CRISPR and Genetic Engineering

This study elucidates the allosteric activation mechanism of CRISPR-Cas13a using molecular dynamics simulations and experiments, revealing key residues critical for RNA cleavage selectivity.

The paper determines the structure of the SPARTA immune system, revealing how it activates NADase activity in response to ssDNA targets.

The paper determines cryo-EM structures of SPARTA in different states to elucidate its auto-inhibition and activation mechanisms.

The paper introduces a modular dCas9-based platform for combinatorial epigenome editing, demonstrating its ability to control effector recruitment and spatial organization for improved transcriptional regulation.

This paper introduces mSwAP-In, a method for efficient genome rewriting in mouse embryonic stem cells, demonstrating its use for Trp53 and ACE2 locus modifications to create more accurate disease models.

The paper introduces a dual sgRNA library design for CRISPRi screens to identify genetic modifiers, showing improved sensitivity and specificity in detecting epistatic relationships.

This paper evaluates five phage-derived recombinases for recombineering in three Pseudomonas strains, achieving mutation efficiencies up to 5 x 10^-5.

The paper evaluates sgRNA design guidelines and in vitro assays for plant CRISPR/Cas9, finding that in vitro cleavage does not reliably predict in vivo efficiency and highlights the need for multiple high-performing sgRNAs.

This study improves the efficiency of biallelic deletions in cattle embryos using CRISPR-Cas and shows OCT4 is critical for blastocyst formation and pluripotency.

The paper uses machine learning to improve Cas12a guide RNA efficiency prediction by analyzing nucleotide bias and mismatches relative to the PAM site.

The paper introduces a new method combining Fusion cloning and CRISPR-Cas9 to clone and edit large bacterial genomes in yeast, demonstrating its effectiveness with Mycoplasma species.

The paper shows that shifting the RNA:DNA hybrid relative to the PAM in SpCas9 generates DNA overhangs and accelerates complex dissociation after cleavage.

This paper presents a temperature-regulated Cas12a-based gene-drive system and demonstrates double gene drives using Cas9 and Cas12a to spread two engineered alleles.

This paper develops a CRISPR/Cas9 system for efficient targeted gene disruption in Histoplasma, enabling high-efficiency mutagenesis and deletion of specific genes.

The paper shows that using the same guide RNA structure for CRISPRi and CRISPRa in E. coli prevents context-dependent effects, ensuring predictable gene circuit behavior.

This study develops a method to efficiently induce somatic gene deletions in adult mouse skeletal muscle fibers using AAV-CRISPR/Cas9, replicating knockout phenotypes without generating knockout mice.

This study shows that transposon-encoded nucleases use guide RNAs to bias transposon inheritance by cleaving donor joints formed during transposition.

GiRAFR improves gRNA detection and annotation in single cell CRISPR screens by identifying mutant gRNAs that are dysfunctional and often overlooked by existing tools.

This paper improves genetic manipulation techniques in Aedes aegypti by introducing transgenic lines for Cre-mediated recombination and a plasmid-based PhiC31 integrase system for stable transgene integration.

The paper develops a high-throughput workflow to assess Cas9 editing precision and identifies a novel Cas9 fusion that improves knockin performance in vivo.

This study evaluates how genetic variation and chromosomal inversions affect CRISPR-Cas9 gene drive homing in Anopheles gambiae strains, finding no significant reduction in homing despite target site heterogeneity.

This paper develops CRISPR-based RNA editing tools for precise deletions and insertions in RNA, enabling recombinant RNA virus engineering.

The paper describes a split Cas9-based synthetic circuit to detect cellular events like cancer cell origin, EMT, and cell fusion by using promoter-specific expression and reporter activation.

This study compares gene drive spread characteristics in continuous space models, finding differences in wave speed and vulnerability to fitness costs and resistance.

GreenGate 2.0 improves modular cloning by increasing module capacity, streamlining entry clone generation, and enabling efficient stacking of transcriptional units for complex genetic constructs.

The paper develops a transfer learning model, crisprHAL, to improve SpCas9/sgRNA activity prediction using small high-quality datasets.

The paper optimizes Cas12a for multiplexed CRISPRa screens in human cells, enabling simultaneous activation of up to four genes and identifying criteria for selecting effective guides.

This paper develops a novel feature set and public resource for predicting CRISPR-Cas9 sgRNA efficiency using quantum chemical tensors and explainable-AI methods.

This study evaluates the durability of epigenome editing for reducing gene expression in cardiovascular disease targets, finding durable effects for PCSK9 but not for ANGPTL3 or AGT.

The paper improves a MAGE protocol to repair mutations in synthetic genome segments, enabling successful complementation of gene deletions in Escherichia coli.