Angela Ruohao Wu

Accurate and scalable decontamination of imaging-based spatial transcriptomics via optimal transport

CellDot improves spatial transcriptomics by accurately decontaminating transcript assignments using optimal transport, enhancing biological interpretation and spatial pattern recovery.

Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices

This paper introduces STitch3D, a framework that reconstructs 3D spatial structures from multiple 2D tissue slices, enabling comprehensive 3D analysis of tissues and organisms.

SpatialScope: A unified approach for integrating spatial and single-cell transcriptomics data using deep generative models

SpatialScope integrates spatial and single-cell transcriptomics data using deep generative models to achieve single-cell resolution and infer transcriptome-wide expression levels.

Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis

The paper defines the single-cell spatiotemporal gene expression landscape of human embryonic development using stem-cell-derived organoids and identifies key developmental signatures and signaling pathways.

Mouse lemur transcriptomic atlas informs primate genes, mutations, physiology, and disease

This paper uses a mouse lemur transcriptomic atlas to identify new genes, splice junctions, and disease-related features, highlighting their relevance to primate biology and human disease.

Cell Fate Determining Molecular Switches and Signaling Pathway in Pax7-expressing Somitic Mesoderm

The paper identifies cell fate determinants in Pax7-expressing somitic mesoderm by analyzing single-cell RNA profiles, revealing lineage-specific markers, transcription factors, and signaling pathways.

FIRM: Flexible Integration of single-cell RNA-sequencing data for large-scale Multi-tissue cell atlas datasets

FIRM integrates heterogeneous scRNA-seq datasets across tissues and platforms, accurately preserving cell type identities and structure.

Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism

The paper creates a comprehensive cell atlas of mouse lemurs using single-cell RNA sequencing, identifying over 750 cell types and comparing their molecular profiles to humans, mice, and macaques.

RNA splicing programs define tissue compartments and cell types at single cell resolution

The paper introduces SpliZ, a statistical method to detect cell-type-specific splicing regulation in single-cell RNA-seq data, finding 9.1% of genes show such regulation in human tissues.

Effect of methanol fixation on single-cell RNA sequencing data

This study evaluates the impact of methanol fixation on scRNA-seq data, showing it preserves biological signals but introduces subtle biases dependent on library construction methods.

MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples

MINERVA enables rapid, high-quality SARS-CoV-2 whole genome sequencing from clinical samples by simplifying library preparation and improving viral enrichment.

Optimization of On-Bead Emulsion Polymerase Chain Reaction Based on Single Particle Analysis

This study optimizes ePCR by analyzing single particles to determine effective conditions and success criteria for amplifying DNA libraries.