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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "ceRNAnetsim" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'ceRNAnetsim: Regulation Simulator of Interaction between miRNA and Competing
  RNAs (ceRNA)'
version: 1.17.0
doi: 10.7717/peerj.11121
abstract: This package simulates regulations of ceRNA (Competing Endogenous) expression
  levels after a expression level change in one or more miRNA/mRNAs. The methodolgy
  adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA,
  etc.) into miRNA:target interaction network. The package basically distributes miRNA
  expression over available ceRNAs where each ceRNA attracks miRNAs proportional to
  its amount. But, the package can utilize multiple parameters that modify miRNA effect
  on its target (seed type, binding energy, binding location, etc.). The functions
  handle the given dataset as graph object and the processes progress via edge and
  node variables.
authors:
- family-names: Ari Yuka
  given-names: Selcen
  email: selcenarii@gmail.com
  orcid: https://orcid.org/0000-0002-0028-2453
- family-names: Yilmaz
  given-names: Alper
  email: alperyilmaz@gmail.com
  orcid: https://orcid.org/0000-0002-8827-4887
preferred-citation:
  type: article
  title: Network based multifactorial modelling of miRNA-target interactions
  authors:
  - family-names: Yuka
    given-names: Selcen Ari
  - family-names: Yilmaz
    given-names: Alper
    email: alperyilmaz@gmail.com
    orcid: https://orcid.org/0000-0002-8827-4887
  year: '2021'
  doi: 10.7717/peerj.11121
  abstract: 'Competing endogenous RNA (ceRNA) regulations and crosstalk between various
    types of non-coding RNA in humans is an important and under-explored subject.
    Several studies have pointed out that an alteration in miRNA: target interaction
    can result in unexpected changes due to indirect and complex interactions. In
    this article, we defined a new network-based model that incorporates miRNA: ceRNA
    interactions with expression values. Our approach calculates network-wide effects
    of perturbations in the expression level of one or more nodes in the presence
    or absence of miRNA interaction factors such as seed type, binding energy. We
    carried out the analysis of large-scale miRNA: target networks from breast cancer
    patients. Highly perturbing genes identified by our approach coincide with breast
    cancer-associated genes and miRNAs. Our network-based approach takes the sponge
    effect into account and helps to unveil the crosstalk between nodes in miRNA:
    target network. The model has potential to reveal unforeseen regulations that
    are only evident in the network context. Our tool is scalable and can be plugged
    in with emerging miRNA effectors such as circRNAs, lncRNAs, and available as R
    package ceRNAnetsim: https://www. bioconductor. org/packages/release/bioc/html/ceRNAnetsim.html.'
  url: https://doi.org/10.1093/bioinformatics/btz314
  journal: PeerJ
repository: https://bioc.r-universe.dev
repository-code: https://github.com/selcenari/ceRNAnetsim
url: https://github.com/selcenari/ceRNAnetsim
contact:
- family-names: Ari Yuka
  given-names: Selcen
  email: selcenarii@gmail.com
  orcid: https://orcid.org/0000-0002-0028-2453