CRISPR screen

An integrated workflow for dual-guide CRISPR-Cas9 targeting and amplicon-based genotyping of Pla2g6 in primary mouse bone marrow-derived macrophages

This paper describes a workflow for dual-guide CRISPR-Cas9 editing of Pla2g6 in mouse BMDMs, showing high editing efficiency and specific deletion patterns.

Where single-cell foundation models help: a benchmark of annotation, perturbation and regulatory inference against simple baselines

This paper benchmarks single-cell foundation models against baselines for annotation, perturbation and regulatory inference using diverse datasets.

Biosensor-guided genome-wide CRISPR screens enable cis,cis-muconic acid overproduction in yeast

This study uses biosensor-guided CRISPR screens in yeast to identify genetic targets that enhance production of cis,cis-muconic acid and protocatechuic acid.

Genome-wide CRISPRi-seq maps essential-gene contributions to aminoglycoside susceptibility in Pseudomonas aeruginosa

This study uses CRISPRi-seq to identify essential genes affecting aminoglycoside susceptibility in Pseudomonas aeruginosa, revealing gene-specific fitness effects and potential targets for antibiotic enhancement.

Tiled base editing screens uncover rare second-site mutations that rescue a misfolded disease protein

The paper uses base editing screens to identify second-site mutations that correct misfolded NPC1 proteins, enabling therapeutic applications for diseases like Niemann-Pick type C.

Cross-modal transfer enables zero-shot prediction of drug responses across cell types

GRAFT predicts drug responses across cell types without direct measurements by transferring genetic perturbation data to chemical perturbations.

Mitochondrial genome editing reveals the impact of complex I heteroplasmic variants on human neurogenesis

This study edits mtDNA variants in human iPSCs to show that heteroplasmic complex I variants impair neuronal commitment.

Carboxymethyl Dextran Coated Iron Oxide Magnetic Nanoparticles as Vehicles for CRISPR Ribonucleoproteins

This paper develops CMD-coated magnetic nanoparticles for delivering CRISPR RNPs, demonstrating efficient genome editing in cell lines and a skin disorder model.

PrEditR: A protein-centric platform for CRISPR-mediated base editor sgRNA design

PrEditR is a tool for designing sgRNAs for CRISPR-based base editors, allowing users to target specific amino acids and annotate resulting mutations.

Expanding the therapeutic window of bacteria for cancer therapy

This paper develops a tumor-targeting engineered bacterium that improves therapeutic efficacy and safety in cancer treatment.

Systematic analysis of genetic vulnerabilities caused by chromosome loss events in cancer

This study identifies genetic vulnerabilities from chromosome loss events in cancer by analyzing CRISPR screening data and copy number profiles, revealing paralogous gene dependencies as therapeutic targets.

Compact CRISPR-based genetic circuitry using a miniature genome-integrated Cas12m protein

A genome-integrated Cas12m in E. coli shows no measurable growth cost, reverses repression faster than dCas9, and supports NOT gates, a two-layer buffer and a two-pathway pigment circuit.

The effects of DNA repair factor-Cas9 fusions on homing gene drive performance

This study evaluates Cas9 fusion proteins in Drosophila to enhance homing gene drive performance by improving HDR and reducing resistance.

Single-vector AAV delivery of En-ISPmu1 and donor DNA for in vivo targeted genome integration

The paper describes the development of En-ISPmu1, a modified TnpB nuclease, and demonstrates its ability to achieve targeted genome integration in mouse liver with a single AAV vector.

Parkin deficiency rewires the genetic dependencies that govern neuronal survival

This study shows that Parkin deficiency alters genetic dependencies for neuronal survival, identifying key pathways and genes involved in this rewiring.

Mitochondrial folate transport becomes essential in serine/glycine-starved triple-negative breast cancer

This study identifies SLC25A32 as a critical mitochondrial folate transporter that becomes essential in serine/glycine-starved triple-negative breast cancer, making it a potential therapeutic target.

In Silico Design and Evaluation of CRISPR Cytosine Base Editing Strategy for Potential Correction of the ASPA Variant Associated with Canavan Disease

The paper designs and computationally evaluates a CRISPR base editing strategy to correct the ASPA variant associated with Canavan disease, identifying a candidate sgRNA with favorable editing characteristics and genome-wide specificity.

U6 promoters in Ulva prolifera enable dual small-RNA/mRNA transcription and vector-based CRISPR-Cas9 genome editing

The paper identifies and characterizes U6 promoters in Ulva prolifera, showing their dual transcriptional activity and utility for CRISPR-Cas9 genome editing.

CRISPR-dPCR: A unified multiplex digital PCR framework for quantitative characterization of targeted knock-in

CRISPR-dPCR quantifies CRISPR knock-in by distinguishing integration from donor abundance and background, using multiplex digital PCR with orthogonal strategies.

An improved CRISPR-LICHT screen of 120 Tdark genes illuminates new biologically relevant SOX2 targets in human brain organoids

The paper uses CRISPR-LICHT to screen SOX2 targets in human brain organoids, identifying 28 new genes involved in neural progenitor lineage expansion and survival.

A light-responsive lipid nanoparticle platform delivering Cas9 RNP for VEGFA editing suppresses choroidal neovascularisation

This study develops a light-responsive lipid nanoparticle platform for VEGFA gene editing to suppress choroidal neovascularisation, showing reduced vascular leakage and structural abnormalities in a rat model.

Centered cross-context perturbation transfer on the public 2025 Virtual Cell Challenge benchmark

The paper develops a method for cross-context perturbation transfer and differential-expression ranking, achieving competitive results on a benchmark challenge.

Evaluating the added value of sequence models in noncoding RNA assays: a baseline-aware framework

The paper evaluates sequence models in noncoding RNA assays by comparing model increments against baselines and highlights the importance of baseline content and regularization.

Multimodal functional characterization of the LDLR noncoding landscape

This study uses multiple functional genomic approaches to identify and characterize cis-regulatory elements (CREs) influencing LDLR expression, revealing overlapping yet distinct CREs across methods.

A heat-assisted ttLbCas12a workflow incorporating crRNA 3'-tailing enables efficient multiplex biallelic genome editing in hybrid poplar

Averaging in gene perturbation benchmarks hides perturbation-strength variation: Consequences for model evaluation

The paper evaluates how averaging perturbation responses in gene perturbation benchmarks affects the ability to assess perturbation-strength variation, finding that current models fail to reliably recover perturbation identity.

Systematic Functional Interrogation of Neurodevelopmental Disorder Risk Variants

This study identifies 38 expression-modulating variants associated with neurodevelopmental disorders and links them to neurodevelopmental transcriptional programs using MPRA and CROP-seq.

Robust Identification of Drug Mechanism of Action Associated Genes Across Heterogeneous Drug Treated Datasets

This paper introduces ConcuRx, a statistical framework that improves gene prioritization across heterogeneous CRISPR drug-response datasets by modeling between-study variability, leading to better identification of MOA-associated genes.

Thermodynamic Quality Control Reshapes Spatially Resolved Metabolic Flux Predictions in Prostate Cancer

Quality-controlled, cycle-certified E-Flux Human-GEM models of twelve regions from one prostate tumor curb implementation-driven flux inflation and show predicted metabolic similarity tracks spatial region, not histology.

Locally deployed AI agents for CRISPR guide discovery from outbreak reports

The paper develops a CRISPR guide-discovery pipeline using locally deployed AI agents and evaluates it with large language models.