Author

Andrew Robbins

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Open access Oct 2026

Beyond the Final Layer: Evaluating Single-Cell Foundation Model Representations for Molecular Prediction

Single-cell foundation models (scFMs) are commonly benchmarked using final-layer embeddings, although useful depth may depend on the task. We evaluate Geneformer, scBERT, scGPT, and scFoundation as frozen feature extractors for cell-type and perturbation-response prediction using layer-wise probes, leave-one-dataset-ou...

Ming Wen, Yiwei Lyu, Andrew Robbins · bioRxiv · 0 citations

Open access Sep 2026

LIGER2: Scalable Single-Cell Integration with On-Disk Datasets

Correcting batch effects and integrating single-cell sequencing datasets has been a crucial step in large-scale biological studies. Many methods have been published for this task, with complementary strengths in various scenarios. Our previous work, LIGER, leveraging integrative non-negative matrix factorization (iNMF)...

Yi-Chen Wang, Andrew Robbins, Gaurav T. Gadhvi et al. · bioRxiv · 0 citations

#protein folding Open access Aug 2026

Autotaxin Inhibition Ameliorates HFpEF Phenotype By Reducing LPA-Mediated Systemic Inflammation and Cardiac Remodeling

In male mice with established two-hit HFpEF, autotaxin inhibition improved diastolic indices and reduced fibrosis, hypertrophy and cardiac myeloid accumulation and the autotaxin–LPA axis is nominated as a tractable therapeutic target.

Rajesh Chaudhary, Andrew Robbins, A. Singh et al. · bioRxiv · 0 citations