ArticleCell reports methods2024
Enhancing immuno-oncology investigations through multidimensional decoding of tumor microenvironment with IOBR 2.0.
Article in Cell reports methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
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- A programmed cell death learning signature predicts immunotherapy response and identifies AP1S1 as a regulator of immune exclusion in breast cancer.Chinese journal of cancer research = Chung-kuo yen cheng yen chiu · 2026Article
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- Myofibroblastic CAF and Malignant Ductal Cell Crosstalk Drives Epithelial-Mesenchymal Transition and Progression in Pancreatic Ductal Adenocarcinoma via THBS2-SDC/Integrin Axes.International journal of molecular sciences · 2026Article
- A HRH1-YAP1 feedback loop drives pancreatic cancer progression and predicts therapeutic response.Oncology letters · 2026Article
- Lower Respiratory Microbiome Dysbiosis Is Associated With Poor Prognosis in Acute Severe Lower Respiratory Tract Infection.MedComm · 2026Article
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- A palmitoylation signature for prognosis immune infiltration and drug sensitivity in esophageal carcinoma.iScience · 2026Article
- NQO1-Mediated Anoikis Resistance and Immune Evasion Define a High-Risk Multi-Omic Subtype for Precision Management of T1 High-Grade Bladder Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Pretreatment intratumoral mature TLSs in non-clear cell renal cell carcinoma are associated with response to immunotherapy rechallenge.Journal for immunotherapy of cancer · 2026Article
- ALG1-mediated PDL1 glycosylation drives macrophage m2 polarization to promote bladder cancer progression.Cell death and differentiation · 2026Article
- Single-cell spatial analysis stratifies lung adenocarcinoma with rare actionable mutations and reveals immune-modulatory cellular crosstalk.Cell reports. Medicine · 2026Article
- Machine learning-based integrative analysis identifies CXCL13-driven tertiary lymphoid structures as favorable immune and prognostic features in osteosarcoma.Cellular oncology (Dordrecht, Netherlands) · 2026Article
- Review
- B7-H3 interaction with cMet enhances lipolysis to drive malignant progression of glioma via pSTAT3-ATGL axis.Journal of translational medicine · 2026Article
- EGR1 lactylation induces tumor cell senescence and immunosuppressive microenvironment in intrahepatic cholangiocarcinoma.Translational oncology · 2026Article
- Overexpression of FOXO1 may suppress proliferation and migration and correlate with tumor immune cells in nasopharyngeal carcinoma.Translational cancer research · 2026Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
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Abstract
The use of large transcriptome datasets has greatly improved our understanding of the tumor microenvironment (TME) and helped develop precise immunotherapies. The growing application of multi-omics, single-cell RNA sequencing (scRNA-seq), and spatial transcriptome sequencing has led to many new insights, yet these findings still require clinical validation in large cohorts. To advance multi-omics integration in TME research, we have upgraded the Immuno-Oncology Biological Research (IOBR) package to IOBR 2.0, restructuring and standardizing its analytical workflow. IOBR 2.0 offers six modules for TME analysis based on multi-omics data, including data preprocessing, TME estimation, TME infiltration pattern identification, cellular interaction analysis, genome and TME interaction, and feature visualization, as well as modeling. Additionally, IOBR 2.0 enables constructing gene signatures and reference matrices from scRNA-seq data for TME deconvolution. The user-friendly pipeline provides comprehensive insights into tumor-immune interactions, and a detailed GitBook(https://iobr.github.io/book/) offers a complete manual and analysis guide for each module.
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