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BEAM specifications


Unique identifier OMICS_10098
Alternative name Bayesian Epistasis Association Mapping
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes


No version available

Publication for Bayesian Epistasis Association Mapping

BEAM citations


A survey about methods dedicated to epistasis detection

Front Genet
PMCID: 4564769
PMID: 26442103
DOI: 10.3389/fgene.2015.00285

[…] Because this learning is an NP-hard problem (Chickering et al., ), specific techniques have to be used to reduce the computational burden.A famous Bayesian network-based software program called BEAM (Bayesian Epistasis Association Mapping) (Zhang and Liu, ) is often used as a Bayesian-based reference for performance comparisons. BEAM relies on a Markov Chain Monte Carlo (MCMC) algorithm to test it […]


Weighted Risk Score Based Multifactor Dimensionality Reduction to Detect Gene Gene Interactions in Nasopharyngeal Carcinoma

Int J Mol Sci
PMCID: 4100176
PMID: 24933637
DOI: 10.3390/ijms150610724

[…] apply. Moreover, MDR methods cannot quantitatively assess the disease risk of genotype combinations; instead, they offer only a binary measure (high or low) of disease risk. Zhang and Liu proposed a Bayesian epistasis association mapping (BEAM) algorithm for identifying both single-marker and epistasis associations in population-based case-control studies []. The BEAM algorithm treats disease-ass […]


Genetic studies of complex human diseases: Characterizing SNP disease associations using Bayesian networks

BMC Syst Biol
PMCID: 3524021
PMID: 23281790
DOI: 10.1186/1752-0509-6-S3-S14

[…] ity. Moreover, almost all prediction/classification-based methods tend to introduce a large number of false positives, which may result in a huge cost for further biological validation experiments [].Bayesian epistasis association mapping (BEAM) is a scalable and association-based method []. It partitions SNPs into three groups: group 0 is for normal SNPs, group 1 contains disease SNPs affecting d […]


A novel method to identify high order gene gene interactions in genome wide association studies: Gene based MDR

BMC Bioinformatics
PMCID: 3372457
PMID: 22901090
DOI: 10.1186/1471-2105-13-S9-S5

[…] in handling large scale GWA data because MDR employs exhaustive searching strategy.Alternatively, Bayesian and regularization approaches have been proposed for gene-gene interaction analysis such as Bayesian epistasis association mapping (BEAM) [] and penalized logistic regression models []. BEAM is a Bayesian marker partition model to select an optimal marker partition with the highest posterior […]


Performance analysis of novel methods for detecting epistasis

BMC Bioinformatics
PMCID: 3259123
PMID: 22172045
DOI: 10.1186/1471-2105-12-475

[…] ain as many informative SNPs as possible while largely reducing computational complexity []. For example, Tang et al proposed epistatic module detection (epiMODE) [], which is a generalized method of Bayesian epistasis association mapping (BEAM) []. Wang et al used AntEpiSeeker [] to identify epistasis, which is a two-stage ant colony optimization algorithm (ACO). Wan et al proposed SNPRuler [] ba […]


SNPInterForest: A new method for detecting epistatic interactions

BMC Bioinformatics
PMCID: 3260223
PMID: 22151604
DOI: 10.1186/1471-2105-12-469

[…] ntly, interest has grown in applying machine learning techniques to analyzing genetic association studies due to their ability to thrive on large-scale and high-dimensional data. In one recent study, Bayesian epistasis association mapping (BEAM; []) designed a form of Bayesian model selection and used a Markov chain Monte Carlo sampling strategy to estimate the model parameters. A recent approach […]


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BEAM institution(s)
Department of Statistics, the Pennsylvania State University, Thomas Building, University Park, PA, USA

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