scRNA-seq

Once yearly cell-based therapy for sustained and dose tunable delivery of monoclonal antibodies

This paper develops a cell-based therapy that enables sustained, dose-tunable delivery of monoclonal antibodies through a single administration, demonstrating long-term efficacy and safety in preclinical models.

Corallimorpharian genome supports the monophyly of Scleractinia and illuminates the cellular evolution of coral calcification

This study presents a corallimorpharian genome and single-cell transcriptomes to show that coral calcification evolved through a derived calicoblast cell state and genomic innovations.

Clonally expanded CD8 T cells in AML adopt an NK-like program distinct from canonical exhaustion

Dataset structure outweighs method choice in single-cell cell-type annotation

In a 63-tool benchmark, dataset identity explained ≈84% of Cohen's κ variance on synthetic data versus ≈4% for tool identity, and k-nearest-neighbor (kNN) purity predicted accuracy near-linearly (R² = 0.85–0.99).

Method-dependent biases in cell type detection between single-cell and single-nucleus RNA sequencing in the photosymbiotic acoel Praesagittifera naikaiensis

The paper compares scRNA-seq and snRNA-seq in Praesagittifera naikaiensis, finding snRNA-seq better recovers neural transcripts and reduces symbiont reads.

Transcriptionally distinct atypical B cell populations contribute to insulin autoreactivity and show differential activation, isotype switching, and somatic hypermutation in early-stage type 1 diabetes individuals

B cells from 24 early-stage type 1 diabetes individuals include four atypical clusters differing in switching and mutation; Cluster 10 had the highest insulin-binding antibody rate (5/16).

Limitations of differential expression for cell-type marker discovery in single-cell RNA sequencing atlases

The paper shows that differential expression methods like Wilcoxon rank-sum test produce unreliable cell-type markers due to cluster size dependence, and proposes a classification-based alternative with better specificity.

Multimodal spatial-omics reveal the heterogeneity and intercellular network characteristics of papillary craniopharyngiomas.

This study uses multimodal spatial-omics to analyze papillary craniopharyngiomas, identifying tumor cell states and microenvironment interactions.

Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport

Species-OT uses Gromov-Wasserstein optimal transport to compare transcriptome geometries across species, identifying gene correspondences and transcriptomic discrepancies.

Multimodal Profiling of Repair-Associated Immune Dynamics in a Mouse Model of Menstruation

This study examines immune dynamics during menstruation in mice, identifying monocytes, macrophages, and neutrophils as key players in endometrial repair and highlighting thrombospondin 1 and secreted phosphoprotein 1 as potential therapeutic targets.

A Metacell Model of Single Cell RNA-seq Counts Yields a Gaussian Mixture Model in PCA Space

The paper shows that applying a metacell model to scRNA-seq data results in PCA embeddings that follow a Gaussian mixture model, but underestimates variance in real datasets due to unaccounted gene correlations.

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

An age-preserving neuronal iSpheroid platform for modeling human aging and Alzheimer disease

This paper introduces an age-preserving neuronal iSpheroid platform that models human aging and Alzheimer's disease, revealing disease-associated metabolic changes and potential therapeutic targets.

SCITRAM: a Single-cell Integrated transcription regulation modeler for predicting master transcription factors

SCITRAM predicts master transcription factors from single-cell transcriptomics data by reconstructing gene regulatory networks and modeling transcriptional cascades.

Quantum Hamiltonian-Based Generative Modeling of Single-Cell Transcriptomics for Gene Regulatory Network Inference

This paper introduces a quantum Hamiltonian-based model for gene regulatory network inference, showing improved performance on synthetic and real single-cell RNA-seq data.

Lineage-informed factor analysis reveals heritable programs of single-cell gene expression

The paper introduces scPFA, a lineage-informed factor analysis method, to uncover heritable gene expression programs from single-cell lineage-tracing data.

Inhibition of hexokinase 2 undermines cartilage health and accelerates osteoarthritis

This study shows that inhibiting hexokinase 2 (HK2) impairs cartilage formation and accelerates osteoarthritis progression in mice.

Cerebral organoids recapitulate interneuron chain migration in the human cortex

This study shows that long-term human cerebral organoids replicate postnatal interneuron migration, revealing chain migration and genetic factors linked to neurodevelopmental disorders.

Interpretable models for scRNA-seq data embedding with multi-scale structure preservation

This paper introduces two tools for improving the trustworthiness of single-cell dimensionality reduction by enhancing quality metrics and multi-scale structure preservation.

Single-cell transcriptomics reveals transcriptional diversity of sea cucumber perivisceral fluid coelomocytes

This study uses scRNA-seq to identify transcriptional diversity in sea cucumber coelomocytes, revealing functional roles and potential progenitor and specialized cell types.

Early dynamics of a neutrophil interferon program drive immunotherapy resistance and limit durable anti-tumor immunity

This study identifies an early neutrophil interferon program that predicts resistance to anti-PD1 therapy and limits durable anti-tumor immunity.

Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments

Nuclear acetyl-CoA accumulation drives reversible RBP hyperacetylation and transcriptome-wide splicing shifts in age-equivalent Alzheimer's disease neurons

This study shows that nuclear acetyl-CoA accumulation in Alzheimer's disease neurons causes RBP hyperacetylation and splicing shifts, which can be reversed by inhibiting ACLY.

Deep Lineage: Single-Cell Lineage Tracing and Fate Inference Using Deep Learning

Deep Lineage uses deep learning to analyze time-series single-cell RNA-sequencing with lineage-tracing data to predict cell fate and gene expression profiles more accurately than existing methods.

Human cerebral assembloids as a model to study the interaction of glioblastoma with resident glial cells

This study develops human cerebral assembloids to model glioblastoma interactions with glial cells, revealing extracellular vesicles' role in peritumoral niche formation.

Quantifying distribution shifts in single-cell data with scXMatch

scXMatch quantifies distribution shifts between single-cell data from different conditions using a non-parametric graph-based test, showing robust performance across gene expression, chromatin accessibility, and morphology data.

Generative modeling reveals the connection between nuclear morphology and gene expression

COSMIC, a generative model, quantifies the relationship between nuclear morphology and gene expression using paired single-cell data, revealing morphology-associated genes in prostate cancer and spatial transcriptomics of zebrafish embryos.

Distinct phases of immune system programming during ART-suppressed immunodeficiency virus infection

The paper identifies two distinct phases of immune system changes in ART-suppressed HIV infection using single-cell transcriptomics and proteomics in rhesus macaques.

Deciphering the Network Architecture of APOBEC3-Driven Mutagenesis in HPV-Positive Head and Neck Cancers

The paper identifies APOBEC3A and APOBEC3B mutagenic effects in HPV-positive HNSCC by analyzing single-cell data, showing distinct mutational signatures linked to tumor stages and vaccine targets.

Age-Dependent Effects of Macrophage Derived Cathelicidin Antimicrobial Peptide on Bone Fracture Repair

This study identifies cathelicidin antimicrobial peptide (CAMP) as an age-dependent regulator of bone fracture repair, showing it promotes healing in young mice but limits it in aged mice through P2X7R-NLRP3 signaling.