perturbation response prediction

This paper introduces scCAPE, a tool for analyzing heterogeneous genetic perturbation effects in single-cell data, and identifies novel interactions in erythroid differentiation.

DrugGym simulates drug discovery processes to evaluate how different strategies affect success rates and costs in achieving target candidate profiles.

This study identifies mitochondrial calcium utilization as a metabolic requirement of venetoclax-resistant acute myeloid leukemia stem cells and shows that targeting mitochondrial calcium uptake can eradicate these cells.

The paper introduces Mobile-CRISPRi, a system for gene knockdown in Vibrio species, showing it effectively modulates gene expression and phenotypes.

This study develops a high-throughput in vivo Perturb-seq platform to analyze gene function across diverse cell types in the brain and peripheral nervous system, identifying cell type-specific transcriptional networks.

The paper identifies gene-perturbation interactions across genetic backgrounds in yeast using CRISPRi and combinatorial DNA barcode sequencing, revealing 460 genes with variable effects and 234 interacting loci.

This study introduces CRISPRai, a bidirectional epigenetic editing system, to investigate gene regulation hierarchies and interactions in T cells and hematopoietic lineage transcription factors.

This study uses CRISPRi-dCas9 to control the lifecycle and infectivity of bacteriophage T7 by targeting host-dependent promoters, showing increased time to lysis and reduced plaque size.

This study shows engineered lysins can target and remodel synthetic human gut microbiomes by altering species preferences through domain recombination.

The paper describes a method to control CRISPR/Cas9 activity using proteasomal degradation of an anti-CRISPR protein fused to a degradation or shutoff tag.

This paper introduces PDSP, a deep learning framework that uses patient-specific single-drug response data to predict personalized drug synergy, improving accuracy by 27% in leukemia patients.

The paper identifies LOAD risk genes through systems biology and shows their impact on memory function via neuronal endosomal dysfunction in C. elegans.

MOSAIC enables high-throughput in situ saturation mutagenesis and CRISPR prime editing guide RNA optimization in human cells, identifying optimized pegRNAs and drug resistance variants.

This study evaluates allele-specific targeting of the mutant TOR1A{Delta}E allele using NmCas9, showing high specificity and efficacy in reducing ubiquitin accumulation in DYT1 fibroblasts.

This study introduces a lightweight graph neural network for protein engineering that predicts fitness and guides the design of effective mutants with improved physicochemical properties.

CODEX models causal effects of perturbations on cancer cell lines using counterfactual reasoning, enabling in-silico exploration of drug combinations and genetic modifications.

The paper investigates off-target activity in CRISPRi by analyzing a genome-wide sgRNA library and finds that seed sequences mediate most off-target effects.

This study evaluates the therapeutic potential of RMC-7977, a broad-spectrum RAS inhibitor, in pancreatic ductal adenocarcinoma models, showing strong anti-tumor effects with minimal impact on normal tissues.

This study tunes the material properties of transcription factor condensates to show their impact on gene expression levels in mammalian cells and mice.

The paper develops CRISPR-Cas tools to independently control transcription and translation in E. coli, showing reduced polar effects with dCas13 and enabling multiplexed gene regulation for biosynthesis.

This paper describes a non-viral CRISPR-Cas9 transfection method for editing primary human dorsal root ganglion neurons and confirms edits at genomic, protein, and functional levels.

This paper develops an orally bioavailable PROTAC degrader of mSWI/SNF ATPases for prostate cancer and identifies resistance mechanisms through long-term treatment.

The paper identifies drug repurposing candidates for low-survival cancers by prioritizing drugs that reverse disease-associated gene signatures using three methods.

This study investigates how early life adversity and adolescent BLA inhibition affect corticolimbic connectivity and anxiety behaviors in animals.

This paper describes a CRISPR-dCas13 system to induce stop codon readthrough in specific transcripts, showing enhanced readthrough in AGO1, VEGFA, and HBB mRNAs.

CROPseq-multi enables multiplexed CRISPR perturbations across various screening methods with improved barcode detection and compatibility.

The paper introduces a modular CRISPR vector assembly system called Fragmid, enabling rapid creation and testing of CRISPR technologies through combinatorial design and pooled screening.

The paper develops CRISPRtOE, a genome-scale overexpression platform for Proteobacteria, demonstrating its use in Escherichia coli and Zymomonas mobilis to identify antibiotic and engineering targets.

The paper develops a CRISPRi-based screening platform to identify genes affecting neuronal excitability in human iPSC-derived neurons, revealing new links to neurodegenerative and neurodevelopmental disorders.