CRISPR screen

Punctuational evolution is pervasive in distal site metastatic colonization

The paper shows that metastatic tumors exhibit more punctuational molecular evolution compared to primary tumors, indicating different evolutionary modes in cancer progression.

Facilitating Gene Editing in Human Lymphoma Cells Using Murine Ecotropic γ-Retroviruses

This paper develops a two-step strategy using ecotropic γ-retrovirus to enable efficient and safe gene editing in B lymphoma cell lines resistant to lentiviral transfection.

Mechanism-guided engineering of a minimal biological particle for genome editing

This study engineers a minimal EDV for genome editing by removing viral components, showing improved efficiency and reduced size.

X-CRISP: Domain-Adaptable and Interpretable CRISPR Repair Outcome Prediction

X-CRISP predicts CRISPR repair outcomes with domain adaptability and interpretability, outperforming existing models and improving with transfer learning across cell lines.

Virus-free continuous directed evolution in human cells using somatic hypermutation

This paper develops a continuous directed evolution platform in human B cells using somatic hypermutation to evolve proteins with diverse mutations.

A self-limiting Sterile Insect Technique alternative for Ceratitis capitata

The paper develops a split-CRISPR/Cas9 system for sex conversion in Mediterranean fruit flies to improve population control strategies.

The cytosolic cysteinyl-tRNA synthetase is capable of regulating ATF4 translation independent of eIF2α phosphorylation state

The paper identifies a novel pathway for ATF4 translation activation through CARS loss, independent of eIF2α phosphorylation and mTOR signaling.

Engineering Adaptive Alleles for Escherichia coli Growth on Sucrose Using the EasyGuide CRISPR System

The paper introduces EasyGuide CRISPR, a CRISPR toolkit for engineering E. coli strains to grow on sucrose, and demonstrates its application in adaptive evolution experiments.

Near 100% genome editing efficiency with a one-step all RNA prime editing system in a human reporter iPSC line

The paper develops an all-RNA prime editing system achieving over 95% editing efficiency in human iPSCs with minimal off-target effects.

Genetic manipulation of Bacteriophage T4 utilizing the CRISPR-Cas13b system

This paper describes a CRISPR-Cas13b-based method to edit the T4 bacteriophage genome, enabling gene deletions, mutations, and fluorescent protein insertion for studying phage biology.

Mapping the Genetic Architecture of the Adaptive Integrated Stress Response in S. cerevisiae

The paper uses CiBER-seq to analyze how genetic perturbations affect ISR dynamics in yeast, finding that translation-related perturbations increase ISR activation while ribosome biogenesis impairments reduce it.

GO-CRISPR: a highly controlled workflow to discover gene essentiality in loss-of-function screens

GO-CRISPR improves loss-of-function CRISPR screens by integrating guide-only controls and TRACS software, identifying novel pathways in tumor dormancy.

Sustained efficacy of CRISPR-Cas13b gene therapy for FSHD is challenged by immune response to Cas13b

This study shows CRISPR-Cas13b effectively reduces DUX4 in FSHD but is limited by immune responses that decrease Cas13b levels over time.

KOnezumi-AID: A Software to Automate the Design of Multiplex Knockouts Using Target-AID

KOnezumi-AID automates gRNA design for Target-AID-mediated gene knockouts, enabling efficient and safe multiplex knockout strategies in mouse and human genomes.

A genetic safeguard for eliminating target genes in synthetic probiotics in a gut environment

This paper introduces a genetic safeguard system for synthetic probiotics that degrades engineered genes without killing host microbes, demonstrating its feasibility in gut environments.

High-accuracy crRNA array assembly strategy for multiplex CRISPR

This paper introduces a high-accuracy CRISPR array assembly strategy that enables efficient assembly of multiple crRNAs in a single reaction, improving the practicality of multiplex CRISPR applications.

Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells

This study shows that gene editing of HSCs without ex vivo culture reduces genotoxicity while maintaining therapeutic efficacy for beta-hemoglobinopathy treatment.

Degron-modified Cas12a enhances single-cell CRISPR screening

This paper develops a degron-modified Cas12a system to enable accurate single-cell detection of pre-crRNAs, enhancing Perturb-seq capabilities for multiplex guide expression.

Cardiac Applications of CRISPR/AAV-Mediated Precise Genome Editing

This study applies CASAAV-HDR to model cardiomyopathies and perform functional genomics in mouse cardiomyocytes, showing its utility for disease modeling and enhancer analysis.

A three-node Turing gene circuit forms periodic spatial patterns in bacteria

The paper engineers a synthetic three-node Turing gene circuit in E. coli that generates periodic spatial patterns, validated by a differential equation model.

Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening

The paper identifies regulators of STING trafficking through genome-wide screening and characterizes their functional impact on STING signaling.

MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis and allostery from deep mutational scanning data

SPLICER: A Highly Efficient Base Editing Toolbox That Enables In Vivo Therapeutic Exon Skipping

SPLICER improves exon skipping by editing both splice acceptor and donor sites, reducing aberrant splicing and enabling therapeutic applications in Alzheimer's disease.

Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation

This paper engineers a synthetic microbial circuit in E. coli to respond to two signals and secrete IL-22 for anti-inflammatory effects in a gut epithelial model.

Engineered transcription-associated Cas9 targeting in eukaryotic cells

This paper introduces a method to temporally control Cas9 DNA targeting by coupling it with transcription through engineered RNA binding, enabling selective gene editing in yeast and human cells.

Paired CRISPR screens to map gene regulation in cis and trans

The paper uses paired CRISPR screens to identify cis- and trans-regulatory elements controlling PD-L1 expression in PDAC cells and links them to clinical outcomes.

Successful delivery of CRISPR-Cas9 with a baculovirus vector for insect brain targets

The paper successfully delivers CRISPR-Cas9 via a baculovirus vector to knock down AmOctβ2R in honey bee brain neurons, leading to appetite suppression.

The interplay of DNA repair context with target sequence predictably biases Cas9-generated mutations

The paper investigates how DNA repair genes influence Cas9-induced mutations by analyzing mutational outcomes across 2,838 synthetic targets in mouse cells, revealing gene-specific roles and improving predictive models.

Epigenetic Regulation of Inflammatory NF-κB Target Genes by IFN-γ via IRF1

This study shows IFN-γ enhances TLR-induced inflammatory gene expression through IRF1, which is critical for synergistic activation of genes like IL6 and TNF in human monocytes.

Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens

The paper introduces Exorcise, a tool to reannotate CRISPR libraries to user-defined genomes, improving targeting accuracy and reducing bias in screens.