Lennard Halle

The paper introduces scAtlasTb, a framework for building and optimizing single-cell reference atlases, demonstrating its application on three Human Cell Atlas projects.

This paper generates cross-species single-cell atlases of pancreatic cancer to study progression, therapy response, and immune evasion across human and mouse models.

The paper analyzes unassigned RNAs in spatial transcriptomics data, identifies biological relevance, and introduces a tool for their study.

This paper creates a human endoderm organoid cell atlas by integrating single-cell transcriptomes from multiple organoid types to compare cell states with primary tissues and disease models.

Pretrained on 57 million dissociated and 53 million spatial human and mouse cells, a 49.3M-parameter transformer predicts niche, region, neighborhood composition and density, and carries spatial labels onto scRNA-seq.

hadge combines hashing and genotype-based deconvolution methods to recover previously discarded cells in single-cell data.