CRISPR and Genetic Engineering

This paper introduces a gene drive called HomeR that efficiently spreads and persists in Drosophila populations by limiting resistance allele accumulation.

CRISPR-Decryptr analyzes noncoding CRISPR screens to infer regulatory elements by accounting for experimental design and validating on published data.

In mouse zygotes, prime editing installed 10 modifications across 6 genes, but undesired products such as large deletions outnumbered intended edits, traced to PE3 double-nicking.

The paper evaluates base editing and PRIME editing techniques to introduce specific mutations in genes associated with Alzheimer's and Duchenne Muscular Dystrophy, assessing their efficiency in cell lines and potential therapeutic impact.

EdiTyper analyzes targeted sequencing data from genome editing experiments to detect mutations and indels with high accuracy and scalability.

This study uses CRISPR-based epigenetic editing to activate pancreatic beta-cell genes in human cells, showing that sequential activation of transcription factors is more effective than simultaneous activation.

This paper develops C:G to G:C base editors to correct specific SNPs in human cells, achieving up to 37% editing efficiency and 90% specificity.

This paper reports unexpected severe hydrops fetalis in CRISPR-Cas9 edited pigs with a FBN1 deletion, highlighting potential off-target effects and the need for comprehensive genomic analysis.

The paper introduces FIVER, a multispectral reporter for in vivo genome editing that detects NHEJ, HDR, and HITI with fluorescent read-outs, demonstrating its utility in primary cells, organoids, and in vivo models.

The paper demonstrates that 2-locus Cleave and Rescue elements create self-limiting gene drive, with spread controlled by a recombination rate-dependent generational clock in Drosophila.

The paper validates off-target effects of CRISPR/Cas9 in rhesus macaques using error-corrected sequencing, showing that in vitro and in silico methods have limited predictive accuracy.

The paper develops a computational method to correct off-target effects in CRISPR-Cas9 essentiality screens, improving specificity while preserving known gene essentialities.

The paper introduces SAGE, a genome engineering system for bacteria that enables efficient, iterative integration of DNA constructs without requiring selection.

The paper introduces MAGIC, a CRISPR/Cas9-based method to generate mosaic animals in Drosophila by inducing DNA double-strand breaks, enabling efficient gene function studies and fluorescent clone generation.

This study investigates CRISPR/Cas9-based gene drives in mice, finding that robust Cas9 expression during meiosis is critical for efficient gene drive generation.

The paper introduces a system for sequentially activating guide RNAs to control genetic manipulations in mammalian cells using Cas9, enabling preprogrammed cascades of gene editing events.

This study shows that gene conversion and NHEJ are major DNA repair mechanisms in human embryos, with gene conversion potentially useful for gene correction but also causing extensive loss of heterozygosity.

The paper enhances Gibson Isothermal Assembly by adding a single-stranded DNA binding protein, improving accuracy and efficiency, especially with multiple fragments.

The paper validates CRISPR-Cas9 editing and identifies transgenic inserts using Xdrop for targeted enrichment followed by short- and long-read sequencing, revealing previously undetected large insertions.

This paper introduces AcrDetector, a tool that identifies Acrs in prokaryotes using six features, achieving high accuracy and demonstrating its effectiveness across species.

Ledidi designs genome edits to induce functional activity by optimizing predictions from a model, validated using Basenji for CTCF and JUND binding.

The paper introduces TRAP-seq to quantify CRISPR editing efficiency and uses it to design improved gRNAs for Cas9, ABE, and CBE with high accuracy and efficiency.

HCR-FlowFISH identifies cis-regulatory elements and their target genes by quantifying gene expression changes after CRISPR perturbations, using >270,000 perturbations to detect CREs for multiple genes.

The paper develops an automated pipeline to design CRISPR prime editors for human pathogenic variants, finding that only a small fraction can be targeted but this number increases to over 50,000 with alternative Cas9 and templates.

FORCAST is a software pipeline that integrates existing tools to design, evaluate, and store Cas-mediated mutagenesis experiments.

This study investigates the portability of RecT-mediated homologous recombination across bacterial species, finding that compatibility with the host's single-stranded DNA-binding protein determines functionality.

The paper characterizes Cas9-generated auxotrophs in Phaeodactylum tricornutum, showing they can be complemented by plasmid-based genes and exhibit metabolic changes.

This paper introduces an inducible CRISPR-Cas9 system for preclinical drug discovery, enabling controlled genome editing in mice to model cancer and test therapies.

The paper demonstrates that a natural gene drive can be used to remove pathogenic traits from Fusarium graminearum populations in three generations.

This study improves gene drive efficacy by reducing resistance and fitness costs through regulatory sequence modifications, leading to better population suppression and delayed resistance.