# John M

John M is a remote worker on Himalayas, Assistant Research Professor at University of Colorado Anschutz Medical Campus, based in United States.

Source: https://himalayas.app/@johnm4

```text
Assistant Research Professor at University of Colorado Anschutz Medical Campus, researching clinical outcomes and developing genomics methods for structural variant detection.
```

| Detail | Value |
| --- | --- |
| Availability | Looking for a job |
| Location | United States |
| Authorized to work in | United States |
| Salary expectations | 135k+ USD |
| Job categories | Bioinformatician, Biostatistician |
| Skills | Bioinformatics, Biostatistics, Statistical Genetics, Clinical Trials Analysis, Outcomes Research, Genomics, Structural Variant Calling, Next Generation Sequencing, Whole Genome Sequencing, Functional Genomics, Population Genetics, Study Design, Time To Event Analysis, Hazard Modeling, Meta Analysis |
| LinkedIn | https://linkedin.com/in/john-stephen-malamon-8ab80932 |

## About

```text
At University of Colorado Anschutz Medical Campus, I conduct original research in clinical outcomes, analytics and methods, actuarial science, and risk management for patient-centric research solutions through CCTCARE. I also teach, mentor, and contribute to project management and grant writing.

At University of Pennsylvania, I worked as a Senior Analyst and Bioinformatician for the Alzheimer’s Disease Sequencing Project and AD Genetic Consortium, developing structural variant analysis plans and workflows. At the FDA, I designed a Python framework for mining cardiovascular outcomes trials and conducted time-to-event meta-analyses; I also researched somatic copy number alterations and immune cell receptor profiling. I developed the DNAnamer and DNASCAN methodologies and analysis pipelines.
```

## Experience

### Assistant Research Professor (current)

[University of Colorado Anschutz Medical Campus](https://himalayas.app/companies/university-of-colorado-anschutz-medical-campus). Sep 2021 - Present

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

### Postdoctoral Research Fellow - Oak Ridge Associated Universities

FDA. Oct 2021 - Feb 2022

```text
- 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
```

### Postdoctoral Research Fellow - Oak Ridge Associated Universities

FDA. Oct 2020 - Oct 2021

```text
- 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
```

### Senior Analyst and Bioinformatician

[University of Pennsylvania](https://himalayas.app/companies/university-of-pennsylvania). Oct 2013 - Aug 2021

```text
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,
```

### Visiting Professor of Bioinformatics

Rowan University. Jul 2018 - Jul 2019

```text
- 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
```

### Adjunct Teaching Professor

Camden County College. Aug 2007 - Jun 2013

```text
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.
```

## Education

### Drexel University

Doctor of Philosophy - PhD, Statistical Genetics and Biomedical Engineering. 2015 - 2019

```text
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
```

### Drexel University

Master's Science, Biomedical Engineering. 2012 - 2015

```text
- 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
```

### Temple University

Bachelor of Science - BSE, Computer Engineering. 1999 - 2005

```text
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.
```

## Tech stack

- SAS
- Python
- Java
- C#
- C++
- MATLAB
- Linux
- SQL
- Stata
- Bash
- Verilog

To contact John, message them from this profile with a Himalayas employer account: [Hire on Himalayas](https://himalayas.app/hire).

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