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Khabre desk
Recent reporting, analysis and explainers from the single-cell biology desk.
health
A medRxiv preprint analysed gene activity in 1.4 million immune cells from 345 people across 13 Indigenous South American populations. Genetic ancestry was associated with many expression differences, often after immune stimulation.
science
A bioRxiv preprint introduces EpiZoo, a 2.6-billion-parameter model trained on about 20.9 million single cells from multiple species. Its authors report performance on several single-cell analysis tasks and describe applications in comparing regulatory patterns and prioritising cancer mutations.
science
Researchers report a single-nucleus atlas spanning 21 adult human tissues and four donors, combining gene-expression and chromatin-accessibility data. It maps candidate regulatory elements and gene links, and uses sequence-to-function models to predict effects of fine-mapped variants.
science
A bioRxiv preprint introduces SPECTRA, a graph-based model that predicts gene-expression responses to CRISPR perturbations by propagating signals through gene regulatory networks. The authors report improved recovery of sparse perturbation-related changes in a large-scale single-cell CRISPRi benchmark.
science
A bioRxiv preprint using data from 1,494 donors finds that many single-cell gene-expression studies may lack sufficient statistical power to detect small effects. Cell counts, gene-expression levels and sequencing depth strongly influenced which findings were detected and reproduced.
science
A bioRxiv preprint finds that randomly dividing single-cell data can leak information between training and test sets when related cells share labels. The authors propose eakcheck, a tool that estimates this leakage before a predictive model is trained.
science
A bioRxiv preprint introduces LucaCell, a foundation model that represents genes through mRNA sequence embeddings instead of fixed gene identifiers. The authors report applications spanning cross-species cell annotation, microbial analysis, chromatin accessibility and influenza infection states.
health
A medRxiv preprint combining genetic and single-cell analyses identifies bone-marrow macrophages as a possible link between aging and osteoporosis. It nominates TGFB1 and HNRNPUL1 as regulators in this relationship, based on observational, genetic and transcriptomic evidence.