Andrew McKenzie’s Home Page

Hello out there. Welcome to my academic website. I’m currently a research scientist at Apex Neuroscience, a non-profit organization in Salem, Oregon. My primary research interests are in the structural basis of neuropsychiatric disorders, brain banking and brain preservation, and computational biology.

To contact me: amckenz @ gmail

About me

• Publications
• Neuroscience blog
• Github

Alzheimer’s disease and related disorders

• PhD thesis on oligodendrocytes in Alzheimer’s disease
• Deep learning of myelin histopathology in cognitive impairment
• A tale of two APOE alleles

Brain preservation and brain banking

• Essays, publications, and links on this topic

General neuroscience

• Celltypes.org: cell type-associated gene expression data
• Neuron typing
• Brain cell type gene expression
• Towards decoding a memory from a static map of the brain

Learning and decision-making

• How I use spaced repetition learning
• Eight years of tracking my life statistics
• The canon of decision-making trade-offs across domains
• Classifying trade-offs on the basis of Berkson’s paradox

Machine learning in medicine

• Generating new protein sequences with a character-level recurrent neural network
• A mock case of neonatal meningitis
• Technical debt: a roadblock in applying machine learning to medicine

Software

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