Research map: SRT-Server: powering the analysis of spatial transcriptomic data

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  1. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles · Aravind N. Subramanian · 2005 · 58106 citations · Cited by this paper
  2. Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets · Jasmine Plummer · 2025 · 27 citations · Cites this paper
  3. Multifeature sequencing-based liquid biopsy for cancer diagnosis and monitoring · Mariano A. Molina · 2026 · 1 citation · Related
  4. KEGG: Kyoto Encyclopedia of Genes and Genomes · Minoru I. Kanehisa · 2000 · 40352 citations · Cited by this paper
  5. STExplore: An Integrated Online Platform for Comprehensive Analysis and Visualization of Spatial Transcriptomics Data · Yongtian Wang · 2025 · 10 citations · Cites this paper
  6. Cumulative cgMLST provides increased discrimination of nested phylogenetic groups · Armen Ovsepian · 2026 · 1 citation · Related
  7. KEGG: Kyoto Encyclopedia of Genes and Genomes · Hiroyuki Ogata · 1999 · 32519 citations · Cited by this paper
  8. ProteoNexus: an integrative database to characterize genetic architecture, estimate mediation effects, and construct and evaluate prediction models of the plasma proteome · Kaixin Shao · 2025 · 9 citations · Cites this paper
  9. Transcriptome signatures for the identification of bevacizumab responders in ovarian cancer · 2026 · Related
  10. Comprehensive Integration of Single-Cell Data · Tim Stuart · 2019 · 17513 citations · Cited by this paper
  11. spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis · Oscar E. Ospina · 2024 · 6 citations · Cites this paper
  12. Circulating tumor DNA precision oncology enables effective and sensitive molecular diagnostics and actionable target detection in pediatric solid tumors - the INFORM experience · 2026 · Related
  13. Integrated analysis of multimodal single-cell data · Yuhan Hao · 2021 · 16919 citations · Cited by this paper
  14. DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments · Vladyslav Honcharuk · 2025 · 6 citations · Cites this paper
  15. Integrative stratification of response to immunotherapy using host and microbial signatures in patients with advanced non-small cell lung cancer · 2026 · Related
  16. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data · Tianzhi Wu · 2021 · 13207 citations · Cited by this paper
  17. PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions · Lan Shui · 2025 · 3 citations · Cites this paper
  18. Cell type-specific contextualisation of the human phenome: towards the systematic treatment of all rare diseases · 2026 · Related
  19. Fast, sensitive and accurate integration of single-cell data with Harmony · Ilya Korsunsky · 2019 · 11385 citations · Cited by this paper
  20. transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics · Weiqiang Lin · 2026 · 2 citations · Cites this paper
  21. Long-read transcriptome sequencing and Drosophila-based functional validation reveal novel gene fusions in fusion panel-negative gliomas · 2026 · Related
  22. Inference and analysis of cell-cell communication using CellChat · Suoqin Jin · 2021 · 8914 citations · Cited by this paper
  23. spatialGE: A user-friendly web application to democratize spatial transcriptomics analysis · Oscar E. Ospina · 2024 · 1 citation · Cites this paper
  24. Comprehensive genomic characterization of extraintestinal pathogenic Escherichia coli isolated from neonates: multiple center insights into virulence, resistance, and transmission dynamics · 2026 · Related
  25. The Gene Ontology Resource: 20 years and still GOing strong · Consortium, The Gene Ontology · 2018 · 5267 citations · Cited by this paper
  26. PoweREST: Statistical Power Estimation for Spatial Transcriptomics Experiments to Detect Differentially Expressed Genes Between Two Conditions · Lan Shui · 2024 · 1 citation · Cites this paper
  27. Infiltrating monocyte-derived macrophages does not survive long term in stroke brain despite their dominance in the acute ischemic core and myeloid derived IGF-1 play dichotomous roles in stroke recovery · 2026 · Related
  28. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression · Christoph Hafemeister · 2019 · 5124 citations · Cited by this paper
  29. Evidence to shared genetic correlation of ischemic stroke and intracerebral hemorrhage and cardiovascular related traits · Wei He · 2025 · 1 citation · Cites this paper
  30. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics · Patrik L. Ståhl · 2016 · 4158 citations · Cited by this paper
  31. Leveraging expression quantitative trait loci information in single-cell resolution to identify cell-specific genes for Basal cell carcinoma · Min Du · 2026 · Cites this paper
  32. A framework for advancing our understanding of cancer-associated fibroblasts · Erik A. Sahai · 2020 · 3981 citations · Cited by this paper
  33. Leveraging expression quantitative trait loci information in single-cell resolution to identify cell-specific genes for gestational diabetes · Wenyan Zhu · 2026 · Cites this paper
  34. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics · Kelly Street · 2018 · 3563 citations · Cited by this paper
  35. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris · Overall coordination · 2018 · 3321 citations · Cited by this paper
  36. A single-cell and spatially resolved atlas of human breast cancers · Sunny Z. Wu · 2021 · 1929 citations · Cited by this paper
  37. DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis · Guangchuang Yu · 2014 · 1405 citations · Cited by this paper
  38. Cell2location maps fine-grained cell types in spatial transcriptomics · Vitalii Kleshchevnikov · 2022 · 1364 citations · Cited by this paper
  39. Squidpy: a scalable framework for spatial omics analysis · Giovanni Palla · 2022 · 1221 citations · Cited by this paper

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