Publications by authors named "Hannah Giba"
The human gut microbiome contains many bacterial strains of the same species ("strain-level variants") that shape microbiome function. The tremendous scale and molecular resolution at which microbial communities are being interrogated motivates addressing how to describe strain-level variants. We introduce the "Spectral Tree"-an inferred tree of relatedness built from patterns of co-evolutionary constraint between greater than 7,000 diverse bacteria.
View Article and Find Full Text PDFHematoxylin and eosin (H&E) is a common and inexpensive histopathology assay. Though widely used and information-rich, it cannot directly inform about specific molecular markers, which require additional experiments to assess. To address this gap, we present a deep-learning framework that computationally imputes the expression and localization of dozens of proteins from H&E images.
View Article and Find Full Text PDFArticle Synopsis
- The human gut microbiome consists of numerous bacterial strains that vary at a genetic level, complicating the process of meaningful classification beyond standard taxonomy.
- Researchers analyzed co-evolution patterns across over 7,000 bacterial strains, which helped them study gut commensal strains they isolated and sequenced.
- By focusing on co-evolutionary signatures, the study enabled predictions of metabolic traits and proposed a new framework for categorizing bacterial strains based on their evolutionary relationships.