Identifiable inverse optimal transport for single-cell state transitions #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.01.756056v1

Differentiation–Proliferation Imbalance and Therapy- Associated State Remodeling in MYCN-Non-Amplified Neuroblastoma: Multi-Cohort and Paired Single-Cell Analyses #SingleCell 🧪🧬🖥️
https://www.researchsquare.com/article/rs-11074318/latest

ECM-CAFs Induce Myeloid M2 Polarization via the HLA- DRA-CD4 Axis and Contribute to Poor Prognosis in Esophageal Squamous Cell Carcinoma #SingleCell 🧪🧬🖥️
https://www.researchsquare.com/article/rs-10979345/latest

Single-cell entropy as a selectable and inducible marker of stem-cell youth: a multi-track technical architecture for producing young autologous hematopoietic stem cells #SingleCell 🧪🧬🖥️
https://www.researchsquare.com/article/rs-11245878/latest

Passive Cell-Flux Partitioning Enables Single-Cell-Constrained Impedance Sensing From High-Density Microbial Cultures #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.09.30.755765v1

📢 Paper Alert! Grateful to have been involved in this amazing work by @thelazarlab.bsky.social and SzilviaJuhasz labs, presenting a framework for dissecting pathogen-host-drug interactions. #Pathogen #Virulence #SingleCell #DeepLearning
Check it at: shorturl.at/LQUFP
🧵👇

Identifiable inverse optimal transport for single-cell state transitions #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.01.756056v1

Conservation of gene co-expression networks and neuropsychiatric-neurological disease gene programs between mouse and human frontal cortex at single-cell resolution #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.05.756860v1

NucLogic: Logic-based geometric 3D nuclear segmentation for fast and robust analysis of challenging biological imaging data #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.05.756154v1

RNA and protein are not interchangeable in single-cell spatial multi-omics #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.05.756660v1

In situ identification of pre-hematopoietic stem cells and their niche #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.05.756028v1

Mechanophenotype of synovial fibroblasts correlates with patients' pathotypes and treatment response in Rheumatoid Arthritis #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.01.755901v1

KRAS-driven metabolic reprogramming of enhanced MFSD2A-mediated lysophosphatidylcholine scavenging promotes survival and progression of pancreatic ductal adenocarcinoma #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.05.756824v1

A new preprint introduces two standardized, end-to-end pipelines for single-cell RNA-seq and imaging-based #spatialtranscriptomics analysis.

EISCA supports droplet- and plate-based scRNA-seq, while EISTA is tailored for high-resolution spatial platforms.

#SingleCell #RNAseq

Our preprint is out! 🎉 methylTFR quantifies transcription factor activity from DNA methylation, for each sample or cell, with GC bias correction.

📄 www.biorxiv.org/content/10.6...
#SingleCell #DNAmethylation #Bioconductor #Epigenomics #Bioinformatics
🧵👇

Single-cell transcriptomics-guided inhalable neutrophil-mimetic nanoplatform restores NET homeostasis through a “block-and-clear” strategy in acute lung injury #SingleCell 🧪🧬🖥️
https://www.researchsquare.com/article/rs-11059111/latest

UBE2D3-mediated ubiquitination of ULK1 drives pathological mitophagy and cuproptosis in myocardial infarction #SingleCell 🧪🧬🖥️
https://www.researchsquare.com/article/rs-10885862/latest

Circular Data Analysis for Spatial Omics #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.09.29.755467v1

Propagating Elevation-Map Uncertainty Through the Contact Maximum in Closed Form #SingleCell 🧪🧬🖥️
https://arxiv.org/abs/2610.06103

TempoBridge: Source-Conditioned Flow Matching with Optimal Transport Couplings for Single-Cell Population Transitions #SingleCell 🧪🧬🖥️
https://arxiv.org/abs/2610.04945