Research graph
References from Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity. Local targets link to admitted publications; unresolved targets remain external evidence.
Spatially resolved single-cell genomics and transcriptomics by imaging
10.1038/s41592-020-01037-8 · 2021 · External reference
Cellpose: a generalist algorithm for cellular segmentation
10.1038/s41592-020-01018-x · 2021 · External reference
Cell segmentation in imaging-based spatial transcriptomics
10.1038/s41587-021-01044-w · 2022 · External reference
RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing
10.1261/rna.074161.119 · 2020 · External reference
mRNA transport and local translation in neurons
10.1016/j.conb.2017.05.005 · 2017 · External reference
mRNA and circRNA mislocalization to synapses are key features of Alzheimer’s disease
10.1371/journal.pgen.1011359 · 2024 · External reference
STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping
10.1038/s41467-023-43915-7 · 2023 · External reference
SEraster: A rasterization preprocessing framework for scalable spatial omics data analysis
10.1093/bioinformatics/btae412 · 2024 · External reference
Towards a general-purpose foundation model for computational pathology
10.1038/s41591-024-02857-3 · 2024 · External reference
Transformer-based unsupervised contrastive learning for histopathological image classification
10.1016/j.media.2022.102559 · 2022 · External reference
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
10.1038/nbt.2859 · 2014 · External reference
A comparison of single-cell trajectory inference methods
10.1038/s41587-019-0071-9 · 2019 · External reference
Spatial organization of the somatosensory cortex revealed by osmFISH
10.1038/s41592-018-0175-z · 2018 · External reference
Highly multiplexed spatial transcriptomics in bacteria
10.1126/science.adr0932 · 2025 · External reference
Unresolved reference
2024 · External reference
σ28-dependent small RNA regulation of flagella biosynthesis
10.7554/elife.87151 · 2023 · External reference
RNA localization in Bacteria
2018 · External reference
Spatiotemporal organization of the E. coli transcriptome: Translation independence and engagement in regulation
10.1016/j.molcel.2019.08.013 · 2019 · External reference
The contribution of mRNA targeting to spatial protein localization in bacteria
10.1111/febs.17054 · 2024 · External reference
Translation inhibition of the Salmonella fliC gene by the fliC 5′ untranslated region, fliC coding sequences, and FlgM
10.1128/jb.01552-05 · 2006 · External reference
10.1101/2025.08.25.672145
10.1101/2025.08.25.672145 · External reference
Evidence of off-target probe binding in the 10x Genomics Xenium v1 human breast gene expression panel compromises accuracy of spatial transcriptomic profiling
2025 · External reference
Deconvolving organogenesis in space and time via spatial transcriptomics in thick tissues
2024 · External reference
Three-dimensional single-cell transcriptome imaging of thick tissues
10.7554/elife.90029 · 2024 · External reference
Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks
10.1038/s41592-025-02867-0 · 2025 · External reference
Four-dimensional molecular mapping from a spatial snapshot reveals the dynamics of hair follicle organogenesis
10.1016/j.cell.2026.06.014 · 2026 · External reference
Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples
10.1038/s41467-025-63414-1 · 2025 · External reference
Comparative analysis of multiplexed in situ gene expression profiling technologies
2024 · External reference
10.1109/iccv.2017.74
10.1109/iccv.2017.74 · External reference
Unresolved reference
2018 · External reference
Statistical analysis supports pervasive RNA subcellular localization and alternative 3’ UTR regulation
10.7554/elife.87517 · 2024 · External reference
Bento: a toolkit for subcellular analysis of spatial transcriptomics data
10.1186/s13059-024-03217-7 · 2024 · External reference
ELLA: Modeling subcellular spatial variation of gene expression within cells in high-resolution spatial transcriptomics
10.1038/s41467-025-64867-0 · 2025 · External reference
Data augmentation for medical imaging: A systematic literature review
10.1016/j.compbiomed.2022.106391 · 2023 · External reference
Unresolved reference
2020 · External reference
Rotation equivariant and invariant neural networks for microscopy image analysis
10.1093/bioinformatics/btz353 · 2019 · External reference
Unresolved reference
2024 · External reference
Graph neural networks learn emergent tissue properties from spatial molecular profiles
10.1038/s41467-025-63758-8 · 2025 · External reference
Modeling intercellular communication in tissues using spatial graphs of cells
10.1038/s41587-022-01467-z · 2023 · External reference
Graph deep learning enabled spatial domains identification for spatial transcriptomics
2023 · External reference
Graph contrastive learning of subcellular-resolution spatial transcriptomics improves cell type annotation and reveals critical molecular pathways
2025 · External reference
A point cloud segmentation framework for image-based spatial transcriptomics
10.1038/s42003-024-06480-3 · 2024 · External reference
Unresolved reference
2023 · External reference
Unresolved reference
2025 · External reference
