Euxhen Hasanaj

Finetuning Foundation Models for Temporal Clinical Transcriptomics Data

The paper finetunes gene embeddings from foundation models for temporal clinical transcriptomics data, improving gene network analysis and detection of disease progression and drug response mechanisms.

Foundation Models Improve Perturbation Response Prediction

This study evaluates foundation models for predicting cellular responses to perturbations, finding that some pretrained embeddings improve predictions while others do not.

Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction

This paper benchmarks foundation model representations for predicting cellular perturbation responses, identifying effective representation learning strategies.

SenSet, a novel human lung senescence cell gene signature, identifies cell-specific senescence mechanisms

The paper develops SenSet, a gene signature for human lung senescence, validated in 3D culture models and identifies cell-type specific senescence mechanisms in aging and disease.

Cellar: Interactive single cell data annotation tool

Cellar is an interactive tool for annotating cell types in single-cell multi-omics and spatial proteomics data using HuBMAP datasets.