ArticleNucleic acids research2026
OmniPath: integrated knowledgebase for multi-omics analysis.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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
12 citing papers in PubMed.
- GRAIL-heart: A graph attention network for inferring ligand-receptor interactions in spatial transcriptomics.MethodsX · 2026Article
- Searching the druggable genome using large language models.Bioinformatics (Oxford, England) · 2026Article
- Metastatic Cancers Exploit Vagal Sensory Neurons and Neural Repair Programs to Colonize New Tissues.Research square · 2026Article
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
- Application of hydrogels in 3D tumor microenvironment modeling and drug screening for cervical cancer: A review.Bioengineering & translational medicine · 2026Review
- BioMedGraphica: an all-in-one platform for joint textual biomedical prior knowledge and numeric graph generation.Bioinformatics (Oxford, England) · 2026Article
- A Scalable Sign-Aware Multi-Omics Knowledge Graph Foundation Model for Mechanistic Drug Action and Clinical Response Predictions.bioRxiv : the preprint server for biology · 2026Article
- Shared gene signatures and biochemical regulatory networks linking Parkinson's disease and ulcerative colitis.NPJ Parkinson's disease · 2026Article
- Reconstructing biologically coherent cellular profiles from imaging-based spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Searching the Druggable Genome using Large Language Models.bioRxiv : the preprint server for biology · 2026Article
- The 2026 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2026Article
- Disease-first public-data integration with local virtual knockout prioritizes shared proteins linking osteoarthritis and osteoporosis.PloS one · 2026Article
Corrections and comments
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Authors and funding
32 authors.
Funding
Abstract
Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods. We developed OmniPath (https://omnipathdb.org/), a database combining diverse molecular knowledge from 168 resources. It covers causal protein-protein, gene regulatory, microRNA, and enzyme-post-translational modification interactions, cell-cell communication, protein complexes, and information about the function, localization, structure, and many other aspects of biomolecules. It prioritizes literature curated data, and complements it with predictions and large scale databases. To enable interactive browsing of this large corpus of knowledge, we developed OmniPath Explorer, which also includes a large language model agent that has direct access to the database. Python and R/Bioconductor client packages and a Cytoscape plugin create easy access to customized prior knowledge for omics analysis environments, such as scverse. OmniPath can be broadly used for the analysis of bulk, single-cell, and spatial multi-omics data, especially for mechanistic and causal modeling.
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What OpenQuestion holds
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 OpenQuestion graph.