Sanja Vicković

SPACE-Tag Enables High-Throughput Spatial Chromatin Profiling With CUT&Tag

The paper introduces SPACE-Tag, a spatial CUT&Tag method for chromatin profiling, and applies it to the mouse brain to reveal age-related chromatin and transcriptome changes.

Dissecting cellular and molecular networks of aging and senescence in the human hippocampus

This study identifies spatially resolved aging and senescence signatures in the human hippocampus using multi-omics approaches, revealing cell-type and sex-specific gene expression changes.

Tissue and cellular spatiotemporal dynamics in colon aging

This study creates a spatial and cellular atlas of the colon across age groups using spatial transcriptomics and single nucleus RNA-seq, identifying age-related molecular gradients and multicellular programs.

Single-Cell RNA Sequencing and Inferred Protein Activity Analysis Reveal a Distinct Tumor Phenotype in Early-Onset Colorectal Cancer Patients

The paper compares early-onset and late-onset colorectal cancer using scRNA-seq and VIPER to identify distinct stromal and epithelial features in early-onset tumors.

INLAomics for Scalable and Interpretable Spatial Multiomic Data Integration

INLAomics integrates spatial transcriptomics and proteomics to identify gene-protein networks and predict protein expression, improving accuracy over single-modality approaches.

Spatial host-microbiome sequencing

This paper introduces a spatial sequencing method to study host-microbiome interactions in the mouse gut using deep learning for spatial niche detection.

Power analysis for spatial omics

The paper develops a computational framework for spatial omics power analysis using in silico tissue generation and applies it across diverse spatial data modalities.

Three-dimensional spatial transcriptomics uncovers cell type dynamics in the rheumatoid arthritis synovium

This study uses spatial transcriptomics to analyze cell type dynamics in rheumatoid arthritis synovium, revealing chemokine-driven interactions in inflamed tissue.

SM-Omics: An automated platform for high-throughput spatial multi-omics

SM-Omics is a platform that combines spatial transcriptomics and proteomics to analyze tissue samples at scale.

Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram

The paper introduces Tangram, a method that aligns single-nucleus RNA-seq data with spatial data to create an anatomically integrated spatial map of the mouse brain.

High-density spatial transcriptomics arrays for in situ tissue profiling

This paper introduces HDST, a high-resolution spatial transcriptomics method, and demonstrates its application in mouse brain tissue to resolve spatial expression patterns and cell types.

Splotch: Robust estimation of aligned spatial temporal gene expression data.

Splotch aligns spatial transcriptomics data across tissue sections and timepoints to improve gene expression estimates and study optimal experimental design.

Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis

The paper was withdrawn due to the inclusion of confidential information about a third party.

Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis

Analysis of the ALS spinal cord using Spatial Transcriptomics reveals spatiotemporal dynamics of disease driven gene regulation.