scRNA-seq

scCont: Interpretable Contrastive Learning for Functional Characterization of Cellular State Transitions

scCont is an unsupervised contrastive learning framework that extracts interpretable functional transition units from scRNA-seq data, outperforming baseline methods in capturing biologically meaningful dynamics.

Rapid, accurate, and memory-frugal sub-gene-level quantification of probe-based, multiplexed single-cell data

This paper introduces simpleaf, a tool for efficient sub-gene-level quantification of probe-based single-cell data, showing improved speed and memory use compared to existing tools.

A comparative transcriptomic framework across kidney organoid, assembloid, and transplantation models

The paper compares transcriptomic profiles across kidney organoid, assembloid, and transplantation models to evaluate their maturity and suitability for research.

Clonally Convergent Tph/Tfh-like CD4+ T Cells are Shared Across Recovery and Recurrence in Experimental Periodontitis

The paper identifies clonally convergent Tfh/Tph-like CD4+ T cells that persist in the mucosa after recovery from periodontitis and contribute to recurrence.

SPECHTacle: An Efficient Detection and Visualization of Cell Specific Regulation in Single Cell-Based Experiments Using a Novel Combinatorial Computational Tool

SPECHTacle efficiently identifies and visualizes cell-specific regulatory changes in single-cell experiments using optimal transport and entropy analysis.

brisc: a multithreaded CPU toolkit for single-cell analysis

brisc is a multithreaded CPU toolkit for single-cell analysis that is faster and more reproducible than existing tools like Scanpy and Seurat.

Single-Cell RNA Sequencing Reveals Distinct Cellular and Molecular Features of Steroid-Induced Osteonecrosis of the Femoral Head Compared to Alcohol-Induced Osteonecrosis and Hip Osteoarthritis

This study uses single-cell RNA sequencing to compare cellular and molecular features of steroid-induced and alcohol-induced osteonecrosis of the femoral head with hip osteoarthritis, identifying distinct immune and stromal cell signatures.

Uncovering cross-signal interactions in single-cell and spatial omics

CRISP identifies and localizes interactions between biological signals in single-cell and spatial transcriptomic data, revealing their effects on tissue function and gene regulation.

High-fat diet promotes exhaustion-associated T-cell remodeling across vascular and lymphoid tissues in atherosclerosis-prone mice

This study shows that a high-fat diet causes T-cell exhaustion in multiple tissues of atherosclerosis-prone mice, which partially reverses with dietary changes.

CD200R1 Marks a Branchpoint During Human Natural Killer Cell Development in Tonsils

The paper identifies CD200R1 as a marker for an immature NK-cell precursor in tonsils, distinguishing between oligopotent and more restricted developmental stages.

gcat, its_a_scam: modular tools for single cell data processing and per-cellquality control

The paper introduces gcat and its_a_scam, modular tools for single cell genomic data processing and quality control, showing they produce results comparable to proprietary pipelines.

CloneVI: A deep generative model for deciphering the relationships between cell state and mitochondrial genotype

CloneVI infers clonal structure from cell states in single-cell RNA-seq and ATAC-seq data, linking mitochondrial DNA mutations to specific cell states.

Endogenous PROM1 activation redistributes liver cancer cells along a preexisting differentiation axis

The paper shows PROM1 activation in liver cancer cells shifts their state along a preexisting differentiation axis, suggesting CD133's role extends beyond being a stem-like marker.

RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure

This paper introduces RAD-seq, a method to quantify RNA accessibility by protein binding, and shows it can detect RBP footprints and RNA structure changes under stress.

KaryoTap-based scDNA seq assessment of aneuploidy induction by hydroquinone in hematopoietic stem cells

This study assesses whether hydroquinone induces aneuploidy in hematopoietic stem cells using KaryoTap and FISH, finding no reproducible increase in whole-chromosome aneuploidy.

The Reasoning Paradox in Scientific Sandboxes: Why Extended Reasoning Fails in Autonomous Bioinformatics and How to Fix It.

This paper identifies two failure modes in extended reasoning models within bioinformatics tasks and introduces DTDR to improve accuracy and reduce errors.

Transcriptional contingency in the early hematopoiesis of inherited bone marrow failure syndromes

This study integrates and analyzes scRNA-seq data from hematopoietic stem and progenitor cells of patients with Fanconi anemia and Telomere Biology disorders, identifying distinct gene expression profiles and shared transcriptional programs.

Integrated transcriptomic and epigenomic profiling of human cartilage reveals coordinated changes in fibronectin expression, splicing, and receptor signaling during osteoarthritis progression

This study profiles human cartilage across OA grades, revealing changes in fibronectin expression, splicing, and receptor signaling during disease progression.

GraphExperiment: infrastructure for high-dimensional quantitative data and associated networks in R/Bioconductor

GraphExperiment provides an R/Bioconductor package to store and manipulate high-dimensional quantitative data alongside associated networks in a unified framework.

Gene regulatory logic underlying the differentiation of mixed lineages in human thymic epithelial cells

The paper identifies 17 human thymic epithelial cell subsets using single-cell data and shows they share a common ancestor and regulatory logic, with some conservation in mice.

Age-based shifts in multicellular community organization and abundance in HPV-Negative Head and Neck Cancer

This study identifies age-related changes in cellular composition and organization in HPV-negative head and neck cancer using single-cell data, highlighting MDK as a key factor in stromal remodeling and immunosuppression.

Development of a multi-organ single-cell atlas of systemic sclerosis reveals shared and tissue-specific pathogenic pathways.

This study creates a multi-organ single-cell atlas of systemic sclerosis to identify shared and tissue-specific transcriptional programs and potential therapeutic targets.

Integrative multi-omics decoding of the host response to Klebsiella pneumoniae infection reveals an itaconate-centred metabolic-immune axis and a spatially organised inflammatory programme

This study integrates multi-omics data from Kp infection to identify an itaconate-centred metabolic-immune axis and a host-response signature with high diagnostic accuracy.

Systemic Analysis of Patient Derived Esophageal Epithelial Organoid Model Reveals Cell State Heterogeneity and Conservation of Differentiation Hierarchy

The paper uses scRNA-seq to compare IL-13-treated esophageal organoids with EoE biopsies, revealing shared cell state heterogeneity and differentiation hierarchy dysregulation.

Single-cell RNA-seq of amniotic fluid provides unique insight into fetal development

This study uses scRNA-seq on amniotic fluid to create a cell atlas of healthy fetal cells, revealing gestational age-related changes in cell composition and gene expression.

High-resolution analysis of T cell subsets, clonality, and trajectories in psoriasis

This study analyzes T cell subsets, clonality, and trajectories in psoriasis using single-cell RNA and TCR sequencing, revealing tissue-specific and shared features of the T-cell repertoire.

Timed binary WNT activity is sufficient to model the early human neural axis

This paper shows that timed WNT pulses can specify distinct neural domains in human pluripotent stem cells, enabling the generation of specific neuron and progenitor types.

Vascular specification from diversified mesoderm culminates in endothelial convergence

This study reconstructs mouse vasculogenesis using single-cell and spatial analyses, revealing a transient vascular-primed state and the role of VEGF in endothelial specification.

Increasing Cancer Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival

This study quantifies cancer stemness in prostate cancer across progression stages, showing its association with therapy resistance, poor survival, and lineage plasticity.

Cardiomyocyte Identity Crisis Without Regenerative Re-entry: A Multi-Scale Atlas of Incomplete Dedifferentiation and Intercellular Communication Rewiring in the Infarcted Human Heart

The paper constructs a multi-scale atlas of cardiomyocyte changes in infarcted hearts, showing partial identity loss without regenerative proliferation and altered intercellular communication.