Feasibility benchmark: can single-cell RNA-seq preprocessing (rapids-singlecell style) be GPU-accelerated on Apple Silicon/Metal? Measured on an M5 Pro. Spoiler: the Apple-GPU linalg gap blocks it....

The performance of single-cell foundation models is dependent on many factors. This study assesses the effect of the pretraining dataset’s size and diversity, revealing potential challenges in pursuin...

Nature Communications - Primary sclerosing cholangitis (PSC) is an autoimmune condition affecting the liver. Here, the authors generate an immunobiliary transcriptomic atlas and show that dendritic...

CellVoyager is an artificial intelligence agent capable of exploring new biological hypotheses by autonomously analyzing single-cell RNA sequencing datasets and accounting for background information a...

The direct contribution of aberrant epithelial cells to lung fibrosis is largely unknown. The authors use murine and human systems to identify how these cells activate fibroblasts, and how reciprocal signals cause them to enter a profibrotic state.

Many single-cell transcriptomics datasets are stored in the HDF5-backed AnnData (H5AD) file format, as popularised by the Python scverse ecosystem. However, accessing these datasets from R, allowing u...

Growing evidence suggests that reduced cerebral blood flow contributes to cognitive decline in ageing and dementia. Attwell and colleagues discuss the underlying mechanisms and functional consequences...

GeneAgent is a language agent using large language models and self-verification to improve gene-set function annotation.

Determining the appropriate sample size (N) for comparative biological experiments is critical for obtaining reliable results. In order to determine the N, the usual approach is to perform a power cal...