CRISPR screen

MUSICiAn: Genome-wide Identification of Genes Involved in DNA Repair via Control-Free Mutational Spectra Analysis

MUSICiAn identifies DNA repair genes by analyzing mutational spectra from CRISPR-Cas9 perturbations without controls, revealing known genes and novel candidates.

Decoding E. coli's Gut Survival Strategies: A CRISPRi Approach Across Diets, Inflammatory Environment and Strains

This study uses CRISPRi to identify genetic factors affecting E. coli adaptation across diets, inflammation, and strains in a mouse model.

Genome writing and Targeted Delivery of the NKX6-3/ANK1 gene cluster and its Type 2 Diabetes GWAS Variants to Human iPSCs

This paper introduces a method to deliver synthetic haplotypes containing T2D GWAS variants to hiPSCs to study their functional impact on differentiation.

Lipid Nanoparticles for the Delivery of CRISPR/Cas9 Machinery to Enable Site-Specific Integration of CFTR and Mutation-Agnostic Disease Rescue

This paper develops lipid nanoparticles to deliver CRISPR/Cas9 for site-specific CFTR gene integration in CF airway cells, achieving 3-3.5% gene editing and 80% Cl- current restoration.

A CURE for synthetic regulation of gene expression: Rapid screening of guide RNA efficacy as a framework for enabling undergraduate research in plant synthetic biology

This paper develops a CURE for undergraduate research in plant synthetic biology using rapid gRNA efficacy screening to study gene regulation in Arabidopsis.

Empirical optimization of dual-sgRNA design for in vivo CRISPR/Cas9-mediated exon deletion in mice

This study develops an in vivo-trained model to predict dual-sgRNA efficiency for exon deletion in mice, achieving an AUC of 0.759.

Identification of Proteins Influencing CRISPR-Associated Transposases for Enhanced Genome Editing

This study identifies host factors that influence VchCAST activity and demonstrates that the λ-Red recombineering system significantly enhances its editing efficiency in E. coli and other bacteria.

Intestinal stem cell marker MEX3A regulates PPARγ expression with functional impact in colorectal carcinogenesis

This study shows MEX3A regulates PPARγ expression in colorectal cancer, affecting tumor growth and chemotherapy response.

CRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance

The paper identifies CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance through CRISPR screens and shows their potential as biomarkers for immunotherapy response.

RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria

The paper introduces CRASP-Seq, a method to identify gene regulators of alternative splicing, and finds ZNF207 regulates LMNA splicing in progeria by interacting with U1 snRNP.

LazyNet: Interpretable ODE Modeling of Sparse CRISPR Single-Cell Screens Reveals New Biological Insights

LazyNet is a neural-ODE model for CRISPR single-cell screens that provides interpretable mechanistic insights and competitive performance on neuronal and T-cell datasets.

eSPLIT and iSWAP: CRISPR-Mediated Conditional Allele Engineering with Short Artificial Introns

The paper introduces eSPLIT and iSWAP, two methods for generating conditional alleles using short artificial introns, validated in human and mouse models.

Allo-defensive, multiplex base-edited, anti-CD38 CAR T cells for "off-the-shelf" Immunotherapy

This paper develops base-edited CAR T cells targeting CD38 to create an off-the-shelf immunotherapy that avoids allo-rejection and shows anti-leukemic activity.

Regulatable In Vivo Gene Expression via Adaptamers

This paper introduces an RNA-based system called adaptamer that allows precise, reversible control of gene expression using small molecules, demonstrating its function in cell lines and mice.

An Efficient Workflow for CHO Cell Genome Engineering with OpenCRISPR-1

This paper validates OpenCRISPR-1 in CHO cells, achieving ≥70% INDEL efficiency across multiple genes using a 39-day workflow.

Mapping cis- and trans-regulatory target genes of human-specific deletions

The paper identifies human-specific deletions that affect gene expression by using CRISPRi screening in chimpanzee stem cells.

Genetic regulators of neuronal survival across metabolic environments

The paper identifies genetic regulators of neuronal survival across different metabolic environments using CRISPRi screens in human neurons.

SPLiCR-seq: A CRISPR-Based Screening Platform for RNA splicing Identifies Novel Regulators of IRE1-XBP1 Signaling Under ER Stress

SPLiCR-seq identifies novel regulators of IRE1-XBP1 signaling under ER stress, revealing GADD34 as a key modulator with therapeutic potential in CAR-T cell immunotherapy.

RAPID-DASH: Fast and Efficient Assembly of Guide RNA Arrays for Multiplexed CRISPR-Cas9 Applications

This paper introduces a method to rapidly construct gRNA arrays for CRISPR-Cas9 applications and provides a web tool for designing oligo sequences.

The Effects of Intraspecies and Interspecies Competition on Genetic Device Construction and Performance

The paper tests genetic device performance in monoculture and co-culture, finding that native promoters improve stability in complex environments.

Plasmid2MC: Efficient cell-free recombination of plasmids into high-purity minicircle DNA for use in genome editing applications

Stage- and tissue-specific gene editing using 4-OHT inducible Cas9 in whole organism

This paper introduces an inducible Cas9 system for tissue- and stage-specific gene editing in zebrafish and mouse embryos, demonstrating its effectiveness in inducing mutations in target genes.

Improved cloning-free one-step CRISPR-Cas12a-assisted tagging of mammalian genes using PCR generated reagents (PCR tagging)

The paper improves CRISPR-Cas12a-assisted gene tagging in mammalian cells by enhancing HDR efficiency and reducing off-target integrations through modified cassettes and repair pathway modulation.

A Pooled Cell Painting CRISPR Screening Platform Enables de novo Inference of Gene Function by Self-supervised Deep Learning

This paper introduces a pooled CRISPR screening platform combined with self-supervised deep learning to infer gene function from morphological phenotypes without target-specific biomarkers.

Evaluating transportability of in-vitro cellular models to in-vivo human phenotypes using gene perturbation data

The paper evaluates the transportability of in-vitro gene perturbation models to in-vivo human phenotypes using CRISPR data and UK Biobank, finding some models are predictive while others are not.

Chemically-inducible CRISPR/Cas9 circuits for ultra-high dynamic range gene perturbation

This paper develops inducible CRISPR/Cas9 systems with improved dynamic range and reduced off-target effects for precise gene perturbation.

Developmental regulators enable rapid and efficient soybean transformation and CRISPR-mediated genome editing

This study develops a method using developmental regulators to improve soybean transformation and CRISPR-mediated genome editing efficiency.

Personalized CRISPR Knock-In Cytokine Gene Therapy to Remodel the Tumor Microenvironment and Enhance CAR T Cell Therapy in Solid Tumors

This paper develops CancerPAM, a bioinformatics pipeline for identifying CRISPR knock-in sites to remodel the tumor microenvironment, enhancing CAR T cell therapy in solid tumors.

Comparison of Interventional Causal Structure Learning Algorithms for Gene Regulatory Network Inference

This paper benchmarks causal structure learning algorithms for gene regulatory network inference using synthetic and CRISPR perturbation data, finding reliable performance on synthetic data but limitations on real data due to noise and scalability.

Conjugation Based CRISPR Antifungals (COBRA)

The paper develops a conjugation-based CRISPR antifungal platform (COBRA) to deliver gene-targeting machinery from E. coli to yeast, demonstrating effective gene elimination and antifungal activity.