SyndrumNET/CITATION.cff at main · nihadaslanzade-02/SyndrumNET · GitHub

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cff-version: 1.2.0
title: >-
  SyndrumNET: a Python implementation of network-based
  prediction of synergistic drug combinations
message: >-
  If you use this software, please cite both this
  repository and the Iida et al. (2024) paper that
  describes the method it implements.
type: software
authors:
  - family-names: Aslanzade
    given-names: Nihad
    alias: nihadaslanzade-02
repository-code: https://github.com/nihadaslanzade-02/SyndrumNET
license: MIT
version: 1.0.0
keywords:
  - drug-combinations
  - drug-synergy
  - network-propagation
  - network-medicine
  - systems-biology
  - bioinformatics
abstract: >-
  A Python implementation of SyndrumNET, a network-based
  trans-omics method for predicting synergistic drug
  combinations. Integrates molecular-interaction resources
  into a single human interactome, builds gene modules for
  diseases and drugs from expression signatures, propagates
  signal with PRINCE, and scores drug pairs on network
  topology, disease proximity and transcriptional reversal.
  The scoring layer is complete and tested; parts of the
  data layer are placeholders, documented in
  docs/PLACEHOLDERS.md.
references:
  - type: article
    title: >-
      A network-based trans-omics approach for predicting
      synergistic drug combinations
    authors:
      - family-names: Iida
        given-names: Michio
      - family-names: Kuniki
        given-names: Yuya
      - family-names: Yagi
        given-names: Kenta
      - family-names: Goda
        given-names: Mitsuhiro
      - family-names: Namba
        given-names: Shinya
      - family-names: Takeshita
        given-names: Jun-ichi
      - family-names: Sawada
        given-names: Ryusuke
      - family-names: Iwata
        given-names: Michio
      - family-names: Zamami
        given-names: Yoshito
      - family-names: Ishizawa
        given-names: Keisuke
      - family-names: Yamanishi
        given-names: Yoshihiro
    year: 2024
    journal: Communications Medicine
    volume: 4
    number: 154
    doi: 10.1038/s43856-024-00571-2
  - type: article
    title: Network-based prediction of drug combinations
    authors:
      - family-names: Cheng
        given-names: Feixiong
      - family-names: Kovács
        given-names: István A.
      - family-names: Barabási
        given-names: Albert-László
    year: 2019
    journal: Nature Communications
    volume: 10
    number: 1197
    doi: 10.1038/s41467-019-09186-x
  - type: article
    title: >-
      Associating genes and protein complexes with disease
      via network propagation
    authors:
      - family-names: Vanunu
        given-names: Oron
    year: 2010
    journal: PLoS Computational Biology
  - type: article
    title: Network-based in silico drug efficacy screening
    authors:
      - family-names: Guney
        given-names: Emre
    year: 2016
    journal: Nature Communications