scRNA-seq

Building virtual cell dynamics that evolve with biological measurements

CellCompass, an agentic AI system, models cell dynamics from single-cell measurements and improves predictions by integrating new biological constraints and experimental data.

How Much Can AI Virtual Cells Gain from Unified Perturbational Modeling?

This paper evaluates how unified perturbational modeling improves AI virtual cell predictors by integrating heterogeneous Perturb-seq datasets and achieving better performance across benchmarks.

Lost and found: beer belly is a novel, ancient regulator of animal development

The paper identifies a novel gene, beer belly, as a regulator of segmentation in spiders using single-cell RNA sequencing and shows its evolutionary loss in mammals and holometabolous insects.

Evaluation design shapes estimates of cross-donor generalization in single-cell classification of cell-type

The paper evaluates how different evaluation designs affect cross-donor generalization in single-cell cell-type classification and finds that random cell-level splitting overestimates performance compared to donor-held-out evaluation.

BLOOM: Biologically Informed Flow Matching for Transcriptomic Virtual Embryo Modeling

BLOOM generates developmental cell-expression distributions across time using conditional flow matching, outperforming baselines in gene and cell-expression correlations.

Single-Cell Atlas of Non-Functioning Gonadotroph Tumors and Anterior Pituitary Reveals Lineage Infidelity and Clinically Associated Transcriptional Programs

This study compares single-cell transcriptomes of non-functioning gonadotroph tumors and normal anterior pituitary to identify lineage infidelity and growth-associated programs.

FluxSprout: Single-cell metabolic modeling of vascular sprouting in zebrafish

FluxSprout identifies metabolic dependencies in zebrafish sprouting angiogenesis by integrating single-cell RNA sequencing with genome-scale metabolic modeling, revealing biosynthetic capacity as a key feature of sprouting vessels.

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.

Decoding & manipulating human intercellular signaling via scalable cell-free protein synthesis

The paper develops scalable cell-free protein synthesis platforms to generate single-cell RNA-sequencing data on immune cell responses to cytokines and other signals, enabling functional discovery and drug target prioritization.

TCF21 loss identifies a conserved inflammation-associated fibroblast state across Crohn's disease and ulcerative colitis

The paper identifies a conserved inflammation-associated fibroblast state in Crohn's disease and ulcerative colitis linked to TCF21 loss and shows TCF21 restoration can suppress inflammatory mediators.

NK Cell Activation as an Immune Mechanism in Depression: Insights from Single-Cell Multi-Omics

The paper identifies NK cell activation as a genetic and functional contributor to MDD susceptibility using single-cell transcriptomics and population genetics.

Distinct muscle stem cell fates correlated with hyperplasia and hypertrophy during skeletal muscle growth in rainbow trout

The epidermal growth factor (EGF) receptor family network in cardiac hypertrophy and heart failure

EGFR-family ligand mRNAs shift in failing human hearts; NRG1 and EGF drive distinct, differently ERBB2-dependent transcriptional programmes in rat cardiomyocytes; afatinib blunts mouse angiotensin II hypertrophy but worsens fibrosis.

SPARK: Bayesian structure learning of enhancer-based gene regulatory networks from single-cell multiomics data and prior knowledge

SPARK reconstructs enhancer-based gene regulatory networks using single-cell multiomics data and prior knowledge, revealing regulatory links associated with immune disease GWAS variants.

Prediction transfer does not imply reliability transfer in single-cell foundation models

The paper investigates reliability transfer in single-cell foundation models across biological contexts and finds it varies independently from prediction transfer.

A unique intestinal epithelial cell that expresses canonical lymphoid genes

The paper identifies and characterizes a novel intestinal epithelial cell type that co-expresses epithelial and lymphoid genes, distinct from known cell types.

RFind-sc maps single cells onto biological axes defined by external gene signatures

RFind-sc maps single cells onto biological axes defined by external gene signatures, revealing cell states and candidate genes for stress responses.

Disrupted glial-mediated synaptic refinement in Fragile X syndrome

This study identifies impaired glial-mediated synaptic refinement in FXS model mice, showing enhanced astrocyte-microglia signaling and synaptic over-engulfment as key features.

Effector-primed TCF1+ CD8+ T cells elicited by a networked epitope vaccine stratify protection against SHIV acquisition

This study identifies an effector-primed TCF1+ CD8+ T cell state linked to delayed SHIV acquisition and reduced viral load in vaccinated non-human primates.

Regulatory architecture tunes gene expression noise in the plant heat shock response

This study shows that the plant heat shock regulatory network controls both the magnitude and distribution of stress-responsive gene expression across cells.

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.

Large-scale integrated single-cell analysis reveals molecular subtypes and microenvironmental remodeling in cutaneous T cell lymphoma

This study integrates a large scRNA-seq dataset of CTCL to identify molecular subtypes and microenvironmental changes with clinical relevance.

Conserved Brain-Associated CD8+ T Cell Programs and Their Regulation by the Brain Microenvironment

This study identifies conserved functional features of brain-associated CD8+ T cells in mice and marmosets and shows how brain signals regulate their effector programs.

CDKL5 deficiency alters cell subtype-specific molecular programmes and intercellular signalling in the mouse hippocampus

This study uses snRNA-seq to analyze gene expression changes in the hippocampus of CDKL5-deficient mice, identifying cell-type-specific transcriptional alterations and intercellular signaling changes.

An integrative cardio-informatics approach identifies positionally conserved ancestors of human lncRNA genes transcribed across vertebrate hearts

The paper identifies conserved genomic positions of human heart-related lncRNA genes across vertebrates using integrative analysis and a neural network tool.

TMEM55B downregulation promotes neurodegeneration in Alzheimer disease models.

The paper shows TMEM55B downregulation contributes to neurodegeneration in Alzheimer's disease models by impairing lysosomal transport and autophagy.

Dosage-dependent disruption of corticofugal neuron development by Fezf2 loss

This study quantifies the cell-type-specific and temporal transcriptional effects of Fezf2 dosage loss in mouse cortical development using single-cell RNA-seq and ATAC-seq data.

A knowledge graph-guided framework for multitask single-cell analysis

scKNIFE integrates gene expression with functional annotations to identify tumor programs and treatment-related functional variation in breast cancer.

Integrative reanalysis of public intracellular and vaccine-challenge transcriptomes, informed by single-cell and metabolomic atlases, refines antigen prioritisation for next-generation veterinary Brucella vaccines

The paper reanalyzes public transcriptomic and metabolomic data to prioritize antigens for improved Brucella vaccines by integrating single-cell and metabolomic atlases.

Single-cell analysis of West Nile virus infection in brain organoids identified a serine synthesis enzyme as a determinant of viral neural tropism and a druggable antiviral target

This study uses human cerebral organoids to identify PHGDH as a key metabolic factor enabling WNV infection and a potential drug target.