Rebecca Neal Culver

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

The paper develops improved mouse models of the small intestine microbiota using region-specific human intestinal sampling and in vitro culturing, showing increased diversity and reproducibility in colonization.

Portal integrates large-scale single-cell datasets efficiently and accurately by preserving biological variation across samples, platforms, and species.

Nearly 500,000 cells from 24 human tissues, many from one donor, characterize over 400 cell types and enable within-donor study of T-cell clones, B-cell mutation rates and splicing.

This paper develops a fast, cheap protocol for assembling ordered transposon insertion libraries in anaerobic bacteria, using cell sorting and barcoded transposons to improve accuracy and efficiency.

This study uses read cloud sequencing to identify mobile elements in Bacteroides caccae that contribute to antibiotic resistance in a patient's microbiome over time.