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Data-driven inference of crosstalk in the tumor microenvironment

https://doi.org/10.1101/835512
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What this work says

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

inferredcites →https://doi.org/10.1002/cncy.22174openalex-snapshot
Tumor mutational burden
inferredcites →https://doi.org/10.1002/emmm.201302625openalex-snapshot
Ret inhibition decreases growth and metastatic potential of estrogen receptor positive breast cancer cells
inferredcites →https://doi.org/10.1002/gcc.10300openalex-snapshot
Contrasting in vivo and in vitro fates of glioblastoma cell subpopulations with amplified EGFR
inferredcites →https://doi.org/10.1002/mrd.22489openalex-snapshot
The ImageJ ecosystem: An open platform for biomedical image analysis
inferredcites →https://doi.org/10.1016/j.ccr.2012.02.022openalex-snapshot
Accessories to the Crime: Functions of Cells Recruited to the Tumor Microenvironment
inferredcites →https://doi.org/10.1016/j.cell.2011.02.013openalex-snapshot
Hallmarks of Cancer: The Next Generation
inferredcites →https://doi.org/10.1016/j.cell.2011.04.029openalex-snapshot
Paracrine and Autocrine Signals Induce and Maintain Mesenchymal and Stem Cell States in the Breast
inferredcites →https://doi.org/10.1016/j.cell.2013.09.034openalex-snapshot
The Somatic Genomic Landscape of Glioblastoma
inferredcites →https://doi.org/10.1016/j.cell.2018.03.022openalex-snapshot
Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer
inferredcites →https://doi.org/10.1016/j.isci.2018.10.028openalex-snapshot
Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration
inferredcites →https://doi.org/10.1021/pr501254jopenalex-snapshot
The CPTAC Data Portal: A Resource for Cancer Proteomics Research
inferredcites →https://doi.org/10.1038/nature12626openalex-snapshot
Influence of tumour micro-environment heterogeneity on therapeutic response
inferredcites →https://doi.org/10.1038/ncomms3612openalex-snapshot
Inferring tumour purity and stromal and immune cell admixture from expression data
inferredcites →https://doi.org/10.1038/ncomms8866openalex-snapshot
A draft network of ligand–receptor-mediated multicellular signalling in human
inferredcites →https://doi.org/10.1038/ncomms9971openalex-snapshot
Systematic pan-cancer analysis of tumour purity
inferredcites →https://doi.org/10.1038/ng.3398openalex-snapshot
Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma
inferredcites →https://doi.org/10.1038/nmeth.1439openalex-snapshot
Cell type–specific gene expression differences in complex tissues
inferredcites →https://doi.org/10.1038/nmeth.1830openalex-snapshot
Gene expression deconvolution in linear space
inferredcites →https://doi.org/10.1038/nmeth.1831openalex-snapshot
Gene expression deconvolution in linear space
inferredcites →https://doi.org/10.1038/nmeth.3337openalex-snapshot
Robust enumeration of cell subsets from tissue expression profiles
inferredcites →https://doi.org/10.1038/nrc3545openalex-snapshot
MSP–RON signalling in cancer: pathogenesis and therapeutic potential
inferredcites →https://doi.org/10.1038/nrclinonc.2016.25openalex-snapshot
The future of cancer treatment: immunomodulation, CARs and combination immunotherapy
inferredcites →https://doi.org/10.1038/onc.2015.139openalex-snapshot
CXCL12/CXCR4: a symbiotic bridge linking cancer cells and their stromal neighbors in oncogenic communication networks
inferredcites →https://doi.org/10.1038/s41467-019-09990-5openalex-snapshot
Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures
inferredcites →https://doi.org/10.1038/s41587-019-0114-2openalex-snapshot
Determining cell type abundance and expression from bulk tissues with digital cytometry
inferredcites →https://doi.org/10.1056/nejmc1713444openalex-snapshot
Tumor Mutational Burden and Response Rate to PD-1 Inhibition
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.1009843107openalex-snapshot
Allele-specific copy number analysis of tumors
inferredcites →https://doi.org/10.1074/jbc.m304204200openalex-snapshot
Endoglycan, a Member of the CD34 Family, Functions as an L-selectin Ligand through Modification with Tyrosine Sulfation and Sialyl Lewis x
inferredcites →https://doi.org/10.1093/bioinformatics/btt293openalex-snapshot
PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btt301openalex-snapshot
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data
inferredcites →https://doi.org/10.1093/bioinformatics/btt759openalex-snapshot
AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data
inferredcites →https://doi.org/10.1097/ppo.0b013e31827459b6openalex-snapshot
Pathology and Molecular Genetics of Pancreatic Neoplasms
inferredcites →https://doi.org/10.1126/science.aaa8172openalex-snapshot
The future of immune checkpoint therapy
inferredcites →https://doi.org/10.1126/science.aad0501openalex-snapshot
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
inferredcites →https://doi.org/10.1126/science.aan2507openalex-snapshot
A pathology atlas of the human cancer transcriptome
inferredcites →https://doi.org/10.1158/0008-5472.can-04-1890openalex-snapshot
Expression of Notch-1 and Its Ligands, Delta-Like-1 and Jagged-1, Is Critical for Glioma Cell Survival and Proliferation
inferredcites →https://doi.org/10.1172/jci32655openalex-snapshot
Bile salt–dependent lipase interacts with platelet CXCR4 and modulates thrombus formation in mice and humans
inferredcites →https://doi.org/10.1186/gm433openalex-snapshot
Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction
inferredcites →https://doi.org/10.1186/s13059-017-1349-1openalex-snapshot
xCell: digitally portraying the tissue cellular heterogeneity landscape
inferredcites →https://doi.org/10.1371/journal.pone.0185208openalex-snapshot
Amplification of the EGFR gene can be maintained and modulated by variation of EGF concentrations in in vitro models of glioblastoma multiforme
inferredcites →https://doi.org/10.18637/jss.v070.i01openalex-snapshot
missMDA : A Package for Handling Missing Values in Multivariate Data Analysis
inferredcites →https://doi.org/10.3389/fonc.2014.00341openalex-snapshot
Notching on Cancer’s Door: Notch Signaling in Brain Tumors

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.celrep.2022.110800openalex-snapshot
A pan-cancer metabolic atlas of the tumor microenvironment
inferred← citeshttps://doi.org/10.1080/08820139.2021.1882484openalex-snapshot
Age-associated Ligand-receptor Interactions Imputed from Nasopharyngeal Transcriptomes of COVID-19 Patients
inferred← citeshttps://doi.org/10.1101/2021.01.20.427515openalex-snapshot
Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS
inferred← citeshttps://doi.org/10.3389/fonc.2020.01027openalex-snapshot
Toward Systems Biomarkers of Response to Immune Checkpoint Blockers
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