CRISPR screen

The paper develops a CRISPR-based platform to scan mutations in essential genes, applying it to Nrd1 to identify critical residues in its CTD-interacting domain.

The paper develops a CRISPR/Cas9 electroporation and single-cell cloning protocol for human myoblasts, achieving high editing success rates and purity.

This study shows that gRNA library representation bias affects gene essentiality predictions in CRISPR screens, with library choice being the most significant factor.

This study shows that transient ATM inhibition improves knock-in efficiency in mouse hematopoietic stem cells by reducing DNA damage response and apoptosis.

This paper demonstrates that the RALA peptide effectively delivers CRISPR components in DNA, RNA, and RNP formats to primary mesenchymal stem cells with high viability and low cytotoxicity.

The paper compares perturbation outcomes in in vivo and ex vivo hematopoietic stem cell models, finding systematic biases and challenges in predicting in vivo effects from ex vivo data.

The paper identifies CRISPRa-responsive enhancers and their target genes in a 2 Mb region around PHOX2B using TESLA-seq, revealing both known and novel regulatory relationships.

The paper identifies human-specific gene expansions linked to brain evolution by analyzing genome sequences and functional models in zebrafish.

The paper identifies BORC as a modifier of TDP-43 protein levels in neurons, showing lysosome transport is required for TDP-43 turnover.

The paper improves orthogonal translation in yeast by enhancing a pyrrolysyl-tRNA synthetase system and identifies ribosomal protein deletions that increase non-canonical amino acid incorporation.

The paper evaluates the AICS-0090 dCas9-KRAB iPSC line for modeling microglia-like cells and their responses to disease-relevant stimuli, finding stimulus-specific transcriptomic and functional responses.

The paper identifies causal genetic mechanisms at CAD GWAS loci using CRISPR screens and chromatin analysis, revealing enhancer-gene links and ancestry/sex-specific risk factors.

This paper demonstrates that a compact ABE corrects the PiZ mutation in AATD mouse models, reducing liver disease and improving lung function.

The paper presents an iterative framework to identify mTOR signaling regulators using multimodal single-cell data and validates novel regulators through experimental testing.

This paper engineers de novo RNA-guided transposition systems using TnpB-family proteins, showing improved specificity and efficiency compared to naturally evolved systems.

The paper introduces CRITR-seq, a CRISPR-based method to measure transcriptional effects, and identifies NELF as a regulator of influenza transcription and interferon response.

This paper develops EGFRvIII-targeted virus-like particles (VLPs) that enable selective genome editing and elimination of glioblastoma cells while sparing non-target cells.

This paper introduces RENDER, a method for transient delivery of CRISPR-based epigenome editors as ribonucleoproteins to modulate gene expression in human cells, achieving durable epigenetic silencing.

This paper engineers type I-F CAST systems for targeted gene insertion in human cells by combining structural insights with rational design to improve efficiency and PAM flexibility.

This paper edits the ADA2 p.R169Q mutation in human hematopoietic stem cells using CRISPR-Cas9 and HDR, showing improved efficiency with NHEJ inhibitors but increased chromosomal deletions.

This paper introduces a computational method to optimize CRISPR/Cas9 guide design by integrating genome composition, PAM diversity, and weighted off-target scoring to improve specificity and efficiency.

This study uses machine learning to predict SaCas9 activity in bacteria, revealing that PAM adenine methylation and flanking sequences significantly influence activity.

The paper introduces Pythia, a tool that uses deep learning to predict CRISPR/Cas9 integration and editing outcomes by leveraging non-random DNA repair patterns.

ALLEGRO designs universal CRISPR sgRNA libraries targeting multiple fungal species, validated experimentally across three fungi and extended to others.

This study uses saturation genome editing to assess BRCA1 variants across cell types, identifying functionally impactful variants and revealing context-dependent cancer risk.

This paper develops a CRISPR-based assay using Cas12a orthologs for detecting NDRV S3 gene with high sensitivity and visual detection capability.

The paper uses CRISPRa Perturb-seq to perturb transcription factors in fibroblasts, recapitulating in vivo transcriptional states and identifying key regulators.

ONE-STEP tagging enables rapid, efficient, and scalable protein tagging in diverse cell types through CRISPR-Cas9 and Bxb1 integrase, with high integration efficiency and multiplexing capabilities.

This paper introduces a CRISPRi-seq platform in Haemophilus influenzae to study gene fitness and essentiality, revealing medium-specific growth determinants and introducing a genome annotation resource.