ArticleBMC systems biology2014
Understanding disease mechanisms with models of signaling pathway activities.
Article in BMC systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 56 citations in OpenAlex.
- Pathway Analysis Interpretation in the Multi-Omic Era.Biotech (Basel (Switzerland)) · 2025Review
- GenPath-PPH: Integrating gene expression and pathway networks via persistent path homology enhances detection of disease-relevant pathways.Computational and structural biotechnology journal · 2025Article
- Whole-exome sequencing and Drosophila modelling reveal mutated genes and pathways contributing to human ovarian failure.Reproductive biology and endocrinology : RB&E · 2024Article
- Substantiate a read-across hypothesis by using transcriptome data-A case study on volatile diketones.Frontiers in toxicology · 2023Article
- Discovering potential interactions between rare diseases and COVID-19 by combining mechanistic models of viral infection with statistical modeling.Human molecular genetics · 2022Article
- Investigating circulating miRNA in transition dairy cows: What miRNAomics tells about metabolic adaptation.Frontiers in genetics · 2022Article
- Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data.Computational and structural biotechnology journal · 2021Article
- Cellular signalling pathways mediating the pathogenesis of chronic inflammatory respiratory diseases: an update.Inflammopharmacology · 2020Review
- Article
- Identifying disease-associated signaling pathways through a novel effector gene analysis.PeerJ · 2020Article
- Using mechanistic models for the clinical interpretation of complex genomic variation.Scientific reports · 2019Article
- SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways.PLoS computational biology · 2019Article
- A comparison of mechanistic signaling pathway activity analysis methods.Briefings in bioinformatics · 2019Review
- An integrative method to predict signalling perturbations for cellular transitions.Nucleic acids research · 2019Article
- Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models.BMC bioinformatics · 2019Article
- Preparticipation Cardiovascular Screening of Student-Athletes with Echocardiography: Ethical, Clinical, Economic, and Legal Considerations.Current cardiology reports · 2019Review
- Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models.NPJ systems biology and applications · 2019Article
- Identifying cancer-related microRNAs based on subpathways.IET systems biology · 2018Article
- Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome.Biology direct · 2018Article
- A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways.PloS one · 2018Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundUnderstanding the aspects of the cell functionality that account for disease or drug action mechanisms is one of the main challenges in the analysis of genomic data and is on the basis of the future implementation of precision medicine.
resultsHere we propose a simple probabilistic model in which signaling pathways are separated into elementary sub-pathways or signal transmission circuits (which ultimately trigger cell functions) and then transforms gene expression measurements into probabilities of activation of such signal transmission circuits. Using this model, differential activation of such circuits between biological conditions can be estimated. Thus, circuit activation statuses can be interpreted as biomarkers that discriminate among the compared conditions. This type of mechanism-based biomarkers accounts for cell functional activities and can easily be associated to disease or drug action mechanisms. The accuracy of the proposed model is demonstrated with simulations and real datasets.
conclusionsThe proposed model provides detailed information that enables the interpretation disease mechanisms as a consequence of the complex combinations of altered gene expression values. Moreover, it offers a framework for suggesting possible ways of therapeutic intervention in a pathologically perturbed system.
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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 OpenQuestion graph.