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Multi-Dendrix specifications

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Unique identifier OMICS_06146
Name Multi-Dendrix
Alternative name Multiple Pathways De novo Driver Exclusivity
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Multiple Pathways De novo Driver Exclusivity

Multi-Dendrix in publications

 (8)
PMCID: 5469877
PMID: 28659971
DOI: 10.3389/fgene.2017.00083

[…] set and the mutual exclusivity of mutations in the set, and uses a markov chain monte carlo (mcmc) approach for identifying mutually exclusive gene sets altered in a large fraction of the patients. multi-dendrix (leiserson et al., ) employs the same score as dendrix and extends it to multiple sets, and uses an integer linear program (ilp) based algorithm to simultaneously find multiple sets […]

PMCID: 5482642
PMID: 28415609
DOI: 10.18632/oncotarget.16433

[…] mcmc algorithm, the blp method is more efficient. a multi-objective optimization model based on a genetic algorithm (moga) was introduced to adjust the trade-off between coverage and exclusivity []. multi-dendrix [] designed a new metric as the sum of dendrix weights and adopted a new programming model to identify multiple modules simultaneously. comdp proposed an exact mathematical programming […]

PMCID: 5449640
PMID: 28168295
DOI: 10.1093/nar/gkx089

[…] among different biological pathways and functional modules may shed new lights on the understanding of the cellular mechanisms underlying carcinogenesis. leiserson et al. () generalized dendrix (multi-dendrix) to simultaneously identify multiple driver gene sets in cancer. more importantly, the collaboration among different pathways means these gene sets are likely simultaneously mutated […]

PMCID: 4575033
PMID: 26379039
DOI: 10.1371/journal.pcbi.1004350

[…] isoforms, variation in mutation types, different background mutation rates, redundancy of the genetic code and others and used a likelihood ratio test to obtain significance levels. moreover, multi-dendrix, drivernet, music, and memo [, , , –] were also developed to identify driver pathways using network-based approaches. an integrated meta-analysis using multiple methods can be accessed […]

PMCID: 4574474
PMID: 26375816
DOI: 10.1371/journal.pone.0138141

[…] these r s scores were grouped according to the crc subtype to determine the p-values, indicating whether a gene contributed significantly to the formation of a specific crc subtype., data input for multi-dendrix analysis was identical to the data input used for nbs analysis, except for genes that shared the same breakpoints, which were now grouped in “pools” (). multi-dendrix parameters […]

Multi-Dendrix institution(s)
Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, USA

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