CRISPR and Genetic Engineering

The paper introduces CRISPRzip, a mechanistic model that predicts CRISPR-Cas9 activity based on sequence and context, validated by experimental data.

This paper introduces a method to deliver synthetic haplotypes containing T2D GWAS variants to hiPSCs to study their functional impact on differentiation.

This paper develops a computational pipeline for designing CRISPR-Cas13b guide RNAs targeting Dengue virus, showing classical machine learning models outperform deep learning in low-data regimes.

This paper introduces CROFT-Seq, a method for detecting Cas9 off-target sites in vitro, which is sensitive, rapid, and cost-effective compared to existing methods.

This paper develops a CURE for undergraduate research in plant synthetic biology using rapid gRNA efficacy screening to study gene regulation in Arabidopsis.

This study develops an in vivo-trained model to predict dual-sgRNA efficiency for exon deletion in mice, achieving an AUC of 0.759.

This study shows OpenCRISPR-1, an AI-derived Cas enzyme, successfully edits genes in tetraploid alfalfa with mono- or bi-allelic editing in 30% of genotypes.

The paper analyzes CRISPR systems in prokaryotes, finding that multiple CRISPR arrays co-occur with Cas loci, vary in structure, and may function independently or collaboratively.

The paper analyzes CRISPR array repeat mutations across prokaryotic genomes, revealing subtype-specific patterns and a link between repeat mutations and spacer dynamics.

This study evaluates genetic mosaicism in Daphnia species after CRISPR-Cas9 gene editing, finding mosaicism in 9 out of 11 targeted genes.

This study identifies host factors that influence VchCAST activity and demonstrates that the λ-Red recombineering system significantly enhances its editing efficiency in E. coli and other bacteria.

This study shows CRISPR-Cas targeting in Haloferax volcanii increases within-species mating and recombination, promoting gene exchange while limiting inter-species transfer.

This study characterizes SuCas9, a compact Cas9 ortholog from Streptococcus uberis, showing it can cleave DNA in vitro and function in human cells with a novel PAM sequence.

This paper develops a high-efficiency, transgene-free CRISPR-Cas12 genome editing method for brown algae, applicable across multiple species and enabling functional genomics studies.

The paper quantifies the effectiveness of all possible trinucleotide sequences as PAMs for the V. cholerae type I-E CRISPR-Cas system, identifying 15 functional PAMs out of 64.

This paper introduces a novel genome engineering method for iPSCs that enables efficient multiplex gene editing and clone selection, improving the precision and speed of iPSC-based therapies.

The paper introduces eSPLIT and iSWAP, two methods for generating conditional alleles using short artificial introns, validated in human and mouse models.

The paper implements a Mobile-CRISPRi system in Piscirickettsia salmonis to silence genes, demonstrating its effectiveness in seven strains and revealing Fur's role in iron metabolism.

This paper validates OpenCRISPR-1 in CHO cells, achieving ≥70% INDEL efficiency across multiple genes using a 39-day workflow.

This study shows that electrostatic interactions in the Nuc domain of Cas12a orthologues regulate trans cleavage activity, with specific mutations enhancing or abolishing cleavage efficiency.

This paper introduces a method to rapidly construct gRNA arrays for CRISPR-Cas9 applications and provides a web tool for designing oligo sequences.

This paper introduces an inducible Cas9 system for tissue- and stage-specific gene editing in zebrafish and mouse embryos, demonstrating its effectiveness in inducing mutations in target genes.

The paper improves CRISPR-Cas12a-assisted gene tagging in mammalian cells by enhancing HDR efficiency and reducing off-target integrations through modified cassettes and repair pathway modulation.

This study describes the structure and mechanism of Crn4, a ring nuclease that degrades cyclic oligoadenylates and modulates type III CRISPR immunity.

This study compares immune responses to AAV-delivered CRISPR-Cas9 and RNP-delivered CRISPR-Cas9 in the retina, finding persistent inflammation with AAV and transient inflammation with RNP.

This study evaluates strategies to improve homing gene drive efficiency using multiplexed gRNAs, finding that population-level multiplexing enhances drive efficiency despite increased vulnerability to resistance.

This paper develops inducible CRISPR/Cas9 systems with improved dynamic range and reduced off-target effects for precise gene perturbation.

This paper introduces CUT&ID, a method that simultaneously profiles protein-DNA and protein-protein interactions without requiring transgenesis.

This paper introduces L-PGI, a ligase-mediated gene editing system that enables efficient and precise genomic integration in both dividing and nondividing cells, overcoming limitations of reverse transcriptase-based methods.