text: user1757: I am a bioinformatics student and I was learning the basics of structural equation modeling (SEM).
  I was wondering, are there any applications of SEM on  bioinformatics? Are there any strong sides for use of structural equation models using data on bioinformatics?
  I did a quick search and found almost nothing. While it seemed like a learning algorithm, I can't say I figured it out completely.
  
  user252: I have came across them in gene regulatory network analysis before. see here and here. However I haven't seen them in other contexts, but that's not to say they don't exist.
  
  user3848: SEM specialises in identifying 'latent variables'.
  SEM are extensively used for questionnaire data. In questionnaire data, latent variables are the 'psychological' factors behind given (human) behaviours. 
  Applying SEM to explicit molecular mechanisms doesn't make much sense unless there is a hidden component in a mechanism that has not been identified. However, even here the SEM will not tell you what the 'latent variable' represents.
  Thus I don't believe there is a good application to bioinformatics, outside human phenotypes derived from questionnaire data, which might be mapped on biological variables, but I could be wrong. 
  
original_text: 1757: <p>I am a bioinformatics student and I was learning the basics of <a href="https://en.wikipedia.org/wiki/Structural_equation_modeling" rel="nofollow noreferrer">structural equation modeling (SEM)</a>.</p>
  
  <p>I was wondering, are there any applications of SEM on  bioinformatics? Are there any strong sides for use of structural equation models using data on bioinformatics?</p>
  
  <p>I did a quick search and found almost nothing. While it seemed like a learning algorithm, I can't say I figured it out completely.</p>
   252: <p>I have came across them in gene regulatory network analysis before. see <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278111/" rel="nofollow noreferrer">here</a> and <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003068" rel="nofollow noreferrer">here</a>. However I haven't seen them in other contexts, but that's not to say they don't exist.</p>
   3848: <p>SEM specialises in identifying 'latent variables'.</p>
  
  <p>SEM are extensively used for questionnaire data. In questionnaire data, latent variables are the 'psychological' factors behind given (human) behaviours. </p>
  
  <p>Applying SEM to explicit molecular mechanisms doesn't make much sense unless there is a hidden component in a mechanism that has not been identified. However, even here the SEM will not tell you what the 'latent variable' represents.</p>
  
  <p>Thus I don't believe there is a good application to bioinformatics, outside human phenotypes derived from questionnaire data, which might be mapped on biological variables, but I could be wrong. </p>
  