CRISPR screen

Simulating a for-loop in the human genome: Design and evaluation of recombinase genetic programs that count to three.

The paper designs and evaluates recombinase-based genetic programs in human cells that simulate a for-loop counting to three, demonstrating heritable memory and sequential gene expression.

Protective antigen-mediated delivery of an anti-CRISPR proteinfor precision genome editing

This paper develops a protein-based delivery system for anti-CRISPR proteins to precisely control Cas9 activity, reducing off-target effects and improving genome editing specificity.

A platform for the systematic interrogation of genetic interactions in human cells: 26 gene by genome-wide double knockout screens as a proof of concept

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.

Optimized iMAP CRISPR Perturbation Illuminates Context-Specific Functions of RNA Modification Factors

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.

Engineering circular guide RNA and CRISPR-Cas13d-encoding mRNA for the RNA editing of Adar1 in triple-negative breast cancer immunotherapy

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.

Systematic Mapping of Bacterial CRISPRa Design Rules and Implications for Synergistic Gene Activation

This study systematically maps bacterial CRISPRa design rules and finds no synergistic activation, highlighting mechanistic differences from eukaryotic systems.

A side-by-side comparison of variant function measurements using deep mutational scanning and base editing

This study compares deep mutational scanning and CRISPR base editing for variant function annotation, finding strong correlation between base editor data and gold standard DMS results.

Engineered ADARs enable single-nucleotide resolution DNA A-to-G editing without bystander effects

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.

Advanced Peptide Nanoparticles Enable Robust and Efficient delivery of gene editors across cell types

This paper develops hPep-based nanoparticles for efficient delivery of gene editors across multiple cell types, achieving high editing efficiency in human cells.

Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness

The paper identifies 58 loci in budding yeast that interact with fitness, showing global epistasis where genetic perturbations have greater effects in more fit individuals.

Integrative analysis of pooled CRISPR screens provide functional insights into AD GWAS risk genes

The paper uses CRISPR screens and Perturb-seq to identify gene programs and functional relationships in AD GWAS risk genes related to lipid and lysosomal pathways.

Self-limiting population suppression gene drive in the West Nile vector mosquito, Culex quinquefasciatus

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.

Higher resolution pooled genome-wide CRISPR knockout screening in Drosophila cells using integration and anti-CRISPR (IntAC)

The paper introduces IntAC, a CRISPR screening method for Drosophila cells that improves accuracy by suppressing early Cas9 activity, leading to a more comprehensive list of fitness genes.

An enhanced Eco1 retron editor enables precision genome engineering in human cells without double-strand breaks

This paper enhances the Eco1 retron editor for precise genome editing in human cells by improving ncRNA stability and reducing sgRNA extension, achieving editing without double-strand breaks.

Context-dependent regulatory variants in Alzheimer's disease

The paper identifies context-dependent regulatory variants in Alzheimer's disease by analyzing their effects across different cellular contexts using MPRAs and machine learning.

Rewiring DNA Repair Activity into CRISPR Signal Transduction via Synthetic DNA Transducers

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.

Comparative CRISPRi screens reveal a human stem cell dependence on mRNA translation-coupled quality control

The paper compares CRISPRi screens in human stem cells and their derivatives to show cell type-dependent roles of translation-coupled quality control factors.

Prevenying vision loss in a mouse model of Leber Congenital Amaurosis by engineered tRNA

This study demonstrates that engineered tRNA can restore vision in a mouse model of Leber Congenital Amaurosis by suppressing a premature termination codon.

Enhanced cleavage of genomic CCR5 using CASX2Max

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

A shotgun approach for highly multiplexed mammalian metabolic engineering

This paper introduces SGE, a method for screening metabolic pathways in mammalian cells, and finds that mitochondrial localization and large synthetic DNA constructs are key for successful pathway engineering.

Specific Modulation of CRISPR Transcriptional Activators through RNA-Sensing Guide RNAs in Mammalian Cells and Zebrafish Embryos

This paper introduces a method to modulate CRISPR activity in response to RNA detection using engineered guide RNAs, demonstrating functionality in mammalian cells and zebrafish embryos.

Directed evolution expands CRISPR-Cas12a genome editing capacity

The paper identifies CRISPR-Cas12a variants with expanded PAM recognition, enabling targeting of ~25% of the human genome.

Benchmarking Genetic Interaction Scoring Methods for Identifying Synthetic Lethality from Combinatorial CRISPR Screens

Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing

This study identifies DDX39B as a global repressor of A-to-I RNA editing using CRISPR screens and shows its potential as a therapeutic target for anti-HDV therapy.

A simplified two-plasmid system for orthogonal control of gene expression using light-activated CRISPR effector for mammalian cells

This paper simplifies the LACE optogenetic system from four to two plasmids, showing similar performance with reduced variability.

Genome-wide CRISPRi-seq identified ferredoxin-NADP reductase FprB as a synergistic target for gallium therapy in Pseudomonas aeruginosa

The paper uses CRISPRi-seq to identify FprB as a synergistic target for gallium therapy in Pseudomonas aeruginosa, enhancing gallium's efficacy against infections.

Temporal Control of CRISPR-Cas9 Activity Using Bio-orthogonal Chemistry.

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

A compendium of nonredundant short Polymerase III promoters for CRISPR applications

The paper presents a collection of minimal Pol III promoters for CRISPR applications, showing they can match longer promoters' performance in dicots.

Quantitative analysis of genetic interactions in human cells from genome-wide CRISPR-Cas9 screens

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

The strength of weird ties: positive genetic interactions have greater scientific impact but are under-represented in the literature

The paper finds that positive genetic interactions have greater scientific impact but are underrepresented in literature, despite equal detection capability.