scRNA-seq

Virtual lineages: in silico lineage tracing from single-cell and spatial transcriptomes

isCORAL infers clonal relationships and cell-fate dynamics from single-cell and spatial transcriptomes, outperforming existing methods in lineage reconstruction and memory-gene identification.

Single-cell characterization of the human immune landscape reveals dysfunction in monocyte-mediated cellular interactions in symptomatic malaria

The paper uses single-cell RNA sequencing to analyze immune cell interactions in asymptomatic and symptomatic malaria patients, finding reduced monocyte-T cell interactions and increased inflammation in symptomatic cases.

multiomeR: a pipeline for reproducible analysis of large-scale single-nucleus Epi Multiome datasets

multiomeR provides a reproducible R pipeline for analyzing large-scale single-nucleus Epi Multiome datasets, improving efficiency and reducing memory usage compared to existing workflows.

Tetraspanin changes in septic blood are organized by cell type, with monocyte CD82 induction and leukocyte CD37 loss associated with mortality

The paper identifies cell-type-specific tetraspanin changes in sepsis, finding CD37 loss and monocyte CD82 induction linked to mortality.

A spatial and single-cell transcriptomic atlas of the embryonic synovial joint and its explant model

The paper creates a spatial and single-cell transcriptomic atlas of mouse embryonic synovial joints and their explants, identifying key markers and regulatory mechanisms in joint formation.

Antigen recognition licenses therapeutic CD8+ T cells to organize a multicellular myeloid interaction network in the tumor microenvironment

This study investigates how therapeutic CD8+ T cells interact with myeloid cells in the tumor microenvironment through antigen recognition, revealing state-selective networks and the role of pMHC-I sources.

Astrocytic sEH-EET signaling regulates microglial lysosomal function and suppresses the STING-Type I interferon pathway in Alzheimer's disease

This study identifies an astrocyte-microglia signaling axis in Alzheimer's disease where astrocytic sEH limits EET availability, promoting lysosomal clearance of pSTING and suppressing type I IFN signaling.

XplainTDA: Explaining the topological structure of single-cell multi-omics data through perturbation

XplainTDA identifies molecular determinants of topological structures in single-cell multi-omics data through perturbation-based analysis.

Developmental trajectories organize the assembly of valence circuits in the central amygdala

The paper identifies developmental trajectories that organize valence-specific circuit assembly in the central amygdala using single-cell profiling and molecular analysis.

Optimal transport reveals unresolved cells in single cell multi-omics

This paper introduces optimal transport to explicitly reveal cell correspondences in single-cell multi-omics, improving integration and label transfer by identifying and removing ambiguous cells.

Developmental origins of thymic B-cell lymphomas

This study identifies a thymus-specific B-cell differentiation program linked to thymic B-cell lymphomagenesis through single-cell multiomics and spatial profiling.

SP1 tethers NR2F2 to drive atrial cardiomyocyte identity

The paper identifies SP1 as a transcription factor necessary for human atrial cardiomyocyte identity, showing it interacts with NR2F2 to drive gene regulation.

Longitudinal single-cell transcriptional profiling identifies dynamic neurodegenerative mechanisms in Christianson Syndrome rat

This study uses single-cell RNA sequencing in a CS rat model to identify dynamic neurodegenerative mechanisms, revealing early mitochondrial dysfunction and microglial activation overlapping with Alzheimer's disease.

Gestational reorganization of cellular niches and communication revealed by a spatially resolved transcriptional atlas of the macaque maternal-fetal interface

This paper constructs a spatial transcriptomic atlas of the macaque maternal-fetal interface across gestation, revealing shifts in cellular composition and signaling pathways.

StoichRNA: A Scalable Framework to Map and Optimize Combinatorial RNA Systems at Single-Cell Resolution

StoichRNA maps and optimizes combinatorial RNA systems at single-cell resolution by analyzing RNA stoichiometry and identifying optimal combinations for desired cellular functions.

Survival-associated cellular communication networks in human solid cancers

The paper develops SKyNet to identify survival-associated cell-cell communication networks in solid cancers using single-cell and bulk RNA-seq data, finding specific interactions linked to patient outcomes.

Two populations with different cell dynamics maintain urethral epithelial homeostasis in female and male mice

The paper identifies two progenitor cell populations in mouse urethra with distinct self-renewal patterns and sex-specific differences in epithelial dynamics.

Cross-species transcriptomic atlas of X-linked Myotubular Myopathy identifies unique, treatment responsive myofiber populations

This study identifies unique myofiber populations in XLMTM using transcriptomics and shows they respond to therapeutic interventions across species.

scOmnom: scalable end-to-end single-cell RNA-seq analysis with auditable resolution selection

scOmnom provides a scalable, semi-automated workflow for single-cell RNA-seq analysis, enabling auditable clustering-resolution selection and annotation refinement across large datasets.

scRBP infers cell-specific RNA-binding protein regulons from single-cell transcriptomes at gene and isoform resolution

scRBP infers cell-specific RNA-binding protein regulons from single-cell transcriptomes, resolving targets at gene and isoform levels and linking genetic risk to disease.

Temporal dynamics of RNA phage infection reveal bacterial recovery despite ongoing viral replication

The paper studies RNA phage infection dynamics in E. coli, showing bacterial population rebound despite viral replication and cell death.

Female microglia show heightened responses to aging and amyloid pathology in mice and humans

The paper identifies conserved sex-biased microglial responses to aging and amyloid pathology in mice and humans using single-cell transcriptomics and proteomics.

Auditing Confidence-Calibrated Benchmarking of Single-Cell Perturbation Models

The paper audits a benchmarking framework for single-cell perturbation models, revealing flaws in metric interpretation and calibration, and identifies a specific calibration failure in split-conformal prediction.

Prenatal immune priming to Plasmodium falciparum is characterized by multi-lineage T-cell responses that are influenced by maternal microchimerism and predict malaria outcomes

Maternal microchimerism in Malian cord blood is associated with fewer Pf-responsive ZBTB16+ CD4 and Vγ9Vδ2 T cells, and with infant malaria outcomes.

LineageFlow: Growth-Corrected State Dynamics for Probabilistic Cell-Fate Prediction

LineageFlow predicts clonal fate and transcriptional profiles by integrating growth dynamics and state transitions in single-cell lineage data.

LIN28B is a post-transcriptional regulator of Wnt signalling in myeloid leukemia cells and dual targeting promotes cytotoxicity

This study identifies LIN28B as a post-transcriptional regulator of Wnt/{beta}-catenin signalling in myeloid leukemia cells and shows that dual targeting enhances cytotoxicity.

CXCL9-Dependent Immune Networks of Spontaneous Tertiary Lymphoid Structures in a Murine Subcutaneous Tumor Model

This study develops a subcutaneous tumor model that naturally forms tertiary lymphoid structures (TLS) and identifies CXCL9 as a key regulator of TLS formation and function.

Sustained antigenic engagement programs multidimensional CTL states with distinct cytotoxic capacities

This study shows that sustained antigenic engagement leads to multidimensional remodeling and functional diversification of CTLs, maintaining cytotoxic activity while creating functionally distinct states.

Ethmoid bone marrow region modulates lymphoid activation and differentiation with distinct myeloid profile in neuroinflammation

The paper investigates how neuroinflammation affects the ethmoid bone marrow region and its role in immune responses using scRNAseq and flow cytometry in a mouse model.

Multiplex programming of mappable, molecularly tagged genomic deletions

The paper introduces OPTIMuS PRIME-Del, a CRISPR-based method for multiplexed, precise deletion of cis-regulatory elements, validated through molecular tagging and scRNA-seq analysis.