CRISPR screen

Engineered mRNA-packaging virus-like particles enable efficient and precise mitochondrial base editing in vitro and in vivo

This study develops mtBE-VLPs for transient mitochondrial base editing, achieving high efficiency and reduced off-target effects in vitro and in vivo.

Programming primary human T cells to deliver gene editing machinery

This study engineers primary human T cells to deliver gene editing machinery using retroviral-based delivery vehicles, demonstrating efficient editing of diverse target cells.

Systematic mapping of chimera-permissive sites by CRISPR-guided PAM scanning

This paper uses CRISPR-guided PAM scanning to identify chimera-permissive sites in proteins, enabling the design of functional chimeras with preserved activity.

Protocol for Non-viral HDR-based CRISPR/Cas9 platform for small custom editing in primary T cells

This paper presents a non-viral HDR-based CRISPR/Cas9 protocol for editing primary T cells with up to 80% HDR efficiency, targeting small pathogenic variants in patient and healthy donor cells.

The phenotypic landscape of the model firmicute Bacillus subtilis

This study uses CRISPRi to screen B. subtilis genes across 150 stress conditions, revealing new roles for conserved firmicute genes in protein secretion, cell wall homeostasis, and bacterial competition.

Transcriptional adaptation influences buffering among essential paralog gene families

The paper investigates transcriptional adaptation in paralog gene families using Perturb-seq, finding six paralog pairs show adaptation and identifying mechanisms like nonsense-mediated decay and nuclear import.

BI-TfR1 CapX rapidly transits the blood-brain barrier for efficient, low-dose gene delivery throughout the CNS

The paper describes BI-TfR1 CapX, a gene delivery vector that efficiently crosses the blood-brain barrier, transduces CNS neurons and astrocytes, and reduces Prnp mRNA with low doses.

Reassessing the contribution of the histone H3 tail to KRAB-DNMT3L-mediated epigenetic silencing

The paper evaluates the role of the histone H3 tail in KRAB-DNMT3L-dCas9-mediated gene silencing and finds it does not provide a general functional advantage.

Stoichiometric m6A regulation of YY1 orchestrates the metabolic switch during cardiac development

The paper identifies a bimodal m6A code in cardiac development, showing how m6A stoichiometry and context regulate metabolic switches and gene expression.

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

The paper uses CRISPRi screening to identify Pol III gene dependencies in cancer cells, finding glioblastoma models are resilient to Pol III gene repression.

Mechanism-selective deep mutational scanning distinguishes ERCC2 disease phenotypes

The paper uses deep mutational scanning to distinguish disease mechanisms in ERCC2 variants, finding that TTD variants have lower fitness than XP variants.

Context-specific genetic interaction mapping reveals combinatorial KRAS/FGFR dependence in pancreatic cancer

The paper identifies combinatorial KRAS/FGFR dependence in pancreatic cancer through genetic interaction mapping and shows that combined inhibition overcomes resistance.

Generative Neuromorphic Programming of Mammalian Cells

This paper introduces a neuromorphic framework for programmable mammalian cells, enabling the design of analog circuits through generative programming and biomorphic neural networks.

Buffer tolerance landscape of LbCas12a trans-cleavage efficiency

This study identifies optimal buffer conditions for LbCas12a trans-cleavage activity, showing that while some buffers enhance catalytic efficiency, they also increase nonspecific cleavage, requiring careful optimization for detection performance.

Auto-SMART: a web-based platform for repair-template design for CRISPR/Cas9 homology-directed editing

Auto-SMART automates the design of CRISPR/Cas9 repair templates, enabling efficient genome editing by optimizing guide RNA selection and donor template construction.

STAR Suite: Transcriptomics processing in a single binary through AI-assisted development

Open-source STAR binary for five transcriptomic assays runs 3.9- to 6.2-fold faster than Cell Ranger 9.0.1 for scRNA-seq and Perturb-seq, 17- to 41-fold for Flex, with closely concordant counts.

Prime Editing Corrects the HBB Codon 8/9 (+G) Mutation in Patient-Derived Induced Pluripotent Stem Cells and Restores β-Globin Expression in iPSC-Derived Erythroid Cells

This study uses prime editing to correct the HBB c.27dupG mutation in patient-derived iPSCs and restores β-globin expression in erythroid cells.

Comparison of CRISPR-Cas-based knockdown of endogenous mRNA in sensory neurons

This study compares CRISPR-Cas systems for RNA knockdown in rat sensory neurons, finding hfCas13d provides robust gene silencing with minimal toxicity.

Twin-prime editing enables endogenous protein visualization and mutant allele tracking

This paper introduces twin-prime editing to visualize endogenous proteins and track mutant alleles at single-cell resolution in vivo.

CRISPR activation of endogenous PKD1 increases polycystin-1 levels and suppresses cellular features of ADPKD

This study uses CRISPR activation to increase PKD1 expression in ADPKD models, reducing cyst formation and improving cellular features.

Engineering Persistent and Rewritable Genetic Memory in Bacteria through Multiscale Plasmid Competition

This paper engineers a reversible genetic memory system in bacteria that maintains two states for up to two weeks while remaining rewritable.

Combinatorial CRISPR/Cas12a excises targeted loci in the mammalian genome at very low efficiency

This study evaluates combinatorial CRISPR/Cas12a for locus excision in mammalian cells and finds low efficiency despite targeting intronic regions.

Cas12a cleavage and trimming kinetics reveal mismatches as a strategy to steer editing

This study shows that reprogrammed gRNAs with mismatches can shift editing outcomes to improve gene knockout efficiency without reducing overall editing efficiency.

Spatiotemporal Control of Genetic and Epigenetic Editing through Covalent Tethering of CRISPR Nanoparticles to Zwitterionic Microgels

This paper introduces a method to covalently tether CRISPR nanoparticles to microgels for sustained and localized gene editing in human cells.

Fishash: A contingency table approach to Perturb-seq guide assignment

Fishash assigns perturbations to cells in Perturb-seq data using Fisher's Exact Test, improving accuracy and speed over existing methods.

Cardiomyocyte vulnerability to lamin polymer disruption revealed by saturation mutagenesis

The paper identifies cardiomyocyte-specific vulnerabilities to LMNA mutations using saturation mutagenesis in hiPSCs and cardiomyocytes, revealing how lamin polymer disruption leads to disease.

SEME enables programmable transcript reconstruction through synthetic microexon incorporation

SEME corrects aberrant splicing in iPSC-CMs by programmable microexon incorporation, restoring filamin C expression in a dilated cardiomyopathy model.

A novel, high-density CRISPR activation platform for mapping cancer dependencies and resistance pathways ex vivo and in vivo

This paper introduces Partita, a high-density CRISPRa platform for comprehensive gene activation studies, demonstrating its utility in identifying cancer dependencies and resistance pathways in vitro and in vivo.

Interrogation of noncoding schizophrenia risk variants using CRISPR-based functional genomics

The paper uses CRISPR-based functional genomics to identify noncoding regulatory elements and variants affecting schizophrenia-associated gene expression.

Universal donor plasmids for biallelic degron-tagging in mammalian cells and organoids

The paper introduces universal donor plasmids for biallelic degron-tagging in mammalian cells and organoids using Cas9-induced double strand breaks and homology-independent repair.