CRISPR and Genetic Engineering

This paper introduces BLU-VIPR, an optogenetic CRISPR tool that enables precise spatiotemporal gene editing in T lymphocytes in vivo by regulating gRNA production with blue light.

This paper introduces an enhanced SCas12a assay (SCas12aV2) for amplification-free detection of highly structured RNA, showing improved sensitivity and specificity for RNA and clinical samples.

The paper introduces a CRISPR-based method to tag human protein-coding genes, achieving 36% tagging efficiency in HEK 293T cells.

This paper introduces PERC, a method for efficient CRISPR editing in primary human immune cells and HSPCs using a peptide reagent, achieving over 90% editing efficiency without specialized equipment.

This paper develops a CRISPR-based therapy targeting Shiga toxin genes in STEC infections, showing efficacy in reducing bacterial load and mitigating disease in animal models.

The paper identifies essential genes in porcine cell lines using CRISPR screening and compares them to human essential genes.

CasGen generates novel Cas9 and Cas12 proteins using a transformer-based model with margin-based regularization, achieving structural similarity and functional integrity.

The paper presents a workflow using machine learning to optimize protein function and reduce immunogenicity in cell and gene therapies.

The paper introduces RepTiles, a system for generating random DNA segments for synthetic genomics, enabling the construction of ultra-long synthetic DNA in Physcomitrium patens.

This study introduces a Sortase-based split-Cas9 system for precise genome editing, demonstrating its feasibility in E. coli and human cells with reduced off-target effects.

The paper develops CRISPR-mediated base-editors to create disarmed Agrobacterium strains with auxotrophy and recombination deficiency for improved plant transformation.

This study shows that U1-driven CRISPR RNAs enhance the efficiency of RNA-targeting CRISPR-Cas13 systems for knockdown and editing without modifying Cas13 proteins.

The paper benchmarks CRISPR sgRNA design algorithms and creates smaller, efficient libraries for loss-of-function screens.

GuideScan2 constructs high-specificity CRISPR gRNA databases and enables design of allele-specific gRNAs, reducing off-target effects in gene essentiality screens.

The paper identifies Cas11b as an internally translated protein in an archaeal CRISPR-Cas system, showing its necessity for effective interference and Cascade complex formation.

H2M is a computational pipeline that models human genetic variants in mice by predicting equivalent mutations and creating a database of mutation pairs for functional studies.

The paper uses in vivo base editing to systematically analyze the functional impact of genetic variants in cancer models, revealing context-dependent effects and limitations of CRISPR-Cas9.

The paper demonstrates that RNA-guided nuclease TnpB enables gene drive in plasmids by biasing the inheritance of insertion sequences.

This study develops a non-viral gene editing method using circular single-stranded DNA templates and TALEN, showing improved engraftment and long-term gene editing in HSPCs compared to AAV.

This study characterizes the genome-editing capabilities of TnpB, IscB, and enIscB in E. coli strains, revealing their activity in specific strains and mechanisms of bacterial escape.

The paper identifies a novel group of Tn7-like transposons in Cyanobacteria that target CRISPR arrays, revealing a new interaction between transposons and CRISPR-Cas systems.

The paper develops PiCTURE and machine learning models to predict RNA off-target effects of CRISPR base editors in tissue-specific transcriptomes, finding higher risks in colon and lungs compared to brain and ovaries.

This paper shows AcrVIB1 inhibits CRISPR-Cas13b by promoting unproductive crRNA binding and degradation, revealing a mechanism to suppress immune defense.

This study uses CRISPR/Cas9 to target a specific mutation in LMNA-associated congenital muscular dystrophy, improving survival and cardiac function in mice.

This study shows that shortening the 4T poly-T tract in gRNA scaffolds improves transcript levels and editing efficiency, especially under low vector conditions, for both SpCas9 and SaCas9.

This paper introduces a method to increase the proportion of correctly repaired hepatocytes in the liver through transient gene inhibition and transgene delivery, achieving a 25% increase in targeted cells and five-fold transgene expression.

This paper introduces P3 editing, a method that links protein-protein proximity to CRISPR-Cas9 dual-component guide RNA formation, enabling genome editing triggered by molecular interactions in human cells.

The paper evaluates collateral RNA cleavage in CRISPR-Cas13d systems and finds that low-copy expression reduces off-target effects while maintaining on-target knockdown.

The paper develops a rapid CRISPR-Cas12a-based assay to measure HIV drug levels, showing it can detect clinically relevant concentrations in complex samples.

The paper introduces CAT-ATAC, a method combining CRISPR, RNA, and ATAC-seq in single cells to identify gene regulatory relationships and validate them with loss-of-function experiments.