CRISPR and Genetic Engineering

ReCo automates the generation of read-count tables for CRISPR gRNAs from NGS data, enabling downstream analysis of gRNA-induced phenotypes.

This paper describes a method to rapidly generate single copy transgenes in C. elegans using RMCE and drug selection, achieving homozygous transgenes in 3 generations.

The paper identifies CRISPR repeat-like RNA elements in CRISPR-Cas systems that function as regulatory guides, showing their prevalence in type I and V-A systems.

This study evaluates the safety and efficacy of in vivo CRISPR gene editing targeting HSV-1 in patients with herpes stromal keratitis, finding no detectable off-target effects or adverse events over 18 months.

The paper describes a method using in vitro transcribed guideRNAs for targeted nanopore sequencing to study structural variations in pancreatic cancer cell lines.

The paper introduces a CRISPR/Cas12a system for efficient genome editing in Methanosarcina acetivorans, enabling deletions, insertions, and multiplex edits with high success rates.

This paper introduces a method to induce targeted recombination in C. elegans using Cas9, enabling high-resolution genetic mapping in species with low natural recombination rates.

This paper introduces CloneSelect, a multi-kingdom genetic barcoding system that enables precise isolation of target clones using CRISPR base editing to trigger reporter gene expression.

This paper introduces PEACE, an in vivo continuous evolution system using AID-T7 PNAP to enable rapid protein engineering by coupling gene polymorphism with toxin-antitoxin growth control.

MaGplotR aggregates and visualizes multiple CRISPR screen datasets to identify common hits and generate publication-quality plots.

This paper introduces a chemically inducible gene editing system in the sea star Patiria miniata using Tet-ON and CRISPR, enabling inducible gene alteration in transgenic cell populations for the first time in echinoderm biology.

CRISPR-Cas-Docker predicts optimal crRNA-Cas pairs using in silico docking and machine learning classification.

The paper introduces the in4mer CRISPR/Cas12a platform for efficient multiplex gene knockout, demonstrating improved sensitivity and reduced clone numbers compared to CRISPR/Cas9.

The paper investigates PlmCas12e cleavage activity on CCR5 by analyzing guide RNA length and PAM sequence variations, identifying optimal conditions for efficient cleavage.

This paper introduces a green-light activated CRISPRi system with a 40-fold dynamic range for precise gene repression in E. coli.

This paper optimizes CRISPR guide RNA library cloning to reduce bias and enables more compact genetic screens with equivalent results using fewer cells.

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

The paper develops PlatinumCRISPr, a tool for selecting efficient sgRNAs for CRISPR-Cas9 genome editing, identifies design constraints, and reports unintended DNA insertions from deletions.

This paper introduces REDRAW, a novel DNA editing method using reverse transcriptase and type V CRISPR-Cas systems, enabling broader sequence replacement beyond type II systems.

This paper develops a temperature-tolerant CRISPR base editor for efficient and precise gene inactivation in Drosophila, showing high efficiency and minimal byproducts.

The paper evaluates a CRISPR toxin-antidote gene drive in a reaction-diffusion model to assess its performance in spatially confined population suppression scenarios.

The paper identifies TREX1 as a suppressor of CRISPR-Cas9 HDR efficiency in human cells and shows that TREX1 removal or use of chemically protected templates can enhance HDR.

This study enhances homology-directed repair (HDR) efficiency by using PRDM9-Cas9 fusion with CtIP, validated through reporter systems for small and longer edits.

The paper develops arabinose-inducible artificial transcription factors for Gram-negative bacteria to control gene expression and demonstrates their use in biosensor and metabolic engineering applications.

GLiDe is a web-based tool for designing CRISPRi sgRNA libraries in prokaryotes, improving off-target detection and providing a database for 1,397 species.

This study systematically reviews gene editing clinical trials, finding a growing trend in CRISPR-based trials and promising phase-I/II trials testing safety and feasibility.

This study develops a CRISPRi tool for Deinococcus radiodurans to knock down gene expression, demonstrating its utility for studying radiation resistance and metabolic engineering.

The paper develops a single-cell CRISPR base editor method to engineer and assess the transcriptional impact of cancer mutations in cell lines.

The paper develops a CRISPR-mediated gene editing protocol in rotifers, demonstrating efficient knockout and knockin mutations in key genes.

This study compares DNA-targeting CRISPR editors in human cells, finding that Cas12f1 is suitable for activation, Cas12a for therapy, and Cas9 for in vitro and animal studies.