CRISPR screen

This paper develops an automated high-throughput workflow for arrayed CRISPRa screening, demonstrating its effectiveness in identifying growth reduction phenotypes in HEK293 cells.

matchbox provides a flexible and scalable read processor for handling diverse sequencing tasks, demonstrating versatility in demultiplexing, restranding, CRISPR efficiency assessment, and haplotyping.

This paper models and minimizes dCas9 competition in CRISPRi-based genetic circuits to improve their performance and dynamic range.

The paper identifies active human neural enhancers and CRISPRa gRNAs that upregulate NDD risk genes, providing a resource for cis-regulatory therapy development.

This paper develops a pooled paired prime editing screen to generate large-scale deletions across the genome, identifying non-coding regions with fitness effects and demonstrating the feasibility of genome-wide deletion perturbation.

The paper introduces CRISPR-rabies virus (CRV) to enable precise circuit-level gene modulation in neurons, demonstrating its ability to regulate synaptic transmission in the hippocampus.

This study uses in vivo CRISPRi-Seq in zebrafish to identify host-adaptive pathways essential for pneumococcal meningitis and discover new therapeutic targets.

The paper introduces MultiCAST, a high-throughput CRISPR-associated transposon system for bacterial gene disruption, enabling rapid and scalable genetic screens using amplicon sequencing.

This paper introduces Star-CDP, a dynamic programming algorithm for accurate cell lineage tree reconstruction from CRISPR-based data, showing improved performance over existing methods.

This paper demonstrates that CRISPR-mediated transcriptional activation can upregulate SYNGAP1 in a mouse model of SRID and human neurons, rescuing deficits without targeting mutations.

This paper maps mutation-defined cancer vulnerabilities across 22 cohorts, identifying OXPHOS addiction in CDKN2A-loss LUSC and highlighting drug repurposing opportunities using a machine learning framework.

This paper discovers and engineers retron-based gene editors for precise genome editing in mammalian cells and vertebrates, achieving high efficiency with novel reverse transcriptases and delivery strategies.

This study corrects a pathogenic ATAD3A variant in iPSCs using CRISPR-Cas9-induced gene conversion without donor templates, showing high efficiency and dependence on HR proteins.

The paper introduces Sleeping ORANGE, a modified CRISPR-Cas9 method that enhances endogenous protein tagging efficiency using a Sleeping Beauty transposase fusion, achieving a 12.85-fold increase in editing efficiency for CYFIP1 tagging.

This study benchmarks five loss-of-function perturbation tools for studying noncoding genome function, finding dual-SpCas9 is most effective for targeting CREs and recommending RNA interference for noncoding RNA genes.

CrisprBuildr is a web-based tool for designing CRISPR constructs in Drosophila to delete genes or insert fluorescent tags, streamlining genome engineering workflows.

This study identifies strategies to improve CRISPR-Cas9 HDR efficiency in generating conditional knockout mice by optimizing DNA templates and using RAD52 protein.

OASIS enables precise, customizable genome editing and subcellular visualization of adult oligodendrocytes using AAV-mediated CRISPR and biotinylation.

This study evaluates inducible transgenic systems in human pluripotent stem cells and differentiated cells, identifying a small molecule-mediated splicing switch that enables tunable transgene expression without protein tags.

The paper identifies Wnt signaling defects and GSK3b overactivity as regulators of lipid accumulation in APOE4 oligodendrocytes, showing that inhibiting GSK3b reduces lipid droplets and improves myelination.

This paper develops ABE10, an improved adenine base editor with enhanced A-to-G editing efficiency and reduced off-target effects, demonstrating its utility in disease modeling and gene therapy.

This paper introduces an activity-based selection method to improve base editing efficiency and precision in identifying functional mutations.

The paper introduces the Knock-in Atlas, a web resource for CRISPR/Cas9-mediated targeted gene knock-in in human and mouse cell lines, providing pre-designed gRNAs and characterization data for 350 proteins.

The paper uses CRISPRi-Seq to identify conserved antibiotic vulnerabilities in S. aureus strains, revealing gene targets for antimicrobial therapies.

The paper develops COMPASS, a method to assess splicing variant effects across cell types, identifying disease-associated variants and cell type-specific splicing programs.

This paper develops an allogeneic T cell therapy strategy using gene editing to reduce immune rejection and enable off-the-shelf use, showing comparable function to autologous cells.

The paper introduces a platform that directly sequences 3'UTRs and guide RNAs in fixed cells alongside protein abundance and morphology, enabling CRISPR screening in lung cancer cells.

This study shows WEE1 inhibitors work better with mRNA translation defects by activating GCN2, and suggests ways to reduce off-target effects.

This study uses prime editing to correct a common TPP1 mutation in cultured cells and eVLPs, achieving on-target editing efficiencies of up to 27.36% and 12.6% in vivo.