CRISPR screen

This study benchmarks association testing methods for low MOI perturb-seq data, identifies analysis challenges, and introduces SCEPTRE low-MOI to improve calibration and power.

This work designs precise base editors with reduced bystander editing using guide RNA libraries and protein language models, improving safety and targeting efficiency.

The paper introduces multiAsCas12a, an engineered CRISPR-Cas12a variant enabling higher-order combinatorial chromatin perturbations, and demonstrates its use in discovering new enhancer elements and dissecting cis-regulatory element functions.

PathoGD designs primers and gRNAs for CRISPR-Cas12a-based pathogen detection with high specificity, validated for Neisseria gonorrhoeae and Streptococcus pyogenes.

The paper describes a method to control CRISPR/Cas9 activity using proteasomal degradation of an anti-CRISPR protein fused to a degradation or shutoff tag.

This study shows that knocking out ALDH3B2 in human pancreatic duct cells converts them into beta-like cells that function and reduce blood glucose in mice.

This paper demonstrates a system that encodes biosignals into genomic DNA of mammalian cells using TdT and CRISPR-Cas9, achieving 91% accuracy in encoding the message 'HELLO WORLD'.

The paper uses pooled CRISPR screens to identify breast cancer risk genes affecting T cell-mediated killing, finding 33 candidates and showing their impact on immune response and patient outcomes.

The paper develops a MINT platform to reprogram serine integrases for precise synthetic DNA integration into specific chromosomal sites in human cells.

ChatNT is a conversational agent that understands biological sequences and achieves state-of-the-art results on genomics tasks while being accessible to non-coders.

The paper identifies genetic vulnerabilities linked to transcription factor activities in cancer cell lines using CRISPR knockout data and validates targets associated with TEAD1.

This study shows that modulating the MMEJ pathway components RPA and POLQ can reduce large deletions and enhance HDR after CRISPR-Cas9 editing.

The paper introduces PERSIST-On, a CRISPR-based method for stable and tunable gene activation by recruiting endogenous transcription factors to target promoters.

MOSAIC enables high-throughput in situ saturation mutagenesis and CRISPR prime editing guide RNA optimization in human cells, identifying optimized pegRNAs and drug resistance variants.

This paper improves variant effect quantification in base editing screens by integrating genotypic and phenotypic data using a Bayesian network called BEAN.

This paper demonstrates successful in vivo editing of ApoE4 to E3 in Alzheimer's model mice using synthetic exosome-delivered CRISPR, achieving low but detectable editing efficiency.

Language models trained on over one million mined CRISPR operons generated Cas9-like effectors and matching guide RNAs, and an AI-designed editor is reported to edit the human genome precisely.

The paper introduces PHAGEPACK, a CRISPR-based assay to systematically identify host genes affecting phage infectivity, revealing new pathways in both permissive and non-permissive E. coli.

This study identifies Rheb as a molecular substrate in the nucleus accumbens that enables drugs of abuse to hijack reward circuits and suppress natural reward responses.

This paper introduces launch-dCas9, a machine learning framework to predict guide RNA effects in CRISPR epigenome editing, showing high accuracy and improved gRNA selection.

The paper introduces a strategy to enhance C>U RNA editors using IDR-derived domains, improving both on- and off-target editing efficiency.

The paper identifies mechanisms by which an RT-Cas1 fusion protein integrates RNA into DNA genomes through cDNA synthesis and site-specific integration.

The paper investigates off-target activity in CRISPRi by analyzing a genome-wide sgRNA library and finds that seed sequences mediate most off-target effects.

This paper introduces a method for targeted gene editing using RNA-templated DNA repair pathways in human cells, achieving high efficiency and fidelity.

This paper edits introns of HSPCs to restrict transgene expression to the myeloid lineage, demonstrating efficacy in treating metabolic diseases and reaching the brain.

The paper develops CRISPR-Cas tools to independently control transcription and translation in E. coli, showing reduced polar effects with dCas13 and enabling multiplexed gene regulation for biosynthesis.

This paper describes a non-viral CRISPR-Cas9 transfection method for editing primary human dorsal root ganglion neurons and confirms edits at genomic, protein, and functional levels.

CRISPR-MIP replaces PCR for sgRNA quantification, revealing GC and oversampling biases in pooled CRISPR screens.

The paper identifies optimized protein-based enhancers of HDR in human HSPCs through functional screening, improving HDR efficiency without increasing off-target effects.