds that fine-tuned scGPT_CP performs best in technical correction while scVI is the top overall performer.

Bridging biomolecular modalities for knowledge transfer in bio-language models

This paper adapts DNA and protein bio-language models for mRNA-focused tasks through various finetuning techniques, showing that medium-scale models perform best for cross-modal knowledge transfer.