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Inflammation & Autoimmunity
Alex K. Shalek Leonard Nettey Zoë Steier Kyle Kimler José Ordovas-Montañes
Autoimmunity
Inflammation

Nettey et al., medRxiv, 2025

Divergent T Cell Phenotypes Define Pediatric Crohn’s Disease and Ulcerative Colitis

DeMeo et al., Science, 2025

Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes

Xu et al., Journal of Experimental Medicine, 2025

Autoimmune disease risk gene ANKRD55 promotes TH17 effector function through metabolic modulation

Adhikari et al., Cell, 2025

Immunometabolic defects of CD8+ T cells disrupt gut barrier integrity in people with HIV

Quinn et al., bioRxiv, 2025

Longitudinal transcriptomic analysis of SIV-infected rhesus macaques reveals peripheral immune dynamics throughout untreated SIV infection and long-term antiretroviral therapy

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Ghirardelli Smith et al., Nature Immunology , 2026

Intratumoral T cell activation kills tumors regardless of T cell specificity

Topics:
Inflammation & Autoimmunity
Subtopics:
Innate & Adaptive Immunity
Multiomics Profiling
Open-source Tools & Repositories
+3
People:
Tyler Dao Son Nguyen Alex K. Shalek

Haradhvala et al., Cancer Discovery, 2026

Follicular Lymphoma Transformation is Characterized by Cytokine-associated Remodeling of Stromal and Macrophage Compartments

Topics:
Cancer
Subtopics:
Cancer Genomics & Transcriptomics
Molecular, Cellular, Niche, & Tissue Dynamics
Multi-modal Data Integration
+5
People:
Ankit Basak Alex K. Shalek

Shay et al., Nature, 2026

Ketogenic diet mediates intestinal tumorigenesis through lipids not ketones

Topics:
Cancer
Subtopics:
Cancer Etiological Agents
Model System Development, Alignment, & Refinement
Tissue-specific Responses
People:
Constantine Tzouanas Alex K. Shalek

Lan et al., Nature aging, 2026

Aging disrupts spatiotemporal coordination in the cycling murine ovary

Topics:
Homeostasis
Inflammation & Autoimmunity
Subtopics:
Health
Inflammation
Women's Health
People:
Tammy Lan David Fischer Alex K. Shalek

Basak et al., biorxiv, 2026

Single-Cell and Spatial Methods for Multimodal Functional Glycan Profiling in Tissues

Topics:
Technology Development
Subtopics:
Custom Instrumentation & Microfluidics
Innate & Adaptive Immunity
Multi-modal Data Integration
+3
People:
Alex K. Shalek Ankit Basak Bokai Zhu +5

Rojas-Hidalgo A. et al., Nat Genetics, 2026

The Single Cell Notebooks for inclusive and accessible training in single-cell and spatial omics

Topics:
Computational Platforms
Subtopics:
Open-source Tools & Repositories
Single-cell & Spatial Data Analysis
Single-cell & Spatial Genomics
People:
Alex K. Shalek Daniela Russo Sergio Triana

Rubin AJ et al., Science, 2026

Disordered protein LAT encodes relative levels of signaling pathways in T cell activation

Topics:
Homeostasis
Subtopics:
Immune Regulation
Innate & Adaptive Immunity
People:
Alex K. Shalek Tyler Dao Adam Rubin

Yeo YY et al., Cell Rep Med, 2026

Epstein-Barr virus orchestrates spatial reorganization and immunomodulation in the classic Hodgkin lymphoma tumor microenvironment

Topics:
Cancer
Subtopics:
Single-cell & Spatial Genomics
Tumor Immunology & Immunotherapy
Tumor Microenvironment (TME)
People:
Alex K. Shalek Bokai Zhu

Farrell-Sherman A et al., bioRxiv, 2026

Early immune responses anticipate HIV rebound and precede viral control

Topics:
Infectious Diseases
Subtopics:
Cure Strategies
Immune Regulation
Innate & Adaptive Immunity
People:
Alex K. Shalek Bokai Zhu

Yiu SPT et al., Cancer Discov, 2026

Same-Slide Spatial Multi-Omics Integration with IN-DEPTH Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment

Topics:
Technology Development
Subtopics:
Multiomics Profiling
Single-cell & Spatial Genomics
People:
Alex K. Shalek Ankit Basak Bokai Zhu
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