Spatial transcriptomics (ST) maps gene expression within tissue architecture, surpassing scRNA-seq by preserving context. This review evaluates 77 platforms—from high-resolution imaging to whole-transcriptome sequencing—and 600 computational tools for analysis and multi-omics integration.

References:

• Zi-Zhen Guo, Renyan Wu, Weixiang Li, Keyu Yang, Xuexiang Ying, Hamid Alinejad-Rokny, Youqiong Ye. Mapping biology in space: from spatial transcriptomics platforms to analytical tools and databases. Science Bulletin. 2026.

Researchers used MERFISH and scRNA-seq to map the neuroimmune landscape of the mouse brain. They found that maternal immune activation and microbiome depletion disrupt fetal neurogenesis and chemokine pathways, leading to sex-specific behavioral deficits in offspring.

References:

• Kukreja B, Jeon S, Cao W, et al. Spatial transcriptomics of the developing mouse brain immune landscape reveals effects of maternal immune activation and microbiome depletion[J]. Nature Neuroscience, 2026: 1-14.

The EpiAgent web platform provides tools for cell type annotation, data mapping, and UMAP visualizations. Built on a Linux Nginx server using PHP and MySQL, it features a JavaScript-based interface for processing H5ad files and rendering complex biological charts.

References:

• Chen X, Gao Z, Li K, et al. Human-scATAC-Corpus: a comprehensive database of scATAC-seq data[J]. Nucleic Acids Research, 2026, 54(D1): D175-D183.

Researchers developed CMAP, a "divide-and-conquer" algorithm that maps single-cell RNA-seq data to precise spatial locations. By integrating transcriptomics with spatial context, it overcomes low gene recovery to reveal cellular heterogeneity and microenvironment interactions.

References:

• Ke, J., Xu, J., Liu, J. et al. High-resolution mapping of single cells in spatial context. Nat Commun 16, 6533 (2025). doi.org

HistoCell is a weakly-supervised AI framework that infers single-nucleus cell profiles from histology images. It integrates morphological and topological features to predict cell types and states, aiding in disease diagnosis, prognosis, and identifying spatial biomarkers.

References:

• Zhang P, Gao C, Zhang Z, et al. Systematic inference of super-resolution cell spatial profiles from histology images[J]. Nature Communications, 2025, 16(1): 1838.

River is an interpretable deep learning framework designed to identify genes with differential spatial expression patterns (DSEP) across multiple conditions. It utilizes a two-branch architecture and attribution methods to outperform existing tools in scalability and accuracy.

References:

• Cui Y, Yuan Z. Prioritizing perturbation-responsive gene patterns using interpretable deep learning[J]. Nature Communications, 2025, 16(1): 6095.

Precise DNA replication depends on the S-phase checkpoint and PCNA dynamics. Research shows PAF15 acts as a "toolbelt" anchor, coordinating Okazaki fragment processing by preventing steric clashes between enzymes. ATR inhibition causes excessive origin firing, exhausting resources.

References:

• Chhetri G, Badugu S B, Petriman N A, et al. PAF15–PCNA exhaustion governs the strand-specific control of DNA replication[J]. Nature, 2026: 1-12.

Researchers developed rhesus macaque placental organoids to model primate pregnancy. Using RNA sequencing, they found these models mirror in vivo development. Comparison with human organoids reveals shared syncytiotrophoblast programs but divergent extravillous trophoblast signatures.

References:

• Comparative analysis of rhesus macaque and human placental organoids highlights evolutionary differences in placentationCaldwell, Allyson et al.Developmental Cell, Volume 0, Issue 0

Researchers analyzed the plasma proteome of continental Africans to understand type 2 diabetes (T2D). They identified 399 pQTLs, many unique to African ancestry. Results highlight 18 proteins, including ACE and SIRPα, as causal drivers or therapeutic targets for T2D.

References:

• Soremekun O, Park Y C, Tutino M, et al. Linking the plasma proteome to genetics in individuals from continental Africa provides insights into type 2 diabetes pathogenesis[J]. Nature Genetics, 2026: 1-8.

This research explores the specialized architecture and defensive utility of umbrella toxins, which are large protein complexes used by Streptomyces bacteria to inhibit competitors. The study reveals that these toxins employ a two-tiered molecular bet-hedging strategy to navigate the vast structural diversity of target cell surfaces. Utilizing cryo-electron microscopy, the authors show how the toxin scaffold interacts with teichuronic acid polymers to form helical filaments. Genomic analysis further demonstrates that these bacteria maintain an extensive repertoire of lectin domains to recognize varying carbohydrate signatures on rival microbes. This complex system allows the bacteria to effectively target multiple species while simultaneously evading viral predation through surface modification. Overall, the findings explain how specific protein-glycan interactions facilitate interbacterial antagonism and survival in diverse soil environments.

References:

• Zhao Q, Vlach J, Park Y J, et al. The unique architecture of umbrella toxins permits a two-tiered molecular bet-hedging strategy for interbacterial antagonism[J]. Cell, 2025.