CRISPR and Genetic Engineering

BARCS extends beta-binomial regression to handle complex CRISPR screen designs, showing improved essential gene recovery but calibration issues in gene-level summaries.

This paper introduces ELXRs, CRISPR-CasX-based epigenetic repressors that use sequential proofreading to enhance specificity and potency by reading chromatin state before DNA methylation.

This study identifies DNA repair mechanisms that influence CRISPR-Cas antifungal efficacy in Candida albicans and shows how to tune Cas9 lethality through repair template availability and enzyme activity.

This paper introduces a knockout and re-expression system for analyzing mutant phenotypes in primary mouse T cells, showing improved integration of mutant proteins and validation for TCR and Zap70 studies.

This paper demonstrates the successful application of AI-designed OpenCRISPR-1 for efficient gene editing in dicot plants, achieving high mutation rates in soybean and Nicotiana benthamiana.

This study compares CRISPR knockout and interference methods using single-cell RNA sequencing to evaluate their strengths in functional genomics.

The paper introduces nCasTLES, a method for targeted sequencing using Cas12a to improve DNA sequence and modification profiling compared to nCATS.

The paper identifies a CRISPR-associated kinase system that uses a tRNA-derived RNA fragment as a second messenger to enhance antiviral defense by upregulating immune genes.

CRISPR-HAWK identifies genetic variants affecting CRISPR guide performance across diverse populations, revealing that 82.5% of therapeutic guides are impacted by variants.

The paper develops a rapid PCR-based screening system to detect type II CRISPR-Cas loci in bacterial species, validated on environmental isolates.

This study investigates the role of the femaleless gene in Anopheles gambiae gametogenesis and its impact on CRISPR-Cas9 gene drive efficacy, showing that disrupting fle causes female sterility and limits gene drive spread.

The paper benchmarks machine learning classifiers for predicting CRISPR-Cas9 off-target cleavage sites using GUIDE-seq data, finding that gradient boosting performs best in a highly imbalanced dataset.

The paper develops a scarless conditional sgRNA system using endogenous RNA processing to enable precise temporal control of genome editing with improved efficiency and fidelity.

This paper develops a CRISPR-Cas method for gene knock-out and endogenous protein tagging in the brown alga Ectocarpus, enhancing functional genomics capabilities.

The paper identifies and characterizes compact Cas9d orthologs with high genome editing efficiency and specificity, suitable for AAV-based therapeutic applications.

The paper benchmarks 12 base editors delivered via VLPs for DNA editing in LentiX-293T cells, showing dosage-dependent efficiency and varying mutation outcomes.

The paper redefines IS110 as a dynamic platform capable of expanding into large elements that disseminate antimicrobial resistance.

Perturb-ME combines CRISPR screening and single-cell profiling to identify regulatory modules governing gene programs in melanoma.

The paper identifies a prespacer-coupling module in Cas1 that interacts with a conformational-coupling module, showing that epistatic interactions between substitutions enhance CRISPR adaptation activity.

The paper develops GuideRefine to identify and remove multi-targeting and off-targeting sgRNAs from CRISPR-KO libraries, improving the accuracy of gene hit lists.

The paper develops a multi-color ddPCR assay to quantitatively distinguish multiple edited alleles in genome editing outcomes, offering a faster and more scalable alternative to sequencing.

The paper generates functional genome editors by combining deep mutational scanning, structural analysis, and evolutionary mining with a generative protein language model.

This paper introduces a self-regulating CRISPRi system that reduces leakiness while maintaining inducible gene repression, enabling portable and multiplexed applications.

The paper identifies and characterizes three compact type II-C Cas9 orthologs with improved PAM compatibility and high fidelity for genome editing in human cells.

This study shows that RecA status influences CRISPR-Cas adaptation through SOS response mechanisms in E. coli, with RecA loss enhancing adaptation via RecBCD-dependent DNA processing.

The paper shows guide RNA binding causes reverse transcription bias in RT-qPCR for CRISPR systems and proposes a denaturation step to correct it.

This paper describes a standardized method to replace T cell receptors in murine CD8 T cells using CRISPR-Cas9 and retroviral transduction, enabling efficient genetic manipulation for in vitro and in vivo studies.

The paper develops CRISPR-Cas9 delivery methods for primary human hepatocytes to enable efficient gene editing and screening of HBV host factors.

This study develops and validates CRISPR guide RNAs to target BRAF oncofusions and V600E mutations in pediatric low-grade glioma cells, achieving high indel frequencies and confirming junction excision.

The paper enhances Cas{Phi}2 activity using EPICA.2, an optimized directed evolution platform, resulting in evoCas{Phi}2 with 70-fold increased activity in human cells.