ArticleMolecular systems biology2021
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.
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 90 papers.
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Who cites it
90 citing papers in PubMed.
- Complex assembly and activity states as multifaceted protein attributes explaining phenotypic variability.Molecular systems biology · 2026Article
- Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz.Molecular systems biology · 2026Article
- Omics Approaches in Hantavirus Research: Current Advances, Challenges, and Future Perspectives.Biotech (Basel (Switzerland)) · 2026Review
- A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.Briefings in bioinformatics · 2026Review
- From Prediction to Creation: Generative Plant Design.Plants (Basel, Switzerland) · 2026Review
- Inference of upstream-mutation and metabolomic-signature causality identifies prognostic biomarkers and therapeutic targets in pancreatic cancer.Nature communications · 2026Article
- Assessing current capabilities for incorporating lipidomics in multiomics data integration.Briefings in bioinformatics · 2026Review
- Integrative multi-omics defines melanoma drug response networks and ARID1A-dependent resistance mechanisms.Molecular systems biology · 2026Article
- MultiOmicsXplorer, a tool to browse, access and analyse multi-omics data.BMC bioinformatics · 2026Article
- AI-derived constrained conditional model for screening marker genes through integrated high-throughput transcriptome big data.BMC medical research methodology · 2026Article
- Review
- Multi-Omics Guided Pathway and Network Analysis of Clinical Metabolomics and Proteomics Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Multi-omics biomarkers for predicting resistance, hyperprogression, and immune-related toxicity during PD-1/PD-L1 therapy in lung cancer: a literature review.Frontiers in immunology · 2026Review
- Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease.Gut microbes · 2025Review
- PatientProfiler: building patient-specific signaling models from proteogenomic data.Molecular systems biology · 2025Article
- Spatial Immunometabolism: Integrating Technologies to Decode Cellular Metabolism in Tissues.European journal of immunology · 2025Review
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- MPAC: a computational framework for inferring pathway activities from multi-omic data.Bioinformatics (Oxford, England) · 2025Article
- Can classical statistics and deep learning converge on explainable, causally driven target discovery?DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Review
- Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression.Molecular systems biology · 2025Article
30 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors.
Funding
Abstract
Multi-omics datasets can provide molecular insights beyond the sum of individual omics. Various tools have been recently developed to integrate such datasets, but there are limited strategies to systematically extract mechanistic hypotheses from them. Here, we present COSMOS (Causal Oriented Search of Multi-Omics Space), a method that integrates phosphoproteomics, transcriptomics, and metabolomics datasets. COSMOS combines extensive prior knowledge of signaling, metabolic, and gene regulatory networks with computational methods to estimate activities of transcription factors and kinases as well as network-level causal reasoning. COSMOS provides mechanistic hypotheses for experimental observations across multi-omics datasets. We applied COSMOS to a dataset comprising transcriptomics, phosphoproteomics, and metabolomics data from healthy and cancerous tissue from eleven clear cell renal cell carcinoma (ccRCC) patients. COSMOS was able to capture relevant crosstalks within and between multiple omics layers, such as known ccRCC drug targets. We expect that our freely available method will be broadly useful to extract mechanistic insights from multi-omics studies.
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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.