CRISPR and Genetic Engineering

CRaTER enriches for on-target gene-edited cells in hiPSCs, enabling efficient generation of variant libraries for studying cardiomyopathy-associated mutations.

The paper shows that clonally selected CRISPR-edited cell lines acquire many culture-specific mutations, making them non-isogenic, and recommends comparing multiple edited and unedited line mixes.

CRISPR-Detector detects, visualizes, and annotates genome-wide mutations from CRISPR/Cas gene editing events with improved speed, scalability, and accuracy.

This paper develops a CRISPR-guided transposon system for DSB-free DNA integration in human cells, improving efficiency and reducing off-target effects.

The paper reduces CRISPR dark matter by analyzing spacers in antibiotic-resistant bacterial genomes and links CRISPR-Cas systems to membrane proteins involved in phage defense.

This paper demonstrates that CbAgo from Clostridium butyricum can be used for targeted genomic DNA cleavage and recombineering by using plasmid-derived gDNAs.

The paper introduces UniDesign, a computational framework for designing protein-nucleic acid interactions, and demonstrates its ability to accurately predict PAM-PIAA interactions for Cas9 proteins.

The paper introduces TARDIS, a high-throughput transgenesis method in C. elegans that generates thousands of genetically unique transgenic individuals by splitting the transgenesis process into two steps.

The paper investigates whether prokaryotes use diversity-generating retroelements to create defense proteins against unknown invaders, identifying and characterizing candidate systems.

This paper demonstrates that CbAgo-mediated DNA cleavage in E. coli is mutagenic and can be used for genetic manipulation.

The paper identifies pervasive gene-by-environment interactions among natural genetic variants in yeast using high-throughput genome editing.

MINORg generates minimal gRNA sets to cover multiple targets across multiple genomes, reducing workload for pangenomic screens.

FLInt enables efficient and safe transgene integration in C. elegans using fluorescent marker loci and CRISPR/Cas9, allowing easy screening through fluorescence interference.

This study compares CRISPR off-target detection tools using ex vivo edited CD34+ HSPCs, finding that HiFi Cas9 reduces off-target sites and some methods outperform others in sensitivity and specificity.

This paper evaluates distant-site rescue elements for CRISPR toxin-antidote gene drives and finds they fail for both haplolethal and haplosufficient target genes.

The paper develops DeepCas13, a deep learning model to predict CRISPR-Cas13d gRNA on-target activity and off-target viability effects, improving accuracy for RNA editing applications.

CriSNPr provides a webserver for designing and querying gRNAs for CRISPR-based diagnostics using multiple Cas systems and includes a curated database of gRNAs for human and SARS-CoV-2 variants.

This paper shows that reducing DNA targeting activity in CRISPR systems improves genome editing efficiency in bacteria by enabling RecA-mediated repair.

This study determines the crystal structures of Crn1/Sso2081 in different states to elucidate the mechanism of cA4 cleavage by the type III CRISPR ring nuclease.

ShrinkCRISPR analyzes CRISPR-Cas9 screen data to detect differential gene fitness effects while accounting for variation across cell populations and replicates.

This paper demonstrates the first successful CRISPR/Cas9-mediated genome editing in non-model nematodes Panagrolaimus sp. PS1159 and Propanagrolaimus sp. JU765, enabling functional studies of developmental genes.

This study develops non-viral nanocapsules for in vivo CRISPR-Cas9 delivery to edit neuronal DNA in mice, achieving efficient and safe genome editing in specific neuron types.

This study optimizes genomewide CRISPR screens using AsCas12a and multi-guide arrays, finding that three guides per gene construct provide optimal performance.

The paper shows Polycomb response elements reduce leaky Cas9 expression under a heat-inducible promoter in Drosophila, but further regulation is needed for precise control.

This paper demonstrates CRISPR/Cas9-mediated gene editing in the nematode Nippostrongylus brasiliensis using extracellular vesicles to deliver Cas9/guide RNA complexes, achieving targeted gene disruption.

The paper develops a system for rapid, site-specific integration of multiple DNA constructs into the E. coli chromosome using recombinases, demonstrating its utility by inserting DNA methyltransferases to enable transformation of Clostridium clariflavum.

The paper shows CRISPR screens have a 20% false negative rate and introduces JLOE to recover false negatives without increasing false discoveries.

This paper introduces an approach called 'inception' that allows base editing at previously inaccessible sites by generating new PAM sequences through sequential combinatorial base editing.

CRISPRcleanRWebApp is a web tool that processes CRISPR-Cas9 viability screens to reduce false positives by correcting biases in gene targeting.

DANGER analysis assesses on/off-target effects of CRISPR editing using RNA-seq data without a reference genome, identifying deleterious off-target sites and quantifying their phenotypic impact.