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GENIE3 specifications


Unique identifier OMICS_01683
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB, R
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Vân Anh Huynh-Thu <>

Publication for GENIE3

GENIE3 citations


A comprehensive evaluation of module detection methods for gene expression data

PMCID: 5854612
PMID: 29545622
DOI: 10.1038/s41467-018-03424-4

[…] most profoundly is the higher performance of certain biclustering methods, such as isa (iterative signature algorithm), qubic (qualitative biclustering), and fabia, and direct ni methods, primarily genie3, on human and/or synthetic data, where these methods can in some cases compete with clustering and decomposition methods. performance was generally very consistent across different module […]


GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6 LIKE 4 in Arabidopsis

PMCID: 5818008
PMID: 29439132
DOI: 10.1242/dev.159707

[…] gtl1 and df1 directly regulate rsl4 and a subset of its downstream targets. to further investigate the regulatory roles of gtl1 and df1, we employed gene network inference with ensemble of tree 3 (genie3) () and inferred a gene regulatory network (grn) among gtl1, df1, rsl4 and their 36 common target genes using our expression data from gtl1 and df1 mutants (gtl1-1, df1-1, gtl1-1 df1-1) […]


Reverse engineering of gene networks for regulating early blood development from single cell measurements

PMCID: 5751697
PMID: 29297370
DOI: 10.1186/s12920-017-0312-z

[…] position in the cell cycle. since there is substantial noise in the generated pseudo-trajectory data, the gaussian processes regression method is used to smooth the expression data []. then the genie3 algorithm is employed to infer the structure of gene regulatory network []. using single-cell quantitative real-time reverse transcription-pcr analysis of 33 transcription factors […]


Prophetic Granger Causality to infer gene regulatory networks

PMCID: 5718405
PMID: 29211761
DOI: 10.1371/journal.pone.0170340

[…] probabilistic dependencies that formalize the previous mutual information approaches to name a few. machine-learning methods have also had success, exemplified by the decision tree approach of the genie3 method [] that has performed well in multiple benchmarks. a recent review and comparison of methods for inferring grns from steady state data can be found in [,]., perturbation and time series […]


Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae

PMCID: 5628832
PMID: 28981547
DOI: 10.1371/journal.pone.0185475

[…] for example, the method of genenet [] converts correlation network into partial correlation graphs and further establishes partial ordering of nodes based on the covariance matrix. the method of genie3 [] solves a regression problem for every gene using tree-based ensemble methods. the method of generalized local learning (gll) performs local learning and feature selection in graphs [, ]., […]


Inference of time delayed gene regulatory networks based on dynamic Bayesian network hybrid learning method

PMCID: 5655205
PMID: 29113310
DOI: 10.18632/oncotarget.21268

[…] is second only to aracne algorithm, reaching 0.800. figure shows the main results of the three algorithms and the dbncs algorithm to infer grns., the fpr of the dbncs algorithm is 9.9% lower than genie3 and aracne algorithm, which is 3.7% lower than that of narromi algorithm. the ppv is 45.2% higher than genie3 algorithm and 25.3% higher than narromi algorithm. the acc is 10% higher […]

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GENIE3 institution(s)
Department of Electrical Engineering and Computer Science, Systems and Modeling, University of Liège, Liège, Belgium

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