Zoltan Maliga

Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Tumour, Stroma, and Immune Structures in Human FFPE Tissue

The paper introduces v-CyCIF, a method for 3D spatial profiling of human FFPE tissue, enabling detailed analysis of tumor, stroma, and immune structures.

Immunogenic tumor mass dormancy as a driver of persistent residual lesions in immunotherapy-treated melanoma

This study shows that immunogenic tumor mass dormancy, not cell-level quiescence, persists in residual melanoma lesions after immunotherapy, with active tumor cells and immune interactions.

Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis

This study uses 3D reconstruction and optimal transport modeling to analyze TLS development in TB-infected lungs, revealing distinct maturation trajectories and spatial dynamics.

Compositional and interpretable representation of histology using AI foundation models and sparse autoencoders

This paper introduces a human-in-the-loop framework using AI foundation models and sparse autoencoders to interpret H&E histology images and integrate them with molecular spatial profiling.

In vivo evidence for bleb-induced survival signaling in metastatic melanoma

This paper shows that bleb-induced septin signaling supports survival of metastatic melanoma cells in vivo, and disrupting this pathway reduces metastasis.

Multiomic profiling of a unique in-transit melanoma cohort identifies melanoma differentiation as predictor of tumor progression and therapy response

The paper identifies melanoma differentiation and immune exhaustion as predictors of tumor progression and therapy response in in-transit melanoma patients through multiomic profiling.

Spatial statistics for identifying and scoring immune clusters in high-plex profiles of primary prostate cancer

The paper introduces statistical tools to analyze immune cluster patterns in prostate cancer and finds high-grade tumors show more immune infiltration and active immune features.

Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours

This study distinguishes tissue-resident memory (TRM) and exhausted T (TEX) cells in tumors by analyzing their antigen reactivity, clonality, and functional outcomes.

Spatial determinants of tumor cell dedifferentiation and plasticity in primary cutaneous melanoma

The paper maps spatial patterns of tumor cell dedifferentiation and plasticity in melanoma by analyzing RNA and protein expression across 300 histological domains.

Multiomic analysis identifies suppressive myeloid cell populations in human TB granulomas.

This study identifies suppressive myeloid cell populations in human TB granulomas using spatial transcriptomics and single-cell immunophenotyping, revealing IDO1+ dendritic cells as key regulators of immune suppression.

SpatialCells: Automated Profiling of Tumor Microenvironments with Spatially Resolved Multiplexed Single-Cell Data

SpatialCells automates the analysis of spatially resolved multiplexed single-cell data to characterize tumor microenvironments, enabling efficient feature extraction and downstream machine learning applications.

UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues

The paper introduces two methods to improve tissue segmentation in highly multiplexed images using real augmentations and nuclear envelope imaging, resulting in more accurate models.

MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging

MCMICRO processes multiplexed tissue images into single-cell data, demonstrating its versatility across different tissues and imaging platforms.