perturbation response prediction

This paper introduces an active learning method to efficiently design Perturb-seq experiments by leveraging multi-modal priors, improving perturbation space exploration with fewer experiments.

This paper demonstrates that IB4-conjugated streptavidin can selectively knock down PKCε in IB4+ nociceptors, reversing hyperalgesic priming in a chronic pain model.

This study examines how pyoverdine and ceftazidime interact with E. coli resistance evolution, showing combination treatment reduces resistance development.

PepPre improves peptide identification by detecting accurate and comprehensive precursor ions, leading to higher PSM and peptide identifications compared to existing methods.

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.

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.

The paper introduces BIOFORMERS, a transformer-based framework for analyzing biological systems, demonstrating its ability to capture biological insights from single-cell transcriptomics data.

The paper introduces a contrastive analysis framework to disentangle perturbation effects from natural cell variation in optical pooled screens, showing improved performance in generating embeddings and reducing technical artifacts.

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

This study applies the SLIPT system to fission yeast to perturb cell cycle-related proteins with improved temporal resolution.

The paper uses base editor screens to assess phosphorylation site functionality in T cell activation, identifying novel sites that modulate transcriptional activity and signaling pathways.

This study shows that burst firing of striatal cholinergic interneurons promotes extinction learning, while their pause is critical for reversing goal-directed behavior, and alcohol disrupts this process.

This paper describes a genetic engineering approach for cell type-specific silencing and in vivo imaging of neuronal responses.

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 investigates the genomic and environmental diversity of Solirubrobacter, revealing its pangenome, flagellin genes, and ecological interactions across soils and rhizospheres.

The paper introduces a method to quantify diverse perturbation responses and discover novel biological insights in single-cell perturbation datasets.

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

This study systematically compares siRNA delivery methods to T cells, finding lipid-conjugate-mediated delivery is most effective for both resting and activated T cells ex vivo.

The paper analyzes how bacterial metabolic systems respond to perturbations using kinetic models, finding that cofactors and network sparsity significantly influence responsiveness.

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.

This paper introduces a life-or-death selection platform for enzyme evolution that identifies highly efficient biocatalysts through serial passaging of carbamoylase variants.

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 uses Perturb-seq to functionally interrogate SARS-CoV-2 host factors in human lung epithelial cells, identifying key factors that influence infection and host response.

This paper introduces a method to predict single-cell perturbation responses using neural optimal transport, showing improved performance over existing methods on drug-treated cells.

The paper develops a CRISPR-UMI-based screening system to study exosome biogenesis, transport, and uptake mechanisms on a genome-wide scale.

The paper optimizes Cas12a for multiplexed CRISPRa screens in human cells, enabling simultaneous activation of up to four genes and identifying criteria for selecting effective guides.

This paper demonstrates the efficient use of auxin-inducible degradation systems in Candida pathogens for rapid protein inactivation.

This study identifies AZD7648 and Pol{Theta} inhibitors as a combination (2iHDR) that enhances CRISPR-Cas9 integration efficiency and precision by targeting DNA-PK and MMEJ repair pathways.

This study shows that combining ATR inhibition with lurbinectedin improves efficacy in SCLC, particularly in MYC-driven non-neuroendocrine tumors.