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Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis

https://doi.org/10.1101/265256
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Automatic single cell segmentation on highly multiplexed tissue images
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Improving the Accuracy and Efficiency of Partitioning Heritability into the Contributions of Genomic Regions
inferredcites →https://doi.org/10.1016/j.cell.2015.05.047openalex-snapshot
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
inferredcites →https://doi.org/10.1016/j.cell.2015.11.018openalex-snapshot
Control of Transcript Variability in Single Mammalian Cells
inferredcites →https://doi.org/10.1016/j.cell.2018.07.010openalex-snapshot
Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging
inferredcites →https://doi.org/10.1016/j.cels.2016.03.008openalex-snapshot
Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications
inferredcites →https://doi.org/10.1016/j.cels.2017.12.001openalex-snapshot
Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry
inferredcites →https://doi.org/10.1016/j.neuron.2017.05.008openalex-snapshot
seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus
inferredcites →https://doi.org/10.1016/s1040-8428(99)00034-7openalex-snapshot
Pathological prognostic factors in breast cancer
inferredcites →https://doi.org/10.1038/labinvest.2014.156openalex-snapshot
MALDI Imaging mass spectrometry: current frontiers and perspectives in pathology research and practice
inferredcites →https://doi.org/10.1038/nbt.3209openalex-snapshot
High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
inferredcites →https://doi.org/10.1038/ncomms9390openalex-snapshot
Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method
inferredcites →https://doi.org/10.1038/ng1180openalex-snapshot
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
inferredcites →https://doi.org/10.1038/nm.3488openalex-snapshot
Multiplexed ion beam imaging of human breast tumors
inferredcites →https://doi.org/10.1038/nmeth.2657openalex-snapshot
Image-based transcriptomics in thousands of single human cells at single-molecule resolution
inferredcites →https://doi.org/10.1038/nmeth.2869openalex-snapshot
Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry
inferredcites →https://doi.org/10.1038/nmeth.4391openalex-snapshot
histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data
inferredcites →https://doi.org/10.1038/nmeth.4636openalex-snapshot
SpatialDE: identification of spatially variable genes
inferredcites →https://doi.org/10.1073/pnas.0506580102openalex-snapshot
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
inferredcites →https://doi.org/10.1073/pnas.1300136110openalex-snapshot
Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue
inferredcites →https://doi.org/10.1073/pnas.1612826113openalex-snapshot
High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization
inferredcites →https://doi.org/10.1093/biomet/35.3-4.246openalex-snapshot
THE TRANSFORMATION OF POISSON, BINOMIAL AND NEGATIVE-BINOMIAL DATA
inferredcites →https://doi.org/10.1093/nar/gkt1102openalex-snapshot
The Reactome pathway knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkv1351openalex-snapshot
The Reactome pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkx1132openalex-snapshot
The Reactome Pathway Knowledgebase
inferredcites →https://doi.org/10.1101/003905openalex-snapshot
LIMIX: genetic analysis of multiple traits
inferredcites →https://doi.org/10.1109/isbi.2011.5872394openalex-snapshot
Ilastik: Interactive learning and segmentation toolkit
inferredcites →https://doi.org/10.1111/j.1365-2559.1991.tb00229.xopenalex-snapshot
pathological prognostic factors in breast cancer. I. The value of histological grade in breast cancer: experience from a large study with long‐term follow‐up
inferredcites →https://doi.org/10.1111/j.1469-1809.2010.00572.xopenalex-snapshot
Permutation and Parametric Bootstrap Tests for Gene-Gene and Gene-Environment Interactions
inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1111/jcmm.12408openalex-snapshot
The role of the cell–cell interactions in cancer progression
inferredcites →https://doi.org/10.1126/science.aaa6090openalex-snapshot
Spatially resolved, highly multiplexed RNA profiling in single cells
inferredcites →https://doi.org/10.1126/science.aaf2403openalex-snapshot
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
inferredcites →https://doi.org/10.1186/gb-2006-7-10-r100openalex-snapshot
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
inferredcites →https://doi.org/10.1186/s13059-017-1334-8openalex-snapshot
f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq
inferredcites →https://doi.org/10.1214/aoms/1177732360openalex-snapshot
The Large-Sample Distribution of the Likelihood Ratio for Testing Composite Hypotheses
inferredcites →https://doi.org/10.1371/journal.pgen.1006498openalex-snapshot
Genetic Variation in the Social Environment Contributes to Health and Disease
inferredcites →https://doi.org/10.1371/journal.pgen.1006693openalex-snapshot
Joint genetic analysis using variant sets reveals polygenic gene-context interactions
inferredcites →https://doi.org/10.5772/48435openalex-snapshot
Cell-Cell Interactions and Cross Talk Described in Normal and Disease Conditions: Morphological Approach
inferredcites →https://doi.org/10.7554/elife.31657openalex-snapshot
Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/cyto.a.24729openalex-snapshot
Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments
inferred← citeshttps://doi.org/10.1101/2020.03.27.001834openalex-snapshot
Online narrative guides for illuminating tissue atlas data and digital pathology images
inferred← citeshttps://doi.org/10.1186/s13059-019-1645-zopenalex-snapshot
clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
inferred← citeshttps://doi.org/10.1186/s13059-020-1926-6openalex-snapshot
Eleven grand challenges in single-cell data science
inferred← citeshttps://doi.org/10.1186/s40478-019-0779-2openalex-snapshot
The landscape of myeloid and astrocyte phenotypes in acute multiple sclerosis lesions
inferred← citeshttps://doi.org/10.18632/oncotarget.26585openalex-snapshot
Emerging approaches to study cell-cell interactions in tumor microenvironment
inferred← citeshttps://doi.org/10.3389/fimmu.2020.591741openalex-snapshot
Angiogenesis in Lymph Nodes Is a Critical Regulator of Immune Response and Lymphoma Growth
inferred← citeshttps://doi.org/10.3389/fonc.2018.00430openalex-snapshot
Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology
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