Single-cell and spatial transcriptomics

Coordinated Enhancement of Molecular and Spatial Fidelity for Biological Inference in Spatial Transcriptomics

FOCUS improves spatial transcriptomics by coordinating molecular and spatial fidelity across multiple tasks and datasets, revealing clearer biological patterns in immunology, development, and oncology.

SORT disentangles multilevel gene programs across heterogeneous spatial transcriptomic atlases

SORT identifies multilevel gene programs and their spatial activities across diverse spatial transcriptomic datasets, revealing both shared and sample-specific patterns.

Scalable methylome-transcriptome profiling resolves clonal organization in human hematopoiesis

This paper introduces Droplet-MT, a method for joint methylome and transcriptome profiling, enabling clonal organization analysis in human hematopoiesis with high scalability and resolution.

Concurrent de novo inference of cell types and gene regulatory networks with NetMap

NetMap jointly infers cell-level gene regulatory networks and clusters cells based on shared regulatory programs, outperforming existing methods on synthetic data and reliably detecting regulons on real data.

From Sparse Visits to Continuous Molecular Trajectories with Flow Matching

CohortFM reconstructs continuous molecular trajectories from sparse longitudinal data, revealing biologically meaningful progression patterns across diseases.

Subtype-Selective Neuronal Vulnerability and Compensatory Neuroglial Remodeling in Human Cortical Dementia

The paper analyzes snRNA-seq and bulk RNA-seq data to identify cellular and transcriptomic changes in dementia, revealing subtype-specific vulnerabilities and neuroglial remodeling.

A perturbation atlas of mouse neural organoids resolves macroglial reactivity and nominates drivers of degeneration

This study creates a perturbation atlas of mouse neural organoids to understand macroglial reactivity and identify drivers of degeneration.

A Unified Comparison of 10X Genomics and Parse Biosciences scRNA-seq Technologies

This study compares 10X Genomics and Parse Biosciences scRNA-seq technologies, finding platform-specific biases in gene counts and composition, with Parse showing GC-content bias and potential nuclear RNA enrichment.

DeSPA uncovers genes with cross-state spatial pattern remodeling and coordinated spatial programs across multi-slice spatial transcriptomics atlases

DeSPA identifies genes with spatial pattern remodeling across biological states and reveals coordinated spatial programs in multi-slice spatial transcriptomics data.

Multi-omic spatial mapping of the human habenula defines the molecular and anatomical organization of medial and lateral subregions

This study maps the spatiomolecular organization of the human habenula using multi-omic approaches, identifying molecular signatures and spatial domains linked to psychiatric disorders.

Point-Process Modelling of Cell-Type Interaction Structure in CosMx Glioma Data for Hypothesis-Driven Tumor Inference from scRNA-seq

The paper develops a spatial-statistical framework to model cell-type interactions in glioblastoma using CosMx data, revealing patient-specific spatial patterns and their molecular correlates.