Giotto: a toolbox for integrative analysis and visualization of spatial expression data

• Next-generation kidney tissue analysis — spatial omics and digital pathology

  2026 Nature Reviews Nephrology review Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics

  1

  citations
• Advancing Cardiovascular Research With Single-Cell and Spatial Transcriptomics

  2026 Circulation Research article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics

  12

  citations
• GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data

  2025 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directions

  2025 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  39

  citations
• STMiner: Gene-centric spatial transcriptomics for deciphering tumor tissues

  2025 Cell Genomics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  10

  citations
• spacedeconv: deconvolution of tissue architecture from spatial transcriptomics

  2024 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  4

  citations
• GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data

  2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases

  2024 Genome Medicine article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  106

  citations
• SpaceWalker enables interactive gradient exploration for spatial transcriptomics data

  2023 Cell Reports Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  4

  citations
• Best practices for single-cell analysis across modalities

  2023 Nature Reviews Genetics review Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 7 patents

  1,043

  citations
• Explainable multiview framework for dissecting spatial relationships from highly multiplexed data

  2022 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  291

  citations
• Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data

  2021 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  10

  citations
• Cell-cell Communication Inference from Single-cell RNA-Seq Data: a Comparison of Methods and Resources

  2021 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  3

  citations
• Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data

  2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  23

  citations
• Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data

  2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  28

  citations

15 results