GENIE3 protocols

View GENIE3 computational protocol

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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 in pipelines

PMCID: 4403341
PMID: 25865119
DOI: 10.1038/ncomms7683

[…] h3k27ac peak of the region with absolute correlation coefficient of 0.3 or more., for , the optimal parameters were selected on the basis of the gsea enrichment results for genes ranked according to genie3 scores of the corresponding factor (for sox10, mitf and ap-1 targets). for tead target predictions, taz perturbation data were used (with gene ranking based on log2fc on taz activation), since […]

PMCID: 4642938
PMID: 26562774
DOI: 10.1371/journal.pcbi.1004590

[…] few top-scoring mutations may contribute to the oncogenic program as cis-regulatory drivers., tfs target genes were selected either from curated tf perturbation gene signatures (msigdb) [] or from a genie3 [] inferred co-expression network focused on melanoma (skin (77): gse7553 [], gse28914 [], gse13355 []; primary melanoma (90): gse7553 [], gse19293 [], gse23376; metastasis (71): gse7553, […]

PMCID: 4670728
PMID: 26577401
DOI: 10.15252/msb.20156236

[…] model (a threshold where precision is calibrated using aupr curves as illustrated in fig a)., in addition to the network inference described above, we built networks using clr (faith et al, ) and genie3 (huynh‐thu et al, )., the combined network was visualized using cytoscape v. 2.8 (smoot et al, )., the meme suite (bailey et al, ) was used for identifying dna sequence motifs characteristic […]

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GENIE3 in publications

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 […]

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) […]

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 […]

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 […]

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 [, ]., […]

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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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