Fundamental Limitations of Foundation Models in Single-Cell Transcriptomics https://www.biorxiv.org/content/10.1101/2025.06.26.661767v1?med=mas

Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction https://www.biorxiv.org/content/10.1101/2025.06.26.661186v1?med=mas

Molecular dynamics reveals a novel Regulatory Ca+2-Binding Site in the Mitochondrial Calcium Uniporter https://www.biorxiv.org/content/10.1101/2025.06.25.661581v1?med=mas

PatternExtract: A facile, scalable pipeline for point pattern generation from spatial imaging data https://www.biorxiv.org/content/10.1101/2025.06.25.661424v1?med=mas

EC-Bench: A Benchmark for Enzyme Commission NumberPrediction https://www.biorxiv.org/content/10.1101/2025.06.25.661207v1?med=mas

Navigating the Lipid Universe with LipidLibrarian: A Cross-Linked Database for Lipidomics Data Integration https://www.biorxiv.org/content/10.1101/2025.06.26.661298v1?med=mas

Alignment-free Bacterial Taxonomy Classification with Genomic Language Models https://www.biorxiv.org/content/10.1101/2025.06.27.662019v1?med=mas

Unsupervised Multi-scale Segmentation of Cellular Cryo-electron Tomograms with Stable Diffusion Foundation Model https://www.biorxiv.org/content/10.1101/2025.06.25.661425v1?med=mas

Interpreting Attention Mechanisms in Genomic Transformer Models: A Framework for Biological Insights https://www.biorxiv.org/content/10.1101/2025.06.26.661544v1?med=mas

STRESS: Spatial Transcriptome Resolution Enhancing Method based on the State Space Model https://www.biorxiv.org/content/10.1101/2025.06.25.661624v1?med=mas