Investigating Spatial Dynamics in Spatial Omics Data with StarTrail
Year: 2026
Type: article
Abstract: Spatial omics technologies revolutionize our view of biological processes within tissues. However, existing methods fail to capture localized, sharp changes characteristic of critical events (e.g., tumor development). Here, we present StarTrail, a novel gradient based method that powerfully defines rapidly changing regions and detects “cliff genes”, genes exhibiting drastic expression changes at highly localized or disjoint boundaries. StarTrail, the first to leverage spatial gradients for spatial omics data, also quantifies directional dynamics. Across multiple datasets, StarTrail accurately delineates boundaries (e.g., brain layers, tumor-immune boundaries), and detects cliff genes that may regulate molecular crosstalk at these biologically relevant boundaries but are missed by existing methods. StarTrail, filling important gaps in current literature, enables deeper insights into tissue spatial architecture. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
Authors: Jiawen Chen, Caiwei Xiong, Quan Sun, Yutong Song, Geoffery W. Wang, Gaorav P. Gupta, Aritra Halder, Yun Li, Didong Li
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: U.S. Department of Defense, National Institute on Aging, National Human Genome Research Institute, National Cancer Institute, National Institute of Environmental Health Sciences, U.S. National Library of Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development
Awards: Clinical Translational Research Center for Neurodevelopmental Disorders, Robust Computational and Data Analytic Tools for In-depth Understanding Postoperative Pain Mechanism with Enhanced Pain Management and Clinical Decision Making, UNC Center for Environmental Health and Susceptibility, SPORE in Breast Cancer, The UNC Chapel Hill Superfund Research Program (UNC-SRP), Study of Selective Cell and System Vulnerability in Alzheimer's Disease, Polygenic risk scores for cardiometabolic disorders: the role of blood cells immune response and evolutionary adaptation
OpenAlex ID: W4396830627