Yuqi Tan

Single-cell multi-omics identify OTP and NOVA1 as regulators of leptin action in hypothalamic feeding circuits

This study uses single-cell multi-omics to identify OTP and NOVA1 as key regulators of leptin action in hypothalamic feeding circuits, revealing cell-type-specific transcriptional and regulatory changes.

REZCUE: Rescuing 3D spatial omics from archived FFPE tissue

REZCUE enables 3D spatial multi-omic analysis of archived FFPE tissue by preserving nucleic acids and proteins for subsequent assays.

bgnorm: A Generative Statistical Framework for Background Correction, Normalisation, and Quality Control in Multiplex Spatial Proteomics

bgnorm improves signal separation and marker positivity classification in multiplex spatial proteomics by addressing technical variation through background correction, normalization, and quality control.

Fault-tolerant 3D reconstruction from 2D spatial proteomics sections

This paper introduces 3D-Omics-Flow, a method that reconstructs 3D molecular volumes from 2D spatial proteomics sections by repairing damaged sections and interpolating between them.

COLOR-3D: a versatile tool for revealing novel 3D histological features

COLOR-3D improves 3D histology by enhancing dye penetration and enables quantitative analysis of tissue morphology and aging-related changes in mouse liver.

SPACEc: A Streamlined, Interactive Python Workflow for Multiplexed Image Processing and Analysis

SPACEc provides a Python workflow for analyzing multiplexed imaging data with interactive tools for image processing, segmentation, and spatial analysis.

Polyamine Depletion by D, L-alpha-difluoromethylornithine Inhibits Ewing Sarcoma Metastasis by Inducing Ferroptosis

This study shows DFMO inhibits Ewing sarcoma metastasis by inducing ferroptosis through polyamine depletion.

Spatially organized inflammatory myeloid-CD8+ T cell aggregates linked to Merkel-cell Polyomavirus driven Reorganization of the Tumor Microenvironment

The paper identifies spatial immune patterns in Merkel cell carcinoma linked to viral status and patient outcomes.

Inhibition of DKK-1 by WAY262611 Inhibits Osteosarcoma Metastasis

This study shows that the small molecule inhibitor WAY262611 inhibits osteosarcoma metastasis by activating Wnt signaling and inducing osteoblastic differentiation.

INSIHGT: Accessible multimodal systems biology with quantitative molecular phenotyping in 3D

The paper introduces INSIHGT, a 3D spatial biology method for multi-modal molecular phenotyping, and demonstrates its application in mapping cellular structures and identifying novel cell types in human and mouse tissues.

Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake

The paper identifies BNC2 neurons in the hypothalamus that acutely suppress food intake by inhibiting AGRP neurons and are regulated by leptin, sensory cues, and nutritional status.

Annotation of Spatially Resolved Single-cell Data with STELLAR

STELLAR annotates spatially resolved single-cell data using geometric deep learning, discovering cell types and states while transferring annotations across tissues and donors.

Signaling and transcriptional networks governing late synovial joint development

The paper uses single-cell RNA-Seq to map transcriptional programs in synovial joint development, identifying a progenitor population and the role of FGF signaling in chondrocyte fate.

Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution

The paper compares in vitro and in vivo embryogenesis using scRNA-seq data and computational tools to evaluate stem cell differentiation protocols.

SingleCellNet: a computational tool to classify single cell RNA-Seq data across platforms and across species

SingleCellNet classifies single cell RNA-Seq data across platforms and species by comparing query data to reference data, showing improved accuracy and cross-species performance.