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TDARACNE specifications


Unique identifier OMICS_02013
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.30.0
Stability Stable
Biobase, Rgraphviz, GenKern
Maintained Yes


No version available



  • person_outline Luigi Cerulo

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Publication for TDARACNE

TDARACNE citations


Data driven reverse engineering of signaling pathways using ensembles of dynamic models

PLoS Comput Biol
PMCID: 5319798
PMID: 28166222
DOI: 10.1371/journal.pcbi.1005379

[…] parameterization. however, these methods are not designed to recover directed networks. to surmount this limitation, we have introduced the comparison with two other methods for directed networks, tdaracne [] and mider []., in , we show the overall results regarding the ability of seldom and other network inference methods to reverse engineer the known synthetic networks associated […]


Incorporating time delays in S System model for reverse engineering genetic networks

BMC Bioinformatics
PMCID: 3839642
PMID: 23777625
DOI: 10.1186/1471-2105-14-196

[…] original publications for comparison where possible., with real-life networks, for irma, the comparison is carried out with 7 other approaches, namely, alg [,], regard [], bitgrn2 [,], banjo [], tdaracne [], nir and tsni [], aracne []. for the e. coli network, the performance has been evaluated with alg [], regard [], s-tree based approach [], two approaches from kimura et al.[,], […]


Simultaneous learning of instantaneous and time delayed genetic interactions using novel information theoretic scoring technique

BMC Syst Biol
PMCID: 3529704
PMID: 22691450
DOI: 10.1186/1752-0509-6-62

[…] the x-axes represent the noise levels while the y-axes represent the corresponding performance measures (se, sp, pr, f). in figure (b)-(d), we compare our approach with three other methods, namely tdaracne, banjo and bnfinder (bde and mdl) using the f-score (results corresponding to other measures are available in additional file ). it is evident from the results that there is no clear winner […]

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TDARACNE institution(s)
Department of Science and Technology, University of Sannio, Benevento, Italy; BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino (AV) Italy; Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
TDARACNE funding source(s)
Supported by a research project funded by MiUR (Ministero dell’Università e della Ricerca) under grant FIRB2012-RBFR12QW4I.

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