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NetControl4BioMed: A Pipeline for Biomedical Data Acquisition and Analysis of Network Controllability

Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre, NetControl4BioMed: A Pipeline for Biomedical Data Acquisition and Analysis of Network Controllability. TUCS Technical Reports 1163, TUCS, 2016.

Abstract:

Network controllability studies focus on discovering combinations of external
interventions that can drive a biological system to a desired configuration. In
practice, this approach translates into finding a combined multi-drug therapy in
order to achieve a desired response from a cell; this can lead to developments
of novel therapeutic approaches for systemic diseases like cancer. We develop a
novel bioinformatics data analysis pipeline (called NetControl4BioMed) based on
structural control of linear networks. Our pipeline generates a cellular molecular
interaction network by combining pathway data from various public databases ac-
cording to the user’s query. The pipeline identifies a minimal set of driven proteins
needed to control a given, user-defined set of target proteins in the network. We
provide here both the source code of the pipeline as well as an online web-service
based on this pipeline. The pipeline can be used by researchers for controlling
and better understanding of molecular interaction networks through combinatorial
multi-drug therapies, for better disease diagnostic, efficient therapeutic approaches
and personalized medicine.

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BibTeX entry:

@TECHREPORT{tKaRoKaCzPe16a,
  title = {NetControl4BioMed: A Pipeline for Biomedical Data Acquisition and Analysis of Network Controllability},
  author = {Kanhaiya, Krishna and Rogojin, Vladimir and Kazemi, Keivan and Czeizler, Eugen and Petre, Ion},
  number = {1163},
  series = {TUCS Technical Reports},
  publisher = {TUCS},
  year = {2016},
  ISBN = {1163},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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