Zlatko Trajanoski

Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer

The paper integrates single-cell data from CRC patients to identify immune subtypes and neutrophil phenotypes, revealing their spatial organization and tumor-induced changes.

Coordinated IFN-γ/TNF Axis Drives Selective Loss of Activated Enteric Glia in Inflammatory Bowel Diseases

This study identifies IBD type-associated EGC activation signatures and reveals TNF/IFN-γ-driven necroptosis of activated enteric glia in inflammatory bowel diseases.

Escherichia-Shigella expansion and metabolite dysregulation in type 3c diabetes

The paper investigates gut microbiome changes in T3cDM patients, finding increased Escherichia-Shigella and reduced diversity, suggesting EPI drives microbial shifts rather than systemic metabolism.

Unraveling the YAP1-TGFβ1 axis: a key driver of androgen receptor loss in prostate cancer-associated fibroblasts

This study identifies the YAP1-TGFβ1 axis as a driver of androgen receptor loss in prostate cancer-associated fibroblasts, showing its role in promoting aggressive disease and resistance to therapy.

Optimised dissociation and multimodal profiling of prostate cancer stroma reveal fibromuscular cell heterogeneity with clinical correlates

The paper optimizes dissociation protocols and uses multimodal profiling to characterize fibromuscular stromal heterogeneity in prostate cancer with clinical relevance.

NovumRNA: accurate prediction of non-canonical tumor antigens from RNA sequencing data

NovumRNA predicts non-canonical tumor antigens from RNA sequencing data, showing robustness across cancer types and identifying therapy-induced antigens in glioblastoma.

Integrated multi-model analysis of intestinal inflammation exposes key molecular features of preclinical and clinical IBD

The paper compares 13 mouse models of intestinal inflammation with human IBD datasets to identify translatable pathways and introduces a web tool for analyzing these models.

IBDome: An integrated molecular, histopathological, and clinical atlas of inflammatory bowel diseases

This study integrates multi-omic and multimodal data from IBD patients to identify molecular, histopathological, and clinical features associated with inflammatory bowel diseases.

Eosinophils restrict CRC metastasis by inhibiting pro-tumorigenic SPP1+ macrophage differentiation

This study shows eosinophils inhibit CRC metastasis by blocking SPP1+ macrophage differentiation, using transcriptomics and a murine model.

Conventional therapy induces tumor immunoediting and modulates the immune contexture in colorectal cancer

This study shows conventional therapy in CRC induces immunoediting and changes immune contexture, with AI identifying mucin deposits as a potential surrogate marker.

Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion

This paper develops a signature, iHet, to capture tumor microenvironment heterogeneity linked to immune activity and evasion using transcriptomic data from lung cancer.

Driver mutations in GNAQ and GNA11 genes as potential targets for precision immunotherapy in uveal melanoma patients

The paper assesses the immunogenic potential of GNAQ and GNA11 mutations in uveal melanoma using genomic and transcriptomic data, finding Q209L mutations are more immunogenic than Q209P.

Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data

Scirpy provides a Python toolkit for analyzing single-cell T-cell receptor data and integrating it with transcriptomic data.

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

quanTIseq estimates absolute fractions of ten immune cell types from bulk RNA-seq; across TCGA, CXCL9/CXCR3 expression, not mutational load, tracks CD8+ T cell infiltration.

Targeting the PD-1/PD-L1 pathway potentiates immunoediting and changes the dynamics of neutral evolution in a mouse model of colorectal cancer

This study shows that neutral evolution dominates tumor shaping in a mouse CRC model, and PD-1/PD-L1 blockade enhances immunoediting and tumor homogeneity.

Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade

Immunogenomic profiling of 8243 TCGA samples across 20 solid cancers yields an immune atlas and a random-forest-derived immunophenoscore stratifying melanoma responders to checkpoint blockade.