ArticleMolecular systems biology2021
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 219 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
219 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Systems-level transcriptomic analysis reveals synapse-related gene dysregulation in peripheral leukocytes of MDD patients.Scientific reports · 2026Pooled it
- Multiomics Integration of Parkinson's Disease Datasets Reveals Unexpected Roles of IRE1 in Its Pathology.International journal of molecular sciences · 2025Pooled it
- Integrated spatial and single-cell transcriptomics uncover IFI6⁺ regulatory T-cells and SPP1⁺ macrophages immunosuppressive niches in colorectal cancer.British journal of cancer · 2026Article
- Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz.Molecular systems biology · 2026Article
- Engineered Microvascular Model of the Blood-Brain-Tumor Barrier Reveals Endothelial Remodeling in Diffuse Midline Glioma.Advanced healthcare materials · 2026Article
- Single-Cell Transcriptomic Profiling Identifies B Cell-Intrinsic Dysregulation of Sphingolipid Biosynthesis and Could Be Improved by Inhibiting UGCG in Primary Immune Thrombocytopenia.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Temporal transcriptomic remodeling after controlled cortical impact reveals delayed AQP4/SNTA1 expression imbalance associated with ion-homeostatic remodeling.bioRxiv : the preprint server for biology · 2026Article
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- Functional impact of Nth like DNA glycosylase 1 on mitochondrial dynamics.Nucleic acids research · 2026Article
- An iguratimod prodrug reduces RA-FLS invasiveness by disrupting STAT1-C3-TNFα-mediated crosstalk between fibroblast-like synoviocytes and macrophages.Journal of orthopaedic translation · 2026Article
- Altered bone marrow niche forms central innate immune memory driving cardiac dysfunction.Nature communications · 2026Article
- Article
- Ten quick tips for causal analysis of biomedical omics data.PLoS computational biology · 2026Article
- M1-linked ubiquitination by LUBAC regulates AMPK signalling and the response to energetic stress.Cell death and differentiation · 2026Article
- Type 2 Diabetes-Induced Molecular and Functional Impairment of Adipose Tissue-Derived Mesenchymal Stromal Cells (ASCs) and Interferon Gamma Priming for Enhanced Diabetic ASC-Based Therapy.Stem cell reviews and reports · 2026Article
- PD-1/PD-L1 Signaling in Non-ICI Myocarditis.JACC. Basic to translational science · 2026Article
- Article
- Omics Approaches in Hantavirus Research: Current Advances, Challenges, and Future Perspectives.Biotech (Basel (Switzerland)) · 2026Review
- An Integrative Bioinformatics Framework Prioritises a Gingival Mesenchymal Stem Cell Paracrine Apoptosis-ROS Axis in HPV-Negative Oral Squamous Cell Carcinoma: Preliminary Experimental Support and Repurposable-Drug Hypotheses.International journal of molecular sciences · 2026Article
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
159 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
Molecular knowledge of biological processes is a cornerstone in omics data analysis. Applied to single-cell data, such analyses provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across resources, and not linked to intracellular processes. To address this gap, we combined over 100 resources covering interactions and roles of proteins in inter- and intracellular signaling, as well as transcriptional and post-transcriptional regulation. We added protein complex information and annotations on function, localization, and role in diseases for each protein. The resource is available for human, and via homology translation for mouse and rat. The data are accessible via OmniPath's web service (https://omnipathdb.org/), a Cytoscape plug-in, and packages in R/Bioconductor and Python, providing access options for computational and experimental scientists. We created workflows with tutorials to facilitate the analysis of cell-cell interactions and affected downstream intracellular signaling processes. OmniPath provides a single access point to knowledge spanning intra- and intercellular processes for data analysis, as we demonstrate in applications studying SARS-CoV-2 infection and ulcerative colitis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.