Nancy Ruonan Zhang

A Measure of Transcriptional Dyscoordination for Quantifying Aging in Single Cells

This paper introduces a measure of transcriptional dyscoordination to quantify aging in single cells, showing it increases with age and is linked to cellular processes like senescence and genome instability.

All-Optical Multimodal Mapping of Single Cell Type-Specific Metabolic Activities via REDCAT

REDCAT maps single-cell type-specific metabolic activities in tissues using multimodal all-optical imaging, revealing metabolic specialization and reprogramming in immune and liver tissues.

Cellular senescence is associated with age-related loss of liver zonation and hepatocyte function

This study shows that cellular senescence disrupts liver zonation and hepatocyte function with age by altering gene expression and cell signaling.

High-Specificity Detection of Chromosomal Mosaicism Reveals Cell-Type-Specific Genomic Alteration Patterns in Aging Tissues

CHASM detects chromosomal copy number alterations in single-cell data, revealing age-related genomic instability in specific cell types and states.

Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq

This paper introduces TraceBIND, a method to correct Tn5 bias in ATAC-seq data, improving TF footprint detection and revealing age-related regulatory changes in scATAC-seq.

A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma

This study creates a longitudinal multiomic atlas of pediatric high-grade glioma, revealing distinct tumor cell states and therapeutic targets not seen in adult glioblastoma.

Dissecting the coordinated progression of cell states in spatial transcriptomics with CoPro

CoPro identifies spatially coordinated gene expression programs across tissues, revealing distinct cellular states and their interactions in colon, brain, liver, and kidney.

SpatialFinder: A Human-in-the-Loop Vision-Language Framework for Prioritizing High-Value Regions in Spatial Transcriptomics

SpatialFinder uses a vision-language model with human feedback to prioritize high-value regions in H&E slides for spatial transcriptomics, improving ROI selection accuracy.

Multiscale confidence quantification for virtual spatial transcriptomics with UTOPIA

UTOPIA quantifies confidence in virtual spatial transcriptomics predictions across scales, improving reliability and preventing false conclusions.

Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

Thermostable RNaseH release of barcoded cDNA keeps sections intact for CODEX imaging, yielding same-section whole-transcriptome and protein maps plus CODEX-guided spot deconvolution in FFPE tissues.

Nephrobase Cell+: Multimodal Single-Cell Foundation Model for Decoding Kidney Biology

Nephrobase Cell+ is a kidney-specific foundation model that outperforms existing models in single-cell analysis, cross-species transfer, and batch effect correction.

Dual checkpoint blockade of glioblastoma with Anti-PD-1 and Anti-LAG-3 promotes expansion of tumor-reactive T cell clones along a unique pathway of differentiation

This study examines how dual checkpoint blockade with Anti-PD-1 and Anti-LAG-3 affects T cell clones in glioblastoma, showing increased clonal expansion and differentiation into effector T cells.

Cancer subclone detection based on DNA copy number in single cell and spatial omic sequencing data

Clonalscope detects cancer subclones using DNA copy number data from single-cell and spatial omic sequencing, identifying spatially segregated subclones and validating them with matched scDNA-seq data.

Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling

Clonotrace integrates gene expression and clonotype data to infer cell state transitions and fate biases, improving understanding of lineage dynamics in various biological systems.

Mitochondrial clone tracing within spatially intact human tissues

SUMMIT traces mitochondrial mutations in human tissues to identify spatially localized clones and their transcriptomic profiles.

Single-Cell Spatial Mapping of Human Kidney Development Reveals the Critical Role of the Local Microenvironment in Cell Fate Decisions

The paper maps human kidney development using single-cell RNA sequencing and spatial transcriptomics, revealing fate decisions influenced by the local microenvironment.

Targeting Interferon-Driven Inflammatory Memory Prevents Epigenetic Evolution of Cancer Immunotherapy Resistance

This study identifies inflammatory memory as a mechanism for cancer resistance to immunotherapy and shows that combining JAK and TBK1 inhibitors can prevent it.

emObject: domain specific data abstraction for spatial omics

The paper introduces emObject, a domain-specific data abstraction for spatial biology, demonstrating its utility for various spatial omics data types.

Signal recovery in single cell batch integration

This paper introduces CellANOVA, a statistical model to recover biological signals lost during single-cell data integration by distinguishing batch effects from true biological variation.

Single cell and spatial alternative splicing analysis with long read sequencing

The paper develops Longcell, a statistical framework for accurate isoform quantification in single cell and spatial long-read sequencing data, revealing intra-cell splicing heterogeneity and validating regulatory targets.

Clonal cell states link Barrett's esophagus and esophageal adenocarcinoma

The paper identifies clonal cell states in Barrett's esophagus and links them to esophageal adenocarcinoma progression through single-cell lineage tracing and transcriptional profiling.

Integration of spatial and single-cell data across modalities with weak linkage

The paper introduces MaxFuse, a method for integrating spatial and single-cell omics data with weak linkage, demonstrating its effectiveness in consolidating proteomic, transcriptomic, and epigenomic information.

Niche differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

The paper introduces niche-differential expression analysis to identify context-dependent cell-cell interactions in spatial transcriptomics data and applies it to colorectal cancer metastases.

Quantifying common and distinct information in single-cell multimodal data with Tilted-CCA

This paper introduces Tilted-CCA, a method to quantify common and distinct information in multimodal single-cell data, demonstrating its application in antibody panel design and multiome analysis.

A multiplex platform to identify mechanisms and modulators of proteotoxicity in neurodegeneration

The paper develops a multiplex reverse genetics platform to identify genetic modifiers of protein misfolding in neurodegenerative diseases and identifies DNAJB6 as a modifier of toxicity and solubility of ALS/FTD-linked RNA-binding proteins.

Nonparametric Interrogation of Transcriptional Regulation in Single-Cell RNA and Chromatin Accessibility Multiomic Data

The paper introduces TRIPOD, a nonparametric method to detect TF-target gene-accessibility relationships in multiomic data, validated across multiple datasets.

A comparative study of structural variant calling strategies using the Alzheimer's Disease Sequencing Project's whole genome family data

The paper evaluates deletion calling accuracy using two pipelines on ADSP whole genome family data, finding Scalpel better for small deletions and Parliament for larger ones, with 78.1% of predicted deletions validated by Sanger sequencing.

Causal Inference for Heritable Phenotypic Risk Factors Using Heterogeneous Genetic Instruments

This paper introduces GRAPPLE, a framework for causal inference using heterogeneous genetic instruments, and applies it to study the causal effects of blood lipids, BMI, and systolic blood pressure on 25 diseases.

Alleloscope: Integrative single cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer

Alleloscope analyzes allele-specific copy number and chromatin accessibility in single-cell cancer data, revealing complex copy number events and their role in intratumor heterogeneity.

A Mendelian randomization study of the role of lipoprotein subfractions in coronary artery disease

This study uses Mendelian randomization to assess the causal effects of lipoprotein subfractions on coronary artery disease risk, finding protective effects for certain HDL particle traits.