CRISPR screen

The paper evaluates sequence models in noncoding RNA assays by comparing model increments against baselines and highlights the importance of baseline content and regularization.

This paper introduces ConcuRx, a statistical framework that improves gene prioritization across heterogeneous CRISPR drug-response datasets by modeling between-study variability, leading to better identification of MOA-associated genes.

This paper improves CRISPR-based genome editing in Toxoplasma gondii by optimizing gRNA expression and introducing a tRNA-based polycistronic system for multiplexed editing.

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

The paper uses deep mutational scanning to distinguish disease mechanisms in ERCC2 variants, finding that TTD variants have lower fitness than XP variants.

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

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

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

BARCS extends beta-binomial regression to handle complex CRISPR screen designs, showing improved essential gene recovery but calibration issues in gene-level summaries.

The paper identifies PQLC2 as a lysosomal pH regulator that affects tau homeostasis through a CRISPRi screen in iPSC-derived neurons.

The paper develops GuideRefine to identify and remove multi-targeting and off-targeting sgRNAs from CRISPR-KO libraries, improving the accuracy of gene hit lists.

A web atlas counts evidence from 24 types for 188,634,118 variant-gene pairs across 50 human tissues; 1,530,420 pairs pass a high-confidence cutoff, 87% of them tissue-specific.

The paper introduces a method to prioritize targets in Perturb-seq by assessing the dependability of perturbation effects using generalizability theory, improving target identification reliability.

Abundance scores for 8,891 TSC2 missense variants, plus mTOR pathway activity scores for 391, were calibrated to ACMG/AMP evidence. They putatively reclassify 212 of 276 clinical-cohort missense VUS.

The paper characterizes nine Cas12a2 orthologs, identifies three with high DNA collateral activity, and defines their PFS preferences and mismatch tolerance.

POCKET-seq maps dCas9 binding genome-wide to distinguish true and false-positive interactions in CRISPR interference screens.

This paper introduces CRISPR-StAR, an in vivo CRISPR screening platform with improved normalization and analysis tools, showing it can identify tumor suppressor gene effects not observable in vitro.

The paper shows HRd is a continuum with functional and mutational heterogeneity, highlighting the need for refined molecular classification for precision interventions.

The paper recalibrates BAP1 MAVE data for different disease phenotypes to enable accurate variant classification across related disorders.

This paper introduces MPRabc, an MPRA-informed model that improves enhancer-gene interaction prediction across cell types.

The paper evaluates CRISPRi system performance across different E. coli strains and develops a dual gRNA system for improved repression in clinical isolates.

The paper uses CRISPR to assess the functional impact of IL2RG variants in human T cells, confirming known annotations and identifying novel loss-of-function mutations.

This paper computationally designs a PAM-relaxed SaCas9 variant, KRH, with expanded targeting capability and enhanced editing efficiency.

EasyCAPS is a web tool that integrates dCAPS primer design with CRISPR-Cas9 strategies to improve genotyping and gene editing efficiency.

This paper introduces CODEMax and CODEMax(exo+) genome editing systems that enable efficient and precise search-and-replace editing in human cells with reduced off-target effects.

The paper shows that humanized Traf6 promoter sequences in mice affect immune responses but not fertility, revealing distinct roles for germ and immune cells in gene regulatory evolution.

This study shows extending the spacer in SuperFi-Cas9 restores cleavage activity while maintaining specificity, offering a strategy to improve CRISPR efficiency and stability.

This study uses tensor decomposition to analyze CRISPR-Cas9 knockout screens, distinguishing essential from non-essential genes with performance comparable to JACKS without requiring control samples or logarithmic transformations.

The paper performs a genome-wide CRISPR activation screen to identify genes modulating PrPC abundance, finding 531 genes with significant effects and validating 45 of them.