CRISPR screen

PrEditR: A protein-centric platform for CRISPR-mediated base editor sgRNA design

PrEditR is a tool for designing sgRNAs for CRISPR-based base editors, allowing users to target specific amino acids and annotate resulting mutations.

iPSC Neurodegenerative Disease Initiative isogenic CAG repeat iPSC line for Huntingtons disease

The paper generates isogenic iPSC lines with CAG repeats and HTT KO for Huntington's disease study, showing differentiation potential and altered gene expression in neurons and astrocytes.

Dependency Map correlation analysis reveals WDR89 as a genome maintenance factor

The paper uses DepMap data to identify WDR89 as a genome maintenance factor through correlation analysis of genetic dependencies.

Systematic mapping of chimera-permissive sites by CRISPR-guided PAM scanning

This paper uses CRISPR-guided PAM scanning to identify chimera-permissive sites in proteins, enabling the design of functional chimeras with preserved activity.

Protocol for Non-viral HDR-based CRISPR/Cas9 platform for small custom editing in primary T cells

This paper presents a non-viral HDR-based CRISPR/Cas9 protocol for editing primary T cells with up to 80% HDR efficiency, targeting small pathogenic variants in patient and healthy donor cells.

The phenotypic landscape of the model firmicute Bacillus subtilis

This study uses CRISPRi to screen B. subtilis genes across 150 stress conditions, revealing new roles for conserved firmicute genes in protein secretion, cell wall homeostasis, and bacterial competition.

Comparison of CRISPR-Cas-based knockdown of endogenous mRNA in sensory neurons

This study compares CRISPR-Cas systems for RNA knockdown in rat sensory neurons, finding hfCas13d provides robust gene silencing with minimal toxicity.

CRISPR activation of endogenous PKD1 increases polycystin-1 levels and suppresses cellular features of ADPKD

This study uses CRISPR activation to increase PKD1 expression in ADPKD models, reducing cyst formation and improving cellular features.

Fishash: A contingency table approach to Perturb-seq guide assignment

Fishash assigns perturbations to cells in Perturb-seq data using Fisher's Exact Test, improving accuracy and speed over existing methods.

A novel, high-density CRISPR activation platform for mapping cancer dependencies and resistance pathways ex vivo and in vivo

This paper introduces Partita, a high-density CRISPRa platform for comprehensive gene activation studies, demonstrating its utility in identifying cancer dependencies and resistance pathways in vitro and in vivo.

Structure-guided discovery and engineering of miniature CRISPR-Cas12m for epigenome editing

This paper identifies and engineers a miniature CRISPR-Cas12m variant for epigenome editing, demonstrating its effectiveness in human cells and a mouse model of HBV infection.

Nuclear Localization Signals Enable the Cellular Delivery of an Anti-CRISPR Protein to Control Genome Editing

This paper develops a cell-permeable anti-CRISPR protein (6xNLS-Acr) that efficiently inhibits Cas9 activity in human cells, enhancing genome-editing specificity.

Optimizing CRISPR/Cas9 mutagenesis in Drosophila da neurons to avoid cytotoxicity

This study optimizes CRISPR/Cas9 mutagenesis in Drosophila da neurons by developing uCas9 transgenes that reduce cytotoxicity while maintaining gene editing efficiency.

Regulators of Interferon-Responsive Microglia Uncovered by Genome-wide CRISPRi Screening

This study identifies 772 genes regulating the interferon-responsive microglia state using CRISPRi screening in human iPSC-derived microglia, including novel regulators like CNOT10.

Cross-species variant-to-function analyses implicate MEIS1 in conferring sleep abnormalities and impaired cerebellar development

The paper identifies MEIS1 as a gene involved in sleep abnormalities and cerebellar development using cross-species variant-to-function analyses in zebrafish.

LDLR variant classification through activity-normalized prime editing screening

This paper uses prime editing to classify LDLR variants by measuring their impact on LDL-C uptake, reclassifying many previously unclassified variants.

Turnip mosaic virus-based gRNA delivery system for plant genome editing

This paper develops a turnip mosaic virus-based gRNA delivery system for plant genome editing, showing improved editing efficiency with Csy4-mediated processing and multiplex targeting capabilities.

CRISPR associated enzymes are mislocalized to the cytoplasm in iPSC-derived neurons resulting in KRAB-specific degradation

This study identifies that dCas9-KRAB mislocalizes to the cytoplasm in iPSC-derived neurons, leading to KRAB-specific degradation, and shows that adding a neuronal-specific NLS restores nuclear localization and expression.

Self-amplifying RNA enables rapid, durable, integration-free programming of hiPSCs

This paper demonstrates that self-amplifying RNA (saRNA) enables durable, integration-free transgene expression in hiPSCs, supporting cell-fate programming and functional reporter analysis.

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits

Genome-scale CRISPRi perturb-seq in 22 million primary human CD4+ T cells maps stimulation-specific regulators and links perturbation signatures to T cell states and autoimmune genetics.

Systematic multivariate analysis of chromatin complex dependencies reveals Set1C/COMPASS as a melanoma-enriched epigenetic vulnerability

Complex-level DepMap dependency modeling across 42 cancer types nominates Set1C/COMPASS as melanoma-enriched; CXXC1 knockdown lowers H3K4me3, curbs proliferation, and suppresses MYC/E2F programs in responsive melanoma lines.

Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells

This paper develops a virus-like particle-based system for CRISPR gene editing and screening in primary human myeloid cells, identifying TNFAIP3 as a key regulator of inflammatory polarization.

SpacerScope: Binary-vectorized, genome-wide off-target profiling for RNA-guided nucleases without prior candidate-site bias

SpacerScope provides a high-speed, high-sensitivity off-target profiling tool for RNA-guided nucleases, accurately recovering all validated off-target sites and detecting complex indel-containing sites.

Genome-Wide CRISPR Screening Identifies Cellular Factors Controlling Nonviral Genome Editing Efficiency

The paper uses CRISPR screening to identify genes that enhance nonviral genome editing efficiency in human cells, finding six genes that increase editing efficiency by up to five-fold.

UNCOVERseq Enables Sensitive and Controlled Gene Editing Off-Target Nomination Across CRISPR-Cas Modalities and Systems

UNCOVERseq is a workflow for sensitive off-target nomination in CRISPR-Cas editing, demonstrating superior performance across multiple modalities and systems.

NF2 lacking exon 11 isoform induced by antisense gene therapy is able to recover partially merlin deficiency on NF2-related Schwannomatosis iPSC-derived spheroid model

This study shows that antisense gene therapy using PMOs can induce exon 11 skipping in NF2-deficient Schwann cells, partially restoring merlin function and key pathways in a spheroid model of NF2-SWN.

Genetic-to-chemical perturbation transfer learning through unified multimodal molecular representations

UniPert-G2CP transfers genetic perturbation insights to chemical perturbation modeling, enabling efficient in silico drug screening with reduced data costs.

In-Depth Characterization of Stem Cell Potency and Genotoxicity for Clinical-Scale Ex Vivo CRISPR/Cas9 Gene Editing

This study develops a clinical-compliant framework for ex vivo CRISPR/Cas9 gene editing of HSPCs to correct WAS, showing improved engraftment and a favorable safety profile with minimal off-target effects.

Pan-cancer proteogenomic interrogation of the Ubiquitin Proteasome System

Proteogenomic analysis of up to 11 CPTAC cohorts shows ubiquitin-proteasome proteins often diverge from transcripts; TP53-mutant tumors elevate UBR5 protein, while TRIM28 prognosis is lineage-dependent.

A Singular Base Editing Platform for Polyfunctional Multiplex Engineering of Immune Cells

This paper develops a base editing platform to efficiently and safely engineer CAR T cells with multiple gene knockouts and insertions.