#SingleCell preprints

CATFISHR: integration of transcriptome and inferred CNV profiles for comprehensive malignant cell identification #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.22.760906v1

Stimulation strategy matters: A B-cell focused single-cell transcriptomic study on in vitro stimulated immune cells #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.22.760934v1

ProtCell: a foundation model for single-cell proteomics #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.22.760932v1

Vascular specification from diversified mesoderm culminates in endothelial convergence #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.25.761646v1

Identification of gene kinetics patterns improves RNA velocity and cell fate prediction using JuloVelo #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.24.761531v1

Regularized logistic regression-based gene selection for functional analysis of heterogeneous scRNA-seq macrophage populations in muscle aging and regeneration. #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.25.761682v1

Evaluation design shapes estimates of cross-donor generalization in single-cell classification of cell-type #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.26.761949v1

BLOOM: Biologically Informed Flow Matching for Transcriptomic Virtual Embryo Modeling #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.26.761895v1

Matrix stiffness shapes immunometabolic states and response to PD-1 blockade in gastric cancer #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.25.761609v1

Quantifying epigenetic reprogramming and cellular plasticity in preneoplastic lesions reveals dedifferentiation as a key precancer hallmark #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.25.761640v1

CEP-IP with CMRF in SEA-AD Microglia: A Mitochondrial Co-expression Module Linked to Cognition #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.22.761284v1

FluxSprout: Single-cell metabolic modeling of vascular sprouting in zebrafish #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.24.761567v1

Lost and found: beer belly is a novel, ancient regulator of animal development #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.24.761492v1

Compartment-specific transcriptional programs of the gravid human myometrium underlie labor and uterine atony #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-11225136/latest

Palmitoylation-associated molecular states implicate FNDC3B in tumor progression and macrophage-associated microenvironmental remodeling in pancreatic cancer #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-11101218/latest

An Ensemble Deep Learning Framework for Single-Cell Phenotypic Profiling of Escherichia coli under Antibiotic Stress #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-11132510/latest

Integrated single cell and bulk transcriptomic analysis reveals disulfidptosis related malignant epithelial states associated with prognosis in gastric cancer #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-10992120/latest

The ACVR1C-GAS6 Antagonistic Axis Drives Metabolic Decompensation and Liver Fibrosis in MASLD: Mechanistic Insights from Multi-omics Analyses #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-10938931/latest

Development of an Accelerated Stress Test Protocol for Rapid Catalyst Degradation Evaluation in Polymer Electrolyte Membrane Fuel Cell Stacks #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-11273460/latest

Shared clones make random cell halves look reproducible in pooled screens #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2610.32962

OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2605.06728

Escaping cells dilute CRISPR screen responses unequally across cell types #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2610.35508

Multiscale Topology-Regulated Nonlinear Dynamics for Protein B-Factor Prediction and Single-Cell Type Classification #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2610.33727

Canonical residual physics-informed neural networks and algorithmic perturbation landscapes map cell-fate transitions in longitudinal H3K27M glioma #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2610.33000

An Exploratory Multiome Analysis of a BCG-Associated HSPC Signature: Trained-Immunity Marker in Blood and an Adverse Prognostic Association in Tumour #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2610.32999

Active Learning of Conditional Generative Models via the Transport Neural Tangent Kernel #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2610.35652

Rethinking Microscopy Generation: Co-Designed Diffusion for Biologically Interpretable Single-Cell Synthesis #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2610.33398

SPARK: Bayesian structure learning of enhancer-based gene regulatory networks from single-cell multiomics data and prior knowledge #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.22.761021v1

RFind-sc maps single cells onto biological axes defined by external gene signatures #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.21.759514v1

19h

TCF21 loss identifies a conserved inflammation-associated fibroblast state across Crohn's disease and ulcerative colitis #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.21.760764v1

19h

Cornealia: automated collective order analysis reveals density-dependent reorganization of donor corneal endothelium #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.21.760745v1

Single-cell landscape of the mouse medial vestibular nucleus after unilateral vestibular loss and the effect of sequencing depth #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-11273549/latest

Spatial niche organization shapes clinical heterogeneity in Ewing sarcoma #SingleCell 🧪🧬🖥️ https://www.medrxiv.org/content/10.64898/2026.10.24.26366384v1

Exhaustive white blood cell extraction and profiling across whole-slide images of blood and bone marrow smears #SingleCell 🧪🧬🖥️ https://www.medrxiv.org/content/10.64898/2026.10.23.26366335v1

Prediction transfer does not imply reliability transfer in single-cell foundation models #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.21.760716v1

Aquaporin-4 Regulates Edema, Sustains Astrocyte Differentiation, and Constrains Immunosuppressive Remodeling in Glioblastoma #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.23.761345v1

Decoding & manipulating human intercellular signaling via scalable cell-free protein synthesis #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.24.761585v1

NK Cell Activation as an Immune Mechanism in Depression: Insights from Single-Cell Multi-Omics #SingleCell 🧪🧬🖥️ https://www.medrxiv.org/content/10.64898/2026.10.23.26366302v1

SC-MAPS: Image-based deep learning for bacterial identification and antibiotic-susceptibility testing #SingleCell 🧪🧬🖥️ https://www.medrxiv.org/content/10.64898/2026.10.23.26366325v1

Multi-scale analysis of the HIF1A hypoxia-inflammation axis in severe COVID-19 #SingleCell 🧪🧬🖥️ https://www.medrxiv.org/content/10.64898/2026.10.23.26366304v1

Normal mucosal fibroblast remodeling during carcinogenesis promotes initial submucosal invasion of early-stage colorectal carcinoma #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-10972596/latest

Dobutamine suppresses YAP1 signaling to disrupt tumor-stroma crosstalk in hepatocellular carcinoma #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-11112779/latest

Single-cell references can reverse, inflate and blur the associations inferred from bulk deconvolution #SingleCell 🧪🧬🖥️ https://www.researchsquare.com/article/rs-11472895/latest

GeneSpeak-FP: Target and Compound Retrieval from Observed Cell-Level Perturbation Signatures #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2607.17671

Shared clones make random cell halves look reproducible in pooled screens #SingleCell 🧪🧬🖥️ https://arxiv.org/abs/2610.32962

ALHENA, an H&E encoder distilled from transcriptomic foundation models for multi-scale slide analysis #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.20.760439v1

Cardiomyocyte Identity Crisis Without Regenerative Re-entry: A Multi-Scale Atlas of Incomplete Dedifferentiation and Intercellular Communication Rewiring in the Infarcted Human Heart #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.20.760578v1

Effector-primed TCF1+ CD8+ T cells elicited by a networked epitope vaccine stratify protection against SHIV acquisition #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.20.760588v1

Uncoupling of STING Accumulation and Activation upon Chromosome-Derived Extrachromosomal Circular DNA Formation #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.23.761201v1