pathTiMEx statistics

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Citations per year

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Associated diseases

Associated diseases

pathTiMEx specifications


Unique identifier OMICS_14082
Name pathTiMEx
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 3.0
Computer skills Advanced
Version 0.99.0
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens



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  • person_outline Niko Beerenwinkel <>

Publication for pathTiMEx

pathTiMEx in publications

PMCID: 5469877
PMID: 28659971
DOI: 10.3389/fgene.2017.00083

[…] above, memo and the method from babur et al. () employ mutual exclusivity to find gene sets, but use an interaction network to limit the candidate gene sets. the method by raphael and vandin () and pathtimex (cristea et al., ) introduce an additional dimension to the characterization of inter-tumor heterogeneity, by reconstructing the order in which mutually exclusive gene sets are mutated. kim […]

PMCID: 5215607
PMID: 27863091
DOI: 10.1002/wsbm.1364

[…] however, more robust models can be derived by considering dependencies among altered pathways, mainly because of the large interpatient gene‐wise mutational heterogeneity., cristea et al. devised pathtimex, an extension timex that introduces a probabilistic waiting time model for mutually exclusive cancer alterations on the level of pathways rather than on the level of genes. the idea […]

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pathTiMEx institution(s)
Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; The Swiss Institute of Bioinformatics, Basel, Switzerland
pathTiMEx funding source(s)
This work was financially supported by the Swiss National Science Foundation (Sinergia project 136247).

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