CRISPR and Genetic Engineering

The paper introduces YYAP, an engineered gene drive system that enforces obligate co-inheritance of alleles, demonstrating efficient population replacement and suppression in Drosophila.

The paper identifies recurrent acquisition of nuclease-protease pairs in bacterial antiviral immunity and shows their proteolytic activation mechanism across different immune systems.

This study reveals how cyclic tetra-adenylate binds to Cap1, inducing conformational changes that open a membrane pore and cause depolarization during the type III CRISPR immune response.

This study benchmarks and optimizes Perturb-seq in human pluripotent stem cells, identifying shared regulatory networks during cardiomyocyte differentiation.

This paper develops a non-viral genome-editing method called STEP-RNPs that effectively treats Angelman syndrome in mice and human neurons, showing functional genetic rescue without off-target effects.

The paper introduces XConTest, a method to assess genetic convergence in CRISPR perturbations, showing it identifies genes with similar downstream effects in autism and immune response studies.

The paper develops iPSC-SGE to assess variant effects in diverse genetic and cell contexts, identifying pathogenic variants and essential disease genes.

This study improves CRISPR/Cas9 off-target prediction by integrating DNABERT with epigenetic features, showing better performance than existing models.

This study identifies design rules for expanding PAM compatibility in CRISPR-Cas9 variants by analyzing structural and functional interactions in VQR, VRER, and EQR variants.

pGGTOX enables efficient, marker-free genome editing across Enterobacteriaceae using homologous recombination, with applications in gene deletion, plasmid modification, and CRISPR delivery.

The paper introduces poolVis and cellPool to improve scalability and decoding of protein barcode-based CRISPR screens through experimental and computational methods.

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

The paper develops a CRISPR/Cas9 gene editing toolkit for transient and stable plant transformation, validated in rice and Arabidopsis, to improve access in low-income regions.

This paper uses machine learning to identify allosteric networks in Cas9, revealing key residues and an electrostatic valley that stabilize its structure and specificity.

The paper uses village editing to study how genetic backgrounds affect the impact of schizophrenia-associated mutations in human neurons.

This study engineers recombinases to improve DNA insertion efficiency and specificity in human cells, achieving 53% integration and 97% genome-wide specificity.

This paper develops a site-directed transposase system for precise genomic insertion of gene-sized DNA without double-strand breaks, achieving on-target insertion with minimal off-target effects.

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

The paper investigates how modifying Cas9 regulatory elements affects gene drive performance in Drosophila, finding that promoter truncation reduces resistance allele formation but decreases germline cutting efficiency.

This paper develops self-limiting genetic strategies using genomic editors to suppress pest populations more efficiently than traditional methods.

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.

The paper shows that a viral SAVED domain, AcrIII-2, degrades the CRISPR second messenger cA4, inhibiting its effectors.

This study investigates LOH caused by CRISPR-Cas9 DSBs, showing large-scale loss and mechanisms, and highlights risks when combined with end joining inhibition.

This study uses CRISPR to target H3K4me3 methyltransferases in Arabidopsis, showing activation of gene expression and increased meiotic crossover recombination near centromeres.

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

The paper introduces P3a site-directed mutagenesis, achieving ~100% efficiency for point mutations and cassette mutagenesis of DNA fragments up to 5 kb.

The paper shows that anoxia activates the CRISPR-Cas system in the mouse intestine via the Fnr regulator, suggesting an adaptation for microbial defense.

This study develops and characterizes a nanosd integral gene drive in Anopheles gambiae, achieving high gene drive rates and showing potential for malaria vector control.

This paper develops a CRISPR/Cas9 gene editing system for Pseudoalteromonas fuliginea, achieving high editing efficiency for gene knockouts and insertions.