Paula Pinto Coelho

Archetype analysis of multiplexed antibody imaging reveals interpretable morphological programs in optical pooled screens

The paper introduces CellMAPP and CHART to analyze multiplexed antibody imaging data, revealing modular morphological programs in response to genetic perturbations.

Scalable multimodal mapping of macrophage regulatory architecture by integrating optical and transcriptomic pooled screens

The paper introduces PerturbPair, a platform integrating transcriptomic and optical screens to map macrophage regulatory networks, revealing cross-modal relationships and disease-relevant gene programs.

SpatialAgent: An Autonomous AI Agent for Spatial Biology

SpatialAgent integrates large language models with dynamic tool retrieval, multimodal interpretation, and claim verification to automate end-to-end spatial biology workflows from gene-panel design to tissue annotation and hypothesis generation.

Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView

PerturbView enables highly multiplexed optical pooled screens in primary cells and tissues by improving barcode amplification, revealing regulators of NFκB signaling and enabling spatial transcriptomics integration.

Evolution of chromosome arm aberrations in breast cancer through genetic network rewiring

The paper investigates the evolution of chromosome 4p loss in basal breast cancer, identifying C4orf19 as a novel gene that suppresses proliferation and is part of a kinase module.