ArticleBioinformatics (Oxford, England)2014
Bayesian network prior: network analysis of biological data using external knowledge.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- AI-based methods for the assessment of DNA damage and repair mechanisms.Frontiers in systems biology · 2026Review
- MRSL: a causal network pruning algorithm based on GWAS summary data.Briefings in bioinformatics · 2024Article
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- Identifying large-scale interaction atlases using probabilistic graphs and external knowledge.Journal of clinical and translational science · 2022Article
- Data Integration Challenges for Machine Learning in Precision Medicine.Frontiers in medicine · 2021Review
- KEGG2Net: Deducing gene interaction networks and acyclic graphs from KEGG pathways.EMBnet.journal · 2021Article
- Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge.BMC bioinformatics · 2019Article
- Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities.Frontiers in genetics · 2019Review
- REFINING CELLULAR PATHWAY MODELS USING AN ENSEMBLE OF HETEROGENEOUS DATA SOURCES.The annals of applied statistics · 2018Article
- Applications of Bayesian network models in predicting types of hematological malignancies.Scientific reports · 2018Article
- Bayesian variable selection with graphical structure learning: Applications in integrative genomics.PloS one · 2018Article
- Inference of time-delayed gene regulatory networks based on dynamic Bayesian network hybrid learning method.Oncotarget · 2017Article
- An empirical Bayes approach to network recovery using external knowledge.Biometrical journal. Biometrische Zeitschrift · 2017Article
- From big data analysis to personalized medicine for all: challenges and opportunities.BMC medical genomics · 2015Review
- Gene network inference by fusing data from diverse distributions.Bioinformatics (Oxford, England) · 2015Article
- Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data.Current genomics · 2015Article
- A review on computational systems biology of pathogen-host interactions.Frontiers in microbiology · 2015Review
- Data- and knowledge-based modeling of gene regulatory networks: an update.EXCLI journal · 2015Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationReverse engineering GI networks from experimental data is a challenging task due to the complex nature of the networks and the noise inherent in the data. One way to overcome these hurdles would be incorporating the vast amounts of external biological knowledge when building interaction networks. We propose a framework where GI networks are learned from experimental data using Bayesian networks (BNs) and the incorporation of external knowledge is also done via a BN that we call Bayesian Network Prior (BNP). BNP depicts the relation between various evidence types that contribute to the event 'gene interaction' and is used to calculate the probability of a candidate graph (G) in the structure learning process.
resultsOur simulation results on synthetic, simulated and real biological data show that the proposed approach can identify the underlying interaction network with high accuracy even when the prior information is distorted and outperforms existing methods. AVAILABILITY: Accompanying BNP software package is freely available for academic use at http://bioe.bilgi.edu.tr/BNP. CONTACT: hasan.otu@bilgi.edu.tr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.