perturbation screen

PIE: Generalizing perturbation effects across unseen perturbations, contexts and datasets

Predicting differentially expressed genes and expression shifts per condition from database embeddings plus per-gene evidence, PIE reaches 1.2–3.2 times the best baseline's AUPRC on unseen contexts, perturbations and datasets.

Reconstructing signaling histories of single cells via perturbation screens and transfer learning

The paper develops a framework combining perturbation screens and transfer learning to reconstruct signaling histories in cells and optimize differentiation protocols.

Predicting cellular responses to perturbation across diverse contexts with STATE

State, a set-based transformer trained on over 100 million perturbed cells, predicts perturbation responses in new cellular contexts better than mean, linear and deep learning baselines.

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.

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.

BrainBridge Characterizes Key Factors affecting Alzheimer's Disease and Associated Phenotypes

BrainBridge integrates single-cell transcriptomic data with phenotypes to model brain biology, prioritizing genes and cell types linked to Alzheimer's, aging, and sex differences.

Novel reporter of the PINK1-Parkin mitophagy pathway identifies its damage sensor in the import gate

A HaloTagged MFN2 reporter enabled CRISPRi screens showing diverse mitochondrial damage activates PINK1-Parkin via membrane potential loss, with TOM retaining PINK1 when TIM23 is blocked.

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling

A 100-million-cell atlas: 50 cancer lines pooled as spheroid villages, treated with 379 drugs at several doses, profiled by combinatorial-barcoding scRNA-seq and embedded with a 10-dimensional scVI model.

Similarity metric learning on perturbational datasets improves functional identification of perturbations

This paper introduces PeML, a similarity metric learning method for perturbational datasets, improving the identification of perturbation mechanisms and biological relationships.

Learning epistatic gene interactions from perturbation screens

The paper develops a model to infer pairwise epistatic gene interactions from siRNA perturbation screens, showing that glinternet outperforms xyz in accuracy for high-dimensional data.

System-wide biochemical analysis reveals ozonide antimalarials initially act by disrupting Plasmodium falciparum haemoglobin digestion

This paper shows ozonide antimalarials disrupt Plasmodium falciparum haemoglobin digestion, leading to parasite death and stress responses.

A protein phosphatase network controls temporal and spatial dynamics of differentiation commitment in human epidermis

In suspended human keratinocytes, five induced phosphatases dampen ERK to drive differentiation commitment, opposed by DUSP10, in a time-rewired network that renders commitment an unstable switch.