Single-cell and spatial transcriptomics

Xenium-based spatial transcriptomic screening identifies candidate mRNAs localized in neuronal and glial processes of the adult mouse cerebellum

The paper uses Xenium spatial transcriptomics to identify mRNAs localized in neuronal and glial processes of the adult mouse cerebellum, finding 126 candidate genes with process-like localization patterns.

{Phi}-Space ST: a platform-agnostic method to identify cell states inspatial transcriptomics studies

Phi-Space ST identifies continuous cell states in spatial transcriptomics data using scRNA-seq references, revealing niche-specific cell types and patterns in cancer tissues.

An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies

This paper creates an integrated multimodal atlas of the female reproductive system across the lifespan, identifying cell types and linking them to gynaecological pathologies.

Evaluating cell type annotations in single-cell omics in the absence of ground truth

This paper introduces ISC, a framework to evaluate cell type annotations in single-cell RNA-seq without ground truth, revealing reproducibility gaps and enabling tool benchmarking.

Deciphering cross-omics complexity of tissues via diagonal integration of unpaired spatial multi-omics data

This paper introduces STAMO, a spatially aware integration method for unpaired spatial multi-omics data, showing improved alignment and domain detection compared to existing methods.

Generalisable tissue-wide molecular reconstruction from histology

GHIST+ reconstructs tissue-wide molecular maps from H&E histology, enabling cohort-scale molecular reconstruction from sparse spatial transcriptomic data.

DyMoTree decodes early cell state transitions and drivers from single-cell transcriptomes using a tree-structured neural network

DyMoTree infers early cell fate transitions and drivers from single-cell transcriptomes using a tree-structured neural network, outperforming existing methods in resolving fate biases.

OCOO-T : A SIMPLE AND SCALABLE VIRTUAL CELL MODEL FOR TRANSCRIPTIONAL PERTURBATION RESPONSE PREDICTION

OCOO-T predicts transcriptional responses to perturbations using a minimalist Transformer-based model, achieving state-of-the-art performance across cell types and perturbations.

GeroEngine: Generative single-cell aging trajectories reveal a bidirectionally traversable identity core and direction-specific inflammatory remodeling

GeroEngine reveals aging trajectories show bidirectional identity recovery and direction-specific inflammation, suggesting homeostatic restoration over inflammation suppression.

Molecular signature of human endometrial stem/progenitor cells at the single cell level

The paper characterizes human endometrial stem/progenitor cells using scRNA-seq, identifying key markers and signaling pathways involved in their function and interactions.

Robust semi-supervised scRNA-seq integration from virtual adversarial learning

scCRAFT+ improves scRNA-seq integration by incorporating marker gene information via virtual adversarial training, enhancing accuracy and robustness to noisy annotations.

MipSScs: Artificial neural network-based data integration of 2D/3D single-cell spatial RNA sequence data from virus-infected human cerebral organoids

The paper develops an artificial neural network approach to integrate 2D/3D single-cell spatial RNA sequence data from virus-infected human cerebral organoids to study neurodegenerative disease mechanisms.

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

ANCHOR improves variant calling and allele-specific expression analysis in single-cell long-read RNA-seq by integrating haplotype-aware methods and beta-binomial modeling.

HESTA: a curated and reusable database for the human early organogenesis spatiotemporal transcriptome atlas

The paper presents a spatiotemporal transcriptome database of human embryogenesis, providing spatial gene expression and substructure data across 50 developing organs.

Conserved Cell Type Signatures Across the Brainstem and Spinal Cord in the Mouse Central Nervous System

The paper maps conserved cell type signatures in the adult mouse brainstem and spinal cord using multi-omics data, revealing shared and region-specific features.

Uncovering Pseudotime-Varying Genetic Causal Effects Along Single-Cell Trajectories for Pulmonary Disease Trait

This study identifies pseudotime-dependent causal effects of genes on pulmonary fibrosis using scRNA-seq and GWAS data.

SPARQ-MI leverages end-to-end spatial single-cell analysis of the tumor microenvironment

SPARQ-MI provides a streamlined spatial single-cell analysis method for tumor microenvironments, revealing CD8 T cell state and spatial location associations with immunotherapy response.

Sciphy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.

SciPhy estimates time-scaled phylogenies and cell population parameters from sequential genetic lineage tracing data using a Bayesian framework, showing improved accuracy over existing methods.

GATHeR: Graph-based Accurate Tool for Immunoglobulin HEavy- and Light-chain Reconstruction

GATHeR reconstructs full-length, paired B-cell receptor sequences from scRNA-seq data, improving subclass, allele, and isoform resolution, especially in naive and memory B cells.

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics

The paper introduces circVDJ-seq for efficient T cell receptor profiling from single-cell and spatial multi-omics data, revealing distinct immune microenvironments and T cell clonality patterns in various clinical contexts.

CellBouncer, A Unified Toolkit for Single-Cell Demultiplexing and Ambient RNA Analysis, Reveals Hominid Mitochondrial Incompatibilities

CellBouncer demultiplexes and analyzes pooled single-cell data, revealing mitochondrial incompatibilities between humans and chimpanzees.

A Unified Spatial AI Framework for Cross-Domain Tissue-State Analysis in Trauma, Oral, and Cardiovascular Pathology

This paper develops a spatial AI framework to identify conserved tissue-state organization across trauma, oral, and cardiovascular pathology using spatial transcriptomic data, finding six conserved fuzzy tissue states.

Gateway: patient olfactory neurons for large-scale discovery in neurodegenerative disease

The paper introduces Gateway, a platform for collecting and analyzing single-cell transcriptomic data from patient olfactory neurons to study neurodegenerative diseases.

NaVis: a virtual microscopy framework for interactive histological interrogation of spatial transcriptomics data

NaVis provides an interactive virtual microscopy framework for analyzing spatial transcriptomics data by integrating gene expression with histological morphology.

Spatially-resolved integration of microglia morphological diversity and gene expression using Visium with protein co-detection

The paper integrates microglia morphology and gene expression using spatial transcriptomics and proteogenomics to identify morphology-related genes in the human brain.

Evaluating agentic AI for biological discovery in autonomous and copilot settings

This study evaluates agentic AI's ability to support biological discovery in autonomous and human-AI copilot settings using multi-omic cancer datasets.

Cell-Cell-Seq resolves contact-associated NK cell activation in defined tumor cell dyads

The paper introduces Cell-Cell-Seq to study NK cell activation in defined tumor cell dyads, finding contact-associated activation programs distinct from suspension co-culture.

Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance

This study evaluates how pre-training dataset size and diversity affect single-cell foundation model performance on zero-shot and fine-tuned tasks using 22.2 million cells.

Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks

This study develops an iSCST framework for FFPE biopsies, identifying colitis-associated cell networks and VDZ response signatures in IBD patients.

Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation

The paper uses hybrid crosses to analyze regulatory variation in mouse tissues, finding cell-type-specific trans-acting effects and highlighting the limitations of bulk tissue analysis.