CRISPR and Genetic Engineering

The paper introduces pCASKD, a single-plasmid system for scarless gene editing in E. coli, demonstrating efficient knock-in and knock-out edits with reduced false positives and faster workflow.

This paper introduces a CRISPRi-seq platform in Haemophilus influenzae to study gene fitness and essentiality, revealing medium-specific growth determinants and introducing a genome annotation resource.

This study investigates CRISPR-Cas9 antimicrobial activity against E. coli ST131 and identifies two escape mechanisms, showing that genetic context of the target gene influences escape frequency.

The paper introduces a method for systematically studying genetic interactions in human cells using CRISPR/Cas9 screens and demonstrates its effectiveness through 26 gene by genome-wide knockout screens.

This study uses long-read sequencing to analyze genomic and transcriptomic changes in AAV-CRISPR therapy for DMD, revealing complex editing outcomes and developing new methods for detection.

The paper describes engineering Cas12a to enable PAM-free, ultra-specific detection by splitting the target DNA duplex and improving structural selectivity and nucleotide specificity.

The paper optimizes the iMAP CRISPR platform to reduce recombination bias, profiles RNA modification factors across mouse tissues, and identifies context-specific functions with therapeutic implications.

This study develops circular guide RNAs (cgRNAs) and Cas13d-encoding mRNA for efficient RNA editing of Adar1 in triple-negative breast cancer, showing improved stability and therapeutic efficacy.

This paper introduces snuABE, a single-nucleotide resolution ABE that reduces bystander effects through engineered ADAR and tagRNA design, achieving precise A-to-G editing in human cells.

This paper describes a CRISPR-based gene drive targeting the doublesex gene in Culex mosquitoes to suppress populations through male-biased propagation and sterile intersexes.

This paper introduces a synthetic DNA transduction platform that links DNA repair activity to CRISPR-Cas12a activation, enabling rapid and sensitive detection of DNA glycosylase activity and inhibitor screening.

The paper evaluates CasX2Max, a modified CRISPR system, showing it enhances cleavage efficiency for the CCR5 gene compared to native CasX2.

This paper demonstrates the use of Mpa Ago for in vitro mRNA processing and analysis, including 3' end polishing and comprehensive assessment of mRNA features using LC-MS/MS.

This paper introduces a method to temporally control CRISPR-Cas9 activity using bio-orthogonal chemistry, demonstrating its effectiveness in live cells and therapeutic applications.

The paper develops a method to quantify genetic interactions from CRISPR-Cas9 screens and identifies systematic variations in screen data.

This study shows that crispant founder mice can be used for phenotypic assessment despite genetic mosaicism, as observed null phenotypes were present in up to 100% of founders.

The paper develops fast-annealed 3'-extended dsDNA templates to improve CRISPR-Cas9-mediated knock-in efficiency in emerging model insects.

This paper introduces an in vivo method to iteratively relocate chromosomal loci in E. coli using synthetic DNA, enabling scarless genome editing without requiring external DNA manipulation.

This study uses deep learning and simulations to uncover the molecular mechanisms of TnsC filament assembly in a CRISPR-associated transposon.

OOGGA optimizes Golden Gate assembly overhangs for accuracy and efficiency, outperforming NEBridge SplitSet in fidelity and efficiency metrics.

This study demonstrates that retron-mediated recombineering can be applied across multiple bacterial species, achieving high editing efficiencies in several phyla.

This paper introduces a method for targeted genomic integration and rearrangement in human cells using CRISPR-targeted dual flap synthesis, enabling DNA sequence assembly without requiring double-stranded DNA donors or cell cycle progression.

The paper introduces a synthetic CRISPR guide sequence for generating entry strains in C. elegans when the standard dpy-10 guide is unsuitable.

The paper develops caffeine-inducible systems for controlling gene expression in human cells using humanized protein components and demonstrates their use in inducible gene expression in T-cells.

This study develops a wireless optogenetic system to control genome editing and tumorigenesis in mice by using light-regulated recombinase and implantable devices.

This study tests a homing gene drive in Drosophila melanogaster and finds that while simple resistance alleles can emerge, complex resistance is unlikely due to no heritable genetic effects on drive efficiency.

This study demonstrates the use of Eco CRISPR-Cas3 in rice to generate heritable large deletions, achieving deletion frequencies of 21-61% and stable inheritance in progenies.

The paper identifies intrinsic ATPase activity in AsCas12a, independent of DNA, using radiometric TLC and bioinformatics.

This paper demonstrates a cytosine base editor that enables efficient and durable multiplexed gene knockout in iPSCs with minimal p53 activation and reduced DNA damage.