Chi-Ming Li

A Compact Regulatory Logic Governs Fibroblast Cell State Plasticity in Fibrosis

The paper identifies a compact regulatory logic governing fibroblast plasticity in fibrosis by analyzing enhancer repression and gene perturbations across multiple tissues.

Collateral Immune Cell Signaling Compromises the Efficacy of T-cell Engaging Therapies for Cardiac Fibrosis

This study shows that FAP-targeted BiTE(R) molecules, intended to reduce cardiac fibrosis, instead worsen heart function by triggering harmful immune responses.

Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy

Single-cell and spatial maps of human coronary arteries identify FAP as a marker of SMC-derived modulated cells; an anti-FAP BiTE reduced plaque burden in mouse models.

Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery

This study identifies RUNX1 as a key regulator of cardiac recovery by reprogramming macrophages, showing that its inhibition promotes heart function recovery in a chronic heart failure model.

Basic-Leucine-Zipper Transcription Factors Regulate Selective Molecular Phenotypes in Regulatory T Cells During IL-2-Induced Activation

The paper identifies bZIP transcription factors as key regulators of IL-2-induced Treg activation, linking chromatin accessibility changes to Th1/Th2 molecular phenotypes and metabolic pathways.

Single cell variant to enhancer to gene map for coronary artery disease

This paper links CAD GWAS variants to causal genes in SMCs using single-cell chromatin accessibility and Hi-C data, creating a scV2E2G map for disease mechanism discovery.

Dissecting Regulatory Non-Coding Heart Disease GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Pathophysiological Relevance to Heart Failure

The paper identifies causal genes in heart disease GWAS loci by integrating Hi-C, chromatin accessibility, and transcriptomic data, revealing regulatory relationships in cardiac fibroblasts.

Functional Genomics in Human iPSC-Derived Sinoatrial Node Cells Reveals Shared Regulatory Determinants of Heart Rate and Atrial Fibrillation

The paper develops a human iPSC-derived sinoatrial node system to study heart rhythm-associated SNPs and identifies causal variants linked to heart rate and atrial fibrillation.

A Highly Efficient Aorta-Gonad-Mesonephros-Like Definitive Hemogenic Endothelium From Human Pluripotent Stem Cells

This paper describes a method to efficiently generate definitive hemogenic endothelium from human pluripotent stem cells, which can differentiate into hematopoietic progenitors and stem cells with multilineage potential.

RAB18 is a key regulator of GalNAc conjugated siRNA induced silencing in Hep3B cells

The paper identifies RAB18 as a key regulator that enhances GalNAc-conjugated siRNA efficacy in Hep3B cells by improving siRNA delivery and RISC access.

In vitro assessment of an engineered tBID-based safety switch system in human T lymphocytes

This study develops and tests a tBID-based safety switch system for engineered T cells to manage toxicity and persistence, showing up to 90% cell elimination in vitro.

Limited differential expression of miRNAs and other small RNAs in LPS-stimulated human monocytes

The paper profiles small RNA expression in LPS-stimulated human monocytes and identifies a limited set of miRNAs upregulated during inflammation.