Dewei Hu

SLIM predicts single-cell genetic perturbation responses using STRING embeddings and a closed-form ridge regression model, achieving competitive accuracy with low computational cost.

The paper constructs disease maps by integrating omics data with protein network embeddings, identifying more disease-relevant proteins than omics analysis alone.

The paper develops cross-species protein embeddings using network data and shows they improve subcellular localization and function prediction when combined with sequence embeddings.

The paper introduces DeepCompARE, an in silico ablation framework to analyze TF cooperativity, finding most TF motifs are independent with defined synergy and redundancy effects.