Anna Kuchina

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics

The paper develops metaSPLiT, a single-cell RNA sequencing method, to reveal sub-species functional specialization in the human gut microbiome.

Pooled single-cell CRISPRa/i screens for functional genomics in bacteria at scale

The paper introduces mapSPLiT, a pooled CRISPRa/i screening platform for bacteria, linking perturbations to single-cell transcriptomes and expanding regulatory networks in E. coli and P. putida.

Combinatorial phenotypic landscape enables bacterial resistance to phage infection

The paper profiles single-cell transcriptomes of Bacteroides fragilis infected with a phage, revealing combinatorial phase-variable expression of defense systems that enable super-resistant cells to avoid phage infection without mutations.

Scaling single cell transcriptomics through split pool barcoding

The paper introduces SPLiT-seq, a scalable scRNA-seq method, and applies it to analyze 109,069 cells from a mouse brain, identifying 13 main cell populations and developmental substructures.

Deep learning of the regulatory grammar of yeast 5’ untranslated regions from 500,000 random sequences

The paper trains a CNN to predict translational efficiency of yeast 5' UTRs using synthetic sequences and validates it on native sequences and evolved designs.