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cats

Coco is a young mitted Ragdoll cat with fluffy white gloves and gentle blue eyes.

Putao is Coco’s dad. He is a gentle and affectionate seal bicolor Ragdoll who loves human company and behaves obediently.

Processed and analyzed multi-disease bulk TCR datasets comprising 465.8M human TCR entries, including 330.3M from 59 NCBI projects and 135.5M from 66 immuneACCESS projects, enabling comprehensive TCR repertoire analysis.
Developed a disease-specific recognition framework utilizing unsupervised learning methodologies with the GIANA tool, enhancing TCR classification accuracy.

Analyzed 246 healthy and diseased samples from three subcellular-level spatial transcriptomic sequencing platforms: Visium HD, Stereo-seq, and Xenium.
Developed an interactive, multi-resolution visualization tool (e.g., 8µm, 16µm bins for Visium HD) with adjustable leiden clustering and differential gene expression (DEG) analysis.
Enabled visualization of cell segmentation with advanced analyses, including cell shape characterization, spatial distribution, and cell-cell interactions.

Developed a LAMP primer design tool based on comprehensive threshold screening of primer characteristics.
Built a predictive model using extensive LAMP experimental data to evaluate primer performance and forecast amplification success under various conditions.

Conducted large-scale benchmarking of 7 integration methods (spaVAE, scVI, scPoli, …) across 6 multi-batch spatial transcriptomic-metabolomic datasets.
Developed quantitative batch integration assessment system:
- Basic ST assessment (Continuity (CHAOS, PAS, …), Marker score (Moran’s, Geary’s, …), Specificity score (Specificity, Logistic regression, …)
- Biological conservation (ASW, Cell-type LISI (cLISI), …)
- Batch correction (Batch ASW, Integration LISI (iLISI), …)
- Reconstruction fidelity (Cosine Similarity, Pearson Correlation)

Developed a high-resolution spatial TCR profiling method leveraging Stereo-seq, enabling accurate reconstruction of TCR alpha and beta chains directly from tissue sections.
Created a dedicated computational pipeline for reliable chain pairing, clonotype mapping, and integration with spatial transcriptomic data.
Applied the platform to human tissues, revealing spatial T cell clonotype distributions and immune microenvironments with high confidence.