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OmicsNet specifications


Unique identifier OMICS_25936
Name OmicsNet
Software type Framework/Library
Interface Web user interface
Restrictions to use None
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Ivo Kwee
  • person_outline Ivo Kwee

Additional information

Publication for OmicsNet

OmicsNet citations


Validation of systems biology derived molecular markers of renal donor organ status associated with long term allograft function

Sci Rep
PMCID: 5934379
PMID: 29725116
DOI: 10.1038/s41598-018-25163-8

[…] ld 260, 46, and 259 molecular features respectively. 391 of the molecular features shared at least one protein interaction to another member of the combined set thus forming the induced subgraph with omicsNET as the underlying biological network. Eleven clusters of highly interconnected proteins were identified by the MCODE algorithm with 89 proteins assigned to these eleven clusters. A set of 34 […]


Integrated Analysis of Transcriptomic and Proteomic Data

Curr Genomics
PMCID: 3637682
PMID: 24082820
DOI: 10.2174/1389202911314020003

[…] PANTHER and KEGG do not cover all the features found in transcriptomic and proteomic dataset used in this study. So, the authors had developed undirected protein interaction network omicsNET [] which includes all protein encoding genes as nodes in the network. It has edges between the nodes with edge weights referring to dependency measures between the pair of nodes. The dependen […]


Concept and application of a computational vaccinology workflow

Immunome Res
PMCID: 2981879
PMID: 21067549
DOI: 10.1186/1745-7580-6-S2-S7

[…] erentially regulated in the course of EBV primary and re-infection presented by Chen (the Meta-A dataset) [] were connected using shortest paths utilizing the human proteome interaction network omicsNET []. This resulting subgraph was merged with the EBV-EBV and EBV-human subgraphs as noted above, and further enriched by direct omicsNET connections between the two sets of proteins. Further p […]


Integrative Bioinformatics Analysis of Proteins Associated with the Cardiorenal Syndrome

PMCID: 3003974
PMID: 21188212
DOI: 10.4061/2011/809378

[…] For network analysis, we used an extended version of the protein dependency network “omicsNET” as described in Bernthaler et al. []. The network is comprised of information from protein-protein interactions, tissue-specific reference coexpression, shared pathway information, gene onto […]


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OmicsNet institution(s)
Università della Svizzera italiana, Institute of Oncology Research, Bellinzona, Switzerland; Dalle Molle Institute for Artificial Intelligence Research, SUPSI, Manno, Switzerland; Oncology Institute of Southern Switzerland, Bellinzona, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; BigOmics Analytics, Bellinzona, Switzerland
OmicsNet funding source(s)
Supported by the Swiss National Science Foundation (205321-147138/1).

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