AI model predicts spatial gene expression from histopathology slides in breast cancer, identifying subgroups with distinct survival outcomes and improving treatment predictions.
- Open access
- 17 cites
Single-cell and spatial transcriptomics
Moving in Cell, Genome Research, Bioinformatics, eLife, GigaScience, Nature, Nature Immunology.
- Moved this week
- 10
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Moved this week
Universal cell embedding (UCE) creates a single biological latent space that accurately represents 36 million cells across eight species, over 1,000 cell types, and diverse tissues.
- Open access
- 14 cites
Distinct pediatric intestinal cell states at diagnosis predict Crohn's disease severity and response to anti-TNF therapy, with treatment shifting toward a more refractory adult-like profile.
- Open access
- 5 cites
scBaseCount is the largest public repository of single-cell gene expression data, containing over 502 million cells from 27 organisms and 75 tissues, standardized through AI automation.
- 1 opens in JClub
- Open access
Tahoe-100M maps 100 million single-cell transcriptomes across 50 cancer cell lines under 1,100 drug conditions, revealing detailed drug-induced molecular phenotypes.
- 1 opens in JClub
- Open access
A novel immunomodulatory CAF population expressing CHL1 promotes Treg recruitment and tumor immune suppression in lung cancer.
- 1 opens in JClub
- Open access
FIERCE accurately reconstructs cellular differentiation trajectories without prior assumptions, outperforming existing methods in complex systems.
- 1 opens in JClub
- Open access
iPSC-derived neurons predominantly retain fetal-like chromatin architecture, with 96 high-coverage contact maps revealing strong compartmentalization and developmental gene enrichment.
Moderated experimental designs can effectively balance batch-effect reduction and cell loss, with cell loss doubling for each additional hashtag used in single-cell experiments.
Latest in Single-cell and spatial transcriptomics
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Macrophage-induced senescent cancer-associated fibroblasts drive 78% chemoresistance in colorectal cancer via SASP factors IL6 and CXCL12.
Persistent expansion of alloreactive T cell clones and phenotypic plasticity drive severe graft-versus-host disease in human transplant recipients.
A spatial atlas of muscle-invasive bladder cancer uncovers lineage-specific vulnerabilities and immune structures across 22 tumors.
- Open access
CAR T cell therapy targeting CD19 can induce long-term remission of intestinal inflammation in ulcerative colitis, revealing a new therapeutic avenue for IBD.
- 1 cites
Deep learning genetic perturbation models outperform uninformative baselines when evaluated with calibrated metrics across multiple datasets.
- Open access
Multimodal lineage tracing combined with advanced computational methods enables detailed reconstruction of cellular development with high accuracy and resolution.
Multi-sample spatial transcriptomics reveals distinct regional fibrotic programs and cellular niches in human IPF, with 10X Xenium validation confirming key findings.
- Open access
- 20 cites
Senescent-like neutrophils expressing BHLHE40 promote immunosuppressive and angiogenic niches in colorectal cancer liver metastasis, correlating with poor prognosis.
Single-cell genomics reveals diverse pathogenic immune cell subsets in rheumatoid arthritis, paving the way for targeted therapies.
3D multi-omics tumour atlases reveal complex cellular interactions and evolution, offering new insights into tumor biology and potential clinical applications.
BatchVaria reveals that subtype-protected ComBat maintains nearly unchanged subtype contributions after correction, unlike naive ComBat which reduces them by 4.23%.
- Open access
Fibro-inflammatory remodeling in bone marrow is a defining feature of clonal hematopoiesis of indeterminate potential, with a significant expansion of fibroblasts and extracellular matrix changes.
- Open access
- 1 cites
ArchMap enables accessible, no-code reference-based analysis of single-cell datasets, democratizing the use of comprehensive atlases for researchers worldwide.
- Open access
CytoVI enables comprehensive analysis of antibody-based single-cell data, accurately modeling 350 proteins and revealing disease-related immune cell states.
- Open access
SpaCEy, an explainable graph neural network, predicts clinical outcomes from spatial proteomics data with 100% accuracy in identifying key tissue patterns.
- Open access
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Moving areas, week to 3 Oct 2026
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