CRISPR and Genetic Engineering

This study investigates how PAM-distal mismatches affect R-loop stability and DNA transposition in the type I-F CRISPR-Cas system using molecular dynamics simulations and network analysis.

This paper introduces NSC-seq, a direct sgRNA capture method for single-cell CRISPR screens using standard knockout libraries, and characterizes sgRNA expression in three whole-genome libraries.

This paper improves prime editing by modulating DNA repair pathways and engineering pegRNA, achieving higher precision and efficiency in human and mouse cells.

This paper introduces Crackling++, a faster and scalable method for off-target assessment of CRISPR guide RNAs by using non-contiguous exact matches, outperforming existing tools.

This study improves CRISPR editing in Daphnia pulex, reveals mutation mosaicism, and identifies gene expression changes linked to neurodegenerative disease genes in scarlet mutants.

The paper introduces graded-CRISPRi, a tool for tuning CRISPRi-mediated knockdown strengths in Vibrio natriegens using gRNA libraries to study gene expression effects.

This study uses single-cell DNA sequencing to evaluate multiplexed CRISPR-Cas9 gene editing for HIV cure strategies, finding limited co-editing across loci within individual cells.

The paper demonstrates that IS110 insertion sequences use a structured RNA to direct sequence-specific DNA recombination, enabling modular genome editing.

The paper develops Int-Plex@, a binary memory switch system using large serine-integrases to modulate plant genomic DNA through excision or inversion.

The paper introduces SPIT, a method using human cells to deliver genetic tools in vivo, demonstrating its application for modifying multiple organs and tissues in immunocompetent mice.

This study identifies gRNA efficiency as the main determinant of CRISPR/Cas9-induced inversion rates and sizes in tomato, with large inversions being less frequent due to potential transport limitations.

The paper introduces LINEMAP, a computational framework that traces and maps mutation networks in single-cell lineage dynamics using homing CRISPR technology.

The paper identifies mechanisms by which CRISPR, base editors, and prime editors cause large DNA deletions and proposes strategies to mitigate them.

This paper introduces baseMEMOIR, a method that reconstructs high-resolution cell lineage trees and spatial dynamics using base editing and imaging, achieving 792 bits of memory in embryonic stem cells.

CRISPRmap enables multi-omic optical pooled screens to map gene function in cells and tissue without sequencing, identifying pathogenic mutations and analyzing spatial phenotypes.

This study improves genetic manipulation of Acinetobacter sp. Tol 5 by deleting restriction enzymes and adapting CRISPR-Cas9 base-editing, enabling efficient electroporation and DNA assembly.

The paper tests multiple promoters and Cas9 NLS configurations in Arabidopsis to improve multiplex mutagenesis efficiency, finding the RPS5A promoter and double-BP NLS to be most effective.

This study combines CRISPR/Cas9 with retargeted adenoviruses to suppress HIV-1 replication in primary CD4+ T cells.

This study uses protein language models and high-throughput screening to engineer an anti-CRISPR protein that enhances CRISPR/Cas genome editing precision in human cells.

The paper demonstrates that loss-of-function mutations in OsLAT5 confer resistance to methylviologen, providing a selectable marker for genome editing in rice.

The paper describes modifications to the CRISPR-Cas12d system, identifies catalytically inactive variants, and demonstrates their high specificity using single-molecule techniques.

This paper describes a method to rapidly create mouse models of human epilepsy variants using in utero prime editing, enabling the study of seizures in a clinically relevant timeframe.

This study investigates X chromosome shredding in mice to control population growth but finds it causes spermatogenic block rather than male-biased offspring.

This study evaluates the safety of using dCas9-ABE8e for editing gamma-globin genes, showing reduced large deletions compared to nCas9-ABE8e while maintaining editing efficiency.

This study develops a CRISPR/Cas9 method to generate heritable mutations in Frankliniella occidentalis, demonstrating gene knockouts and phenotypic changes.

This paper describes a homing gene drive targeting the hairy gene in insects, which spreads to high frequency in cage populations but generates functional resistance alleles despite using multiple gRNAs.

The paper demonstrates that fusing CRISPR endonucleases to specific 5'-exonucleases significantly increases scar-free multikilobase knock-in frequencies in plants.

Krisp designs CRISPR and amplification-based diagnostic assays from whole genome data to differentiate pathogen groups, validated with Phytophthora ramorum data.

This paper develops a cryptographic encoding scheme called GSE to ensure information confidentiality and integrity in biological substrates using multi-site base editing in mammalian cells.

The paper develops CRISPR-based strategies to correct a complex genomic rearrangement in EYA1 linked to haploinsufficiency, showing successful gene expression restoration in patient-derived cells.