CRISPR screen

A Three-View System for CRISPR-Cas12a crRNA Activity Ranking: When to Ensemble, When Context Matters More

The paper develops TriCasRank, a model for ranking CRISPR-Cas12a crRNA activity using sequence features, reference mapping, and historical data, showing improved correlation but comparable performance to an XGBoost model.

HERACLES for fast and accurate likelihood-based reconstruction of massive lineages

HERACLES improves lineage reconstruction accuracy and scalability by optimizing cell coordinates in hyperbolic space using a composite likelihood model of CRISPR editing.

An integrated workflow for dual-guide CRISPR-Cas9 targeting and amplicon-based genotyping of Pla2g6 in primary mouse bone marrow-derived macrophages

This paper describes a workflow for dual-guide CRISPR-Cas9 editing of Pla2g6 in mouse BMDMs, showing high editing efficiency and specific deletion patterns.

Where single-cell foundation models help: a benchmark of annotation, perturbation and regulatory inference against simple baselines

This paper benchmarks single-cell foundation models against baselines for annotation, perturbation and regulatory inference using diverse datasets.

Biosensor-guided genome-wide CRISPR screens enable cis,cis-muconic acid overproduction in yeast

This study uses biosensor-guided CRISPR screens in yeast to identify genetic targets that enhance production of cis,cis-muconic acid and protocatechuic acid.

Genome-wide CRISPRi-seq maps essential-gene contributions to aminoglycoside susceptibility in Pseudomonas aeruginosa

This study uses CRISPRi-seq to identify essential genes affecting aminoglycoside susceptibility in Pseudomonas aeruginosa, revealing gene-specific fitness effects and potential targets for antibiotic enhancement.

Tiled base editing screens uncover rare second-site mutations that rescue a misfolded disease protein

The paper uses base editing screens to identify second-site mutations that correct misfolded NPC1 proteins, enabling therapeutic applications for diseases like Niemann-Pick type C.