About

Stephen Wong is an experienced computer scientist, physicist, and educator specializing in object-oriented programming, software engineering, and computer science pedagogy. His current research includes the use of design patterns in redesigning traditional algorithms, serious gaming systems, cloud-based enterprise information management systems, large-scale high-fidelity simulation systems, and technologies for massive open online courses. He holds a PhD in Physics from MIT, obtained in 1989, and a BA in Physics with minors in Digital Electronics and Physical Chemistry from Swarthmore College, earned in 1981.

Research topics

• Genetics
• Biology
• Cancer research
• Computational biology
• Mathematics
• Evolutionary biology
• Combinatorics

Selected publications

• Supplementary Figure 1 from Tumor NOS2 and COX2 Spatial Juxtaposition with CD8<sup>+</sup> T Cells Promote Metastatic and Cancer Stem Cell Niches that Lead to Poor Outcome in ER<sup>−</sup> Breast Cancer

  2026-03-16

  articleOpen access

  <p>Tumor NOS2 and COX2 expression induced by IFNg and TNFa</p>

  PublisherDOI

• Supplementary Figure 6 from Tumor NOS2 and COX2 Spatial Juxtaposition with CD8<sup>+</sup> T Cells Promote Metastatic and Cancer Stem Cell Niches that Lead to Poor Outcome in ER<sup>−</sup> Breast Cancer

  2026-03-16

  articleOpen access

  <p>Modulation of EpCAM and CD44v6+.</p>

  PublisherDOI

• Supplementary Table II from Tumor NOS2 and COX2 Spatial Juxtaposition with CD8<sup>+</sup> T Cells Promote Metastatic and Cancer Stem Cell Niches that Lead to Poor Outcome in ER<sup>−</sup> Breast Cancer

  2026-03-16

  articleOpen access

  <p>Supplementary Table II summarizes �8+ T cells in designated regions of the tumors.</p>

  PublisherDOI

• Supplementary Figure 2 from Tumor NOS2 and COX2 Spatial Juxtaposition with CD8<sup>+</sup> T Cells Promote Metastatic and Cancer Stem Cell Niches that Lead to Poor Outcome in ER<sup>−</sup> Breast Cancer

  2026-03-16

  articleOpen access

  <p>Tumor analysis of NOS2 and COX2.</p>

  PublisherDOI

• Supplementary Figure 4 from Tumor NOS2 and COX2 Spatial Juxtaposition with CD8<sup>+</sup> T Cells Promote Metastatic and Cancer Stem Cell Niches that Lead to Poor Outcome in ER<sup>−</sup> Breast Cancer

  2026-03-16

  articleOpen access

  <p>Supplementary Fig. 4. Supplementary Fig. 4. Spatial UMAP analysis of CD8+/-NOS2+/-COX2+/- phenotypes in Deceased vs Alive patient tumors. Single cell neighborhood profile summary.</p>

  PublisherDOI

• Supplementary Table I from Tumor NOS2 and COX2 Spatial Juxtaposition with CD8<sup>+</sup> T Cells Promote Metastatic and Cancer Stem Cell Niches that Lead to Poor Outcome in ER<sup>−</sup> Breast Cancer

  2026-03-16

  articleOpen access

  <p>Supplementary Table I summarizes pathological features of tumor immune microenvironment where NOS2+ inflamed regions are significantly higher in tumors from Deceased patients.</p>

  PublisherDOI

• iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk

  Signal Transduction and Targeted Therapy · 2026-05-11

  articleOpen accessSenior author

  Large language models (LLMs) have demonstrated impressive capabilities in summarization, reasoning, and content generation, yet their inability to directly interpret large-scale omics data has limited their utility in data-driven hypothesis generation-particularly in mechanism discovery that demands the integration and interpretation of multimodal datasets, heterogeneous models, and deep domain expertise. Conversely, traditional computational algorithms excel at quantitative analysis of omics data but often rely heavily on labor-intensive, expert-driven interpretation to extract biologically meaningful insights. Here, we introduce (cointelligent single-cell spatial cell‒cell communication: iS2C2), a novel cointelligent platform that synergizes mathematically rigorous computational algorithms with the contextual reasoning capabilities of LLMs to automatically generate biologically interpretable hypotheses from single-cell RNA-seq and spatial transcriptomics data. The iS2C2 platform incorporates a transparent and reproducible cell-cell communication analysis pipeline built upon mathematically rigorous algorithms designed to enhance interpretability for integration with LLMs that contextualize algorithmic outputs or predictions using domain-specific knowledge and literature-derived evidence. When applied to Alzheimer's disease and cancer datasets, iS2C2 generated accurate, reproducible, and expert-validated hypotheses, unveiling previously unrecognized signaling pathways and mechanistic insights in disease microenvironments. This cointelligent approach bridges the gap between structured computational analysis and generative reasoning, heralding a paradigm shift toward fully automated, interpretable biological discovery and advancing the frontiers of next-generation precision medicine and systems biology.

  PublisherOA PDFDOI

• Supplementary Figure 5 from Tumor NOS2 and COX2 Spatial Juxtaposition with CD8<sup>+</sup> T Cells Promote Metastatic and Cancer Stem Cell Niches that Lead to Poor Outcome in ER<sup>−</sup> Breast Cancer

  2026-03-16

  articleOpen access

  <p>Spatial dot plot of CD8+/-NOS2+/-COX2+/- phenotypes in tumor from deceased patient.</p>

  PublisherDOI

• Tumor-derived cystatin C enables amyloid clearance

  Trends in Immunology · 2026-03-11

  articleSenior author
  PublisherDOI

• Supplementary Figure 3 from Tumor NOS2 and COX2 Spatial Juxtaposition with CD8<sup>+</sup> T Cells Promote Metastatic and Cancer Stem Cell Niches that Lead to Poor Outcome in ER<sup>−</sup> Breast Cancer

  2026-03-16

  articleOpen access

  <p>Immune and tumor quantification</p>

  PublisherDOI

Recent grants

• Systematic Alzheimer's disease drug repositioning (SMART) based on bioinformatics-guided phenotype screening and image-omics

  NIH · $3.5M · 2018–2024

• NIH Grant R01LM008696

  NIH · $1.0M · 2009

• Systematic identification of astrocyte-tumor crosstalk regulating brain metastatic tumors

  NIH · $2.6M · 2020–2025

• NIH Grant R01AG028928

  NIH · $1.3M · 2012

• NIH Grant R01LM009161

  NIH · $1.3M · 2013

Frequent coauthors

• Xiaobo Zhou

  369 shared

• Hong Zhao

  Children's Hospital of Zhejiang University

  323 shared

• Kelvin Wong

  Houston Methodist

  297 shared

• Jianting Sheng

  Weill Cornell Medicine

  252 shared

• Fuhai Li

  Washington University in St. Louis

  239 shared

• Zheng Yin

  Houston Methodist

  225 shared

• Zhong Xue

  200 shared

• Kemi Cui

  Albany Medical Center Hospital

  180 shared