Han M. Chen

Lymphatic constraint of germinal centers optimizes protective antibody responses

This study shows that lymphatic remodeling in skin and lymph nodes constrains germinal center size and function to optimize protective antibody responses during viral infection.

Tfh dysfunction is associated with poor responses to HBV vaccination

HBV vaccine-draining lymph node biopsies tie low antibody titers to reduced, interferon-skewed GNG4+ germinal center T follicular helper cells; public B cell clonotypes did not track response.

Temporal AI model predicts drivers of cell state trajectories across human aging

The paper introduces a temporal AI model, MaxToki, trained on extensive gene data to predict cell state changes across human aging and identifies age-modulating targets.

Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment

This study uses spatial multi-omics to compare EBV-positive and EBV-negative cHL, identifying distinct TME features and immunological signatures linked to EBV.

Neighborhood nonnegative matrix factorization identifies patterns and spatially-variable genes in large-scale spatial transcriptomics data

The paper introduces NNMF, a spatially-aware method for analyzing spatial transcriptomics data, identifying multicellular patterns and spatially-variable genes in large datasets.

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment

This study introduces MicroCart, a framework for spatial multi-omics analysis of host-microbiome interactions in colitis, revealing tissue-level immune responses and microbial shifts.

Quantized multi-task learning for context-specific representations of gene network dynamics

The paper develops a multi-task learning approach to create context-specific gene network representations, applying it to colorectal tumors to predict therapeutic targets.

Robust Single-cell Matching and Multi-modalAnalysis Using Shared and Distinct FeaturesReveals Orchestrated Immune Responses

The paper introduces MARIO, a cell matching algorithm that integrates single-cell proteomic and multi-modal data, revealing orchestrated immune responses in lung tissue.