John M

- Original research (basic, clinical and translational)
- Mentoring
- Teaching
- Education
- Administration
- Grant Writing
- Project Management
- Public Speaking

- analysis of somatic copy number alterations in human lymphocyte cancer cell lines
- immune cell receptor profiling using ultra-high NGS
- in-depth knowledge of NGS platforms and technologies
- help to kick-start precisionFDA, a collaborative research network

- Designed and built framework in python for data mining of cardiovascular outcomes trials (CVOTs)
- Time-to-event (Hazard Modeling) meta-analyses for over twenty Type 2 diabetes (T2D) trials for major adverse cardiac events
- Comparative analysis of pediatric versus adult T2D drug trials
- Statistical analysis plan design and publication

Core analyst and technical leader for the Alzheimer's Disease Sequencing Project (ADSP) and AD Genetic Consortium (ADGC). My contributions have been numerous and wide-spread, including association/population-based analysis; genotype quality control; algorithms/methods/pipeline development; reducing cost of laboratory procedures in genetic experiments; improving structural variant calling accuracy,

- Lecturer for introduction to advanced bioinformatics; human, yeast, and fly (D. melanogaster) genetics; cell biology; neuroscience; and graduate seminar in advanced bioinformatics
- Mentored Master's thesis on hypoxic effects on the metabolism of Saccharomyces cerevisiae
- Mentored Master's thesis on 3D protein modeling (Maestro Schrodinger) from primary DNA structure of five common alleles tha

100% Teaching (night courses):
1. Engineering Circuit Analysis (EGR-211)
2. Robotics and Automation (EGR-241)
3. Engineering Co-op I (EGR-208) Circuits, Software, Automation, Embedded Programing, and Robotics
4. Embedded Hardware and Sofware Seminar (MATLAB, VB, and VERILOG),
5. I picked up courses in the Math department as needed.

The goal of my thesis was to apply, develop, and improve methods for quantitative trait, genome-wide association, functional, and single-cell RNA analyses by combining multi-omics platforms and novel approaches in large AD cohorts to better understand and decribe the complexitiies and systems biology of demenia, especially microglial and immune processes. These aims were applied to the ROSMAP and

- Developed Michaelis-Menten simulation models for enzyme kinetics based on gene dosage data from cognitively healthy aged controls, AD patients, and trisomy-21 cases to predict amyloid-beta production based on the post-translation modifications to APP.
- MM model predicted extreme plaque deposition at a mean age of 40 years in trisomy-21 individuals, similar to that of an 82 year-old patient wit

algorithms (design and development), advanced linear algebra, circuits (design and dev), multivariable calculus, data reduction (Laplacian Eigenmaps, PCA), statistical mechanics, Fourier transformation in ultra-fast retrieval of image data, stochastic processes and analysis (speech and language), control systems, and information theory.