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Colin Stroud Hackathon 2026

Overview

  • Event: Colin Stroud Hackathon
  • Dates: April 30 - May 1, 2026
  • Location: MD Anderson Cancer Center
  • Organizer: Linghua Wang
  • Theme: "Decoding Functional Niches in Cancer by Leveraging Spatial Omics and AI"

The Organizer

Linghua Wang is a professor at MD Anderson Cancer Center whose research focuses on integrating computational pathology with spatial transcriptomics to characterize tumor microenvironments. Her group developed:

  • TESLA (Cell Systems, 2023) — H&E-guided super-resolution annotation for spatial transcriptomics.
  • METI (Nature Communications, 2024) — Tumor microenvironment interaction mapping combining morphology and spatial gene expression.
  • SpaGCN (Nature Methods, 2021) — Graph convolutional network for spatial domain identification integrating expression, spatial location, and histology.

All three methods share a common thread: integrating H&E morphology with molecular spatial data. This reflects Wang's core insight that tissue architecture visible in routine clinical stains encodes information about the molecular microenvironment.

Theme Breakdown

"Decoding Functional Niches in Cancer by Leveraging Spatial Omics and AI"

  • Functional Niches: Not just identifying niches, but understanding what they do — how niches influence cell behavior, treatment response, and patient outcome. See Functional Niche.
  • Spatial Omics: Technologies that measure molecular features (RNA, protein) with spatial resolution in tissue.
  • AI: Computational methods from deep learning, foundation models, and statistical learning.

The theme directly aligns with the core tension in the niche field: we have many methods to identify niches (correlative) but few to understand their function (causal). The hackathon is positioned at the frontier between niche identification and functional niche characterization.

Relevant Background

Key Papers to Read

  1. Schurch et al. (Cell, 2020) — The origin of computational cellular neighborhoods. Deep read.
  2. TESLA (Cell Systems, 2023) — Wang's method for H&E-guided spatial annotation. Deep read.
  3. METI (Nature Communications, 2024) — Wang's method for TME interaction mapping.
  4. Niche-DE (Genome Biology, 2024) — Testing whether gene expression depends on niche context. Deep read.
  5. NicheCompass (Nature Genetics, 2025) — Communication-aware niche atlas. Deep read.

Key Concepts

Relevant Datasets

  • CRC CODEX — The standard niche dataset (Schurch et al., 2020).
  • TISCH2 — Curated tumor microenvironment atlas with 190 datasets covering 50+ cancer types.
  • CZ CELLxGENE Census — 100M+ cells with standardized APIs.
  • Any cancer spatial transcriptomics dataset with paired H&E (relevant for Wang's morphology-integration approach).