Guo‐Cheng Yuan

Plasticity of Human Microglia and Brain Perivascular Macrophages in Aging and Alzheimer's Disease

The paper profiles human myeloid cells across aging and Alzheimer's disease, identifies AD-associated changes, and links GPNMB to neuroprotection via TREM2.

Optimal Gene Panel Selection for Targeted Spatial Transcriptomics Experiments

This paper introduces ReconST, a method for optimal gene panel design in spatial transcriptomics, outperforming existing methods in reconstruction accuracy and spatial pattern preservation.

sCCIgen: A high-fidelity spatially resolved transcriptomics data simulator for cell-cell interaction studies.

sCCIgen generates synthetic spatial transcriptomics data with known cell-cell interaction features to evaluate analytical tools.

SpaDiff: Denoising for Sequence-based Spatial Transcriptomics via Diffusion Process

SpaDiff improves spatial transcriptomics by reversing RNA molecule displacement, enhancing spatial specificity and data integrity for downstream analyses.

Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis

ONTraC uses a graph neural network to analyze spatial transcriptomics data, improving trajectory reconstruction and revealing microenvironment-dependent changes in gene regulation and cell interactions during development.

Broad H3K4me3 Domain Is Associated with Spatial Coherence during Mammalian Embryonic Development

The paper uses spatial-CUT&Tag data to analyze H3K4me3 domain organization in a mouse embryo, finding spatially coherent gene patterns associated with tissue boundaries and distinct chromatin state transitions.

QuadST: A Powerful and Robust Approach for Identifying Cell-Cell Interaction-Changed Genes on Spatially Resolved Transcriptomics

QuadST identifies interaction-changed genes in spatially resolved transcriptomics by analyzing distance-expression associations in cell-type pairs.

Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

Giotto Suite provides a modular, open-source framework for analyzing spatial multi-omics data across scales and technologies.

Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease

The paper uses spatial transcriptomics to identify injury-specific microenvironments and molecular interactions in the mouse kidney during injury and regeneration.

Multi-omic profiling of the developing human cerebral cortex at the single cell level

The paper profiles gene expression and chromatin accessibility in 45,549 cortical nuclei across 6 developmental timepoints to study cell fate determination and neuropsychiatric disease mechanisms.

Matrin3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and YY1 mediated enhancer-promoter interactions

The paper shows Matrin3 stabilizes chromatin accessibility and loop-domain interactions, and facilitates YY1-mediated enhancer-promoter interactions during differentiation.

Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture

The paper uses integrated spatial genomics to study nuclear architecture in mouse brain cortex cells, revealing chromatin fixed points and cell-type specific organization of nuclear bodies.

CUT&RUNTools 2.0: A pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis

CUT&RUNTools 2.0 is a computational pipeline for analyzing single-cell and bulk CUT&RUN and CUT&Tag data, offering alignment, quality control, clustering, and visualization tools.

SpatialDWLS: accurate deconvolution of spatial transcriptomic data

SpatialDWLS improves accuracy and speed in deconvolving spatial transcriptomic data, revealing spatial-temporal cell-type changes in human heart development.

Giotto, a toolbox for integrative analysis and visualization of spatial expression data

Giotto is a toolbox for analyzing and visualizing spatial transcriptomic and proteomic data, offering integration with single-cell RNA-seq and supporting diverse datasets.

Global architecture of the nucleus in single cells by DNA seqFISH+ and multiplexed immunofluorescence

The paper maps chromatin states, DNA loci, and gene expression in single mouse embryonic stem cells using DNA seqFISH+ and immunofluorescence, revealing nuclear zones and subpopulations with distinct chromatin features.

The landscape of human brain immune response in patients with severe COVID-19

The paper analyzes single-nucleus transcriptomes from brain regions of COVID-19 patients to show increased neuroinflammation and microglial transcriptome changes, without evidence of viral brain tropism.

Multi-scale annotations of chromatin states in 127 human cell-types

The paper improves a chromatin state annotation method and applies it to 127 human cell types, revealing patterns related to cell origin and 3D chromatin structure.

Histone demethylome map reveals combinatorial gene regulatory functions in embryonic stem cells

The paper identifies combinatorial functions of histone demethylases in gene regulation of mouse embryonic stem cells by analyzing their genome-wide binding patterns.

GiniClust3: a fast and memory-efficient tool for rare cell type identification

GiniClust3 identifies rare cell types in large single-cell RNA sequencing datasets efficiently and robustly.

Sarcomeres regulate cardiomyocyte maturation through MRTF-SRF signaling

This study shows that sarcomere assembly via ACTN2 and MRTF-SRF signaling promotes cardiomyocyte maturation through a positive feedback loop.

In vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis

CUT&RUNTools processes CUT&RUN data to identify protein binding and genomic footprints through read analysis and visualization.

Enhancer-dependence of gene expression increases with developmental age

The paper shows that enhancer-dependence of gene expression increases with developmental age in mouse and human cells.

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

STREAM is an interactive pipeline for reconstructing and visualizing complex branching trajectories from single-cell transcriptomic and epigenomic data.

Revealing the critical regulators of cell identity in the mouse cell atlas

The paper identifies 202 variable gene regulatory networks and predicts essential regulators for over 800 cell types in the mouse using the mouse cell atlas data.

Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity

The paper integrates single-cell transcriptomic and spatial data to analyze cell-type and spatial domain contributions to heterogeneity in the mouse visual cortex.

A cluster-aware, weighted ensemble clustering method for cell-type detection

GiniClust2 is a cluster-aware, weighted ensemble clustering method that improves cell-type detection by identifying both common and rare cell types across diverse datasets.

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome editing experiments

The paper presents a protocol for designing, executing, and analyzing CRISPR genome editing experiments using CRISPOR and CRISPResso.

Dissecting super-enhancer hierarchy based on chromatin interactions

The paper identifies hub enhancers within super-enhancers using Hi-C and ChIP-seq data, showing their role in gene activation and chromatin structure.