CRISPR screen

This paper introduces LAML, a method for inferring time-scaled cell lineage trees from CRISPR-based lineage tracing data, showing improved accuracy over existing methods.

CRISPRmap enables multi-omic optical pooled screens to map gene function in cells and tissue without sequencing, identifying pathogenic mutations and analyzing spatial phenotypes.

This study identifies a Sox2 mutation that enhances Sox/Oct cooperativity, improving iPSC reprogramming efficiency and enabling reprogramming of aged cells across species.

This study uses CRISPR screening to identify genes critical for human primordial germ cell-like cell development, finding TCL1A regulates AKT-mTOR signaling and protein synthesis.

The paper uses a CRISPRi screen in human iNeurons to identify novel FCD genes that increase mTOR signaling, finding two genes mutated in FCD patient tissue.

This study uses protein language models and high-throughput screening to engineer an anti-CRISPR protein that enhances CRISPR/Cas genome editing precision in human cells.

This paper introduces a CRISPR-associated transposon system for targeted gene activation in E. coli and shows its ability to induce antibiotic resistance.

This study shows that reducing MMR gene expression in HD iPSCs slows CAG repeat expansion, suggesting these genes as therapeutic targets for HD.

This study evaluates the safety of using dCas9-ABE8e for editing gamma-globin genes, showing reduced large deletions compared to nCas9-ABE8e while maintaining editing efficiency.

The paper develops a pipeline using Recursive Feature Machines to identify synthetic lethal gene pairs from CRISPR viability data, improving accuracy over prior methods and discovering new candidates.

Startle is a method for inferring CRISPR-Cas9 lineage trees using a star homoplasy model, showing improved accuracy on simulated and real datasets.

This study uses CRISPR-Cas9 to investigate BCL11A zinc finger domains' role in gamma-globin regulation and hemoglobinopathy treatment, finding Znf4 deletion increases HbF levels.

The paper demonstrates that fusing CRISPR endonucleases to specific 5'-exonucleases significantly increases scar-free multikilobase knock-in frequencies in plants.

The paper shows that increasing FAN1 expression in HD patient astrocytes reduces CAG repeat expansion using mRNA-LNP.

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

This paper develops new CRISPR-Cas13a variants and crRNA design strategies to improve RNA-detection specificity, achieving better discrimination of SARS-CoV-2 strains.

This paper develops an AAV-based CRISPRi system to silence gene expression in cardiac myocytes, showing dose-dependent reduction of Nppa expression in vitro and in vivo.

The paper introduces a modular dCas9-based platform for combinatorial epigenome editing, demonstrating its ability to control effector recruitment and spatial organization for improved transcriptional regulation.

This study uses CRISPR/Cas9 HITI to repair CTNS in ciPTEC cells, achieving functional cystinosin restoration and reversing the cystinotic phenotype.

The paper introduces a CRISPR-based system called qTAG to improve the efficiency and flexibility of endogenous protein tagging through optimized repair cassettes.

The paper introduces a dual sgRNA library design for CRISPRi screens to identify genetic modifiers, showing improved sensitivity and specificity in detecting epistatic relationships.

The paper evaluates sgRNA design guidelines and in vitro assays for plant CRISPR/Cas9, finding that in vitro cleavage does not reliably predict in vivo efficiency and highlights the need for multiple high-performing sgRNAs.

This study improves the efficiency of biallelic deletions in cattle embryos using CRISPR-Cas and shows OCT4 is critical for blastocyst formation and pluripotency.

This study delivers Cas9 or base editor RNP complexes directly to retinal cells, achieving gene editing in photoreceptors and RPE, but with toxicity at high concentrations.

The paper compares CRISPR-Cas9 RNP and nickase systems for inducing Aire gene mutations in murine mTECs, finding recurrent mutations with RNP but not nickase.

The paper uses interventional data to infer causal networks for blood traits, revealing regulatory relationships among 788 genes.

The paper assesses whether gene regulatory networks can predict gene sensitivity in cancer cell lines and finds that mRNA abundance is a better predictor than inferred regulatory activity.

The paper shows that using the same guide RNA structure for CRISPRi and CRISPRa in E. coli prevents context-dependent effects, ensuring predictable gene circuit behavior.

This study investigates the 3D genome organization in human brain development, finding differences in compartment and loop domain formation between neurons and glia.