perturbation response prediction

The paper uses a CRISPR base editor screen in yeast to identify regulators of protein abundance, revealing both specific and broad regulatory relationships.

sciCAN integrates single-cell chromatin accessibility and gene expression data using an adversarial network, outperforming existing methods in cross-modal transfer and preserving biological structure in hematopoietic data.

The paper demonstrates that adaptive model predictive control can steer cancer cell signaling dynamics to mimic wild-type cells and support combination therapy design.

This study uses a P1 bacteriophage to deliver CRISPR-Cas9 for targeted killing of Shigella flexneri in zebrafish larvae, reducing bacterial load and improving survival.

This study establishes a canine mammary tumor organoid biobank to model human breast cancer, showing genetic and phenotypic conservation and utility for drug testing and CRISPR screening.

CellDrift identifies temporally varied perturbation patterns in single-cell data by analyzing covarying gene expression across time, outperforming existing methods in imputation and pattern detection.

This study uses a virus-based guide RNA delivery system to enable efficient gene editing in wheat, demonstrating multiplexed editing of agronomic genes and heritable targeted deletions.

This study shows that genetic silencing of AKT paralogs in melanoma cells leads to cell death via mTORC signaling disruption, which can be rescued by activated SGK1, suggesting dual targeting of AKT and SGK1 as a potential therapy.

This paper introduces nanoblade technology for efficient, low-toxicity genome editing in organoids, achieving up to 80% gene knockout in murine and human organoids.

The paper investigates collateral RNase activity of Cas13d in mammalian cells and introduces GENO to mitigate it for repeat-targeting RNA therapies.

This paper introduces ACES, absorbable conductive scaffolds that enhance peripheral nerve regeneration and stimulation in animal models.

This study uses in vivo CRISPR screening to identify SAGA complex members as key regulators of hematopoiesis, showing their loss impairs blood production and activates interferon pathways.

This paper introduces structured hierarchical models for probabilistic inference of causal effects from perturbation screening data, showing that incorporating prior knowledge improves parameter inference in noisy datasets.

This study shows DNA oligonucleotides can inhibit Cas9 activity in human cells and in vitro by targeting the guide RNA and requiring a PAM-loop for effective inhibition.

This study uses EdU-click and FACS-Seq to identify actively replicating gut bacteria in human and murine samples, revealing Ileibacterium as resistant to antibiotic perturbations.

This paper demonstrates that PVX-delivered CRISPRa systems can induce strong gene activation and metabolic reprogramming in N. benthamiana.

GEARS predicts transcriptional responses to single and multi-gene perturbations using single-cell RNA-sequencing data and geometric deep learning, outperforming existing methods in identifying genetic interactions.

MultiCPA predicts multimodal perturbation responses at the single-cell level using a generative model trained on CRISPR perturbation data.

This paper introduces CAKE, a method for multiplex CRISPR/Cas9 gene editing in neurons to label and manipulate endogenous proteins with high accuracy and low crosstalk.

This paper introduces Haystack, a method to prioritize causal transcription factors from single-cell data, validated in Drosophila, showing high accuracy in identifying drivers of differentiation.

This study improves sgRNA activity predictions by incorporating tracrRNA sequence variations, showing better performance than existing models on a new dataset.

This study demonstrates that the CRISPR-Csm complex efficiently and precisely targets and degrades both nuclear and cytoplasmic transcripts in human cells with minimal off-target effects.

The paper introduces SEED/Harvest, a CRISPR-based method for efficient and controlled knock-in generation in multicellular animals, enabling seamless cassette removal and spatio-temporal protein labeling.

The paper identifies suppressor mutations that enable rapid compensatory evolution in a yeast transcriptional network disrupted by a primary mutation.

A mouse embryo multiome atlas (E7.5 to E8.75) and an unsupervised transcription factor binding predictor; a Brachyury knockout supports its network predictions in neuromesodermal progenitors.

The paper develops a bio-orthogonal conjugation strategy to efficiently assemble modified sgRNAs and investigates their impact on CRISPR activity.

This study shows CRISPR base editors can reduce gene expression by editing cis-regulatory elements, with examples in human and mouse models.

The paper constructs genome-wide CRISPR libraries for gene ablation, activation, and silencing with high efficacy and reports novel gene regulators and modifiers.

The paper shows that task complexity extends the time window in which V1 is necessary for perceptual decisions, overlapping with report-related activity and affecting behavioral performance.

This study evaluates three CRISPR/Cas9 approaches to correct C9orf72 repeat expansion in patient-derived neurons, finding that repeat and mutant allele excision fully eliminate dipeptide repeats.