University of Alabama at Birmingham — Weaver Lab

The CD4 T cell, mapped.

We study how CD4 T cells direct immunity at the body's largest barrier — the intestine — and how their programs fail in chronic disease. Below: our working atlas of an infection, live in your browser. Every point is one cell.

Research → 128 publications → Join the lab →

Cells profiled 558,304 scRNA-seq · mouse intestine

Cell states 87 grouped into 9 lineages

Time course d0 → d42 C. rodentium infection

Genotypes 2 wild-type · MHC-II ΔIEC

Genes live here 9 of 19,790 measured

Fig. 01 Single-cell atlas · epithelial MHC-II × infection n = 80,003 rendered / 558,304 profiled · WebGL

View

Genotype

Time

Tissue

Color by

drag to pan · click, then scroll to zoom

Loading the atlas… Single-cell RNA-seq of the mouse intestine across a Citrobacter rodentium infection (days 0–42), comparing normal mice with a conditional knockout whose gut epithelium cannot present antigen on MHC-II (H2-Ab1 deleted in epithelial cells only). The view opens as a slowly orbiting 3D overview — drag to orbit, right- or ⌘-drag to pan, scroll to zoom, R to reset. Points are gray where a gene is not detected. Rendered with the lab's own RNA-FLEEK engine, simplified for the web.

Try H2-Ab1 · wild-type epithelium H2-Ab1 · knockout — goes dark Itgae · d42 resident memory Il22 · d14 peak defense

Research modules

Axis 02 · what we work on

M.01 — Foundations

Th17 biology

In 2005 this lab reported a third effector lineage of CD4 T cells — Th17 — beyond the Th1/Th2 paradigm. We still dissect the circuitry that commits a cell to that fate, keeps it stable, or lets it convert.

Module 01 →

M.02 — Tissue

Mucosal & intestinal immunity

The gut is a constant negotiation between tolerance and defense. We follow effector and regulatory CD4 T cells through differentiation in their native tissue — including whether the epithelium itself presents antigen.

Module 02 →

M.03 — Disease

Disease & dysregulation

The pathways that defend the gut drive disease when control is lost. Our work spans inflammatory bowel disease, the inflammation-to-colorectal-cancer transition, and late-onset neonatal sepsis.

Module 03 →

Log

Axis 03 · lab news

2026-05-15

Placeholder: lab welcomes new postdoctoral fellow

Replace these entries with real lab news — a current log is the clearest signal a lab is active.

2026-02-01

Placeholder: new paper accepted

Link log items to the paper, press release, or talk where possible.

2025-09-10

Placeholder: Dr. Weaver gives invited lecture

Awards, invited talks, and new arrivals all make good entries.