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Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Updated: Mar 28, 2026

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

Single-cell spatial multi-omics molecular pathology enabled by SuperFocus.

Yao Lu, Xiaolong Tian, Marco Vicari

Biorxiv : the Preprint Server for Biology

|March 27, 2026

Summary

This summary is machine-generated.

SuperFocus computationally integrates genome-scale molecular data with histopathology images, enabling single-cell spatial multi-omics analysis without external references. This advances next-generation pathology by bridging tissue morphology and molecular profiling.

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Area of Science:

Computational Biology
Pathology
Genomics

Background:

Histopathology and molecular pathology are currently distinct diagnostic fields.
Integrating spatial context with molecular data at single-cell resolution is a key goal for advanced pathology.

Purpose of the Study:

To present SuperFocus, a computational platform for integrating histopathology with single-cell spatial multi-omics.
To enable cell-resolved molecular analyses across whole tissue sections.

Main Methods:

SuperFocus is a modality-agnostic platform using constrained cascading imputation and quality control.
It generates spatial multi-omics from spot-based measurements on adjacent tissue sections.
No external reference data is required.

Main Results:

SuperFocus significantly improves accuracy metrics (28-73%) on spatial transcriptomics benchmarks.
It enables cell-resolved analyses in various datasets, including MALT lymphoma, hippocampus, MASH, and Parkinsonian mouse brain.
Demonstrates integration of transcriptomic and metabolomic data.

Conclusions:

SuperFocus provides scalable whole-slide, single-cell spatial multi-omics integrated with histopathology.
It bridges the gap between histology and genome-scale molecular profiling for next-generation molecular pathology.