scRNA-seq

PhenoMapR: scalable mapping of sample phenotypes to single-cell, spatial, and bulk transcriptomics data

PhenoMapR maps bulk expression phenotypes to single-cell and spatial transcriptomics data to identify biologically relevant cellular populations and spatial niches.

Selective collateralization of transcriptomically distinct neurons organizes visual-stream output from the primary visual cortex

The paper maps gene expression and axonal projections of neurons in the mouse primary visual cortex to reveal how retinotopy and cell-type-specific collateralization organize visual-stream output.

A Systematic Comparison of Single-Cell Perturbation Response Prediction Models

The paper benchmarks 13 models for predicting single-cell perturbation responses across 25 datasets, finding performance varies with perturbation effect size and evaluation metric.

Resolving cell lineages and gene functions in the developing mouse gastrointestinal tract using in utero transduction

This study uses in utero lentiviral transduction to resolve clonal relationships and gene functions in developing mouse gut lineages, revealing distinct developmental patterns in mesenchyme and enteric nervous system.

Adaptive immunity is dispensable for salamander appendage regeneration

Rag1-knockout newts lacking adaptive immunity regenerate larval limbs, tails and adult limbs without overt gross differences from controls; newt blastema tolerates allografts, and axolotl regenerating limbs show immunosuppressive transcriptional shifts.

Loss of Mitochondrial Respiratory Capacity Reshapes Myeloid Cell Function during Mycobacterium tuberculosis infection

The paper shows that reduced mitochondrial respiratory capacity in myeloid cells during Mtb infection impairs immune function and Mtb control, with similar findings in human data.

Müller glia subtypes define neuro-glial associations and spatial morphogen axes in the zebrafish retina

The paper identifies three constitutive Muller glia subtypes in the zebrafish retina that define spatial morphogen axes and neuron-associated programs, showing functional heterogeneity in the healthy retina.

Flexible use of conserved motif vocabularies constrains genome access in cell type evolution

The paper shows that conserved motif vocabularies constrain genome access in cell type evolution across species.

Cell-type-specific circadian and light-responsive transcriptional dynamics in adult Drosophila neurons

The paper profiles circadian neuron transcriptomes across timepoints under different light conditions to reveal transcriptional and light-dependent gene regulation in Drosophila.

Primordial cardiomyocytes orchestrate myocardial morphogenesis and vascularization but are dispensable for regeneration

The paper identifies a unique cardiomyocyte subpopulation in zebrafish hearts that is essential for development but not regeneration.

Single-cell characterization of human periodontal ligament (PDL) cells reveals uniformly mesenchymal populations in matched maxilla and mandible pairs from four donors

The paper uses single-cell RNA sequencing to analyze PDL cells from maxilla and mandible pairs, finding uniform mesenchymal populations with donor-specific substates and limited jaw-related transcriptional differences.

Reconstructing signaling histories of single cells via perturbation screens and transfer learning

The paper develops a framework combining perturbation screens and transfer learning to reconstruct signaling histories in cells and optimize differentiation protocols.

Distinct depressive-like behavioural phenotypes in mice exhibit unique patterns of transcriptional perturbations across habenular cell subtypes

The paper identifies distinct transcriptional changes in habenular cell subtypes associated with different depressive-like behavioural phenotypes in mice.

A single-nucleus multiomic and spatial atlas of gene regulation in human spermatogenesis

This study creates a single-nucleus multiomic and spatial atlas of human spermatogenesis, linking gene regulatory networks to infertility-associated genetic variation and disease perturbations.

Coupled transcriptomic divergence establishes a human-specific synaptic glial precursor state

The paper identifies a human-specific synaptic glial precursor state by analyzing single-cell differentiation trajectories across multiple species and shows its role in human cortical evolution.

Atlas-scale single-cell analysis beyond in-memory paradigm with scAtlasPy

scAtlasPy enables efficient analysis of large single-cell atlases by using disk-resident computing, achieving high speed and low memory usage compared to existing tools.

scFLAME: a unified generative model for interpretable clustering, hierarchical structure discovery and marker-gene identification in single-cell RNA-seq data

scFLAME is a generative model that unifies clustering, marker-gene identification, and hierarchical structure discovery in scRNA-seq data, achieving state-of-the-art accuracy and scalability.

Dynamic regulation of a domesticated DNA transposon-derived gene, in human germline and early embryonic development

The paper identifies THAP9, a domesticated DNA transposon-derived gene, as dynamically regulated during human germline and early embryonic development, with lineage-specific expression patterns and epigenomic changes.

Culture-free single-cell transcriptomics shows short term functional and associative stability in non-model microeukaryotes under shading stress

This study uses culture-free single-cell transcriptomics to analyze microeukaryotes under shading stress, revealing stable prokaryotic associations and functional changes in gene expression.

Intravital single-cell behavior profiling reveals disrupted germinal center B cell motility and interactions by EZH2 gain-of-function mutation

This study uses intravital imaging and single-cell analysis to show that EZH2 mutations alter GC B cell motility and interactions, promoting lymphomagenesis.

Single-Cell Indel Detection Enhances Genetic Ancestry and Cellular Lineage Analysis

Monopogen-Indel calls germline indels from single-cell and single-nucleus RNA data at 73.0% (retina) and ~87% (ovarian cancer) WGS-validated precision, though no single-cell somatic indel matched a WGS somatic indel.

PSEN1 Expression Identifies a Developmentally Distinct Favorable-Prognosis State in SHH α Medulloblastoma

This study identifies high PSEN1 expression as a favorable-prognosis state in SHH medulloblastoma, associated with a distinct transcriptional program.

Campylobacter jejuni Infection Is Associated With Cell-Cycle, Redox, and Metabolic Remodeling of Human Intestinal Epithelial Cells at Single-Cell Resolution

This study uses single-cell RNA sequencing to show that C. jejuni infection alters cell-cycle, redox, and metabolic states in human intestinal epithelial cells.

Altered Purinergic Signaling and CD8+ T Cell Dysregulation in STAT3 GOF Syndrome

This study identifies altered purinergic signaling and CD8+ T cell dysregulation in STAT3 GOF syndrome, showing partial normalization with JAK inhibitors.

Systematic Comparison of 10X Genomics and Parse Single Cell RNA Technologies across PBMC and CD8+ TEMRA Cells

Side-by-side PBMC and CD8+ TEMRA profiling shows Parse favors longer transcripts but underdetects cytotoxic genes (GNLY, PRF1, GZMB), so 10X Chromium better resolves TEMRA subsets.

Comparative Analysis of Primary and Liver Fibroblasts Reveals MET as a Potent Target in Pancreatic Cancer Metastasis

The paper compares primary and liver PDAC lesions using single-cell transcriptomics to identify MET as a target in pancreatic cancer metastasis.

The Notch signaling pathway is a master regulator of CD8+ T cell exhaustion and differentiation during chronic infection

This study shows that Notch signaling regulates CD8+ T cell exhaustion and differentiation during chronic infection by promoting the transition from progenitor to effector-like cells and preventing terminal exhaustion.

Evaluating the Robustness of Path-Preservation Benchmarks for Dimensionality Reduction Across Point-Density Thresholds: Linear and Cyclic Single-Cell Trajectories

This paper evaluates how dimensionality reduction methods affect trajectory geometry by testing their path-preservation across different point-density thresholds on linear and cyclic single-cell datasets.

Global tree encoding of atlas-scale single-cell genomics

The paper introduces MILK, a framework for organizing single-cell genomic data into tree representations, enabling scalable analysis and preserving information across large datasets.

Function-driven geometry directs human pilosebaceous unit development

The paper builds a spatiotemporal map of human pilosebaceous unit development using single-cell multiomics and machine learning, showing how epithelial-mesenchymal interactions drive organogenesis and how sebaceous gland programs are disrupted in tumors.