Understanding biology in space: platforms, tools, and databases for spatial transcriptomics
Peer-Reviewed Publication
Updates every hour. Last Updated: 3-Jun-2026 21:15 ET (4-Jun-2026 01:15 GMT/UTC)
Recently, the research team led by Prof. Youqiong Ye at the Shanghai Institute of Immunology published a comprehensive review entitled “Mapping Biology in Space: From Spatial Transcriptomics Platforms to Analytical Tools and Databases” in Science Bulletin.The review summarizes the key challenges currently facing the field of spatial transcriptomics and outlines future directions for its development. In addition, the authors developed SpatialToolDB (https://www.spatialtooldb.yelab.site/), a systematically curated, classified, and continuously updated database that currently catalogs 77 spatial transcriptomics technologies and 594 spatial transcriptomics analysis tools.By integrating the existing analytical tool ecosystem and providing an interactive resource portal, this review and SpatialToolDB offer a data-driven foundation to support researchers in selecting appropriate spatial transcriptomics platforms and analytical methods across diverse biological and translational research contexts.
Biodiversity is changing across the planet, yet governments still lack the robust, consistent data needed to track these changes and guide effective conservation. Now, a new study led by the University of Amsterdam (UvA), the German Centre for Integrative Biodiversity Research (iDiv), and the Martin Luther University Halle-Wittenberg (MLU), proposes a comprehensive roadmap to build a modern, integrated Biodiversity Observation Network (BON) for Europe – one that could become a global model for biodiversity monitoring in the 21st century. The study has been published in the journal Nature Reviews Biodiversity.
Wide-field quantum sensing with fluorescent nanodiamonds (FNDs) in biological systems offers significant potential for understanding intracellular dynamics at the nanoscale.
We describe the statistical characteristics of optical speckle patterns formed by illuminating biological tissues, commonly called biospeckles. The predominant techniques used to gather information from the movement of speckle patterns are detailed.
Cancer remains a leading cause of death worldwide, with early and accurate diagnosis being paramount for effective treatment. However, traditional diagnostic methods like biopsies are invasive and carry risks, while non-invasive approaches often struggle to identify reliable biomarkers due to tumor heterogeneity and the complexity of biological data. Integrating information across different molecular layers—genomics, transcriptomics, proteomics, and metabolomics—holds promise but is technically challenging, particularly in capturing the dynamic metabolic state of tumors.
A collaborative team led by Bing Li from Shanghai Jiao Tong University School of Medicine published an article titled "BCL7A’s arginine anchor links nucleosome recognition to chromatin remodeling and diffuse large B-cell lymphoma tumor suppression" in Protein & Cell. This study demonstrates that the conserved arginine anchor within the N-terminal α-helix of BCL7A is crucial for its function across all genomic contexts. This anchor acts as a key molecular switch connecting nucleosome binding to chromatin remodeling and tumor suppression, positioning it as a potential therapeutic target for DLBCL.
Radiotherapy (RT) is one of the most widely used cancer treatment modalities, applied in over half of all patients with cancer. In clinical oncology, positron emission tomography (PET) with 18F-fluorodeoxyglucose (18F-FDG) is widely used to noninvasively monitor tumor glucose metabolism and evaluate therapeutic responses, including those to RT. However, transient increases in 18F-FDG uptake—referred to as post-RT “metabolic flares”—are frequently observed in responding tumors and have traditionally been attributed to localized inflammatory reactions. Whether these flares reflect underlying immune cell dynamics, particularly tumor-infiltrating T cells, has remained poorly understood.
Scientists have deciphered a long-standing paradox of the histone variant H3.3: how the same protein can mark both active and silenced regions of the genome. The key lies in a specific combination of modifications—phosphorylation at serine 31 (Ser31p) together with trimethylation at lysine 27 (K27me3). This dual “code” on H3.3 acts as a master switch, recruiting protein complexes that establish H3K9me3-marked heterochromatin, a repressive chromatin state. The study demonstrates that this “H3.3–CBX7–KAP1–H3K9me3” pathway is essential for silencing repetitive DNA elements and, crucially, for the epigenetic silencing of one X chromosome in females, a process vital for mammalian development.