CRISPR screen

This study uses allele-specific CRISPR/Cas9 to inactivate a pathogenic variant in COL6A1, showing improved editing efficiency and collagen VI matrix restoration in patient fibroblasts.

This study uses CRUDO to show that cohesin and 3D contacts influence enhancer-promoter regulation, with distal enhancers showing stronger cohesin dependence.

This paper presents a transfection-free method for delivering Cas9:gRNA ribonucleoprotein using gold nanoparticles, achieving effective gene editing in human melanoma cells.

This paper introduces a CRISPRi system using dHyperLbCas12a for highly multiplexed epigenome editing and demonstrates its application in proliferation and CRE analysis screens.

The paper introduces GABI, a Bayesian framework in BEAST 2 for analyzing lineage tracing data, demonstrating its application to zebrafish development.

This study shows that CRISPRa systems experience resource competition between scRNAs, leading to gene repression and non-modular behavior, and introduces predictive modeling tools for multi-module networks.

The paper fine-tunes a CRISPRi screen in Vibrio cholerae to enable pooled genome-wide screening with minimal cytotoxicity and identifies 368 essential genes.

This study analyzes end-modified long dsDNA donors in CRISPR-mediated endogenous tagging, showing that 5 biotinylation reduces imprecise insertions and enhances HDR efficiency.

This paper improves the efficiency of noncanonical amino acid incorporation in mammalian cells by evolving tRNAEcLeu through directed evolution in mammalian cells.

The paper designs a high-activity CRISPR sgRNA library for Yarrowia lipolytica and uses it to identify genes involved in acetate and hydrocarbon tolerance.

This study uses CRISPR/Cas9 screening to identify novel regulators of mitochondrial oxidative metabolism, revealing key genes involved in complex I assembly and BCAA catabolism.

This study demonstrates the functional benefit of deleting a dominant RYR1 mutation using CRISPR/Cas9 in patient-derived muscle cells.

The paper develops a Bayesian model and software for analyzing CRISPR screens and validates its effectiveness in maintaining statistical power under low coverage conditions.

The paper identifies miR-142 as a regulator of EBV reactivation through CRISPR/Cas9 screening and shows it suppresses SOS1/Ras/Raf/Mek/Erk signaling initiated by the BCR.

This study develops and evaluates TadA-8e-derived cytosine and dual base editors in plants, showing high efficiency, purity, and specificity with no off-target effects.

The paper develops a CRISPR/Cas9 gene editing strategy using a single AAV vector and Cre-dependent Cas9 in mice to enable cell-type specific editing and tool delivery in the nervous system.

EXPosition is a computational tool for CRISPR gRNA design that optimizes gene expression effects using deep learning models for transcription, splicing, and translation initiation.

The paper identifies ancestry-related biases in CRISPR experiments caused by germline variants, showing disproportionate effects in cell models from recent African descent.

This study improves retron-based gene editing efficiency by reducing competition between msDNA and genomic DNA, achieving 100% editing efficiency.

The paper generates a comprehensive GUIDE-seq dataset with bulges, trains and evaluates machine-learning models to predict off-target sites with bulges, and visualizes model features.

This study develops a deep learning model to generate nonrepetitive and diverse CRISPR sgRNAs with high activity, validated for gene editing and regulation in Bacillus subtilis.

The paper identifies a proximity bias in CRISPR-Cas9 knockouts, showing phenotypic similarity between unrelated genes on the same chromosome arm, and proposes a correction method.

This study uses a CRISPR-Cas9 screen in zebrafish to identify genes involved in enteric nervous system development, revealing opioid receptor involvement in ENS establishment.

This paper develops a method to efficiently insert fluorescent tags into genes not expressed in hiPSCs using AAV6 delivery, optimized CRISPR conditions, and ddPCR/ICE to minimize INDELs and isolate tagged clones.

The paper introduces Mobile-CRISPRi, a system for gene knockdown in Vibrio species, showing it effectively modulates gene expression and phenotypes.

The paper shows that engineered GeoCas9 variants enhance genome editing by accelerating DNA unwinding, revealing a new role for the WED domain in this process.

This paper introduces CRISPRi-DR, a dose-response model to analyze chemical-genetic interactions in CRISPRi screens, showing improved precision over existing methods.

The paper identifies gene-perturbation interactions across genetic backgrounds in yeast using CRISPRi and combinatorial DNA barcode sequencing, revealing 460 genes with variable effects and 234 interacting loci.

This study introduces CRISPRai, a bidirectional epigenetic editing system, to investigate gene regulation hierarchies and interactions in T cells and hematopoietic lineage transcription factors.