Arabidopsis Spaceflight Tropism Autodecoder

01 Study Overview & Key Findings

Plants read directional environmental cues—gravity, light, mechanical touch, and moisture gradients—to coordinate organ growth. Microgravity dismantles fundamental gravitropic setpoints, forcing plants to reprioritize their tropic signaling networks. This study integrates 1,337 transcriptomic samples from 24 NASA GeneLab OSDR studies and 6 NCBI GEO series with the Salk Institute Arabidopsis Developmental Atlas (432,919 single nuclei across 183 cell-type clusters) as a foundation model.

Figure 1: Full Multi-Scale Pipeline Architecture. Integration of NASA OSDR and NCBI GEO transcriptomic callsets, single-cell atlas representation learning via a 32-dimensional variational auto-decoder, non-negative least squares (NNLS) deconvolution, DerSimonian-Laird random-effects meta-analysis, elastic-net spaceflight prediction, and ggPlantMap anatomical spatial projection.

02 Draft Manuscript & PDF Reader

Explore the complete 12-page research manuscript below, prepared in Springer Nature format (sn-jnl). You can read the paper directly within the browser, expand it to fullscreen, or download the compiled PDF.

03 Publication Figures & Multi-Omics Atlas

High-resolution analytical figures generated by the pipeline. Click any figure to open the interactive full-resolution lightbox viewer with official publication captions.

Figure 1 · Cohort

Harmonized Multi-Omics Dataset

Distribution of 1,337 samples across 24 OSDR + 6 GEO experiments and tropic conditions.

Figure 2 · Single-Cell

Cell-Type Deconvolution Profiles

Mapping 398 bulk transcriptomes onto 183 single-cell reference clusters.

Figure 3 · Auto-Decoder

32-D Latent Stimulus Activation

Variational latent representation of cell-type specific stress and stimulus states.

Figure 4 · Meta-Analysis

11-Study Spaceflight Volcano Plot

Identification of 16,002 statistically significant cross-mission spaceflight genes.

Figure 5 · Spatial Anatomy

Stem Vascular Tropism Hotspot

ggPlantMap projection identifying inflorescence stem vascular cambium as prime responder.

Figure 6 · Spatial Anatomy

Root Tip Columella Remodeling

Columella statocyte and procambium shifts in microgravity-grown roots.

Figure 7 · Machine Learning

Spaceflight Classifier Weights (AUC 0.919)

Key discriminative cell types (silique_20, stem_9) and stimulus code dimensions.

Figure 8 · Pathways

KEGG Pathway Functional Network

Functional cross-talk between gravitropism, cell-wall biogenesis, and auxin response.

04 Interactive Decoder & Analysis Tool

Upload an expression matrix from Arabidopsis or non-plant spaceflight model organisms (Human, Mouse, Fruit fly, Worm). Runs 100% client-side in your browser; your research data never touches a remote server.

05 Phase 3: Cross-Species Functional Conservation

While upstream plant tropism sensor proteins (PIN auxin efflux carriers, phototropins, and MIZ1) are largely angiosperm-specific, spaceflight perturbs an evolutionarily conserved core of downstream cellular and physiological functions shared across the tree of life. Phase 3 systematically maps the Arabidopsis spaceflight signature against human astronaut multi-omics, mouse spaceflight models, fruit flies, and nematodes.

Conserved Protein Domain & Molecular Function Enrichment

Cross-species enrichment scores across 18 major Pfam/InterPro functional domain families and GO molecular functions. Red indicates coordinate up-regulation in microgravity; blue indicates coordinate down-regulation.

Gene-Domain Drill-Down Explorer

Filterable, searchable index connecting ortholog groups across the 5 model organisms with their conserved functional domains, biological functions, and observed spaceflight expression shifts.

06 Pipeline Architecture & Foundation Model

Traditional bulk transcriptomics averages gene expression over whole organs, obscuring tissue- and cell-type-specific responses to microgravity. Our computational pipeline bridges single-cell resolution and bulk archives using deep generative models:

07 Harmonized Datasets & FAIR Open Science

The dataset aggregates 1,337 transcriptomic samples from NASA GeneLab OSDR and NCBI GEO, fully standardized with DataCite 4.x metadata, containerized Docker environments, and reproducible analysis scripts.

08 Lead Researcher & CoSE Network

Connected Space Omics & Astrobiology Decoders

Explore companion browser-based decoders and analysis platforms developed across the Barker Lab / CoSE ecosystem:

How to Cite This Work

If you utilize the Tropism Autodecoder, the single-cell foundation model weights, or the cross-species conservation explorer in your research, please cite:

@article{barker2026tropism,
  title={Arabidopsis thaliana Spaceflight Tropism Recognition: Integrating Bulk Transcriptomics with a Single-Cell Developmental Atlas Foundation Model},
  author={Barker, Richard},
  journal={Draft Manuscript},
  year={2026},
  doi={10.5281/zenodo.arabidopsis-tropism},
  url={https://dr-richard-barker.github.io/Tropism_autodecoder_2026/}
}