Public sequencing repositories contain large amounts of gut microbiome data that could support cross-study comparison, reproducibility analysis, and microbiome foundation model development. However, the extent to which these data are structured, harmonized, and reusable at archive scale remains unclear. Here, we charac...
Kiersten Oderman, T. Nandi, J. Malas et al.· bioRxiv· 0 citations
Linkage disequilibrium (LD) information from one’s own dataset is considered optimal for downstream analyses such as statistical fine-mapping. However, the computational complexity ( computations for N variants) lead most studies to use external reference panels, such as from 1000 Genomes. To capture LD across all vari...
Rachit Kumar, Pankhuri Singhal, David Y. Zhang et al.· bioRxiv· 0 citations
To advance precision medicine in pathology, artificial intelligence (AI)-driven foundation models must generalize across diverse datasets, tissues, and clinical tasks. However, their comparative performance and generalizability in computational pathology remain incompletely characterized. Here, we benchmark 32 AI found...
R. Bareja, F. Carrillo-Perez, Yuan-Ning Zheng et al.· Nature Communications· 3 citations
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