Andrew T McKenzie

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Projects

Software

  • bayesbio: Miscellaneous functions for bioinformatics and Bayesian statistics (R package)
  • DGCA: Differential Gene Correlation Analysis (R package)
  • BRETIGEA: Brain Cell Type Specific Gene Expression Analysis (R package)
  • demedify: Demystifying and expanding medical acronyms and terms (Python Reddit bot)

Decision Theory

  • The “canon” of common trade-offs across domains 
  • Classifying trade-offs on the basis of Berkson’s paradox
  • My short-list of the most interesting biomedical trade-offs

Gene Expression

  • Bayesian transcription start site estimation in sparsely sampled RNA-seq data
  • Generating new protein sequences with a character-level recurrent neural network
  • Visualizing mouse brain cell type gene expression data

Machine Learning & Medicine 

  • Technical debt: probably the main roadblack in applying machine learning to medicine
  • A mock case of neonatal meningitis 

Quantified Self 

  • Eight years of tracking my life statistics
  • Five years of spaced repetition flashcards
  • Does whole genome sequencing add value above SNP arrays?

Neuroscience

  • Neuron typing
  • Lucidity in dementia

Rating Systems

  • Patterns of favorite music preferences on Facebook across countries with different GDPs
  • Shrinkage estimation of movie directors’ average IMDb rating
  • The best books of all time based on shrinkage estimation 
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