Ahmet F. Coskun

The paper maps NF-κB multiprotein signalosome dynamics in 3D using iseqPLA and scGPT, revealing spatial organization and disease-related changes in inflammation.

This paper introduces CurvSeq and CurvSee to analyze prostate cancer morphology and molecular profiles, identifying cancer-associated genes and morphomechanical niches linked to progression.

CellWHISPER infers direct cell-cell communication from spatial transcriptomics data, reducing errors by accounting for cell-type-specific expression and spatial organization.

This study shows that IL-6 restricts pre-thymic T cell lineage commitment in SIV-infected rhesus macaques, contributing to loss of viral control.

MetaboFM is a foundation model for spatial metabolomics that uses Vision Transformers to create embeddings from MSI data, achieving high accuracy in metadata prediction and enabling interpretable, multimodal interactions.

The paper enhances the spatial resolution of mass spectrometry imaging data using high-resolution imaging mass cytometry images to create detailed single-cell metabolite maps.

The paper describes engineered chromatin-binding proteins that preferentially bind H3K27me3 over H3K9me3, validated using a novel CHIA assay.

This study develops a 3D bone marrow-on-a-chip model to investigate interactions between CAR-T cells and multiple myeloma cells in different niches and assess therapeutic responses.

The paper introduces SNOWFLAKE, a graph neural network framework that predicts disease status from multiplex imaging data in human B-cell follicles, showing improved performance over other methods.

The paper introduces spaGNN, a method to analyze subcellular spatial gene neighborhoods in MSCs and chondrocytes, revealing tissue-specific transcriptional and spatial features.

The paper introduces srIBI, a super-resolution imaging technique, to visualize subcellular localization of biomolecules and drugs at the nanometer scale.

This paper introduces ion beam tomography (IBT), a 3D subcellular imaging technique, and demonstrates its ability to visualize genomic regions, RNA transcripts, and protein factors with high resolution.