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.

I also have a private practice in psychiatry, where I see patients located in Oregon and New York via telemedicine. Please see my practice website for more details and contact information.

About me

• Publications
• Neuroscience blog
• Github
• LinkedIn

Alzheimer’s disease and related disorders

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

Brain preservation and brain banking

• Essays, publications, and links on this topic

General neuroscience

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

Learning and decision-making

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

Machine learning in medicine

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

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)

Contact

To contact me directly (I regret I am not always able to respond to emails): amckenz @ gmail