CRISPR screen

This paper introduces CRISPR-PspCas13b as a method to systematically silence oncogenic fusion transcripts, showing effectiveness against drug-resistant cancer drivers.

The paper uses population-scale GUIDE-seq-2 and CHANCE-seq to analyze how genetic variants affect Cas9 activity, finding frequent context-dependent effects on off-target sites.

The paper introduces CRISPuRe-seq, a pooled CRISPR screening method that identifies genetic perturbations affecting protein-based phenotypes, and demonstrates its use in uncovering components of the type 1 Interferon JAK/STAT pathway.

Superb-seq captures single-cell Cas9 edits and transcriptomes, revealing on- and off-target effects on gene expression in over 34,000 cells.

This study compares electroporation and packaged RNP delivery for genome editing, finding that packaged delivery is significantly more efficient and faster.

The paper investigates how patient sex affects cancer cell function by analyzing gene essentiality and drug sensitivity across 1,209 cell lines.

This paper develops a CRISPRi approach using truncated guides to screen multiple transcription factor binding sites, showing they can disrupt enhancer activity and repress transcription factor binding.

This paper shows that adding anionic polymers like polyglutamic acid to protoplast transfection protocols improves CRISPR-Cas9 genome editing efficiency in plants.

The paper develops CLEANSER, a model to filter ambient gRNAs in single-cell CRISPR screens, improving gRNA-cell assignment accuracy and differential gene expression analysis.

The paper introduces an enAsCas12a mouse model and associated libraries for efficient gene editing and screening, identifying drug resistance genes and enabling simultaneous gene knockouts and activations.

This paper develops NanoCas, a compact CRISPR nuclease, and demonstrates its efficacy in editing non-liver tissues in non-human primates.

The paper identifies context-dependent gene essentiality in GBM using CRISPR screening and develops a platform to link biomarkers to therapeutic targets.

The paper presents a genome-wide perturbation atlas using CRISPR-Cas9 knockouts to link genes to cellular phenotypes, identifying TMEM251/LYSET as a Golgi-resident protein involved in lysosomal enzyme trafficking.

The paper performs a CRISPR/Cas9 screen of sORFs to identify microproteins involved in cancer cell growth, finding several candidates with functional roles and localization data.

scEDIT is a lightweight software tool for analyzing CRISPR-edited single-cell data, revealing indel patterns and detecting unintended deletions in base editing experiments.

The paper presents a screening assay to identify efficient sgRNAs for CRISPR activation and provides a cloning workflow for viral vector integration.

The paper identifies ACP1 and AURKB as regulators of cortactin-driven actin remodeling in glioblastoma invasion using CRISPRi screens in 3D hydrogels.

The paper uses single-cell CRISPRi screens to show variant-associated enhancers regulate cancer genes in breast cancer, revealing network motifs and subtype-specific functions.

This paper uses a modified CRISPR method to replace the entire coding sequence of LRRTM2 in rat neurons, revealing its synaptic distribution and interactions with AMPARs.

This study eliminates the Warburg Effect in mammalian cells by knocking out lactate dehydrogenase and feedback regulators, maintaining growth rate while reducing lactate production.

This paper introduces a CRISPR-mediated platform for intracellular directed evolution of RNA aptamers, identifying novel orthogonal aptamer-RBP pairs for multiplexed gene regulation.

The paper develops a scalable CRISPR-Cas9 system for Plasmodium berghei to enable genome-wide knockout screens.

The paper introduces CREATE, an RNA-based gene editing system that delivers large genes without DSBs or DNA templates, achieving specific genomic integration in human cells.

This paper develops a CRISPR knockout screening method using viral replicons to identify host factors essential for viral replication, successfully identifying known and novel genes for dengue, chikungunya, and Ebola viruses.

The paper designs synthetic promoters that respond to TFs differentially expressed in activated and exhausted T cells, enabling functional state classification and dynamic gene expression control.

This paper introduces CRISPR MiRAGE, a miRNA-sensing guide RNA system that enables tissue-specific gene editing by modulating CRISPR activity based on miRNA signatures.

edgeR v4 adds a continuous negative binomial for fractional counts, bias-corrected quasi-likelihood for small counts, C-based fitting, and new transcript, exon, methylation and fold-change-threshold analyses.

This study demonstrates that CRISPR-CasRx reduces C9orf72 repeat RNAs and DPRs in vitro and in vivo, suggesting its therapeutic potential for ALS/FTD.

The paper uses a deep ensemble approach to improve CRISPR guide RNA selection by incorporating uncertainty quantification, achieving over 91% precision in guide identification for most mouse genes.