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Genetic Interactions (Multi-omics (gene interaction network (protein…

- - - - multifactor dimensionality reduction (MDR)
        https://sourceforge.net/projects/mdr/
      - http://doi.org/10.1007/978-1-4939-2155-3
      - https://doi.org/10.1038/nrg2579
  - - - https://string-db.org/
        (2000) a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations
      - http://www.geneticinteractions.org/research.html
        To faciliate experimentation and integrated computational analysis with model organism PPI networks, we have integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database.
    - - gene-gene interaction
        
        BOOST: A Fast Approach to Detecting Gene-Gene Interactions in Genome-wide Case-Control Studies
        Author links open overlay
        https://doi.org/10.1016/j.ajhg.2010.07.021
        
        Detecting gene-gene interactions using support vector machines with L1 penalty
        https://doi-org.ezproxy.lib.ucalgary.ca/10.1109/BIBMW.2010.5703819
        
        Detecting gene–gene interactions that underlie human diseases
        Nature Reviews Genetics volume 10, pages 392–404 (2009)
      - combined
        
        https://genemania.org/
        (2010) finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity
    - - https://omictools.com/clr-tool
        (2007) Infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles.
- - - - Develop training strategy
        
        Testing and validation strategy
        
        Identify possible pitfalls
        
        Test cases? Benchmark?
        
        Algorithm to use based on features