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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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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

Russo DD et al., Nat Protoc, 2026

A scalable, low-cost, sample hashing workflow for multiomic single-cell analysis using the Seq-Well S3 platform

Topics:
Technology Development
Subtopics:
Low-input & Low-resource Technology
Multiomics Profiling
Single-cell & Spatial Genomics
People:
Alex K. Shalek Brittany Goods Daniela Russo +2

Li W et al., bioRxiv, 2026

Toward Computationally Complete Spatial Omics

Topics:
Computational Platforms
Subtopics:
Machine Learning & Active Learning
Multi-modal Data Integration
Single-cell & Spatial Data Analysis
People:
Alex K. Shalek Ankit Basak

Tzouanas CN et al., Cell, 2026

Hepatic adaptation to chronic metabolic stress primes tumorigenesis

Topics:
Cancer
Subtopics:
Cancer Genomics & Transcriptomics
Cell Circuitry & Predictive Modeling
Health
+7
People:
Alex K. Shalek Adam Rubin Ben Mead +4
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